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Sample records for sequencing technologies permit

  1. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

    Directory of Open Access Journals (Sweden)

    Materne Michael

    2011-05-01

    Full Text Available Abstract Background Lentil (Lens culinaris Medik. is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Results Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs. De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. Conclusions A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

  2. Taxes, permits, and the diffusion of a new technology

    International Nuclear Information System (INIS)

    Coria, Jessica

    2009-01-01

    This study looks at the effects of the choice between taxes and permits on the pattern of adoption of a new (pollution) emissions abatement technology. It uses a dynamic setting, where the regulator observes the arrival and initial use of the technology and determines the optimal ex post amount of emissions before firms start to adopt the technology. In the model here, the adoption benefits and costs depend on the number of firms that are already using the technology. Thus, each firm decides the optimal date to adopt the technology, considering its benefits and costs, as well as the advantage they will gain over their rivals, producing a sequence of adoption that is ''diffused'' into the industry over time. With this framework, the study shows that when the output demand is elastic, auctioned permits induce an earlier diffusion than taxes. (author)

  3. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  4. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  5. 78 FR 42520 - Control Technology, Inc.; Notice of Preliminary Permit Application Accepted for Filing and...

    Science.gov (United States)

    2013-07-16

    ... Technology, Inc.; Notice of Preliminary Permit Application Accepted for Filing and Soliciting Comments, Motions To Intervene, and Competing Applications On December 18, 2012, Control Technology, Inc. filed an... lower reservoir, (3) a reinforced concrete penstock with intake/outlet structure in the upper reservoir...

  6. The clean development mechanism versus international permit trading: The effect on technological change

    International Nuclear Information System (INIS)

    Hagem, Cathrine

    2009-01-01

    The clean development mechanism of the Kyoto Protocol may induce technological change in developing countries. As an alternative to the clean development mechanism regime, developing countries may accept a (generous) cap on their own emissions, allow domestic producers to invest in new efficient technologies, and sell the excess emission permits on the international permit market. The purpose of this article is to show how the gains from investment, and hence the incentive to invest in new technology in developing countries, differ between the two alternative regimes. We show that the difference in the gains from investment depends on whether the producers in developing countries face competitive or noncompetitive output markets, whether the investment affects fixed or variable production costs, and whether producers can reduce emissions through means other than investing in new technology. (author)

  7. 40 CFR 125.3 - Technology-based treatment requirements in permits.

    Science.gov (United States)

    2010-07-01

    ... fundamentally different control technology than under permits for an industrial category issued before such date... reduction benefits to be achieved from such application; (ii) The age of equipment and facilities involved... to the cost and level of reduction of such pollutants from a class or category of industrial sources...

  8. [Sequencing technology in gene diagnosis and its application].

    Science.gov (United States)

    Yibin, Guo

    2014-11-01

    The study of gene mutation is one of the hot topics in the field of life science nowadays, and the related detection methods and diagnostic technology have been developed rapidly. Sequencing technology plays an indispensable role in the definite diagnosis and classification of genetic diseases. In this review, we summarize the research progress in sequencing technology, evaluate the advantages and disadvantages of 1(st) ~3(rd) generation of sequencing technology, and describe its application in gene diagnosis. Also we made forecasts and prospects on its development trend.

  9. Next-Generation Sequencing of the Chrysanthemum nankingense (Asteraceae) Transcriptome Permits Large-Scale Unigene Assembly and SSR Marker Discovery

    Science.gov (United States)

    Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Peng, Hui; Li, Pirui; Song, Aiping; Guan, Zhiyong; Fang, Weimin; Liao, Yuan; Chen, Fadi

    2013-01-01

    Background Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. Methodology/Principal Findings Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. Conclusions/Significance SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera. PMID:23626799

  10. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  11. Comparison of next generation sequencing technologies for transcriptome characterization

    Directory of Open Access Journals (Sweden)

    Soltis Douglas E

    2009-08-01

    Full Text Available Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19. We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica and the magnoliid avocado (Persea americana using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB, 119,518 (88.7% mapped exactly to known exons, while 1,117 (0.8% mapped to introns, 11,524 (8.6% spanned annotated intron/exon boundaries, and 3,066 (2.3% extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance

  12. Next generation sequencing (NGS)technologies and applications

    Energy Technology Data Exchange (ETDEWEB)

    Vuyisich, Momchilo [Los Alamos National Laboratory

    2012-09-11

    NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

  13. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  14. Targeted genotyping-by-sequencing permits cost-effective identification and discrimination of pasture grass species and cultivars.

    Science.gov (United States)

    Pembleton, Luke W; Drayton, Michelle C; Bain, Melissa; Baillie, Rebecca C; Inch, Courtney; Spangenberg, German C; Wang, Junping; Forster, John W; Cogan, Noel O I

    2016-05-01

    A targeted amplicon-based genotyping-by-sequencing approach has permitted cost-effective and accurate discrimination between ryegrass species (perennial, Italian and inter-species hybrid), and identification of cultivars based on bulked samples. Perennial ryegrass and Italian ryegrass are the most important temperate forage species for global agriculture, and are represented in the commercial pasture seed market by numerous cultivars each composed of multiple highly heterozygous individuals. Previous studies have identified difficulties in the use of morphophysiological criteria to discriminate between these two closely related taxa. Recently, a highly multiplexed single nucleotide polymorphism (SNP)-based genotyping assay has been developed that permits accurate differentiation between both species and cultivars of ryegrasses at the genetic level. This assay has since been further developed into an amplicon-based genotyping-by-sequencing (GBS) approach implemented on a second-generation sequencing platform, allowing accelerated throughput and ca. sixfold reduction in cost. Using the GBS approach, 63 cultivars of perennial, Italian and interspecific hybrid ryegrasses, as well as intergeneric Festulolium hybrids, were genotyped. The genetic relationships between cultivars were interpreted in terms of known breeding histories and indistinct species boundaries within the Lolium genus, as well as suitability of current cultivar registration methodologies. An example of applicability to quality assurance and control (QA/QC) of seed purity is also described. Rapid, low-cost genotypic assays provide new opportunities for breeders to more fully explore genetic diversity within breeding programs, allowing the combination of novel unique genetic backgrounds. Such tools also offer the potential to more accurately define cultivar identities, allowing protection of varieties in the commercial market and supporting processes of cultivar accreditation and quality assurance.

  15. RCRA permitting strategies for the development of innovative technologies: Lessons from Hanford

    International Nuclear Information System (INIS)

    Gajewski, S.W.; Donaghue, J.F.

    1994-01-01

    The Hanford Site restoration is the largest waste cleanup operation in history. The Hanford plutonium production mission generated two-thirds of all the nuclear waste, by volume, in the Department of Energy (DOE) Complex. Cleanup challenges include not only large stored volumes of radioactive, hazardous, and mixed waste, but contaminated soil and groundwater and scores of major structures slated for decontamination, decommissioning, and demolition. DOE and its contractors will need to invent the technology required to do the job on a timetable driven by negotiated milestones, public concerns, and budgetary constraints. This paper will discuss the effort at Hanford to develop an integrated, streamlined strategy for compliance with the Resource Conservation and Recovery Act (RCRA) and the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) in the conduct of research, development, and demonstration (RD ampersand D) of innovative cleanup technologies. The aspects that will be discussed include the following: the genesis of the RD ampersand D permitting challenge at Hanford; permitting options in the existing regulatory framework; regulatory options that offered the best fit for Hanford RD ampersand D activities, and the problems associated with them; and conclusions and recommendations made to regulatory bodies

  16. FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies.

    Science.gov (United States)

    Wilson, Carolyn A; Simonyan, Vahan

    2014-01-01

    Applications of next-generation sequencing (NGS) technologies require availability and access to an information technology (IT) infrastructure and bioinformatics tools for large amounts of data storage and analyses. The U.S. Food and Drug Administration (FDA) anticipates that the use of NGS data to support regulatory submissions will continue to increase as the scientific and clinical communities become more familiar with the technologies and identify more ways to apply these advanced methods to support development and evaluation of new biomedical products. FDA laboratories are conducting research on different NGS platforms and developing the IT infrastructure and bioinformatics tools needed to enable regulatory evaluation of the technologies and the data sponsors will submit. A High-performance Integrated Virtual Environment, or HIVE, has been launched, and development and refinement continues as a collaborative effort between the FDA and George Washington University to provide the tools to support these needs. The use of a highly parallelized environment facilitated by use of distributed cloud storage and computation has resulted in a platform that is both rapid and responsive to changing scientific needs. The FDA plans to further develop in-house capacity in this area, while also supporting engagement by the external community, by sponsoring an open, public workshop to discuss NGS technologies and data formats standardization, and to promote the adoption of interoperability protocols in September 2014. Next-generation sequencing (NGS) technologies are enabling breakthroughs in how the biomedical community is developing and evaluating medical products. One example is the potential application of this method to the detection and identification of microbial contaminants in biologic products. In order for the U.S. Food and Drug Administration (FDA) to be able to evaluate the utility of this technology, we need to have the information technology infrastructure and

  17. Technology development for gene discovery and full-length sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Marcelo Bento Soares

    2004-07-19

    In previous years, with support from the U.S. Department of Energy, we developed methods for construction of normalized and subtracted cDNA libraries, and constructed hundreds of high-quality libraries for production of Expressed Sequence Tags (ESTs). Our clones were made widely available to the scientific community through the IMAGE Consortium, and millions of ESTs were produced from our libraries either by collaborators or by our own sequencing laboratory at the University of Iowa. During this grant period, we focused on (1) the development of a method for preferential cloning of tissue-specific and/or rare transcripts, (2) its utilization to expedite EST-based gene discovery for the NIH Mouse Brain Molecular Anatomy Project, (3) further development and optimization of a method for construction of full-length-enriched cDNA libraries, and (4) modification of a plasmid vector to maximize efficiency of full-length cDNA sequencing by the transposon-mediated approach. It is noteworthy that the technology developed for preferential cloning of rare mRNAs enabled identification of over 2,000 mouse transcripts differentially expressed in the hippocampus. In addition, the method that we optimized for construction of full-length-enriched cDNA libraries was successfully utilized for the production of approximately fifty libraries from the developing mouse nervous system, from which over 2,500 full-ORF-containing cDNAs have been identified and accurately sequenced in their entirety either by our group or by the NIH-Mammalian Gene Collection Program Sequencing Team.

  18. RCRA Part B permit modifications for cost savings and increased flexibility at the Rocky Flats Environmental Technology Site

    International Nuclear Information System (INIS)

    Jierree, C.; Ticknor, K.

    1996-10-01

    With shrinking budgets and downsizing, a need for streamlined compliance initiatives became evident at the Rocky Flats Environmental Technology Site (RFETS). Therefore, Rocky Mountain Remediation Services (RMRS) at the RFETS successfully and quickly modified the RFETS RCRA Part B Permit to obtain significant cost savings and increased flexibility. This 'was accomplished by requesting operations personnel to suggest changes to the Part B Permit which did not diminish overall compliance and which would be most. cost beneficial. The U.S. Department of Energy (DOE) subsequently obtained approval of those changes from the Colorado Department of Public Health and the Environment (CDPHE)

  19. SEQUENCING BATCH REACTOR: A PROMISING TECHNOLOGY IN WASTEWATER TREATMENT

    Directory of Open Access Journals (Sweden)

    A. H. Mahvi

    2008-04-01

    Full Text Available Discharge of domestic and industrial wastewater to surface or groundwater is very dangerous to the environment. Therefore treatment of any kind of wastewater to produce effluent with good quality is necessary. In this regard choosing an effective treatment system is important. Sequencing batch reactor is a modification of activated sludge process which has been successfully used to treat municipal and industrial wastewater. The process could be applied for nutrients removal, high biochemical oxygen demand containing industrial wastewater, wastewater containing toxic materials such as cyanide, copper, chromium, lead and nickel, food industries effluents, landfill leachates and tannery wastewater. Of the process advantages are single-tank configuration, small foot print, easily expandable, simple operation and low capital costs. Many researches have been conducted on this treatment technology. The authors had been conducted some investigations on a modification of sequencing batch reactor. Their studies resulted in very high percentage removal of biochemical oxygen demand, chemical oxygen demand, total kjeldahl nitrogen, total nitrogen, total phosphorus and total suspended solids respectively. This paper reviews some of the published works in addition to experiences of the authors.

  20. Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Nutrition and Agriculture.

    Science.gov (United States)

    Next-generation sequencing technologies are able to produce high-throughput short sequence reads in a cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also changed the landscape of life sciences. Here I survey their major applications ranging...

  1. Biomolecule Sequencer: Next-Generation DNA Sequencing Technology for In-Flight Environmental Monitoring, Research, and Beyond

    Science.gov (United States)

    Smith, David J.; Burton, Aaron; Castro-Wallace, Sarah; John, Kristen; Stahl, Sarah E.; Dworkin, Jason Peter; Lupisella, Mark L.

    2016-01-01

    On the International Space Station (ISS), technologies capable of rapid microbial identification and disease diagnostics are not currently available. NASA still relies upon sample return for comprehensive, molecular-based sample characterization. Next-generation DNA sequencing is a powerful approach for identifying microorganisms in air, water, and surfaces onboard spacecraft. The Biomolecule Sequencer payload, manifested to SpaceX-9 and scheduled on the Increment 4748 research plan (June 2016), will assess the functionality of a commercially-available next-generation DNA sequencer in the microgravity environment of ISS. The MinION device from Oxford Nanopore Technologies (Oxford, UK) measures picoamp changes in electrical current dependent on nucleotide sequences of the DNA strand migrating through nanopores in the system. The hardware is exceptionally small (9.5 x 3.2 x 1.6 cm), lightweight (120 grams), and powered only by a USB connection. For the ISS technology demonstration, the Biomolecule Sequencer will be powered by a Microsoft Surface Pro3. Ground-prepared samples containing lambda bacteriophage, Escherichia coli, and mouse genomic DNA, will be launched and stored frozen on the ISS until experiment initiation. Immediately prior to sequencing, a crew member will collect and thaw frozen DNA samples, connect the sequencer to the Surface Pro3, inject thawed samples into a MinION flow cell, and initiate sequencing. At the completion of the sequencing run, data will be downlinked for ground analysis. Identical, synchronous ground controls will be used for data comparisons to determine sequencer functionality, run-time sequence, current dynamics, and overall accuracy. We will present our latest results from the ISS flight experiment the first time DNA has ever been sequenced in space and discuss the many potential applications of the Biomolecule Sequencer for environmental monitoring, medical diagnostics, higher fidelity and more adaptable Space Biology Human

  2. Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

    Directory of Open Access Journals (Sweden)

    Giorgio Palù

    2011-11-01

    Full Text Available Novel DNA sequencing techniques, referred to as “next-generation” sequencing (NGS, provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics.

  3. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

    Science.gov (United States)

    Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

    2012-01-01

    The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

  4. DNA Polymerases Drive DNA Sequencing-by-Synthesis Technologies: Both Past and Present

    Directory of Open Access Journals (Sweden)

    Cheng-Yao eChen

    2014-06-01

    Full Text Available Next-generation sequencing (NGS technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. E. coli DNA polymerase I proteolytic (Klenow fragment was originally utilized in Sanger's dideoxy chain terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ⱷ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ⱷ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies.

  5. The application of the high throughput sequencing technology in the transposable elements.

    Science.gov (United States)

    Liu, Zhen; Xu, Jian-hong

    2015-09-01

    High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.

  6. The history and advances of reversible terminators used in new generations of sequencing technology.

    Science.gov (United States)

    Chen, Fei; Dong, Mengxing; Ge, Meng; Zhu, Lingxiang; Ren, Lufeng; Liu, Guocheng; Mu, Rong

    2013-02-01

    DNA sequencing using reversible terminators, as one sequencing by synthesis strategy, has garnered a great deal of interest due to its popular application in the second-generation high-throughput DNA sequencing technology. In this review, we provided its history of development, classification, and working mechanism of this technology. We also outlined the screening strategies for DNA polymerases to accommodate the reversible terminators as substrates during polymerization; particularly, we introduced the "REAP" method developed by us. At the end of this review, we discussed current limitations of this approach and provided potential solutions to extend its application. Copyright © 2013. Production and hosting by Elsevier Ltd.

  7. Treatment of Laboratory Wastewater by Sequence Batch reactor technology

    International Nuclear Information System (INIS)

    Imtiaz, N.; Butt, M.; Khan, R.A.; Saeed, M.T.; Irfan, M.

    2012-01-01

    These studies were conducted on the characterization and treatment of sewage mixed with waste -water of research and testing laboratory (PCSIR Laboratories Lahore). In this study all the parameters COD, BOD and TSS etc of influent (untreated waste-water) and effluent (treated waste-water) were characterized using the standard methods of examination for water and waste-water. All the results of the analyzed waste-water parameters were above the National Environmental Quality Standards (NEQS) set at National level. Treatment of waste-water was carried out by conventional sequencing batch reactor technique (SBR) using aeration and settling technique in the same treatment reactor at laboratory scale. The results of COD after treatment were reduced from (90-95 %), BOD (95-97 %) and TSS (96-99 %) and the reclaimed effluent quality was suitable for gardening purposes. (author)

  8. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

    Directory of Open Access Journals (Sweden)

    Jiang Du

    2009-07-01

    Full Text Available The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen, with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs. SV reconstruction is considered the most challenging step in human genome re-sequencing. (It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome. To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of

  9. DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants.

    Science.gov (United States)

    Sucher, Nikolaus J; Hennell, James R; Carles, Maria C

    2012-01-01

    DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in "next generation sequencing" (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of "NGS" technology for DNA fingerprinting and DNA barcoding applications.

  10. Transforming environmental permitting and compliance policies to promote pollution prevention: Removing barriers and providing incentives to foster technology innovation, economic productivity, and environmental protection. Final report

    International Nuclear Information System (INIS)

    Berg, D.R.; Kerr, R.L.; Fleischer, S.; Gorsen, M.; Harris, E.

    1993-04-01

    The Technology Innovation and Economics (TIE) Committee, a standing committee of EPA's National Advisory Council for Environmental Policy and Technology (NACEPT), has concluded that major changes are needed in federal and state permitting and compliance programs to encourage adoption of practical pollution prevention approaches to environmental protection. The Committee recommends seven major areas for improvement, including: (1) Redesigning permit procedures to encourage regulated facilities to expand multi-media and pollution prevention environmental improvement efforts; (2) Accelerating development and use of innovative pollution prevention technologies and techniques through special permitting and review procedures during RD ampersand D and commercialization phases; (3) Developing and expanding federal and state pollution prevention enforcement initiative; (4) Supporting state initiatives in pollution prevention facility planning; (5) Expanding pollution prevention-related training, educational and technology diffusion efforts to better reach managers in all sectors of the economy; (6) Altering personnel reward systems to encourage EPA staff to champion pollution prevention; (7) Expanding and publicizing the system of national awards honoring outstanding pollution prevention research, training and technology implementation

  11. Application of genotyping by sequencing technology to a variety of crop breeding programs.

    Science.gov (United States)

    Kim, Changsoo; Guo, Hui; Kong, Wenqian; Chandnani, Rahul; Shuang, Lan-Shuan; Paterson, Andrew H

    2016-01-01

    Since the Arabidopsis genome was completed, draft sequences or pseudomolecules have been published for more than 100 plant genomes including green algae, in large part due to advances in sequencing technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, a recurring complication in crop genotyping that differs from other taxa is a higher level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. In the current article, we briefly review current genotyping methods using next-generation sequencing (NGS) technologies. We also explore case studies of genotyping-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system (paleopolyploids, neo-allopolyploids, neo-autopolyploids). GBS typically shows good results when it is applied to an inbred diploid species with a well-established reference genome. However, we have also made some progress toward GBS of outcrossing species lacking reference genomes and of polyploid populations, which still need much improvement. Regardless of some limitations, low-cost and multiplexed genotyping offered by GBS will be beneficial to breed superior cultivars in many crop species. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Stepwise threshold clustering: a new method for genotyping MHC loci using next-generation sequencing technology.

    Directory of Open Access Journals (Sweden)

    William E Stutz

    Full Text Available Genes of the vertebrate major histocompatibility complex (MHC are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems:1 a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2 a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci--Stepwise Threshold Clustering (STC--that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.

  13. Students' Guided Reinvention of Definition of Limit of a Sequence with Interactive Technology

    Science.gov (United States)

    Flores, Alfinio; Park, Jungeun

    2016-01-01

    In a course emphasizing interactive technology, 19 students, including 18 mathematics education majors, mostly in their first year, reinvented the definition of limit of a sequence while working in small cooperative groups. The class spent four sessions of 75 minutes each on a cyclical process of guided reinvention of the definition of limit of a…

  14. Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology.

    Science.gov (United States)

    Tanase, Koji; Nishitani, Chikako; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Ohmiya, Akemi; Onozaki, Takashi

    2012-07-02

    Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. We constructed a normalized cDNA library and a 3'-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

  15. Transcriptome analysis of carnation (Dianthus caryophyllus L. based on next-generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Tanase Koji

    2012-07-01

    Full Text Available Abstract Background Carnation (Dianthus caryophyllus L., in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. Results We constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380 of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. Conclusions We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

  16. Comparing microarrays and next-generation sequencing technologies for microbial ecology research.

    Science.gov (United States)

    Roh, Seong Woon; Abell, Guy C J; Kim, Kyoung-Ho; Nam, Young-Do; Bae, Jin-Woo

    2010-06-01

    Recent advances in molecular biology have resulted in the application of DNA microarrays and next-generation sequencing (NGS) technologies to the field of microbial ecology. This review aims to examine the strengths and weaknesses of each of the methodologies, including depth and ease of analysis, throughput and cost-effectiveness. It also intends to highlight the optimal application of each of the individual technologies toward the study of a particular environment and identify potential synergies between the two main technologies, whereby both sample number and coverage can be maximized. We suggest that the efficient use of microarray and NGS technologies will allow researchers to advance the field of microbial ecology, and importantly, improve our understanding of the role of microorganisms in their various environments.

  17. [Application of next-generation semiconductor sequencing technologies in genetic diagnosis of inherited cardiomyopathies].

    Science.gov (United States)

    Zhao, Yue; Zhang, Hong; Xia, Xue-shan

    2015-07-01

    Inherited cardiomyopathy is the most common hereditary cardiac disease. It also causes a significant proportion of sudden cardiac deaths in young adults and athletes. So far, approximately one hundred genes have been reported to be involved in cardiomyopathies through different mechanisms. Therefore, the identification of the genetic basis and disease mechanisms of cardiomyopathies are important for establishing a clinical diagnosis and genetic testing. Next-generation semiconductor sequencing (NGSS) technology platform is a high-throughput sequencer capable of analyzing clinically derived genomes with high productivity, sensitivity and specificity. It was launched in 2010 by Life Technologies of USA, and it is based on a high density semiconductor chip, which was covered with tens of thousands of wells. NGSS has been successfully used in candidate gene mutation screening to identify hereditary disease. In this review, we summarize these genetic variations, challenge and application of NGSS in inherited cardiomyopathy, and its value in disease diagnosis, prevention and treatment.

  18. Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

    Directory of Open Access Journals (Sweden)

    Matt J Cahill

    Full Text Available BACKGROUND: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. METHODOLOGY/PRINCIPAL FINDINGS: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. CONCLUSIONS: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length.

  19. Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

    KAUST Repository

    Cahill, Matt J.

    2010-07-12

    Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

  20. Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

    KAUST Repository

    Cahill, Matt J.; Kö ser, Claudio U.; Ross, Nicholas E.; Archer, John A.C.

    2010-01-01

    Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

  1. Ci PERMIT

    CERN Multimedia

    Relations with the Host States Service

    1999-01-01

    The Swiss Permanent Mission to the International Organisations at Geneva recalls that only the spouses and children of members of personnel resident in Switzerland and in possession of a legitimation card of types 'B', 'C', 'D' or 'E' issued by the Swiss Federal Department of Foreign Affairs are entitled to benefit from a Ci Permit.The 'demande d'attestation de permis Ci' (request for a Ci permit attestation) can be sent to the Mission only through Personnel Division (Administrative Services, Office 33/1-025).Additional information on access by family members of CERN officials to the Swiss labour market are available to you on the Web site of the Relations with the Host States Service (cf. document entitled 'Employment in Switzerland for spouses and children of CERN officials' dated March 1996).Relations with the Host States Servicehttp://www.cern.ch/relations/Tel. 72848

  2. Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences

    Directory of Open Access Journals (Sweden)

    Alessandra Traini

    2013-01-01

    Full Text Available Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

  3. Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences.

    Science.gov (United States)

    Traini, Alessandra; Iorizzo, Massimo; Mann, Harpartap; Bradeen, James M; Carputo, Domenico; Frusciante, Luigi; Chiusano, Maria Luisa

    2013-01-01

    Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

  4. Academic performance in a pharmacotherapeutics course sequence taught synchronously on two campuses using distance education technology.

    Science.gov (United States)

    Steinberg, Michael; Morin, Anna K

    2011-10-10

    To compare the academic performance of campus-based students in a pharmacotherapeutics course with that of students at a distant campus taught via synchronous teleconferencing. Examination scores and final course grades for campus-based and distant students completing the case-based pharmacotherapeutics course sequence over a 5-year period were collected and analyzed. The mean examination scores and final course grades were not significantly different between students on the 2 campuses. The use of synchronous distance education technology to teach students does not affect students' academic performance when used in an active-learning, case-based pharmacotherapeutics course.

  5. A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology.

    Science.gov (United States)

    Ustek, Duran; Sirma, Sema; Gumus, Ergun; Arikan, Muzaffer; Cakiris, Aris; Abaci, Neslihan; Mathew, Jaicy; Emrence, Zeliha; Azakli, Hulya; Cosan, Fulya; Cakar, Atilla; Parlak, Mahmut; Kursun, Olcay

    2012-10-01

    One application of next-generation sequencing (NGS) is the targeted resequencing of interested genes which has not been used in viral integration site analysis of gene therapy applications. Here, we combined targeted sequence capture array and next generation sequencing to address the whole genome profiling of viral integration sites. Human 293T and K562 cells were transduced with a HIV-1 derived vector. A custom made DNA probe sets targeted pLVTHM vector used to capture lentiviral vector/human genome junctions. The captured DNA was sequenced using GS FLX platform. Seven thousand four hundred and eighty four human genome sequences flanking the long terminal repeats (LTR) of pLVTHM fragment sequences matched with an identity of at least 98% and minimum 50 bp criteria in both cells. In total, 203 unique integration sites were identified. The integrations in both cell lines were totally distant from the CpG islands and from the transcription start sites and preferentially located in introns. A comparison between the two cell lines showed that the lentiviral-transduced DNA does not have the same preferred regions in the two different cell lines. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

    Directory of Open Access Journals (Sweden)

    Wenyu Zhang

    Full Text Available 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.

  7. Characterizing ncRNAs in human pathogenic protists using high-throughput sequencing technology

    Directory of Open Access Journals (Sweden)

    Lesley Joan Collins

    2011-12-01

    Full Text Available ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, snoRNAs and long ncRNAs on a genomic scale making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases.

  8. Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology

    Science.gov (United States)

    Collins, Lesley Joan

    2011-01-01

    ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases. PMID:22303390

  9. Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.

    Science.gov (United States)

    Gimode, Davis; Odeny, Damaris A; de Villiers, Etienne P; Wanyonyi, Solomon; Dida, Mathews M; Mneney, Emmarold E; Muchugi, Alice; Machuka, Jesse; de Villiers, Santie M

    2016-01-01

    Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional

  10. Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.

    Directory of Open Access Journals (Sweden)

    Davis Gimode

    Full Text Available Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS technologies to develop both Simple Sequence Repeat (SSR and Single Nucleotide Polymorphism (SNP markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included

  11. The first FDA marketing authorizations of next-generation sequencing technology and tests: challenges, solutions and impact for future assays.

    Science.gov (United States)

    Bijwaard, Karen; Dickey, Jennifer S; Kelm, Kellie; Težak, Živana

    2015-01-01

    The rapid emergence and clinical translation of novel high-throughput sequencing technologies created a need to clarify the regulatory pathway for the evaluation and authorization of these unique technologies. Recently, the US FDA authorized for marketing four next generation sequencing (NGS)-based diagnostic devices which consisted of two heritable disease-specific assays, library preparation reagents and a NGS platform that are intended for human germline targeted sequencing from whole blood. These first authorizations can serve as a case study in how different types of NGS-based technology are reviewed by the FDA. In this manuscript we describe challenges associated with the evaluation of these novel technologies and provide an overview of what was reviewed. Besides making validated NGS-based devices available for in vitro diagnostic use, these first authorizations create a regulatory path for similar future instruments and assays.

  12. Automatic start-up system of nuclear reactor based on sequence control technology

    International Nuclear Information System (INIS)

    Zhang Yao; Zhang Dafa; Peng Huaqing

    2009-01-01

    A conceptive design of an automatic start-up system based on the sequence control for the nuclear reactors is given in this paper, so as to solve the problems during the start-up process, such as the long operation time, low automatic control level and high accident rate. The start-up process and its requirements are analyzed in detail at first. Then,the principle, the architecture, the key technologies of the automatic start-up system of nuclear reactors are designed and discussed. With the designed system, the automatic start-up of the nuclear reactor can be realized,the work load of the operator can be reduced,and the safety and efficiency of the nuclear power plant during its start-up can be improved. (authors)

  13. Killer Immunoglobulin-Like Receptor Allele Determination Using Next-Generation Sequencing Technology

    Directory of Open Access Journals (Sweden)

    Bercelin Maniangou

    2017-05-01

    Full Text Available The impact of natural killer (NK cell alloreactivity on hematopoietic stem cell transplantation (HSCT outcome is still debated due to the complexity of graft parameters, HLA class I environment, the nature of killer cell immunoglobulin-like receptor (KIR/KIR ligand genetic combinations studied, and KIR+ NK cell repertoire size. KIR genes are known to be polymorphic in terms of gene content, copy number variation, and number of alleles. These allelic polymorphisms may impact both the phenotype and function of KIR+ NK cells. We, therefore, speculate that polymorphisms may alter donor KIR+ NK cell phenotype/function thus modulating post-HSCT KIR+ NK cell alloreactivity. To investigate KIR allele polymorphisms of all KIR genes, we developed a next-generation sequencing (NGS technology on a MiSeq platform. To ensure the reliability and specificity of our method, genomic DNA from well-characterized cell lines were used; high-resolution KIR typing results obtained were then compared to those previously reported. Two different bioinformatic pipelines were used allowing the attribution of sequencing reads to specific KIR genes and the assignment of KIR alleles for each KIR gene. Our results demonstrated successful long-range KIR gene amplifications of all reference samples using intergenic KIR primers. The alignment of reads to the human genome reference (hg19 using BiRD pipeline or visualization of data using Profiler software demonstrated that all KIR genes were completely sequenced with a sufficient read depth (mean 317× for all loci and a high percentage of mapping (mean 93% for all loci. Comparison of high-resolution KIR typing obtained to those published data using exome capture resulted in a reported concordance rate of 95% for centromeric and telomeric KIR genes. Overall, our results suggest that NGS can be used to investigate the broad KIR allelic polymorphism. Hence, these data improve our knowledge, not only on KIR+ NK cell alloreactivity in

  14. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

    Science.gov (United States)

    Senol Cali, Damla; Kim, Jeremie S; Ghose, Saugata; Alkan, Can; Mutlu, Onur

    2018-04-02

    Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious

  15. Detecting novel genetic mutations in Chinese Usher syndrome families using next-generation sequencing technology.

    Science.gov (United States)

    Qu, Ling-Hui; Jin, Xin; Xu, Hai-Wei; Li, Shi-Ying; Yin, Zheng-Qin

    2015-02-01

    Usher syndrome (USH) is the most common cause of combined blindness and deafness inherited in an autosomal recessive mode. Molecular diagnosis is of great significance in revealing the molecular pathogenesis and aiding the clinical diagnosis of this disease. However, molecular diagnosis remains a challenge due to high phenotypic and genetic heterogeneity in USH. This study explored an approach for detecting disease-causing genetic mutations in candidate genes in five index cases from unrelated USH families based on targeted next-generation sequencing (NGS) technology. Through systematic data analysis using an established bioinformatics pipeline and segregation analysis, 10 pathogenic mutations in the USH disease genes were identified in the five USH families. Six of these mutations were novel: c.4398G > A and EX38-49del in MYO7A, c.988_989delAT in USH1C, c.15104_15105delCA and c.6875_6876insG in USH2A. All novel variations segregated with the disease phenotypes in their respective families and were absent from ethnically matched control individuals. This study expanded the mutation spectrum of USH and revealed the genotype-phenotype relationships of the novel USH mutations in Chinese patients. Moreover, this study proved that targeted NGS is an accurate and effective method for detecting genetic mutations related to USH. The identification of pathogenic mutations is of great significance for elucidating the underlying pathophysiology of USH.

  16. Integration of microbiological, epidemiological and next generation sequencing technologies data for the managing of nosocomial infections

    Directory of Open Access Journals (Sweden)

    Matteo Brilli

    2018-02-01

    Full Text Available At its core, the work of clinical microbiologists consists in the retrieving of a few bytes of information (species identification; metabolic capacities; staining and antigenic properties; antibiotic resistance profiles, etc. from pathogenic agents. The development of next generation sequencing technologies (NGS, and the possibility to determine the entire genome for bacterial pathogens, fungi and protozoans will likely introduce a breakthrough in the amount of information generated by clinical microbiology laboratories: from bytes to Megabytes of information, for a single isolate. In parallel, the development of novel informatics tools, designed for the management and analysis of the so-called Big Data, offers the possibility to search for patterns in databases collecting genomic and microbiological information on the pathogens, as well as epidemiological data and information on the clinical parameters of the patients. Nosocomial infections and antibiotic resistance will likely represent major challenges for clinical microbiologists, in the next decades. In this paper, we describe how bacterial genomics based on NGS, integrated with novel informatic tools, could contribute to the control of hospital infections and multi-drug resistant pathogens.

  17. A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

    Directory of Open Access Journals (Sweden)

    Yu Cao

    2017-09-01

    Full Text Available The development of next generation sequencing (NGS techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents or a food manufacturing facility econiche (e.g., floor drain. To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.

  18. A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

    Science.gov (United States)

    Cao, Yu; Fanning, Séamus; Proos, Sinéad; Jordan, Kieran; Srikumar, Shabarinath

    2017-01-01

    The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods. PMID:29033905

  19. Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.

    Science.gov (United States)

    DeMaere, Matthew Z; Darling, Aaron E

    2018-02-01

    Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences. The simulator models the basic spatial structure in genomes that is commonly observed in Hi-C and 3C datasets, including the distance-decay relationship in proximity ligation, differences in the frequency of interaction within and across chromosomes, and the structure imposed by cells. A means to model the 3D structure of randomly generated topologically associating domains is provided. The simulator considers several sources of error common to 3C and Hi-C library preparation and sequencing methods, including spurious proximity ligation events and sequencing error. We have introduced the first comprehensive simulator for 3C and Hi-C sequencing protocols. We expect the simulator to have use in testing of Hi-C data analysis algorithms, as well as more general value for experimental design, where questions such as the required depth of sequencing, enzyme choice, and other decisions can be made in advance in order to ensure adequate statistical power with respect to experimental hypothesis testing.

  20. Is Whole Exome Sequencing an Ethically Disruptive Technology? Perspectives of Pediatric Oncologists and Parents of Pediatric Patients with Solid Tumors

    Science.gov (United States)

    McCullough, Laurence B.; Slashinski, Melody J.; McGuire, Amy L.; Street, Richard L.; Eng, Christine M.; Gibbs, Richard A.; Parsons, D. Williams; Plon, Sharon E.

    2016-01-01

    Background Some anticipate that physician and parents will be ill-prepared or unprepared for the clinical introduction of genome sequencing, making it ethically disruptive. Procedure As part of the Baylor Advancing Sequencing in Childhood Cancer Care (BASIC3) study, we conducted semi-structured interviews with 16 pediatric oncologists and 40 parents of pediatric patients with cancer prior to the return of sequencing results. We elicited expectations and attitudes concerning the impact of sequencing on clinical decision-making, clinical utility, and treatment expectations from both groups. Using accepted methods of qualitative research to analyze interview transcripts, we completed a thematic analysis to provide inductive insights into their views of sequencing. Results Our major findings reveal that neither pediatric oncologists nor parents anticipate sequencing to be an ethically disruptive technology, because they expect to be prepared to integrate sequencing results into their existing approaches to learning and using new clinical information for care. Pediatric oncologists do not expect sequencing results to be more complex than other diagnostic information and plan simply to incorporate these data into their evidence-based approach to clinical practice although they were concerned about impact on parents. For parents, there is an urgency to protect their chil's health and in this context they expect genomic information to better prepare them to participate in decisions about their chil's care. Conclusion Our data do not support concern that introducing genome sequencing into childhood cancer care will be ethically disruptive, i.e., leave physicians or parents ill-prepared or unprepared to make responsible decisions about patient care. PMID:26505993

  1. Technology trajectories and the selection of optimal R and D project sequences

    NARCIS (Netherlands)

    van Bommel, Ties; Mahieu, R.J.; Nijssen, E.J.

    2014-01-01

    Given a set of R&D projects drawing on the same underlying technology, a technology trajectory refers to the order in which projects are executed. Due to their technological interdependence, the successful execution of one project can increase a firm's technological capability, and help to

  2. Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.

    Science.gov (United States)

    Ma, Peng-Fei; Guo, Zhen-Hua; Li, De-Zhu

    2012-01-01

    Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast

  3. Federal Fisheries Permit (FFP)/ Federal Processor Permit (FPP) Permit Program

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Federal Fisheries Permit (FFP) is required for vessels of the United States which are used to fish for groundfish in the Gulf of Alaska or Bering Sea and...

  4. Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

    OpenAIRE

    Yang, Xiang; Noyes, Noelle R.; Doster, Enrique; Martin, Jennifer N.; Linke, Lyndsey M.; Magnuson, Roberta J.; Yang, Hua; Geornaras, Ifigenia; Woerner, Dale R.; Jones, Kenneth L.; Ruiz, Jaime; Boucher, Christina; Morley, Paul S.; Belk, Keith E.

    2016-01-01

    Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bact...

  5. Molecular-Sized DNA or RNA Sequencing Machine | NCI Technology Transfer Center | TTC

    Science.gov (United States)

    The National Cancer Institute's Gene Regulation and Chromosome Biology Laboratory is seeking statements of capability or interest from parties interested in collaborative research to co-develop a molecular-sized DNA or RNA sequencing machine.

  6. Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology.

    Science.gov (United States)

    Sasaki, Katsutomo; Mitsuda, Nobutaka; Nashima, Kenji; Kishimoto, Kyutaro; Katayose, Yuichi; Kanamori, Hiroyuki; Ohmiya, Akemi

    2017-09-04

    Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. To obtain useful information about molecular bases for floral traits of chrysanthemums, we read expressed sequence tags (ESTs) of chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3'-UTR, and 5'-UTR cDNAs derived from various tissues of chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in chrysanthemums. We confirmed that our chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of chrysanthemums including the myriad cultivars at the molecular level.

  7. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  8. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Directory of Open Access Journals (Sweden)

    Chengwei Luo

    Full Text Available Next-generation sequencing (NGS is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage correlated highly between the two platforms (R(2>0.9. Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  9. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Science.gov (United States)

    Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos; Read, Timothy; Konstantinidis, Konstantinos T

    2012-01-01

    Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R(2)>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  10. Permit.LOA table

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This table includes the effective dates by vessel and permit number for each issued letter of authorization (LOA) by the Permit Office (APSD)

  11. State Licenses & Permits

    Data.gov (United States)

    Small Business Administration — Starting a business? Confused about whether you need a business license or permit? Virtually every business needs some form of license or permit to operate legally....

  12. Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO.

    Science.gov (United States)

    Fraiture, Marie-Alice; Saltykova, Assia; Hoffman, Stefan; Winand, Raf; Deforce, Dieter; Vanneste, Kevin; De Keersmaecker, Sigrid C J; Roosens, Nancy H C

    2018-05-21

    In order to strengthen the current genetically modified organism (GMO) detection system for unauthorized GMO, we have recently developed a new workflow based on DNA walking to amplify unknown sequences surrounding a known DNA region. This DNA walking is performed on transgenic elements, commonly found in GMO, that were earlier detected by real-time PCR (qPCR) screening. Previously, we have demonstrated the ability of this approach to detect unauthorized GMO via the identification of unique transgene flanking regions and the unnatural associations of elements from the transgenic cassette. In the present study, we investigate the feasibility to integrate the described workflow with the MinION Next-Generation-Sequencing (NGS). The MinION sequencing platform can provide long read-lengths and deal with heterogenic DNA libraries, allowing for rapid and efficient delivery of sequences of interest. In addition, the ability of this NGS platform to characterize unauthorized and unknown GMO without any a priori knowledge has been assessed.

  13. Technological sequence of creating components of the training system of the future officers to the management of physical training

    Directory of Open Access Journals (Sweden)

    Olkhovy O.M.

    2012-09-01

    Full Text Available The goal is to determine constructive ways of sequence of constructing components of the training system of the future officers to carry out official questions of managing the physical training in the process of the further military career. The structural logic circuit of the interconnections stages of optimum cycle management and technological sequence of constructing the components of the training system of the future officers to the management of physical training, which provides: definition of requirements to the typical problems of professional activities on the issues of the leadership, organization and conducting of physical training, the creation of the phased system model cadets training, training of the curriculum discipline ″Physical education, special physical training and sport″; model creation and definition of criteria of the integral evaluation of the readiness of the future officers to the management of physical training was determined through the analysis more than thirty documentary and scientific literature.

  14. 76 FR 75897 - Endangered and Threatened Species Permit Applications

    Science.gov (United States)

    2011-12-05

    ...: EA Engineering, Science, and Technology, Lewisville, Texas. Applicant requests a new permit for... atricapilla) within Texas. Permit TE-37047A Applicant: Sea World Parks and Entertainment, San Antonio, Texas...

  15. New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Schmutz, Jeremy

    2013-03-01

    Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on New approaches and technologies to sequence de novo plant reference genomes at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

  16. CRISPR-Cas9 technology: applications in genome engineering, development of sequence-specific antimicrobials, and future prospects.

    Science.gov (United States)

    de la Fuente-Núñez, César; Lu, Timothy K

    2017-02-20

    The development of CRISPR-Cas9 technology has revolutionized our ability to edit DNA and to modulate expression levels of genes of interest, thus providing powerful tools to accelerate the precise engineering of a wide range of organisms. In addition, the CRISPR-Cas system can be harnessed to design "precision" antimicrobials that target bacterial pathogens in a DNA sequence-specific manner. This capability will enable killing of drug-resistant microbes by selectively targeting genes involved in antibiotic resistance, biofilm formation and virulence. Here, we review the origins and mechanistic basis of CRISPR-Cas systems, discuss how this technology can be leveraged to provide a range of applications in both eukaryotic and prokaryotic systems, and finish by outlining limitations and future prospects.

  17. The Application of Next Generation Sequencing Technology on Noninvasive Prenatal Test

    DEFF Research Database (Denmark)

    Jiang, Hui

    There are nearly 7000 rare diseases that have been reported in the world. Although most of them occur with a frequency of less than one in 2000, in total about 6% of the population suffers from rare diseases. These rare diseases are often caused by changes in genes, which is currently lack of eff...... diseases and monogenetic diseases in a noninvasively manner. The new approach has great potential to be wildly used in the worldwide with the decreasing in sequencing costs, and therefore play an incredible role to prevent rare diseases....

  18. Complete genome sequencing of the luminescent bacterium, Vibrio qinghaiensis sp. Q67 using PacBio technology

    Science.gov (United States)

    Gong, Liang; Wu, Yu; Jian, Qijie; Yin, Chunxiao; Li, Taotao; Gupta, Vijai Kumar; Duan, Xuewu; Jiang, Yueming

    2018-01-01

    Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands. Our dataset can be useful as a comparative genome for evolution and speciation studies, as well as for the analysis of protein-coding gene families, the pathogenicity of different Vibrio species in fish, the evolution of non-coding RNA and transposon, and the regulation of gene expression in relation to the bioluminescence of Vqin-Q67.

  19. 76 FR 50246 - Endangered and Threatened Wildlife and Plants; Permit Applications

    Science.gov (United States)

    2011-08-12

    ... species in the wild. Permit Application Number: TE212427. Applicant: Ecology and Environment, Inc... wild. Permit Application Number: TE48835A. Applicant: Applied Science & Technology, Inc., Brighton, MI...

  20. Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection.

    Science.gov (United States)

    Zopf, Agnes; Raim, Roman; Danzer, Martin; Niklas, Norbert; Spilka, Rita; Pröll, Johannes; Gabriel, Christian; Nechansky, Andreas; Roucka, Markus

    2015-03-01

    The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.

  1. Understanding invasion history and predicting invasive niches using genetic sequencing technology in Australia: case studies from Cucurbitaceae and Boraginaceae.

    Science.gov (United States)

    Shaik, Razia S; Zhu, Xiaocheng; Clements, David R; Weston, Leslie A

    2016-01-01

    Part of the challenge in dealing with invasive plant species is that they seldom represent a uniform, static entity. Often, an accurate understanding of the history of plant introduction and knowledge of the real levels of genetic diversity present in species and populations of importance is lacking. Currently, the role of genetic diversity in promoting the successful establishment of invasive plants is not well defined. Genetic profiling of invasive plants should enhance our understanding of the dynamics of colonization in the invaded range. Recent advances in DNA sequencing technology have greatly facilitated the rapid and complete assessment of plant population genetics. Here, we apply our current understanding of the genetics and ecophysiology of plant invasions to recent work on Australian plant invaders from the Cucurbitaceae and Boraginaceae. The Cucurbitaceae study showed that both prickly paddy melon ( Cucumis myriocarpus ) and camel melon ( Citrullus lanatus ) were represented by only a single genotype in Australia, implying that each was probably introduced as a single introduction event. In contrast, a third invasive melon, Citrullus colocynthis , possessed a moderate level of genetic diversity in Australia and was potentially introduced to the continent at least twice. The Boraginaceae study demonstrated the value of comparing two similar congeneric species; one, Echium plantagineum , is highly invasive and genetically diverse, whereas the other, Echium vulgare , exhibits less genetic diversity and occupies a more limited ecological niche. Sequence analysis provided precise identification of invasive plant species, as well as information on genetic diversity and phylogeographic history. Improved sequencing technologies will continue to allow greater resolution of genetic relationships among invasive plant populations, thereby potentially improving our ability to predict the impact of these relationships upon future spread and better manage invaders

  2. Tradeable carbon permits

    International Nuclear Information System (INIS)

    Koutstaal, P.R.

    1995-01-01

    The research project on tradeable carbon permits has focused on three elements. First of all, the practical implications of designing a system of tradeable emission permits for reducing CO2 has been studied. In the second part, the consequences of introducing a system of tradeable carbon permits for entry barriers have been considered. Finally, the institutional requirements and welfare effects of coordination of CO2 abatement in a second-best world have been examined

  3. Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa

    Directory of Open Access Journals (Sweden)

    Pazos-Navarro María

    2011-12-01

    Full Text Available Abstract Background Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three botanical varieties have previously been identified in this species: albomarginata, bituminosa and crassiuscula. B. bituminosa can be considered a genomic 'orphan' species with very few genomic resources available. New DNA sequencing technologies provide an opportunity to develop high quality molecular markers for such orphan species. Results 432,306 mRNA molecules were sampled from a leaf transcriptome of a single B. bituminosa plant using Roche 454 pyrosequencing, resulting in an average read length of 345 bp (149.1 Mbp in total. Sequences were assembled into 3,838 isotigs/contigs representing putatively unique gene transcripts. Gene ontology descriptors were identified for 3,419 sequences. Raw sequence reads containing simple sequence repeat (SSR motifs were identified, and 240 primer pairs flanking these motifs were designed. Of 87 primer pairs developed this way, 75 (86.2% successfully amplified primarily single fragments by PCR. Fragment analysis using 20 primer pairs in 79 accessions of B. bituminosa detected 130 alleles at 21 SSR loci. Genetic diversity analyses confirmed that variation at these SSR loci accurately reflected known taxonomic relationships in original collections of B. bituminosa and provided additional evidence that a division of the botanical variety bituminosa into two according to geographical origin (Mediterranean region and Canary Islands may be appropriate. Evidence of cross-pollination was also found between botanical varieties within a B. bituminosa breeding programme. Conclusions B. bituminosa can no longer be considered a genomic orphan species, having now a large (albeit incomplete repertoire of expressed gene sequences that can serve as a resource for future genetic studies. This

  4. Characterization of microflora in Latin-style cheeses by next-generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Lusk Tina S

    2012-11-01

    Full Text Available Abstract Background Cheese contamination can occur at numerous stages in the manufacturing process including the use of improperly pasteurized or raw milk. Of concern is the potential contamination by Listeria monocytogenes and other pathogenic bacteria that find the high moisture levels and moderate pH of popular Latin-style cheeses like queso fresco a hospitable environment. In the investigation of a foodborne outbreak, samples typically undergo enrichment in broth for 24 hours followed by selective agar plating to isolate bacterial colonies for confirmatory testing. The broth enrichment step may also enable background microflora to proliferate, which can confound subsequent analysis if not inhibited by effective broth or agar additives. We used 16S rRNA gene sequencing to provide a preliminary survey of bacterial species associated with three brands of Latin-style cheeses after 24-hour broth enrichment. Results Brand A showed a greater diversity than the other two cheese brands (Brands B and C at nearly every taxonomic level except phylum. Brand B showed the least diversity and was dominated by a single bacterial taxon, Exiguobacterium, not previously reported in cheese. This genus was also found in Brand C, although Lactococcus was prominent, an expected finding since this bacteria belongs to the group of lactic acid bacteria (LAB commonly found in fermented foods. Conclusions The contrasting diversity observed in Latin-style cheese was surprising, demonstrating that despite similarity of cheese type, raw materials and cheese making conditions appear to play a critical role in the microflora composition of the final product. The high bacterial diversity associated with Brand A suggests it may have been prepared with raw materials of high bacterial diversity or influenced by the ecology of the processing environment. Additionally, the presence of Exiguobacterium in high proportions (96% in Brand B and, to a lesser extent, Brand C (46%, may

  5. Automatic Commercial Permit Sets

    Energy Technology Data Exchange (ETDEWEB)

    Grana, Paul [Folsom Labs, Inc., San Francisco, CA (United States)

    2017-12-21

    Final report for Folsom Labs’ Solar Permit Generator project, which has successfully completed, resulting in the development and commercialization of a software toolkit within the cloud-based HelioScope software environment that enables solar engineers to automatically generate and manage draft documents for permit submission.

  6. A New Targeted CFTR Mutation Panel Based on Next-Generation Sequencing Technology.

    Science.gov (United States)

    Lucarelli, Marco; Porcaro, Luigi; Biffignandi, Alice; Costantino, Lucy; Giannone, Valentina; Alberti, Luisella; Bruno, Sabina Maria; Corbetta, Carlo; Torresani, Erminio; Colombo, Carla; Seia, Manuela

    2017-09-01

    Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we developed, validated, and tested a laboratory assay for an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population. Overall, 1426 dried blood spots from neonatal screening, 402 genomic DNA samples from various origins, and 1138 genomic DNA samples from patients with CF were analyzed. The assay showed excellent analytical and diagnostic operative characteristics. We identified and experimentally validated 159 (of 188) CFTR mutations. The assay achieved detection rates of 95.0% and 95.6% in two large-scale case series of CF patients from central and northern Italy, respectively. These detection rates are among the highest reported so far with a genetic test for CF based on a mutation panel. This assay appears to be well suited for diagnostics, neonatal and carrier screening, and assisted reproduction, and it represents a considerable advantage in CF genetic counseling. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  7. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  8. Investigating the mechanisms of glyphosate resistance in goosegrass (Eleusine indica (L.) Gaertn.) by RNA sequencing technology.

    Science.gov (United States)

    Chen, Jingchao; Huang, Hongjuan; Wei, Shouhui; Huang, Zhaofeng; Wang, Xu; Zhang, Chaoxian

    2017-01-01

    Glyphosate is an important non-selective herbicide that is in common use worldwide. However, evolved glyphosate-resistant (GR) weeds significantly affect crop yields. Unfortunately, the mechanisms underlying resistance in GR weeds, such as goosegrass (Eleusine indica (L.) Gaertn.), an annual weed found worldwide, have not been fully elucidated. In this study, transcriptome analysis was conducted to further assess the potential mechanisms of glyphosate resistance in goosegrass. The RNA sequencing libraries generated 24 597 462 clean reads. De novo assembly analysis produced 48 852 UniGenes with an average length of 847 bp. All UniGenes were annotated using seven databases. Sixteen candidate differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time PCR (qRT-PCR). Among these UniGenes, the EPSPS and PFK genes were constitutively up-regulated in resistant (R) individuals and showed a higher copy number than that in susceptible (S) individuals. The expressions of four UniGenes relevant to photosynthesis were inhibited by glyphosate in S individuals, and this toxic response was confirmed by gas exchange analysis. Two UniGenes annotated as glutathione transferase (GST) were constitutively up-regulated in R individuals, and were induced by glyphosate both in R and S. In addition, the GST activities in R individuals were higher than in S. Our research confirmed that two UniGenes (PFK, EPSPS) were strongly associated with target resistance, and two GST-annotated UniGenes may play a role in metabolic glyphosate resistance in goosegrass. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  9. A high-throughput method to detect RNA profiling by integration of RT-MLPA with next generation sequencing technology.

    Science.gov (United States)

    Wang, Jing; Yang, Xue; Chen, Haofeng; Wang, Xuewei; Wang, Xiangyu; Fang, Yi; Jia, Zhenyu; Gao, Jidong

    2017-07-11

    RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples. By combining Reverse Transcription-Multiple Ligation-dependent Amplification method and next generation sequencing technology, RT-MLPSeq overcomes the limit of probe length in multiplex ligation-dependent probe amplification assay and thus could detect expression levels of transcripts without quantitative limitations. We proved that different RT-MLPSeq probes targeting on the same transcripts have highly consistent results and the starting RNA/cDNA input could be as little as 1 ng. RT-MLPSeq also presented consistent relative RNA levels of selected 13 genes with reverse transcription quantitative PCR. Finally, we demonstrated the application of the new RT-MLPSeq method by measuring the mRNA expression levels of 21 genes which can be used for accurate calculation of the breast cancer recurrence score - an index that has been widely used for managing breast cancer patients.

  10. [Research on soil bacteria under the impact of sealed CO2 leakage by high-throughput sequencing technology].

    Science.gov (United States)

    Tian, Di; Ma, Xin; Li, Yu-E; Zha, Liang-Song; Wu, Yang; Zou, Xiao-Xia; Liu, Shuang

    2013-10-01

    Carbon dioxide Capture and Storage has provided a new option for mitigating global anthropogenic CO2 emission with its unique advantages. However, there is a risk of the sealed CO2 leakage, bringing a serious threat to the ecology system. It is widely known that soil microorganisms are closely related to soil health, while the study on the impact of sequestered CO2 leakage on soil microorganisms is quite deficient. In this study, the leakage scenarios of sealed CO2 were constructed and the 16S rRNA genes of soil bacteria were sequenced by Illumina high-throughput sequencing technology on Miseq platform, and related biological analysis was conducted to explore the changes of soil bacterial abundance, diversity and structure. There were 486,645 reads for 43,017 OTUs of 15 soil samples and the results of biological analysis showed that there were differences in the abundance, diversity and community structure of soil bacterial community under different CO, leakage scenarios while the abundance and diversity of the bacterial community declined with the amplification of CO2 leakage quantity and leakage time, and some bacteria species became the dominant bacteria species in the bacteria community, therefore the increase of Acidobacteria species would be a biological indicator for the impact of sealed CO2 leakage on soil ecology system.

  11. Shedding light on the Early Pleistocene of TD6 (Gran Dolina, Atapuerca, Spain): The technological sequence and occupational inferences.

    Science.gov (United States)

    Mosquera, Marina; Ollé, Andreu; Rodríguez-Álvarez, Xose Pedro; Carbonell, Eudald

    2018-01-01

    This paper aims to update the information available on the lithic assemblage from the entire sequence of TD6 now that the most recent excavations have been completed, and to explore possible changes in both occupational patterns and technological strategies evidenced in the unit. This is the first study to analyse the entire TD6 sequence, including subunits TD6.3 and TD6.1, which have never been studied, along with the better-known TD6.2 Homo antecessor-bearing subunit. We also present an analysis of several lithic refits found in TD6, as well as certain technical features that may help characterise the hominin occupations. The archaeo-palaeontological record from TD6 consists of 9,452 faunal remains, 443 coprolites, 1,046 lithic pieces, 170 hominin remains and 91 Celtis seeds. The characteristics of this record seem to indicate two main stages of occupation. In the oldest subunit, TD6.3, the lithic assemblage points to the light and limited hominin occupation of the cave, which does, however, grow over the course of the level. In contrast, the lithic assemblages from TD6.2 and TD6.1 are rich and varied, which may reflect Gran Dolina cave's establishment as a landmark in the region. Despite the occupational differences between the lowermost subunit and the rest of the deposit, technologically the TD6 lithic assemblage is extremely homogeneous throughout. In addition, the composition and spatial distribution of the 12 groups of lithic refits found in unit TD6, as well as the in situ nature of the assemblage demonstrate the high degree of preservation at the site. This may help clarify the nature of the Early Pleistocene hominin occupations of TD6, and raise reasonable doubt about the latest interpretations that support the ex situ character of the assemblage as a whole.

  12. Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.

    Science.gov (United States)

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Mu-Chiou; Wang, Li-Tin; Huang, Lina; Lee, Fwu-Ling

    2012-10-01

    To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification. The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing. Copyright © 2012 Society of Chemical Industry.

  13. Permitted Marine Hydrokinetic Projects

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data represents pending or issued preliminary permits or issued licenses for marine hydrokinetic projects that produce energy from waves or directly from the...

  14. BCDC Minor Permits

    Data.gov (United States)

    California Natural Resource Agency — An administrative permit can be issued for an activity that qualifies as a minor repair or improvement in a relatively short period of time and without a public...

  15. Allegheny County Asbestos Permits

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Current asbestos permit data issued by the County for commercial building demolitions and renovations as required by the EPA. This file is updated daily and can be...

  16. Floodplain District Permit

    Data.gov (United States)

    Montgomery County of Maryland — The purpose of a Floodplain District Permit (FPDP) is to control floodplain development in order to protect persons and property from danger and destruction and to...

  17. Coal Mine Permit Boundaries

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — ESRI ArcView shapefile depicting New Mexico coal mines permitted under the Surface Mining Control and Reclamation Act of 1977 (SMCRA), by either the NM Mining these...

  18. Multilocus sequence typing of Pseudomonas syringae sensu lato confirms previously described genomospecies and permits rapid identification of P. syringae pv. coriandricola and P. syringae pv. apii causing bacterial leaf spot on parsley.

    Science.gov (United States)

    Bull, Carolee T; Clarke, Christopher R; Cai, Rongman; Vinatzer, Boris A; Jardini, Teresa M; Koike, Steven T

    2011-07-01

    Since 2002, severe leaf spotting on parsley (Petroselinum crispum) has occurred in Monterey County, CA. Either of two different pathovars of Pseudomonas syringae sensu lato were isolated from diseased leaves from eight distinct outbreaks and once from the same outbreak. Fragment analysis of DNA amplified between repetitive sequence polymerase chain reaction; 16S rDNA sequence analysis; and biochemical, physiological, and host range tests identified the pathogens as Pseudomonas syringae pv. apii and P. syringae pv. coriandricola. Koch's postulates were completed for the isolates from parsley, and host range tests with parsley isolates and pathotype strains demonstrated that P. syringae pv. apii and P. syringae pv. coriandricola cause leaf spot diseases on parsley, celery, and coriander or cilantro. In a multilocus sequence typing (MLST) approach, four housekeeping gene fragments were sequenced from 10 strains isolated from parsley and 56 pathotype strains of P. syringae. Allele sequences were uploaded to the Plant-Associated Microbes Database and a phylogenetic tree was built based on concatenated sequences. Tree topology directly corresponded to P. syringae genomospecies and P. syringae pv. apii was allocated appropriately to genomospecies 3. This is the first demonstration that MLST can accurately allocate new pathogens directly to P. syringae sensu lato genomospecies. According to MLST, P. syringae pv. coriandricola is a member of genomospecies 9, P. cannabina. In a blind test, both P. syringae pv. coriandricola and P. syringae pv. apii isolates from parsley were correctly identified to pathovar. In both cases, MLST described diversity within each pathovar that was previously unknown.

  19. Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain.

    Science.gov (United States)

    Yang, Xiang; Noyes, Noelle R; Doster, Enrique; Martin, Jennifer N; Linke, Lyndsey M; Magnuson, Roberta J; Yang, Hua; Geornaras, Ifigenia; Woerner, Dale R; Jones, Kenneth L; Ruiz, Jaime; Boucher, Christina; Morley, Paul S; Belk, Keith E

    2016-04-01

    Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for Salmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus, Clostridium spp. (C. botulinum and C. perfringens), and Campylobacter spp. (C. jejuni,C. coli, and C. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts for S. enterica,E. coli, and C. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes. Copyright © 2016 Yang et al.

  20. In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip® technology

    Directory of Open Access Journals (Sweden)

    Ye Shui Q

    2005-05-01

    Full Text Available Abstract Background Genomic approaches in large animal models (canine, ovine etc are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To address this problem, we speculated that conserved interspecies genetic sequences can be experimentally detected by cross-species hybridization. The Affymetrix platform probe redundancy offers flexibility in selecting individual probes with high sequence similarities between related species for gene expression analysis. Results Gene expression profiles of 40 canine samples were generated using the human HG-U133A GeneChip (U133A. Due to interspecies genetic differences, only 14 ± 2% of canine transcripts were detected by U133A probe sets whereas profiling of 40 human samples detected 49 ± 6% of human transcripts. However, when these probe sets were deconstructed into individual probes and examined performance of each probe, we found that 47% of human probes were able to find their targets in canine tissues and generate a detectable hybridization signal. Therefore, we restricted gene expression analysis to these probes and observed the 60% increase in the number of identified canine transcripts. These results were validated by comparison of transcripts identified by our restricted analysis of cross-species hybridization with transcripts identified by hybridization of total lung canine mRNA to new Affymetrix Canine GeneChip®. Conclusion The experimental identification and restriction of gene expression analysis to probes with detectable hybridization signal drastically increases transcript detection of canine-human hybridization suggesting the possibility of broad utilization of cross-hybridizations of related species using GeneChip technology.

  1. Hanford Facility RCRA permit handbook

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-03-01

    Purpose of this Hanford Facility (HF) RCRA Permit Handbook is to provide, in one document, information to be used for clarification of permit conditions and guidance for implementing the HF RCRA Permit.

  2. Title V Permitting Statistics Inventory

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Title V Permitting Statistics Inventory contains measured and estimated nationwide statistical data, consisting of counts of permitted sources, types of permits...

  3. Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies.

    Science.gov (United States)

    Goddard, Katrina A B; Whitlock, Evelyn P; Berg, Jonathan S; Williams, Marc S; Webber, Elizabeth M; Webster, Jennifer A; Lin, Jennifer S; Schrader, Kasmintan A; Campos-Outcalt, Doug; Offit, Kenneth; Feigelson, Heather Spencer; Hollombe, Celine

    2013-09-01

    The aim of this study was to develop, operationalize, and pilot test a transparent, reproducible, and evidence-informed method to determine when to report incidental findings from next-generation sequencing technologies. Using evidence-based principles, we proposed a three-stage process. Stage I "rules out" incidental findings below a minimal threshold of evidence and is evaluated using inter-rater agreement and comparison with an expert-based approach. Stage II documents criteria for clinical actionability using a standardized approach to allow experts to consistently consider and recommend whether results should be routinely reported (stage III). We used expert opinion to determine the face validity of stages II and III using three case studies. We evaluated the time and effort for stages I and II. For stage I, we assessed 99 conditions and found high inter-rater agreement (89%), and strong agreement with a separate expert-based method. Case studies for familial adenomatous polyposis, hereditary hemochromatosis, and α1-antitrypsin deficiency were all recommended for routine reporting as incidental findings. The method requires definition of clinically actionable incidental findings and provide documentation and pilot testing of a feasible method that is scalable to the whole genome.

  4. 33 CFR 325.1 - Applications for permits.

    Science.gov (United States)

    2010-07-01

    ... process. Whenever the district engineer becomes aware of planning for work which may require a DA permit... in the basic timing sequence used by the Corps of Engineers in processing applications for DA permits.... Upon receipt of such request, the district engineer will assure the conduct of an orderly process which...

  5. First Complete Genomic Sequence of a Rabies Virus from the Republic of Tajikistan Obtained Directly from a Flinders Technology Associates Card

    OpenAIRE

    Goharriz, H.; Marston, D. A.; Sharifzoda, F.; Ellis, R. J.; Horton, D. L.; Khakimov, T.; Whatmore, A.; Khamroev, K.; Makhmadshoev, A. N.; Bazarov, M.; Fooks, A. R.; Banyard, A. C.

    2017-01-01

    ABSTRACT A brain homogenate derived from a rabid dog in the district of Tojikobod, Republic of Tajikistan, was applied to a Flinders Technology Associates (FTA) card. A full-genome sequence of rabies virus (RABV) was generated from the FTA card directly without extraction, demonstrating the utility of these cards for readily obtaining genetic data.

  6. First Complete Genomic Sequence of a Rabies Virus from the Republic of Tajikistan Obtained Directly from a Flinders Technology Associates Card.

    Science.gov (United States)

    Goharriz, H; Marston, D A; Sharifzoda, F; Ellis, R J; Horton, D L; Khakimov, T; Whatmore, A; Khamroev, K; Makhmadshoev, A N; Bazarov, M; Fooks, A R; Banyard, A C

    2017-07-06

    A brain homogenate derived from a rabid dog in the district of Tojikobod, Republic of Tajikistan, was applied to a Flinders Technology Associates (FTA) card. A full-genome sequence of rabies virus (RABV) was generated from the FTA card directly without extraction, demonstrating the utility of these cards for readily obtaining genetic data. © Crown copyright 2017.

  7. A Framework for Building Efficient Environmental Permitting Processes

    Directory of Open Access Journals (Sweden)

    Nicola Ulibarri

    2017-01-01

    Full Text Available Despite its importance as a tool for protecting air and water quality, and for mitigating impacts to protected species and ecosystems, the environmental permitting process is widely recognized to be inefficient and marked by delays. This article draws on a literature review and interviews with permitting practitioners to identify factors that contribute to delayed permit decisions. The sociopolitical context, projects that are complex or use novel technology, a fragmented and bureaucratic regulatory regime, serial permit applications and reviews, and applicant and permitting agency knowledge and resources each contribute to permitting inefficiency when they foster uncertainty, increase transaction costs, and allow divergent interests to multiply, yet remain unresolved. We then use the interviews to consider the potential of a collaborative dialogue between permitting agencies and applicants to mitigate these challenges, and argue that collaboration is well positioned to lessen permitting inefficiency.

  8. Permit application modifications

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-11-01

    This document contains the Permit Application Modifications for the Y-12 Industrial Landfill V site on the Oak Ridge Reservation. These modifications include the assessment of stability of the proposed Landfill V under static and loading conditions. Analyses performed include the general slope stability, veneer stability of the bottom liner and cover system, and a liquefaction potential assessment of the foundation soils.

  9. Permit application modifications

    International Nuclear Information System (INIS)

    1995-11-01

    This document contains the Permit Application Modifications for the Y-12 Industrial Landfill V site on the Oak Ridge Reservation. These modifications include the assessment of stability of the proposed Landfill V under static and loading conditions. Analyses performed include the general slope stability, veneer stability of the bottom liner and cover system, and a liquefaction potential assessment of the foundation soils

  10. PERMITTING HAZARDOUS WASTE INCINERATORS

    Science.gov (United States)

    This publication is a compilation of information presented at a seminar series designed to address the issues that affect the issuance of hazardous waste incineration permits and to improve the overall understanding of trial burn testing. pecifically, the document provides guidan...

  11. Is Whole-Exome Sequencing an Ethically Disruptive Technology? Perspectives of Pediatric Oncologists and Parents of Pediatric Patients With Solid Tumors.

    Science.gov (United States)

    McCullough, Laurence B; Slashinski, Melody J; McGuire, Amy L; Street, Richard L; Eng, Christine M; Gibbs, Richard A; Parsons, D William; Plon, Sharon E

    2016-03-01

    It has been anticipated that physician and parents will be ill prepared or unprepared for the clinical introduction of genome sequencing, making it ethically disruptive. As a part of the Baylor Advancing Sequencing in Childhood Cancer Care study, we conducted semistructured interviews with 16 pediatric oncologists and 40 parents of pediatric patients with cancer prior to the return of sequencing results. We elicited expectations and attitudes concerning the impact of sequencing on clinical decision making, clinical utility, and treatment expectations from both groups. Using accepted methods of qualitative research to analyze interview transcripts, we completed a thematic analysis to provide inductive insights into their views of sequencing. Our major findings reveal that neither pediatric oncologists nor parents anticipate sequencing to be an ethically disruptive technology, because they expect to be prepared to integrate sequencing results into their existing approaches to learning and using new clinical information for care. Pediatric oncologists do not expect sequencing results to be more complex than other diagnostic information and plan simply to incorporate these data into their evidence-based approach to clinical practice, although they were concerned about impact on parents. For parents, there is an urgency to protect their child's health and in this context they expect genomic information to better prepare them to participate in decisions about their child's care. Our data do not support the concern that introducing genome sequencing into childhood cancer care will be ethically disruptive, that is, leave physicians or parents ill prepared or unprepared to make responsible decisions about patient care. © 2015 Wiley Periodicals, Inc.

  12. 78 FR 43268 - Special Permit Applications

    Science.gov (United States)

    2013-07-19

    ... an amount qualifying as hazardous material. (modes 1, 2, 3, 4) 15860-N......... Apple Inc. 49 CFR To... strength stiffness. 13581-M......... Bengal Products 49 CFR To modify the Inc. Baton 173.306(a)(3). special............ Carleton 49 CFR 173.302a To modify the Technologies special permit to Inc. (Former change a drawing Grantee...

  13. Permitting issues in Virginia

    International Nuclear Information System (INIS)

    Kennel, R.P.

    1992-01-01

    As background, LG and E Development Corporation (formerly Hadson) has successfully put 16 Qualifying Facilities in the ground over the past 9 years in California, Maine, Virginia, and North Carolina. Each of these qualifying facilities has had some environmental innovative first, so there is no apology for the authors' environmental credentials. In Virginia, there are four identical 60 MW stoker coal cogeneration projects in Southampton County, Altavista, Hopewell, and -lastly-Buena Vista. The Buena Vista cogeneration project becomes the exception that proves the permitting rules. It has been in the permitting process for over 4 years; and despite being the cleanest coal project ever considered east of the Mississippi (design at 0.1 lbs/MMBtu for both So 2 and NO x ), it has suffered serous consequences from permitting delays and BACT ratcheting. As a simple comparison of importance, the Virginia Power Mt. Storm coal power facility emits approximately 150,000 tons of So 2 per year, while the Buena Vista project will actually emit approximately 150 tons of SO 2 per year (not including 1,500' tons of purchased SO 2 offsets). Both are similar distances from the Shenandoah National Park which has been the primary environmental point of concern in Virginia

  14. Air permitting of IGCC plants

    Energy Technology Data Exchange (ETDEWEB)

    Chitikela, S.R.

    2007-07-01

    The IGCC process is, currently, the preferred choice over conventional thermal power production in regard to cleanup of fuel and significantly reduced contaminant emissions. The air permitting requirements include the review of: feed preparation and PM emissions; feed gasification and contaminant emissions; elemental sulfur recovery and SO{sub 2} emissions; options for carbon-dioxide recovery; syngas characteristics for combustion; CT design and combustion mechanisms; air contaminant emissions of CT; controlled CT emissions of nitrogen-oxides and carbon-monoxide gases using the SCR and oxidation catalysts, respectively; and, emission of volatile organic compounds (VOCs), and hazardous air pollutants (HAPs). However, the IGCC processes are being rigorously reviewed for the system integration and reliability, and significant reduction of air contaminant emissions (including the greenhouse gases). This paper included a review of IGCC air contaminant emission rates, and various applicable regulatory requirements, such as NSR (New Source Review), NSPS (New Source Performance Standards), and MACT (Maximum Achievable Control Technology). The IGCC facility's NOX, CO, SO{sub 2}, PM, VOCs, and HAPs emission rates would be significantly low. Thus, effective, construction and installation, and operation air permits would be necessary for IGCC facilities.

  15. The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation

    International Nuclear Information System (INIS)

    Chen, Chung H.

    2004-01-01

    The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation

  16. Tradable CO2 permits in Danish and European energy policy

    DEFF Research Database (Denmark)

    Varming, S.; Eriksen, P.B.; Grohnheit, Poul Erik

    2000-01-01

    This report presents the results of the project "Tradable CO2 permits in Danish and European energy policy". The project was financed by a grant from the Danish Energy Research Programme 1998 (Grant 1753/98-0002). The project was conducted in co-operationbetween Elsamprojekt A/S (project manager...... for a tradable CO_2 permit market for the energy sector in the EU. Experience from the tradable SO_2 permit market in the US is taken into consideration as well. Topresent an overview of price estimates of CO_2 and greenhouse gas permits in different models as well as discussing the assumptions leading...... to the different outcomes. Furthermore, the special role of backstop technologies in relation to permit prices isanalysed. To analyse the connection between CO_2 permit prices and technology choice in the energy sector in the medium and longer term (i.e., 2010 and 2020) with a special emphasis on combined heat...

  17. Lean in Air Permitting Guide

    Science.gov (United States)

    The Lean in Air Permitting Guide is designed to help air program managers at public agencies better understand the potential value and results that can be achieved by applying Lean improvement methods to air permitting processes.

  18. Pacific Islands Region Fishing Permits

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Sustainable Fisheries Division Permits Program issues around 300 permits annually for pelagic longline and troll & handline, bottomfish, crustacean (lobster...

  19. Vessel Permit System Data Set

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — GARFO issues federal fishing permits annually to owners of fishing vessels who fish in the Greater Atlantic region, as required by federal regulation. These permits...

  20. Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry.

    Science.gov (United States)

    Babrak, Lmar; McGarvey, Jeffery A; Stanker, Larry H; Hnasko, Robert

    2017-10-01

    Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibodies (rAb). This determination can be achieved by sequence analysis of immunoglobulin (Ig) transcripts obtained from a monoclonal antibody (MAb) producing hybridoma and subsequent expression of a rAb. However the polyploidy nature of a hybridoma cell often results in the added expression of aberrant immunoglobulin-like transcripts or even production of anomalous antibodies which can confound production of rAb. An incorrect VR sequence will result in a non-functional rAb and de novo assembly of Ig primary structure without a sequence map is challenging. To address these problems, we have developed a methodology which combines: 1) selective PCR amplification of VR from both the heavy and light chain IgG from hybridoma, 2) molecular cloning and DNA sequence analysis and 3) tandem mass spectrometry (MS/MS) on enzyme digests obtained from the purified IgG. Peptide analysis proceeds by evaluating coverage of the predicted primary protein sequence provided by the initial DNA maps for the VR. This methodology serves to both identify and verify the primary structure of the MAb VR for production as rAb. Published by Elsevier Ltd.

  1. A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep-Sequencing Technology.

    Science.gov (United States)

    Kravatsky, Yuri; Chechetkin, Vladimir; Fedoseeva, Daria; Gorbacheva, Maria; Kravatskaya, Galina; Kretova, Olga; Tchurikov, Nickolai

    2017-11-23

    The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs), requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s). Deep sequencing is able to provide an assessment of both the general target conservation and the frequency of particular mutations in the different target sites. The aim of this study was to develop a reliable bioinformatic pipeline for the analysis of millions of short, deep sequencing reads corresponding to selected highly variable viral sequences that are drug target(s). The suggested bioinformatic pipeline combines the available programs and the ad hoc scripts based on an original algorithm of the search for the conserved targets in the deep sequencing data. We also present the statistical criteria for the threshold of reliable mutation detection and for the assessment of variations between corresponding data sets. These criteria are robust against the possible sequencing errors in the reads. As an example, the bioinformatic pipeline is applied to the study of the conservation of RNA interference (RNAi) targets in human immunodeficiency virus 1 (HIV-1) subtype A. The developed pipeline is freely available to download at the website http://virmut.eimb.ru/. Brief comments and comparisons between VirMut and other pipelines are also presented.

  2. A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep-Sequencing Technology

    Directory of Open Access Journals (Sweden)

    Yuri Kravatsky

    2017-11-01

    Full Text Available The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs, requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s. Deep sequencing is able to provide an assessment of both the general target conservation and the frequency of particular mutations in the different target sites. The aim of this study was to develop a reliable bioinformatic pipeline for the analysis of millions of short, deep sequencing reads corresponding to selected highly variable viral sequences that are drug target(s. The suggested bioinformatic pipeline combines the available programs and the ad hoc scripts based on an original algorithm of the search for the conserved targets in the deep sequencing data. We also present the statistical criteria for the threshold of reliable mutation detection and for the assessment of variations between corresponding data sets. These criteria are robust against the possible sequencing errors in the reads. As an example, the bioinformatic pipeline is applied to the study of the conservation of RNA interference (RNAi targets in human immunodeficiency virus 1 (HIV-1 subtype A. The developed pipeline is freely available to download at the website http://virmut.eimb.ru/. Brief comments and comparisons between VirMut and other pipelines are also presented.

  3. High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology

    DEFF Research Database (Denmark)

    Nag, Sidsel; Dalgaard, Marlene Danner; Kofoed, Poul-Erik

    2017-01-01

    Genetic polymorphisms in P. falciparum can be used to indicate the parasite's susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom...... designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well...

  4. SRComp: short read sequence compression using burstsort and Elias omega coding.

    Directory of Open Access Journals (Sweden)

    Jeremy John Selva

    Full Text Available Next-generation sequencing (NGS technologies permit the rapid production of vast amounts of data at low cost. Economical data storage and transmission hence becomes an increasingly important challenge for NGS experiments. In this paper, we introduce a new non-reference based read sequence compression tool called SRComp. It works by first employing a fast string-sorting algorithm called burstsort to sort read sequences in lexicographical order and then Elias omega-based integer coding to encode the sorted read sequences. SRComp has been benchmarked on four large NGS datasets, where experimental results show that it can run 5-35 times faster than current state-of-the-art read sequence compression tools such as BEETL and SCALCE, while retaining comparable compression efficiency for large collections of short read sequences. SRComp is a read sequence compression tool that is particularly valuable in certain applications where compression time is of major concern.

  5. Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi?

    Science.gov (United States)

    Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Erturan, Zayre; Ener, Beyza; Akdagli, Sevtap Arikan; Muslumanoglu, Hamza; Cetinkaya, Zafer

    2015-10-01

    Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis. © 2015 Blackwell Verlag GmbH.

  6. Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry

    Science.gov (United States)

    Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibo...

  7. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.

    Science.gov (United States)

    Chandrasekharappa, Settara C; Lach, Francis P; Kimble, Danielle C; Kamat, Aparna; Teer, Jamie K; Donovan, Frank X; Flynn, Elizabeth; Sen, Shurjo K; Thongthip, Supawat; Sanborn, Erica; Smogorzewska, Agata; Auerbach, Arleen D; Ostrander, Elaine A

    2013-05-30

    Current methods for detecting mutations in Fanconi anemia (FA)-suspected patients are inefficient and often miss mutations. We have applied recent advances in DNA sequencing and genomic capture to the diagnosis of FA. Specifically, we used custom molecular inversion probes or TruSeq-enrichment oligos to capture and sequence FA and related genes, including introns, from 27 samples from the International Fanconi Anemia Registry at The Rockefeller University. DNA sequencing was complemented with custom array comparative genomic hybridization (aCGH) and RNA sequencing (RNA-seq) analysis. aCGH identified deletions/duplications in 4 different FA genes. RNA-seq analysis revealed lack of allele specific expression associated with a deletion and splicing defects caused by missense, synonymous, and deep-in-intron variants. The combination of TruSeq-targeted capture, aCGH, and RNA-seq enabled us to identify the complementation group and biallelic germline mutations in all 27 families: FANCA (7), FANCB (3), FANCC (3), FANCD1 (1), FANCD2 (3), FANCF (2), FANCG (2), FANCI (1), FANCJ (2), and FANCL (3). FANCC mutations are often the cause of FA in patients of Ashkenazi Jewish (AJ) ancestry, and we identified 2 novel FANCC mutations in 2 patients of AJ ancestry. We describe here a strategy for efficient molecular diagnosis of FA.

  8. Learning with Technology: Video Modeling with Concrete-Representational-Abstract Sequencing for Students with Autism Spectrum Disorder

    Science.gov (United States)

    Yakubova, Gulnoza; Hughes, Elizabeth M.; Shinaberry, Megan

    2016-01-01

    The purpose of this study was to determine the effectiveness of a video modeling intervention with concrete-representational-abstract instructional sequence in teaching mathematics concepts to students with autism spectrum disorder (ASD). A multiple baseline across skills design of single-case experimental methodology was used to determine the…

  9. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

    Directory of Open Access Journals (Sweden)

    Chao Shiaoman

    2011-01-01

    Full Text Available Abstract Background Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Results Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM analysis. Of these, 52 (54% were polymorphic between parents of the Ogle1040 × TAM O-301 (OT mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. Conclusions The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide

  10. Marketable pollution permits with uncertainty and transaction costs

    International Nuclear Information System (INIS)

    Montero, Juan-Pablo

    1998-01-01

    Increasing interest in the use of marketable permits for pollution control has become evident in recent years. Concern regarding their performance still remains because empirical evidence has shown transaction costs and uncertainty to be significant in past and existing marketable permits programs. In this paper we develop theoretical and numerical models that include transaction costs and uncertainty (in trade approval) to show their effects on market performance (i.e., equilibrium price of permits and trading volume) and aggregate control costs. We also show that in the presence of transaction costs and uncertainty the initial allocation of permits may not be neutral in terms of efficiency. Furthermore, using a numerical model for a hypothetical NO x trading program in which participants have discrete control technology choices, we find that aggregate control costs and the equilibrium price of permits are sensitive to the initial allocation of permits, even for constant marginal transaction costs and certainty

  11. Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

    Science.gov (United States)

    Ramos, Antonio M.; Crooijmans, Richard P. M. A.; Affara, Nabeel A.; Amaral, Andreia J.; Archibald, Alan L.; Beever, Jonathan E.; Bendixen, Christian; Churcher, Carol; Clark, Richard; Dehais, Patrick; Hansen, Mark S.; Hedegaard, Jakob; Hu, Zhi-Liang; Kerstens, Hindrik H.; Law, Andy S.; Megens, Hendrik-Jan; Milan, Denis; Nonneman, Danny J.; Rohrer, Gary A.; Rothschild, Max F.; Smith, Tim P. L.; Schnabel, Robert D.; Van Tassell, Curt P.; Taylor, Jeremy F.; Wiedmann, Ralph T.; Schook, Lawrence B.; Groenen, Martien A. M.

    2009-01-01

    Background The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs. PMID:19654876

  12. Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.

    Science.gov (United States)

    Humble, Emily; Thorne, Michael A S; Forcada, Jaume; Hoffman, Joseph I

    2016-08-26

    Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be

  13. Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology

    OpenAIRE

    Tanase Koji; Nishitani Chikako; Hirakawa Hideki; Isobe Sachiko; Tabata Satoshi; Ohmiya Akemi; Onozaki Takashi

    2012-01-01

    Abstract Background Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, ...

  14. Learning with Technology: Video Modeling with Concrete-Representational-Abstract Sequencing for Students with Autism Spectrum Disorder.

    Science.gov (United States)

    Yakubova, Gulnoza; Hughes, Elizabeth M; Shinaberry, Megan

    2016-07-01

    The purpose of this study was to determine the effectiveness of a video modeling intervention with concrete-representational-abstract instructional sequence in teaching mathematics concepts to students with autism spectrum disorder (ASD). A multiple baseline across skills design of single-case experimental methodology was used to determine the effectiveness of the intervention on the acquisition and maintenance of addition, subtraction, and number comparison skills for four elementary school students with ASD. Findings supported the effectiveness of the intervention in improving skill acquisition and maintenance at a 3-week follow-up. Implications for practice and future research are discussed.

  15. First study on gene expression of cement proteins and potential adhesion-related genes of a membranous-based barnacle as revealed from Next-Generation Sequencing technology

    KAUST Repository

    Lin, Hsiu Chin; Wong, Yue Him; Tsang, Ling Ming; Chu, Ka Hou; Qian, Pei Yuan; Chan, Benny K K

    2013-01-01

    This is the first study applying Next-Generation Sequencing (NGS) technology to survey the kinds, expression location, and pattern of adhesion-related genes in a membranous-based barnacle. A total of 77,528,326 and 59,244,468 raw sequence reads of total RNA were generated from the prosoma and the basis of Tetraclita japonica formosana, respectively. In addition, 55,441 and 67,774 genes were further assembled and analyzed. The combined sequence data from both body parts generates a total of 79,833 genes of which 47.7% were shared. Homologues of barnacle cement proteins - CP-19K, -52K, and -100K - were found and all were dominantly expressed at the basis where the cement gland complex is located. This is the main area where transcripts of cement proteins and other potential adhesion-related genes were detected. The absence of another common barnacle cement protein, CP-20K, in the adult transcriptome suggested a possible life-stage restricted gene function and/or a different mechanism in adhesion between membranous-based and calcareous-based barnacles. © 2013 © 2013 Taylor & Francis.

  16. First study on gene expression of cement proteins and potential adhesion-related genes of a membranous-based barnacle as revealed from Next-Generation Sequencing technology

    KAUST Repository

    Lin, Hsiu Chin

    2013-12-12

    This is the first study applying Next-Generation Sequencing (NGS) technology to survey the kinds, expression location, and pattern of adhesion-related genes in a membranous-based barnacle. A total of 77,528,326 and 59,244,468 raw sequence reads of total RNA were generated from the prosoma and the basis of Tetraclita japonica formosana, respectively. In addition, 55,441 and 67,774 genes were further assembled and analyzed. The combined sequence data from both body parts generates a total of 79,833 genes of which 47.7% were shared. Homologues of barnacle cement proteins - CP-19K, -52K, and -100K - were found and all were dominantly expressed at the basis where the cement gland complex is located. This is the main area where transcripts of cement proteins and other potential adhesion-related genes were detected. The absence of another common barnacle cement protein, CP-20K, in the adult transcriptome suggested a possible life-stage restricted gene function and/or a different mechanism in adhesion between membranous-based and calcareous-based barnacles. © 2013 © 2013 Taylor & Francis.

  17. The usefulness of DNA sequencing after extraction by Whatman FTA filter matrix technology and phenotypic tests for differentiation of Candida albicans and Candida dubliniensis.

    Science.gov (United States)

    Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Muslumanoglu, Hamza

    2014-02-01

    Since C. dubliniensis is similar to C. albicans phenotypically, it can be misidentified as C. albicans. We aimed to investigate the prevalence of C. dubliniensis among isolates previously identified as C. albicans in our stocks and to compare the phenotypic methods and DNA sequencing of D1/D2 region on the ribosomal large subunit (rLSU) gene. A total of 850 isolates included in this study. Phenotypic identification was performed based on germ tube formation, chlamydospore production, colony colors on chromogenic agar, inability of growth at 45 °C and growth on hypertonic Sabouraud dextrose agar. Eighty isolates compatible with C. dubliniensis by at least one phenotypic test were included in the sequence analysis. Nested PCR amplification of D1/D2 region of the rLSU gene was performed after the fungal DNA extraction by Whatman FTA filter paper technology. The sequencing analysis of PCR products carried out by an automated capillary gel electrophoresis device. The rate of C. dubliniensis was 2.35 % (n = 20) among isolates previously described as C. albicans. Consequently, none of the phenotypic tests provided satisfactory performance alone in our study, and molecular methods required special equipment and high cost. Thus, at least two phenotypic methods can be used for identification of C. dubliniensis, and molecular methods can be used for confirmation.

  18. Identification and Characterization of Epstein-Barr Virus Genomes in Lung Carcinoma Biopsy Samples by Next-Generation Sequencing Technology.

    Science.gov (United States)

    Wang, Shanshan; Xiong, Hongchao; Yan, Shi; Wu, Nan; Lu, Zheming

    2016-05-18

    Epstein-Barr virus (EBV) has been detected in the tumor cells of several cancers, including some cases of lung carcinoma (LC). However, the genomic characteristics and diversity of EBV strains associated with LC are poorly understood. In this study, we sequenced the EBV genomes isolated from four primary LC tumor biopsy samples, designated LC1 to LC4. Comparative analysis demonstrated that LC strains were more closely related to GD1 strain. Compared to GD1 reference genome, a total of 520 variations in all, including 498 substitutions, 12 insertions, and 10 deletions were found. Latent genes were found to harbor the most numbers of nonsynonymous mutations. Phylogenetic analysis showed that all LC strains were closely related to Asian EBV strains, whereas different from African/American strains. LC2 genome was distinct from the other three LC genomes, suggesting at least two parental lineages of EBV among the LC genomes may exist. All LC strains could be classified as China 1 and V-val subtype according to the amino acid sequence of LMP1 and EBNA1, respectively. In conclusion, our results showed the genomic diversity among EBV genomes isolated from LC, which might facilitate to uncover the previously unknown variations of pathogenic significance.

  19. Existing and emerging detection technologies for DNA (Deoxyribonucleic Acid) finger printing, sequencing, bio- and analytical chips: a multidisciplinary development unifying molecular biology, chemical and electronics engineering.

    Science.gov (United States)

    Kumar Khanna, Vinod

    2007-01-01

    The current status and research trends of detection techniques for DNA-based analysis such as DNA finger printing, sequencing, biochips and allied fields are examined. An overview of main detectors is presented vis-à-vis these DNA operations. The biochip method is explained, the role of micro- and nanoelectronic technologies in biochip realization is highlighted, various optical and electrical detection principles employed in biochips are indicated, and the operational mechanisms of these detection devices are described. Although a diversity of biochips for diagnostic and therapeutic applications has been demonstrated in research laboratories worldwide, only some of these chips have entered the clinical market, and more chips are awaiting commercialization. The necessity of tagging is eliminated in refractive-index change based devices, but the basic flaw of indirect nature of most detection methodologies can only be overcome by generic and/or reagentless DNA sensors such as the conductance-based approach and the DNA-single electron transistor (DNA-SET) structure. Devices of the electrical detection-based category are expected to pave the pathway for the next-generation DNA chips. The review provides a comprehensive coverage of the detection technologies for DNA finger printing, sequencing and related techniques, encompassing a variety of methods from the primitive art to the state-of-the-art scenario as well as promising methods for the future.

  20. Genetic diagnosis of Duchenne and Becker muscular dystrophy using next-generation sequencing technology: comprehensive mutational search in a single platform.

    Science.gov (United States)

    Lim, Byung Chan; Lee, Seungbok; Shin, Jong-Yeon; Kim, Jong-Il; Hwang, Hee; Kim, Ki Joong; Hwang, Yong Seung; Seo, Jeong-Sun; Chae, Jong Hee

    2011-11-01

    Duchenne muscular dystrophy or Becker muscular dystrophy might be a suitable candidate disease for application of next-generation sequencing in the genetic diagnosis because the complex mutational spectrum and the large size of the dystrophin gene require two or more analytical methods and have a high cost. The authors tested whether large deletions/duplications or small mutations, such as point mutations or short insertions/deletions of the dystrophin gene, could be predicted accurately in a single platform using next-generation sequencing technology. A custom solution-based target enrichment kit was designed to capture whole genomic regions of the dystrophin gene and other muscular-dystrophy-related genes. A multiplexing strategy, wherein four differently bar-coded samples were captured and sequenced together in a single lane of the Illumina Genome Analyser, was applied. The study subjects were 25 16 with deficient dystrophin expression without a large deletion/duplication and 9 with a known large deletion/duplication. Nearly 100% of the exonic region of the dystrophin gene was covered by at least eight reads with a mean read depth of 107. Pathogenic small mutations were identified in 15 of the 16 patients without a large deletion/duplication. Using these 16 patients as the standard, the authors' method accurately predicted the deleted or duplicated exons in the 9 patients with known mutations. Inclusion of non-coding regions and paired-end sequence analysis enabled accurate identification by increasing the read depth and providing information about the breakpoint junction. The current method has an advantage for the genetic diagnosis of Duchenne muscular dystrophy and Becker muscular dystrophy wherein a comprehensive mutational search may be feasible using a single platform.

  1. PERMITTING LEADERSHIP IN THE UNITED STATES

    International Nuclear Information System (INIS)

    Ken Nemeth

    2002-01-01

    In accordance with the Southern States Energy Board (SSEB) proposal, as incorporated into NETL/DE-FC26-97FT34199, the objective of this agreement is to streamline the environmental technology permitting process site-to-site, state-to-state, and industry-to-industry to achieve remediation and waste processing faster, better and cheaper. SSEB is working with member Governors, legislators and regulators to build consensus on streamlining the permitting process for new and innovative technologies for addressing the legacy of environmental problems from 50 years of weapons research, development and production. This report reviews mechanisms whereby industry consortiums and the Department of Energy (DOE) have been working with State regulators and other officials in technology deployment decisions within the DOE complex. The historic development of relationships with State regulators is reviewed and the current nature of the relationships examined. The report contains observations from internal DOE reviews as well as recommendations from the General Accounting Office (GAO) and other external organizations. The report discusses reorganization initiatives leading up to a DOE Top-to-Bottom review of the Environmental Management (EM) Program and highlights points of consideration for maintaining effective linkages with State regulators. It notes how the proposed changes will place new demands upon the National Energy Technology Laboratory (NETL) and how NETL can leverage its resources by refocusing existing EM efforts specifically to states that have DOE facilities within their borders (host-states). Finally, the report discusses how SSEB's Permitting Leadership in the United States (PLUS) program can provide the foundation for elements of NETL's technical assistance program that are delivered to regulators and other decision- makers in host-states. As a regional compact commission, SSEB provides important direct linkages to regulators and stakeholders who need technical

  2. 2008 Contruction General Permits & Multi-Sector General Permits

    Data.gov (United States)

    U.S. Environmental Protection Agency — View stormwater notices of intent (NOIs) for construction projects under EPA's 2008 Construction General Permit (CGP), for Low Erosivity Waivers (LEWs) submitted...

  3. Noncooperative models of permit markets

    Energy Technology Data Exchange (ETDEWEB)

    Godal, Odd

    2011-07-15

    The applicability of some popular and basic permit market theories has been questioned. Drawing on noncooperative equilibrium theory for pure exchange economies, this article adapts several well-established alternative models to permit exchange. Some qualitative properties of the associated equilibria are provided, including two games with equilibria that in a sense coincide. Nevertheless, as there exist quite a few models potentially applicable to emissions trading, with equilibria that range from autarky to Pareto optimality, it seems that economics lacks a broadly accepted basic theory for permit markets. (Author)

  4. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  5. Permit trading and credit trading

    DEFF Research Database (Denmark)

    Boom, Jan-Tjeerd; R. Dijstra, Bouwe

    This paper compares emissions trading based on a cap on total emissions (permit trading) and on relative standards per unit of output (credit trading). Two types of market structure are considered: perfect competition and Cournot oligopoly. We find that output, abatement costs and the number...... of firms are higher under credit trading. Allowing trade between permit-trading and credit-trading sectors may increase in welfare. With perfect competition, permit trading always leads to higher welfare than credit trading. With imperfect competition, credit trading may outperform permit trading....... Environmental policy can lead to exit, but also to entry of firms. Entry and exit have a profound impact on the performance of the schemes, especially under imperfect competition. We find that it may be impossible to implement certain levels of total industry emissions. Under credit trading several levels...

  6. Pricing emission permits in the absence of abatement

    International Nuclear Information System (INIS)

    Hintermann, Beat

    2012-01-01

    If emissions are stochastic and firms are unable to control them through abatement, the cap in a permit market may be exceeded, or not be reached. I derive a binary options pricing formula that expresses the permit price as a function of the penalty for noncompliance and the probability of an exceeded cap under the assumption of no abatement. I apply my model to the EU ETS, where the rapid introduction of the market made it difficult for firms to adjust their production technology in time for the first phase. The model fits the data well, implying that the permit price may have been driven by firms hedging against stochastic emissions.

  7. Factors Influencing Learner Permit Duration

    Directory of Open Access Journals (Sweden)

    Johnathon P. Ehsani

    2016-12-01

    Full Text Available An increasing number of countries are requiring an extended learner permit prior to independent driving. The question of when drivers begin the learner permit period, and how long they hold the permit before advancing to independent licensure has received little research attention. Licensure timing is likely to be related to “push” and “pull” factors which may encourage or inhibit the process. To examine this question, we recruited a sample of 90 novice drivers (49 females and 41 males, average age of 15.6 years soon after they obtained a learner permit and instrumented their vehicles to collect a range of driving data. Participants completed a series of surveys at recruitment related to factors that may influence licensure timing. Two distinct findings emerged from the time-to-event analysis that tested these push and pull factors in relation to licensure timing. The first can be conceptualized as teens’ motivation to drive (push, reflected in a younger age when obtaining a learner permit and extensive pre-permit driving experience. The second finding was teens’ perceptions of their parents’ knowledge of their activities (pull; a proxy for a parents’ attentiveness to their teens’ lives. Teens who reported higher levels of their parents’ knowledge of their activities took longer to advance to independent driving. These findings suggest time-to-licensure may be related to teens’ internal motivation to drive, and the ability of parents to facilitate or impede early licensure.

  8. The National Solar Permitting Database

    Energy Technology Data Exchange (ETDEWEB)

    2014-08-31

    "The soft costs of solar — costs not associated with hardware — remain stubbornly high. Among the biggest soft costs are those associated with inefficiencies in local permitting and inspection. A study by the National Renewable Energy Laboratory and Lawrence Berkeley National Laboratory estimates that these costs add an average of $0.22/W per residential installation. This project helps reduce non-hardware/balance of system (BOS) costs by creating and maintaining a free and available site of permitting requirements and solar system verification software that installers can use to reduce time, capital, and resource investments in tracking permitting requirements. Software tools to identify best permitting practices can enable government stakeholders to optimize their permitting process and remove superfluous costs and requirements. Like ""a Wikipedia for solar permitting"", users can add, edit, delete, and update information for a given jurisdiction. We incentivize this crowdsourcing approach by recognizing users for their contributions in the form of SEO benefits to their company or organization by linking back to users' websites."

  9. Development and characterization of 26 novel microsatellite loci for the trochid gastropod Gibbula divaricata (Linnaeus, 1758, using Illumina MiSeq next generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Violeta López-Márquez

    2016-03-01

    Full Text Available In the present study we used the high-throughput sequencing technology Illumina MiSeq to develop 26 polymorphic microsatellite loci for the marine snail Gibbula divaricata. Four to 32 alleles were detected per locus across 30 samples analyzed. Observed and expected heterozygosities ranged from 0.130 to 0.933 and from 0.294 to 0.956, respectively. No significant linkage disequilibrium existed. Seven loci deviated from Hardy-Weinberg equilibrium that could not totally be explained by the presence of null alleles. Sympatric distribution with other species of the genus Gibbula, as G. rarilineata and G. varia, lead us to test the cross utility of the developed markers in these two species, which could be useful to test common biogeographic patterns or potential hybridization phenomena, since morphological intermediate specimens were found.

  10. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  11. Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples.

    Science.gov (United States)

    Borsu, Laetitia; Intrieri, Julie; Thampi, Linta; Yu, Helena; Riely, Gregory; Nafa, Khedoudja; Chandramohan, Raghu; Ladanyi, Marc; Arcila, Maria E

    2016-11-01

    Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  12. 50 CFR 679.4 - Permits.

    Science.gov (United States)

    2010-10-01

    ... this section, with the exception that an IFQ hired master permit or a CDQ hired master permit need not... program permit or card type is: Permit is in effect from issue date through the end of: For more... section (C) Halibut & sablefish hired master permits Specified fishing year Paragraph (d)(2) of this...

  13. High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA.

    Science.gov (United States)

    Kebschull, Justus M; Garcia da Silva, Pedro; Reid, Ashlan P; Peikon, Ian D; Albeanu, Dinu F; Zador, Anthony M

    2016-09-07

    Neurons transmit information to distant brain regions via long-range axonal projections. In the mouse, area-to-area connections have only been systematically mapped using bulk labeling techniques, which obscure the diverse projections of intermingled single neurons. Here we describe MAPseq (Multiplexed Analysis of Projections by Sequencing), a technique that can map the projections of thousands or even millions of single neurons by labeling large sets of neurons with random RNA sequences ("barcodes"). Axons are filled with barcode mRNA, each putative projection area is dissected, and the barcode mRNA is extracted and sequenced. Applying MAPseq to the locus coeruleus (LC), we find that individual LC neurons have preferred cortical targets. By recasting neuroanatomy, which is traditionally viewed as a problem of microscopy, as a problem of sequencing, MAPseq harnesses advances in sequencing technology to permit high-throughput interrogation of brain circuits. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Review of Project Permits under the London Protocol - An Assessment of the Proposed P18-4 CO2 Storage Site: 13th International Conference on Greenhouse Gas Control Technologies, GHGT 2016. 14 November 2016 through 18 November

    OpenAIRE

    Mikunda, T.; Dixon, T.

    2017-01-01

    The London Protocol (1996) is a global agreement to promote the protection of the marine environment by prohibiting the dumping of wastes and other matter into the sea. Under the Protocol all dumping is prohibited, with the exception of a limited number of selected wastes on the so-called "reverse list", which can be considered for dumping. In 2007, an amendment entered into force which permitted CO2 streams to be considered for dumping under the London Protocol. The amendment was shortly fol...

  15. FIRE PERMIT NOW ON EDH!

    CERN Multimedia

    TIS General Safety Group or

    2001-01-01

    The electronic version of the Fire Permit form is now active. The aim of the Fire Permit procedure is to reduce the risk of fire or explosion. It is mandatory when performing 'hot work' (mainly activities which involve the use of naked flames or other heat sources - e.g. welding, brazing, cutting, grinding, etc.). Its use is explained in the CERN Fire Protection Code E. (Fire Protection) The new electronic form, which is substantially unchanged from the previous authorizing procedure, will be available on the Electronic Document Handling system (https://edh.cern.ch/) as of 1st September 2001. From this date use of the paper version should be discontinued.

  16. De novo transcriptome sequencing of the Octopus vulgaris hemocytes using Illumina RNA-Seq technology: response to the infection by the gastrointestinal parasite Aggregata octopiana.

    Science.gov (United States)

    Castellanos-Martínez, Sheila; Arteta, David; Catarino, Susana; Gestal, Camino

    2014-01-01

    Octopus vulgaris is a highly valuable species of great commercial interest and excellent candidate for aquaculture diversification; however, the octopus' well-being is impaired by pathogens, of which the gastrointestinal coccidian parasite Aggregata octopiana is one of the most important. The knowledge of the molecular mechanisms of the immune response in cephalopods, especially in octopus is scarce. The transcriptome of the hemocytes of O. vulgaris was de novo sequenced using the high-throughput paired-end Illumina technology to identify genes involved in immune defense and to understand the molecular basis of octopus tolerance/resistance to coccidiosis. A bi-directional mRNA library was constructed from hemocytes of two groups of octopus according to the infection by A. octopiana, sick octopus, suffering coccidiosis, and healthy octopus, and reads were de novo assembled together. The differential expression of transcripts was analysed using the general assembly as a reference for mapping the reads from each condition. After sequencing, a total of 75,571,280 high quality reads were obtained from the sick octopus group and 74,731,646 from the healthy group. The general transcriptome of the O. vulgaris hemocytes was assembled in 254,506 contigs. A total of 48,225 contigs were successfully identified, and 538 transcripts exhibited differential expression between groups of infection. The general transcriptome revealed genes involved in pathways like NF-kB, TLR and Complement. Differential expression of TLR-2, PGRP, C1q and PRDX genes due to infection was validated using RT-qPCR. In sick octopuses, only TLR-2 was up-regulated in hemocytes, but all of them were up-regulated in caecum and gills. The transcriptome reported here de novo establishes the first molecular clues to understand how the octopus immune system works and interacts with a highly pathogenic coccidian. The data provided here will contribute to identification of biomarkers for octopus resistance against

  17. Hydroelectric Generating Facilities General Permit ...

    Science.gov (United States)

    2017-08-28

    The Notice of Availability of the Final NPDES General Permits (HYDROGP) for Discharges at Hydroelectric Generating Facilities in Massachusetts (MAG360000) and New Hampshire (NHG360000) and Tribal Lands in the State of Massachusetts was published in the Federal Register on December 7, 2009 (see 74 Fed. Reg. No. 233, pages 64074 - 64075).

  18. 50 CFR 660.25 - Permits.

    Science.gov (United States)

    2010-10-01

    ... change and the reasons for the request. If the permit requested to be changed to the base permit is..., vessel owner, or permit owner for any reason. The sablefish at-sea processing exemption will expire upon... ownership. (G) For a request to change a permit's ownership that is necessitated by divorce, the individual...

  19. 10 CFR 50.23 - Construction permits.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Construction permits. 50.23 Section 50.23 Energy NUCLEAR... Description of Licenses § 50.23 Construction permits. A construction permit for the construction of a... part 52 of this chapter, the construction permit and operating license are deemed to be combined in a...

  20. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

    Science.gov (United States)

    Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.

  1. Genetic mapping using the Diversity Arrays Technology (DArT) : application and validation using the whole-genome sequences of Arabidopsis thaliana and the fungal wheat pathogen Mycosphaerella graminicola

    NARCIS (Netherlands)

    Wittenberg, A.H.J.

    2007-01-01

    Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds- to thousands of restriction site based polymorphisms between genotypes and does not require DNA sequence

  2. Waste-to-energy permitting sourcebook

    International Nuclear Information System (INIS)

    Longwell, D.; Wegrecki, A.; Williams, D.

    1992-10-01

    Environmental issues, regulatory processes and approvals important in obtaining a permit to construct and/or operate a waste-to-energy (WTE) facility are identified and discussed. Environmental issues include: (1) air emission levels, their control and potential impacts, (2) ash leachability, treatment, and disposal, (3) potential health risks from emissions, and (4) other issues such as need/benefit and public perception of WTE. Laws, regulations and approvals that can affect project development are identified and listed, and potential regulatory trends are discussed. A general permit acquisition plan is also presented. An analysis of environmental and regulatory data obtained from the literature, regulatory agencies, and specific projects is presented. California and Massachusetts, both with regulations generally more stringent than federal regulations and considered environmentally conservative, were selected for detailed state regulatory review. Two project case histories (Commerce Refuse-to-Energy (RTE) Project in California and SEMASS WTE Project in Massachusetts) were selected to illustrate: (1) how regulations are actually applied to a project, (2) project-specific permit and operating conditions, and (3) project-specific environmental issues. Modern WTE plots employ state-of-the-art air emission control technologies and strategies to reduce air emission is to levels below regulatory requirements and to reduce estimated health risks to within EPA's acceptable risk range. WTE ash leachate can exhibit hazardous waste characteristics, primarily lead and cadmium. However, modern landfills utilize liners and leachate collection systems to prevent infiltration of leachate into the groundwater supply. Modern WTE plants employ dry systems and have zero process wastewater discharge

  3. 78 FR 42540 - Endangered and Threatened Species; Permits

    Science.gov (United States)

    2013-07-16

    ... to the disadvantage of the listed species, and that the terms and conditions of the permit were... UNIVERSITY 207948 3/4/2013 12/31/2017 WESTERN ECOSYSTEMS TECHNOLOGY, INC 050706 10/1/2012 12/31/2015 WESTERN...

  4. 75 FR 34445 - Audit Program for Texas Flexible Permit Holders

    Science.gov (United States)

    2010-06-17

    ... flexible permit. The third-party auditor would identify for each emission unit regulated under the source's... Technology, State Implementation Plan citation). The auditor will also need to review and assess the adequacy... unit-specific emission limitations. Where deficiencies exist, the auditor will provide recommendations...

  5. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  6. NPDES permits and water analyses

    International Nuclear Information System (INIS)

    Pojasek, R.B.

    1975-01-01

    Provisions of the Federal Water Pollution Control Act, as amended by P. L. 92-500, including an explanation of the National Pollutant Discharge Elimination System (NPDES), and EPA's criteria for the analysis of pollutants are discussed. The need for a revision of current restrictive variance procedures is pointed out. References for the comparison of analytical methods for water pollutants under permits, including radioactive parameters, are tabulated. (U.S.)

  7. Technology.

    Science.gov (United States)

    Online-Offline, 1998

    1998-01-01

    Focuses on technology, on advances in such areas as aeronautics, electronics, physics, the space sciences, as well as computers and the attendant progress in medicine, robotics, and artificial intelligence. Describes educational resources for elementary and middle school students, including Web sites, CD-ROMs and software, videotapes, books,…

  8. 300 Area Treated Effluent Disposal Facility permit reopener run plan

    International Nuclear Information System (INIS)

    Olander, A.R.

    1995-01-01

    The 300 Area Treated Effluent Disposal Facility (TEDF) is authorized to discharge treated effluent to the Columbia River by National Pollutant Discharge Elimination System permit WA-002591-7. The letter accompanying the final permit noted the following: EPA recognizes that the TEDF is a new waste treatment facility for which full scale operation and effluent data has not been generated. The permit being issued by EPA contains discharge limits that are intended to force DOE's treatment technology to the limit of its capability.'' Because of the excessively tight limits the permit contains a reopener clause which may allow limits to be renegotiated after at least one year of operation. The restrictions for reopening the permit are as follows: (1) The permittee has properly operated and maintained the TEDF for a sufficient period to stabilize treatment plant operations, but has nevertheless been unable to achieve the limitation specified in the permit. (2) Effluent data submitted by the permittee supports the effluent limitation modifications(s). (3) The permittee has submitted a formal request for the effluent limitation modification(s) to the Director. The purpose of this document is to guide plant operations for approximately one year to ensure appropriate data is collected for reopener negotiations

  9. A System of Tradable Permits to Control Emission of Greenhouse Gases in Norway. Challenges for the Petroleum Industry

    Energy Technology Data Exchange (ETDEWEB)

    Schreiner, Per

    1998-07-01

    This presentation discusses the instruments of climate policy, comments on carbon taxes, outlines a tradable permits system, tradable permits and the petroleum industry, revenue from the offshore, and clarifies impact for the petroleum industry. Measures to reduce emissions are grouped into four: (1) Taxes on the emitted quantity, (2) Regulations that force companies to use certain processes or technologies, (3) Emission permits, (4) Information.

  10. Watershed-based point sources permitting strategy and dynamic permit-trading analysis.

    Science.gov (United States)

    Ning, Shu-Kuang; Chang, Ni-Bin

    2007-09-01

    Permit-trading policy in a total maximum daily load (TMDL) program may provide an additional avenue to produce environmental benefit, which closely approximates what would be achieved through a command and control approach, with relatively lower costs. One of the important considerations that might affect the effective trading mechanism is to determine the dynamic transaction prices and trading ratios in response to seasonal changes of assimilative capacity in the river. Advanced studies associated with multi-temporal spatially varied trading ratios among point sources to manage water pollution hold considerable potential for industries and policy makers alike. This paper aims to present an integrated simulation and optimization analysis for generating spatially varied trading ratios and evaluating seasonal transaction prices accordingly. It is designed to configure a permit-trading structure basin-wide and provide decision makers with a wealth of cost-effective, technology-oriented, risk-informed, and community-based management strategies. The case study, seamlessly integrating a QUAL2E simulation model with an optimal waste load allocation (WLA) scheme in a designated TMDL study area, helps understand the complexity of varying environmental resources values over space and time. The pollutants of concern in this region, which are eligible for trading, mainly include both biochemical oxygen demand (BOD) and ammonia-nitrogen (NH3-N). The problem solution, as a consequence, suggests an array of waste load reduction targets in a well-defined WLA scheme and exhibits a dynamic permit-trading framework among different sub-watersheds in the study area. Research findings gained in this paper may extend to any transferable dynamic-discharge permit (TDDP) program worldwide.

  11. The Biomolecule Sequencer Project: Nanopore Sequencing as a Dual-Use Tool for Crew Health and Astrobiology Investigations

    Science.gov (United States)

    John, K. K.; Botkin, D. S.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lehman, N.; Lupisella, M. L.; Mason, C. E.; Smith, D. J.; hide

    2016-01-01

    Human missions to Mars will fundamentally transform how the planet is explored, enabling new scientific discoveries through more sophisticated sample acquisition and processing than can currently be implemented in robotic exploration. The presence of humans also poses new challenges, including ensuring astronaut safety and health and monitoring contamination. Because the capability to transfer materials to Earth will be extremely limited, there is a strong need for in situ diagnostic capabilities. Nucleotide sequencing is a particularly powerful tool because it can be used to: (1) mitigate microbial risks to crew by allowing identification of microbes in water, in air, and on surfaces; (2) identify optimal treatment strategies for infections that arise in crew members; and (3) track how crew members, microbes, and mission-relevant organisms (e.g., farmed plants) respond to conditions on Mars through transcriptomic and genomic changes. Sequencing would also offer benefits for science investigations occurring on the surface of Mars by permitting identification of Earth-derived contamination in samples. If Mars contains indigenous life, and that life is based on nucleic acids or other closely related molecules, sequencing would serve as a critical tool for the characterization of those molecules. Therefore, spaceflight-compatible nucleic acid sequencing would be an important capability for both crew health and astrobiology exploration. Advances in sequencing technology on Earth have been driven largely by needs for higher throughput and read accuracy. Although some reduction in size has been achieved, nearly all commercially available sequencers are not compatible with spaceflight due to size, power, and operational requirements. Exceptions are nanopore-based sequencers that measure changes in current caused by DNA passing through pores; these devices are inherently much smaller and require significantly less power than sequencers using other detection methods

  12. Technology

    Directory of Open Access Journals (Sweden)

    Xu Jing

    2016-01-01

    Full Text Available The traditional answer card reading method using OMR (Optical Mark Reader, most commonly, OMR special card special use, less versatile, high cost, aiming at the existing problems proposed a method based on pattern recognition of the answer card identification method. Using the method based on Line Segment Detector to detect the tilt of the image, the existence of tilt image rotation correction, and eventually achieve positioning and detection of answers to the answer sheet .Pattern recognition technology for automatic reading, high accuracy, detect faster

  13. Forest Products Industry Permitting Information

    Science.gov (United States)

    This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

  14. State Waste Discharge Permit Application: Electric resistance tomography testing

    Energy Technology Data Exchange (ETDEWEB)

    1994-04-01

    This permit application documentation is for a State Waste Discharge Permit issued in accordance with requirements of Washington Administrative Code 173-216. The activity being permitted is a technology test using electrical resistance tomography. The electrical resistance tomography technology was developed at Lawrence Livermore National Laboratory and has been used at other waste sites to track underground contamination plumes. The electrical resistance tomography technology measures soil electrical resistance between two electrodes. If a fluid contaminated with electrolytes is introduced into the soil, the soil resistance is expected to drop. By using an array of measurement electrodes in several boreholes, the areal extent of contamination can be estimated. At the Hanford Site, the purpose of the testing is to determine if the electrical resistance tomography technology can be used in the vicinity of large underground metal tanks without the metal tank interfering with the test. It is anticipated that the electrical resistance tomography technology will provide a method for accurately detecting leaks from the bottom of underground tanks, such as the Hanford Site single-shell tanks.

  15. State Waste Discharge Permit Application: Electric resistance tomography testing

    International Nuclear Information System (INIS)

    1994-04-01

    This permit application documentation is for a State Waste Discharge Permit issued in accordance with requirements of Washington Administrative Code 173-216. The activity being permitted is a technology test using electrical resistance tomography. The electrical resistance tomography technology was developed at Lawrence Livermore National Laboratory and has been used at other waste sites to track underground contamination plumes. The electrical resistance tomography technology measures soil electrical resistance between two electrodes. If a fluid contaminated with electrolytes is introduced into the soil, the soil resistance is expected to drop. By using an array of measurement electrodes in several boreholes, the areal extent of contamination can be estimated. At the Hanford Site, the purpose of the testing is to determine if the electrical resistance tomography technology can be used in the vicinity of large underground metal tanks without the metal tank interfering with the test. It is anticipated that the electrical resistance tomography technology will provide a method for accurately detecting leaks from the bottom of underground tanks, such as the Hanford Site single-shell tanks

  16. 5 CFR 734.202 - Permitted activities.

    Science.gov (United States)

    2010-01-01

    ... (CONTINUED) POLITICAL ACTIVITIES OF FEDERAL EMPLOYEES Permitted Activities § 734.202 Permitted activities. Employees may take an active part in political activities, including political management and political campaigns, to the extent not expressly prohibited by law and this part. ...

  17. 300 area TEDF permit compliance monitoring plan

    International Nuclear Information System (INIS)

    BERNESKI, L.D.

    1998-01-01

    This document presents the permit compliance monitoring plan for the 300 Area Treated Effluent Disposal Facility (TEDF). It addresses the compliance with the National Pollutant Discharge Elimination System (NPDES) permit and Department of Natural Resources Aquatic Lands Sewer Outfall Lease

  18. Rosebud Casino and Hotel NPDES Proposed Permit

    Science.gov (United States)

    Indian Country, Minor Permit, proposed permit SD-0034584, Rosebud Casino and Hotel, South Dakota, is authorized to discharge from its wastewater treatment facility in Todd County, South Dakota to an unnamed drainageway(s) tributary to Rock Creek.

  19. 300 area TEDF permit compliance monitoring plan

    Energy Technology Data Exchange (ETDEWEB)

    BERNESKI, L.D.

    1998-11-20

    This document presents the permit compliance monitoring plan for the 300 Area Treated Effluent Disposal Facility (TEDF). It addresses the compliance with the National Pollutant Discharge Elimination System (NPDES) permit and Department of Natural Resources Aquatic Lands Sewer Outfall Lease.

  20. 7 CFR 319.75-3 - Permits.

    Science.gov (United States)

    2010-01-01

    ... Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Port Operations, Permit Unit... article may be imported only after issuance of a written permit by Plant Protection and Quarantine. (b) An application for a written permit should be submitted to the Animal and Plant Health Inspection Service, Plant...

  1. 77 FR 25082 - Picture Permit Imprint Indicia

    Science.gov (United States)

    2012-04-27

    ... POSTAL SERVICE 39 CFR Part 111 Picture Permit Imprint Indicia AGENCY: Postal Service\\TM\\. ACTION... Service, Domestic Mail Manual (DMM[supreg]) 604.5 to add picture permit imprint indicia standards allowing...: The use of picture permit imprint indicia is designed to improve the effectiveness of a mailpiece by...

  2. 40 CFR 70.6 - Permit content.

    Science.gov (United States)

    2010-07-01

    ... § 70.5(d) of this part. (B) Prompt reporting of deviations from permit requirements, including those... corrective actions or preventive measures taken. The permitting authority shall define “prompt” in relation... and air pollution control equipment), practices, or operations regulated or required under the permit...

  3. A Review of the Environmental Impacts for Marine and Hydrokinetic Projects to Inform Regulatory Permitting: Summary Findings from the 2015 Workshop on Marine and Hydrokinetic Technologies, Washington, D.C.

    Energy Technology Data Exchange (ETDEWEB)

    Baring-Gould, E. Ian [National Renewable Energy Lab. (NREL), Golden, CO (United States); Christol, Corrie [National Renewable Energy Lab. (NREL), Golden, CO (United States); LiVecchi, Al [National Renewable Energy Lab. (NREL), Golden, CO (United States); Kramer, Sharon [H.T. Harvey and Associates, Los Gatos, CA (United States); West, Anna [Kearns & West, Inc., San Francisco, CA (United States)

    2016-07-01

    In 2014 and 2015, the U.S. Department of Energy initiated efforts to develop and implement technology- and application-focused marine and hydrokinetic (MHK) workshops to share the global experience and knowledge base on evolving MHK technologies, observed and not-observed impacts, monitoring and measurement methods, and regulatory needs. The resulting MHK Regulator Workshops engaged resource managers and other decision makers at key regulatory organizations, scientists, researchers, facilitators, and technical experts and provided an opportunity to examine the risks of single-device and small-scale deployments, explore what can be learned and observed from single devices and small-scale arrays, and consider requirements for projects at varying scales of deployment. Experts and stakeholders identified key remaining information gaps. Initial discussions focused on differentiating between monitoring required for single or small-scale deployments and MHK impact research that, although important, goes beyond what is feasible or should be needed to meet specific project regulatory requirements but is appropriate for broader research and development. Four areas of identified potential environmental impacts provided the focus for the workshop: acoustic output impacts, electromagnetic field (EMF) emissions, physical interactions, and environmental effects of MHK energy development on the physical environment. Discussions also focused on the regulatory process and experience, adaptive management, industry drivers, and lessons that can be learned from the wind energy industry. The discussion was set in the context of the types of MHK technologies that are currently proposed or planned in the United States. All presentations and the following discussions are summarized in this document.

  4. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  5. 75 FR 43536 - Agency Information Collection Activities: Permit To Transfer Containers to a Container Station

    Science.gov (United States)

    2010-07-26

    ... Activities: Permit To Transfer Containers to a Container Station AGENCY: U.S. Customs and Border Protection... Transfer Containers to a Container Station. This is a proposed extension of an information collection that... other technological techniques or other forms of information. Title: Permit to Transfer Containers to a...

  6. XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.

    Science.gov (United States)

    Frank, Daniel N

    2008-10-07

    Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects. XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST (Basic Local Alignment and Search Tool; 123) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file. XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.

  7. Annual Hanford Site Environmental Permitting Status Report

    International Nuclear Information System (INIS)

    HOMAN, N.A.

    2000-01-01

    The information contained in, and/or referenced in, this Annual Hanford Site Environmental Permitting Status Report addresses Permit Condition II.W (Other Permits and/or Approvals) of the Dangerous Waste Portion of the Resource Conservation and Recovery Act Permit for the Treatment, Storage, and Disposal of Dangerous Waste, issued by the Washington State Department of Ecology (WA7890008967). Condition II.W specifies that the Permittees are responsible for obtaining all other applicable federal, state, and local permits authorizing the development and operation of the Hanford Facility. This status report also addresses Permit Condition I.E.22, as interpreted in Section 12.1.25 of the Hanford Facility Dangerous Waste Permit Application, General Information Portion (DOE/RL-91-28, Rev. 4), that states this report will be prepared annually and a copy of this report will be placed in the Facility Operating Record, General Information file by October 1 of each year

  8. Annual Hanford Site Environmental Permitting status report

    International Nuclear Information System (INIS)

    SONNICHSEN, J.C.

    1999-01-01

    The information contained in, and/or referenced in, this Annual Hanford Site Environmental Permitting Status Report addresses Permit Condition II.W (Other Permits and/or Approvals) of the Dangerous Waste Portion of the Resource Conservation and Recovery Act Permit for the Treatment, Storage, and Disposal of Dangerous Waste, issued by the Washington State Department of Ecology (WA7890008967). Condition II.W specifies that the Permittees are responsible for obtaining all other applicable federal, state, and local permits authorizing the development and operation of the Hanford Facility. Condition II.W further specifies that the Permittees are to use their best efforts to obtain such permits. For the purposes of this Permit Condition, ''best efforts'' mean submittal of documentation and/or approval(s) in accordance with schedules specified in applicable regulations, or as determined through negotiations with the applicable regulatory agencies

  9. 41 CFR 102-74.500 - Can Federal agencies disapprove permit applications or cancel issued permits?

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Can Federal agencies disapprove permit applications or cancel issued permits? 102-74.500 Section 102-74.500 Public Contracts and... cancel issued permits? Yes, Federal agencies may disapprove any permit application or cancel an issued...

  10. Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

    Science.gov (United States)

    Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

    2016-09-01

    Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

  11. Emerging Technologies for Gut Microbiome Research

    Science.gov (United States)

    Arnold, Jason W.; Roach, Jeffrey; Azcarate-Peril, M. Andrea

    2016-01-01

    Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches will improve the efficiency and quality of microbiome research. Here, we will discuss emerging technologies and their potential impact on gut microbiome studies. PMID:27426971

  12. An economic analysis of tradeable emission permits for sulphur dioxide emissions in Europe

    International Nuclear Information System (INIS)

    Kruitwagen, S.

    1996-01-01

    are reviewed. To provide a complete overview of models, non-European models are reviewed as well. Secondly, the advantages and drawbacks of the different models are weighed up against each other, concluding in a selection of one of the European integrated assessment models to be used in the analysis of this thesis. The first four chapters provide all elements necessary for developing and subsequently simulating a new permit trading system for SO2 emissions. Building on Chapter 3, Chapter 5 develops in steps the concept of guided bilateral permit trading. This system aims at cost-effective emission abatement given pre-specified deposition targets, assuming that permit trading is a bilateral and sequential process. The need to restrict (guide) trade is extensively discussed and the implications of trade restrictions for a bilateral and sequential trade process are explained. In Chapter 6 guided bilateral permit trading will be simulated for SO2 permits in Europe. It is assumed that permit trading takes place among countries. First, the simulation model is described. Next, the simulation results for the base case and two variants are successively discussed. Since in this thesis it is assumed that permit trading is a bilateral and sequential process, special attention is paid to the trade sequence. By simulating different trade sequences the effect of the sequence of transactions is examined. refs

  13. Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

    Directory of Open Access Journals (Sweden)

    Rodrigo Pessôa

    Full Text Available BACKGROUND: Here, we report on the partial and full-length genomic (FLG variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs, 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP and 7 adult T-cell leukemia/lymphoma (ATLL patients, using an Illumina paired-end protocol. METHODS: Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. RESULTS: A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14 and FLG (n = 76 data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5% individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA and that 4 individuals (4.5% were infected with the Japanese sub-subtypes (aB. A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. CONCLUSIONS: This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data

  14. Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

    Science.gov (United States)

    Pessôa, Rodrigo; Watanabe, Jaqueline Tomoko; Nukui, Youko; Pereira, Juliana; Casseb, Jorge; Kasseb, Jorge; de Oliveira, Augusto César Penalva; Segurado, Aluisio Cotrim; Sanabani, Sabri Saeed

    2014-01-01

    Here, we report on the partial and full-length genomic (FLG) variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs), 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and 7 adult T-cell leukemia/lymphoma (ATLL) patients, using an Illumina paired-end protocol. Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14) and FLG (n = 76) data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5%) individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA) and that 4 individuals (4.5%) were infected with the Japanese sub-subtypes (aB). A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data will add to our current understanding of the

  15. Simultaneous discrimination of species and strains in Lactobacillus rhamnosus using species-specific PCR combined with multiplex mini-sequencing technology.

    Science.gov (United States)

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Lina; Chu, Wen-Shen

    2015-12-01

    This study described the use of species-specific PCR in combination with SNaPshot mini-sequencing to achieve species identification and strain differentiation in Lactobacillus rhamnosus. To develop species-specific PCR and strain subtyping primers, the dnaJ gene was used as a target, and its corresponding sequences were analyzed both in Lb. rhamnosus and in a subset of its phylogenetically closest species. The results indicated that the species-specific primer pair was indeed specific for Lb. rhamnosus, and the mini-sequencing assay was able to unambiguously distinguish Lb. rhamnosus strains into different haplotypes. In conclusion, we have successfully developed a rapid, accurate and cost-effective assay for inter- and intraspecies discrimination of Lb. rhamnosus, which can be applied to achieve efficient quality control of probiotic products. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. RPP Environmental Permits and Related Documentation

    International Nuclear Information System (INIS)

    DEXTER, M.L.

    2001-01-01

    This document contains the current list of environmental permits and related documentation for RPP facilities and activities. Copies of these permits and related approvals are maintained by RPP Environmental. In addition, notices of Correction and Notices of Violation are issued by State and Federal Regulators which are tracked by RPP Environmental to resolve any recently identified deficiencies. A listing of these recent Notices is provided as an attachment to this document. These permits, approval conditions, and recent regulatory agency notices, constitute an important element of the RPP Authorization Envelope. Permits are issued frequently and the reader is advised to check with RPP environmental for new permits or approval conditions. Interpretation of permit or approval conditions should be coordinated with RPP Environmental. This document is updated on a quarterly basis

  17. RPP Environmental Permits and Related Documentation

    International Nuclear Information System (INIS)

    DEXTER, M.L.

    2000-01-01

    This document contains the current list of environmental permits and related documentation for RPP facilities and activities. Copies of these permits and related approvals are maintained by RPP Environmental. In addition, Notices of Correction and Notices of Violation are issued by State and Federal Regulators which are tracked by RPP Environmental to resolve any recently identified deficiencies. A listing of these recent Notices is provided as an attachment to this document. These permits, approval conditions, and recent regulatory agency notices, constitute an important element of the RPP Authorization Envelope. Permits are issued frequently and the reader is advised to check with RPP environmental for new permits or approval conditions. Interpretation of permit or approval conditions should be coordinated with RPP Environmental. This document will be updated on a quarterly basis

  18. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  19. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  20. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  1. Conference report : PERM-IT '97

    International Nuclear Information System (INIS)

    Smyth, V.; Yeabsley, A.

    1997-01-01

    The PERM-IT conference (Physics Engineering Radiation Medicine with a special emphasis on Information Technology) which was held in Adelaide with an attendance of about 250, was the joint annual meeting of the Australasian Radiation Protection Society, the Australasian College of Physical Scientists and Engineers in Medicine, the College of Biomedical Engineers of the Institution of Engineers Australia and the Society for Medical and Biological Engineering. The program was organised with three parallel sessions running most of the time, with plenary sessions for items of particular interest featuring keynote speakers from around the world. Attendance at this conference allowed the opportunity to meet with colleagues in other regulatory agencies, and Australia has a number of these. But what should be done about radioactive waste? A universal groan is raised by radiation protection regulatory authority staff at this question. Plans are afoot to develop a whole of Australia radioactive waste repository with both burial and above ground facilities. An announcement on the suitability of various sites in order of preference is expected, but in the meantime, facilities are fragemented. Discussions were held with staff from the radiation standards section of the Australian Radiation Laboratory who face similar problems to NRL including reducing funding, the move to cost recovery, and working towards quality managment accreditation. Plans for a further intercomparison between the Australian and NZ primary standards are being made. (author)

  2. 40 CFR 71.6 - Permit content.

    Science.gov (United States)

    2010-07-01

    ... § 71.5(d). (B) Prompt reporting of deviations from permit requirements, including those attributable to... prompt or otherwise specifies a time frame for reporting deviations, that definition or time frame shall... and air pollution control equipment), practices, or operations regulated or required under the permit...

  3. 40 CFR 71.25 - Permit content.

    Science.gov (United States)

    2010-07-01

    ... such reports; and (ii) Prompt reporting of any deviations from permit requirements, including those... “prompt” in the permit for each situation and will do so in relation to the degree and type of deviation... reasonable times any facilities, equipment (including monitoring and air pollution control equipment...

  4. Review and revision of overload permit classification.

    Science.gov (United States)

    2013-02-01

    The Michigan Department of Transportation (MDOT) allows trucks that exceed their legal loads to cross : bridges if they apply and are approved for a permit. More than 30,000 permits have been processed each : year since 2002, providing a vital servic...

  5. 7 CFR 330.208 - Courtesy permits.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 5 2010-01-01 2010-01-01 false Courtesy permits. 330.208 Section 330.208 Agriculture... PRODUCTS; GARBAGE Movement of Plant Pests § 330.208 Courtesy permits. The Deputy Administrator may issue... subject to regulation under the Plant Protection Actor any other act, as a courtesy to facilitate movement...

  6. 32 CFR 552.90 - Permit office.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 3 2010-07-01 2010-07-01 true Permit office. 552.90 Section 552.90 National... CEMETERIES REGULATIONS AFFECTING MILITARY RESERVATIONS Fort Lewis Land Use Policy § 552.90 Permit office... non-training acess to the range complex. The office is open 0700-1900 hours, seven days a week, for...

  7. 50 CFR 21.31 - Rehabilitation permits.

    Science.gov (United States)

    2010-10-01

    ..., foster parenting, research projects, or other permitted activities with persons permitted or otherwise... Response Coordinator or other designated Service representative and obtain permission from the On-Scene Coordinator. All activities within the location of the spill are subject to the authority of the On-Scene...

  8. 77 FR 10183 - Reissuance of Nationwide Permits

    Science.gov (United States)

    2012-02-21

    ... Civil Works Program (Engineer Circular 1165- 2-211). The current Engineer Circular applies to Corps..., Corps of Engineers Reissuance of Nationwide Permits; Notice #0;#0;Federal Register / Vol. 77 , No. 34..., Corps of Engineers RIN 0710-AA71 Reissuance of Nationwide Permits AGENCY: Army Corps of Engineers, DoD...

  9. 40 CFR 233.21 - General permits.

    Science.gov (United States)

    2010-07-01

    ... ensure compliance with existing permit conditions an any reporting monitoring, or prenotification... apply for an individual permit. This discretionary authority will be based on concerns for the aquatic environment including compliance with paragraph (b) of this section and the 404(b)(1) Guidelines (40 CFR part...

  10. 75 FR 2560 - Issuance of Permits

    Science.gov (United States)

    2010-01-15

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R9-IA-2010-N006] [96300-1671-0000-P5] Issuance of Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of issuance of permits..., 2009 PH.D, Department of 16, 2009. Cardiology Children's Hospital. Dated: January 8, 2010. Brenda Tapia...

  11. 50 CFR 21.41 - Depredation permits.

    Science.gov (United States)

    2010-10-01

    ... PLANTS (CONTINUED) MIGRATORY BIRD PERMITS Control of Depredating and Otherwise Injurious Birds § 21.41... control purposes. No permit is required merely to scare or herd depredating migratory birds other than... other means of concealment, decoys, duck calls, or other devices to lure or entice birds within gun...

  12. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

    Directory of Open Access Journals (Sweden)

    Graner Andreas

    2008-10-01

    Full Text Available Abstract Background Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR index can be generated to map repetitive regions in genomic sequences. Results We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. Conclusion An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences regions in uncharacterised genomic sequences. The restriction that a particular

  13. EPA Region 2 Discharge Pipes for Facilites with NPDES Permits from the Permit Compliance GIS Layer

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Permit and Compliance System (PCS) contains data on the National Pollution Discharge Elimination Systems (NPDES) permit-holding facilities. This includes...

  14. Annual Hanford Site environmental permitting status report

    International Nuclear Information System (INIS)

    Sonnichsen, J.C.

    1998-01-01

    The information contained and/or referenced in this Annual Hanford Site Environmental Permitting Status Report (Status Report) addresses the State Environmental Policy Act (SEPA) of 1971 and Condition II.W. of the Resource Conservation and Recovery Act (RCRA) of 1976 Permit, Dangerous Waste Portion (DW Portion). Condition II.W. of the RCRA Permit specifies the Permittees are responsible for all other applicable federal, state, and local permits for the development and operation of the Hanford Facility. Condition II.W. of the RCRA Permit specifies that the Permittees are to use their best efforts to obtain such permits. For the purposes of permit condition, 'best efforts' means submittal of documentation and/or approval(s) in accordance with schedules specified in applicable regulations, or as determined through negotiations with the applicable regulatory agencies. This Status Report includes information on all existing and anticipated environmental permitting. Environmental permitting required by RCRA, the Hazardous and Solid Waste Amendments (HSWA) of 1984, and non-RCRA permitting (solid waste handling, Clean Air Act Amendments of 1990, Clean Water Act Amendments of 1987, Washington State waste discharge, and onsite sewage system) is addressed. Information on RCRA and non-RCRA is current as of July 31, 1998. For the purposes of RCRA and the State of Washington Hazardous Waste Management Act of 1976 [as administered through the Dangerous Waste Regulations, Washington Active Code (WAC) 173-303], the Hanford Facility is considered a single facility. As such, the Hanford Facility has been issued one US Environmental Protection Agency (EPA)/State Identification Number (WA7890008967). This EPA/State identification number encompasses over 60 treatment, storage, and/or disposal (TSD) units. The Washington State Department of Ecology (Ecology) has been delegated authority by the EPA to administer the RCRA, including mixed waste authority. The RCRA permitting approach for

  15. 77 FR 22267 - Eagle Permits; Changes in the Regulations Governing Eagle Permitting

    Science.gov (United States)

    2012-04-13

    ... with rotating wind turbines. Permit Duration and Transferability In February 2011, we published draft... permit applicants, because of the known risk to eagles from collisions with wind turbines and electric... change does not affect the tenure of any other migratory bird or eagle permit type. DATES: Electronic...

  16. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  17. ALASKA OIL AND GAS EXPLORATION, DEVELOPMENT, AND PERMITTING PROJECT

    Energy Technology Data Exchange (ETDEWEB)

    Richard McMahon; Robert Crandall; Chas Dense; Sean Weems

    2003-11-19

    This is the second technical report, covering the period from April 1, 2003 through September 30, 2003. This project brings together three parts of the oil exploration, development, and permitting process to form the foundation for a more fully integrated information technology infrastructure for the State of Alaska. The geo-technical component is a shared effort between the State Department of Administration and the US Department of Energy. The Alaska Oil and Gas Conservation Commission is rapidly converting high volumes of paper documents and geo-technical information to formats suitable for search and retrieval over the Internet. The permitting component is under the lead of the DNR Office of Project Management and Permitting. A web-based system will enable the public and other review participants to track permit status, submit and view comments, and obtain important project information on-line. By automating several functions of the current manual process, permit applications will be completed more quickly and accurately, and agencies will be able to complete reviews with fewer delays. Structural changes are taking place in terms of organization, statutory authority, and regulatory requirements. Geographic Information Systems are a central component to the organization of information, and the delivery of on-line services. Progress has been made to deploy the foundation system for the shared GIS based on open GIS protocols to the extent feasible. Alaska has nearly one-quarter of the nation's supply of crude oil, at least five billion barrels of proven reserves. The American Association of Petroleum Geologists report that the 1995 National Assessment identified the North Slope as having 7.4 billion barrels of technically recoverable oil and over 63 trillion cubic feet of natural gas. From these reserves, Alaska produces roughly one-fifth of the nation's daily crude oil production, or approximately one million barrels per day from over 1,800 active wells.

  18. Permit to Work System in Nuclear Malaysia

    International Nuclear Information System (INIS)

    Shyen, A.K.S.; Azwafarina Zarmira Aznan; Md Derus Ibrahim

    2015-01-01

    A Permit-To-Work System is an essential part of the job risk assessment process. An effective Permit-To-Work System would help to prevent accident that usually involves maintenance and construction activities. In Malaysian Nuclear Agency, Radiation Safety and Health Division (BKS) has been given the responsibility to implement the system in order to fulfill the requirement of providing a safe and healthy workplace and environment for its employees as pledged in the Occupational Safety, Health and Environmental Policy. This paper presents the roles and functions of Permit-To-Work System, together with the process flow and challenges ahead. (author)

  19. Asymmetric learning by doing and dynamically efficient policy: implications for domestic and international emissions permit trading of allocating permits usefully

    International Nuclear Information System (INIS)

    Read, Peter

    2000-01-01

    Learning by doing leads to cost reductions as suppliers move down the 'experience curve'. This results in a beneficial supply side inter-temporal externality that, for dynamic efficiency, requires a higher incentive for abatement innovations than the penalty on emissions. This effect can be achieved by a dedicated emissions tax or by a proportionate abatement obligation or by allocating permits usefully. The latter arrangement is compatible with the effective cap on emissions that is secured by an emissions trading scheme. Each of the three possibilities results in a reduced loss of international competitivity in policy-committed regions, in less 'leakage, and in more technology transfer. Implications for trading in emissions permits and in project-related credits are discussed. (Author)

  20. Development of severe accident evaluation technology (level 2 PSA) for sodium-cooled fast reactors. (5) Identification of dominant factors in ex-vessel accident sequences

    International Nuclear Information System (INIS)

    Ohno, Shuji; Seino, Hiroshi; Miyahara, Shinya

    2009-01-01

    The evaluation of accident progression outside of a reactor vessel (ex-vessel) and subsequent transfer behavior of radioactive materials is of great importance from the viewpoint of Level 2 PSA. Hence typical ex-vessel accident sequences in the JAEA Sodium-cooled Fast Reactor are qualitatively discussed in this paper and dominant behaviors or factors in the sequences are investigated through parametric calculations using the CONTAIN/LMR code. Scenarios to be focused on are, 1) sodium vapor leakage from the reactor vessel and 2) sodium-concrete reaction, which are both to be considered in the accident category of LOHRS (loss of heat removal system) and might be followed by an early containment failure due to the thermal effect of sodium combustion and hydrogen burning respectively. The calculated results clarify that the sodium vapor leak rate and the scale of sodium-concrete reaction are the important factors to dominate the ex-vessel accident progression. In addition to the understandings of the dominant factors, the analyzed results also provide the specific information such as pressure loading value to the containment and the timing of pressurization, which is indispensable as technical base in Level 2 PSA for developing event trees and for quantifying the accident consequences. (author)

  1. Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology.

    Science.gov (United States)

    Yi, Liuxi; Gao, Fengyun; Siqin, Bateer; Zhou, Yu; Li, Qiang; Zhao, Xiaoqing; Jia, Xiaoyun; Zhang, Hui

    2017-01-01

    Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.

  2. ALASKA OIL AND GAS EXPLORATION, DEVELOPMENT, AND PERMITTING PROJECT

    Energy Technology Data Exchange (ETDEWEB)

    Richard McMahon; Robert Crandall; Chas Dense; Sean Weems

    2003-08-04

    The objective of this project is to eliminate three closely inter-related barriers to oil production in Alaska through the use of a geographic information system (GIS) and other information technology strategies. These barriers involve identification of oil development potential from existing wells, planning projects to efficiently avoid conflicts with other interests, and gaining state approvals for exploration and development projects. Each barrier is the result of either current labor-intensive methods or poorly accessible information. This project brings together three parts of the oil exploration, development, and permitting process to form the foundation for a more fully integrated information technology infrastructure for the State of Alaska. This web-based system will enable the public and other review participants to track permit status, submit and view comments, and obtain important project information online. By automating several functions of the current manual process, permit applications will be completed more quickly and accurately, and agencies will be able to complete reviews with fewer delays. The application will include an on-line diagnostic Coastal Project Questionnaire to determine the suite of permits required for a specific project. The application will also automatically create distribution lists based on the location and type of project, populate document templates for project review start-ups, public notices and findings, allow submission of e-comments, and post project status information on the Internet. Alaska has nearly one-quarter of the nation's supply of crude oil, at least five billion barrels of proven reserves. The American Association of Petroleum Geologists report that the 1995 National Assessment identified the North Slope as having 7.4 billion barrels of technically recoverable oil and over 63 trillion cubic feet of natural gas. From these reserves, Alaska produces roughly one-fifth of the nation's daily crude oil

  3. 基于二次参数化技术的风电机组序列化建模%Wind turbine sequence modeling based on secondary parametric technology

    Institute of Scientific and Technical Information of China (English)

    高青风; 孙振兴; 滕伟; 柳亦兵

    2012-01-01

    针对常规建模方法在庞大复杂风电机组应用上的不足,在建立单台风电机组全参数化模型的基础上,以风电机组序列整体为研究对象,根据同序列不同功率机组之间各零部件设计参数变化规律,研究应用二次参数化技术和参数序列化方法实现了高效的风电机组模型建立与管理;并结合三维模型参数驱动技术,研发了风电机组序列建模系统,可有效减少建模和造型工作量、降低设计失误率、提高设计效率,验证了该建模方法的正确性与合理性.%According to the disadvantages of conventional modeling methods for large and complex wind turbines, a highly efficient modeling method is proposed in this paper. Based on a fully parametric model of a single wind turbine, it took the whole sequence of wind turbines as the research object, and realized the fast modeling via secondary parametric technology according to the change law of design parameters of different wind turbines in the same sequence. A sequence modeling system for wind turbines was also developed by combining with parameter-driven modeling technology. The system can effectively reduce the workload and design error rate, improve design efficiency, and prove the correctness and rationality of the modeling method.

  4. 78 FR 36822 - Special Permit Applications

    Science.gov (United States)

    2013-06-19

    ... lithium battery that exceeds the net quantity weight restriction when transported by motor vehicle and... Dassault Falcon Jet Corp. Little Ferry, NJ May 13, 2013. To modify the special permit to add an additional...

  5. 32 CFR 935.11 - Permits.

    Science.gov (United States)

    2010-07-01

    ... shall be issued under other authority that is inconsistent with this part. The Commander may issue.... (b) To the extent it is not inconsistent with this part, any permit or registration issued pursuant...

  6. Storm Water General Permit 2 for Construction

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — General permit #2 for storm water discharges associated with industrial activity for Construction Activities in Iowa for the National Pollutant Discharge Elimination...

  7. 50 CFR 660.707 - Permits.

    Science.gov (United States)

    2010-10-01

    ... or downloaded from the Southwest Region home page (http://swr.nmfs.noaa.gov/permits.htm) to apply for... the vessel is fishing for, taking, retaining, possessing, or landing HMS shoreward of the outer...

  8. 77 FR 4271 - Special Permit Marking Removal

    Science.gov (United States)

    2012-01-27

    ... the logistical and cost concerns regarding the ability of the railroad industry to comply with the... incorporating the applicable GRL Special Permits into the HMR (and FRA's subsequent approval notice) those...

  9. Web Air Permits (WAP R7)

    Data.gov (United States)

    U.S. Environmental Protection Agency — THIS DATA ASSET NO LONGER ACTIVE: This is metadata documentation for Web Air Permits in Region 7 (WAP R7), a Lotus Notes application that once tracked comment...

  10. 2013 EPA Vessels General Permit (VGP)

    Data.gov (United States)

    U.S. Environmental Protection Agency — Information for any vessel that submitted a Notice of Intent (NOI), Notice of Termination (NOT), or annual report under EPA's 2013 Vessel General Permit (VGP)....

  11. Gulf of Mexico Shrimp Permit Gear Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data set contains annual vessel gear characterization of permit holders shrimp vessel. Data includes net type, TED type, BRD type, etc.

  12. 2011 EPA Pesticide General Permit (PGP)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The 2011 EPA Pesticide General Permit (PGP) covers discharges of biological pesticides, and chemical pesticides that leave a residue, in areas where EPA is the NPDES...

  13. WIPP's Hazardous Waste Facility Permit Renewal Application

    International Nuclear Information System (INIS)

    Most, W.A.; Kehrman, R.F.

    2009-01-01

    Hazardous waste permits issued by the New Mexico Environment Department (NMED) have a maximum term of 10-years from the permit's effective date. The permit condition in the Waste Isolation Pilot Plant's (WIPP) Hazardous Waste Facility Permit (HWFP) governing renewal applications, directs the Permittees to submit a permit application 180 days prior to expiration of the Permit. On October 27, 1999, the Secretary of the NMED issued to the United States Department of Energy (DOE), the owner and operator of WIPP, and to Washington TRU Solutions LLC (WTS), the Management and Operating Contractor and the cooperator of WIPP, a HWFP to manage, store, and dispose hazardous waste at WIPP. The DOE and WTS are collectively known as the Permittees. The HWFP is effective for a fixed term not to exceed ten years from the effective date of the Permit. The Permittees may renew the HWFP by submitting a new permit application at least 180 calendar days before the expiration date, of the HWFP. The Permittees are not proposing any substantial changes in the Renewal Application. First, the Permittees are seeking the authority to dispose of Contact-Handled and Remote-Handled TRU mixed waste in Panel 8. Panels 4 through 7 have been approved in the WIPP Hazardous Waste Facility Permit as it currently exists. No other change to the facility or to the manner in which hazardous waste is characterized, managed, stored, or disposed is being requested. Second, the Permittees also seek to include the Mine Ventilation Rate Monitoring Plan, as Attachment Q in the HWFP. This Plan has existed as a separate document since May 2000. The NMED has requested that the Plan be submitted as part of the Renewal Application. The Permittees have been operating to the Mine Ventilation Rate Monitoring Plan since the Plan was submitted. Third, some information submitted in the original WIPP RCRA Part B Application has been updated, such as demographic information. The Permittees will submit this information in the

  14. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  15. 40 CFR 270.62 - Hazardous waste incinerator permits.

    Science.gov (United States)

    2010-07-01

    ... WASTES (CONTINUED) EPA ADMINISTERED PERMIT PROGRAMS: THE HAZARDOUS WASTE PERMIT PROGRAM Special Forms of Permits § 270.62 Hazardous waste incinerator permits. When an owner or operator of a hazardous waste... 40 Protection of Environment 26 2010-07-01 2010-07-01 false Hazardous waste incinerator permits...

  16. 30 CFR 773.10 - Review of permit history.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Review of permit history. 773.10 Section 773.10... REQUIREMENTS FOR PERMITS AND PERMIT PROCESSING § 773.10 Review of permit history. (a) We, the regulatory authority, will rely upon the permit history information you, the applicant, submit under § 778.12 of this...

  17. 40 CFR 60.4124 - Hg budget permit revisions.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 6 2010-07-01 2010-07-01 false Hg budget permit revisions. 60.4124... Coal-Fired Electric Steam Generating Units Permits § 60.4124 Hg budget permit revisions. Except as provided in § 60.4123(b), the permitting authority will revise the Hg Budget permit, as necessary, in...

  18. Next-generation sequencing technology a new tool for killer cell immunoglobulin-like receptor allele typing in hematopoietic stem cell transplantation.

    Science.gov (United States)

    Maniangou, B; Retière, C; Gagne, K

    2018-02-01

    Killer cell Immunoglobulin-like Receptor (KIR) genes are a family of genes located together within the leukocyte receptor cluster on human chromosome 19q13.4. To date, 17 KIR genes have been identified including nine inhibitory genes (2DL1/L2/L3/L4/L5A/L5B, 3DL1/L2/L3), six activating genes (2DS1/S2/S3/S4/S5, 3DS1) and two pseudogenes (2DP1, 3DP1) classified into group A (KIR A) and group B (KIR B) haplotypes. The number and the nature of KIR genes vary between the individuals. In addition, these KIR genes are known to be polymorphic at allelic level (907 alleles described in July 2017). KIR genes encode for receptors which are predominantly expressed by Natural Killer (NK) cells. KIR receptors recognize HLA class I molecules and are able to kill residual recipient leukemia cells, and thus reduce the likelihood of relapse. KIR alleles of Hematopoietic Stem Cell (HSC) donor would require to be known (Alicata et al. Eur J Immunol 2016) because the KIR allele polymorphism may affect both the KIR + NK cell phenotype and function (Gagne et al. Eur J Immunol 2013; Bari R, et al. Sci Rep 2016) as well as HSCT outcome (Boudreau et al. JCO 2017). The introduction of the Next Generation Sequencing (NGS) has overcome current conventional DNA sequencing method limitations, known to be time consuming. Recently, a novel NGS KIR allele typing approach of all KIR genes was developed by our team in Nantes from 30 reference DNAs (Maniangou et al. Front in Immunol 2017). This NGS KIR allele typing approach is simple, fast, reliable, specific and showed a concordance rate of 95% for centromeric and telomeric KIR genes in comparison with high-resolution KIR typing obtained to those published data using exome capture (Norman PJ et al. Am J Hum Genet 2016). This NGS KIR allele typing approach may also be used in reproduction and to better study KIR + NK cell implication in the control of viral infections. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  19. 9 CFR 78.2 - Handling of certificates, permits, and “S” brand permits for interstate movement of animals.

    Science.gov (United States)

    2010-01-01

    ... âSâ brand permits for interstate movement of animals. 78.2 Section 78.2 Animals and Animal Products... certificates, permits, and “S” brand permits for interstate movement of animals. (a) Any certificate, permit, or “S” brand permit required by this part for the interstate movement of animals shall be delivered...

  20. Inhibition of expression in Escherichia coli of a virulence regulator MglB of Francisella tularensis using external guide sequence technology.

    Directory of Open Access Journals (Sweden)

    Gaoping Xiao

    Full Text Available External guide sequences (EGSs have successfully been used to inhibit expression of target genes at the post-transcriptional level in both prokaryotes and eukaryotes. We previously reported that EGS accessible and cleavable sites in the target RNAs can rapidly be identified by screening random EGS (rEGS libraries. Here the method of screening rEGS libraries and a partial RNase T1 digestion assay were used to identify sites accessible to EGSs in the mRNA of a global virulence regulator MglB from Francisella tularensis, a Gram-negative pathogenic bacterium. Specific EGSs were subsequently designed and their activities in terms of the cleavage of mglB mRNA by RNase P were tested in vitro and in vivo. EGS73, EGS148, and EGS155 in both stem and M1 EGS constructs induced mglB mRNA cleavage in vitro. Expression of stem EGS73 and EGS155 in Escherichia coli resulted in significant reduction of the mglB mRNA level coded for the F. tularensis mglB gene inserted in those cells.

  1. 77 FR 71818 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2012-12-04

    ... following permit requests. Applicant Permit No. TE-78622A Applicant: William J. Mautz, Hilo, Hawaii The...-179036 Applicant: Cullen A. Wilkerson, Richmond, California The applicant requests a permit renewal to...

  2. State Waste Discharge Permit ST-4502 Implementation Plan

    Energy Technology Data Exchange (ETDEWEB)

    BROWN, M.J.; LECLAIR, M.D.

    2000-09-27

    Plan has been developed to demonstrate compliance with regulatory requirements set forth in Permit ST-3502 and as a line management tool for use in maintaining configuration control of permit as well as documentation used to implement permit requirements.

  3. State Waste Discharge Permit ST-4502 Implementation Plan

    International Nuclear Information System (INIS)

    BROWN, M.J.; LECLAIR, M.D.

    2000-01-01

    Plan has been developed to demonstrate compliance with regulatory requirements set forth in Permit ST-3502 and as a line management tool for use in maintaining configuration control of permit as well as documentation used to implement permit requirements

  4. IFQ Halibut/Sablefish and CDQ Halibut Permit Program

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Under the IFQ Halibut/Sablefish Permit Program and CDQ Halibut Permit Program permits are issued for harvesting and receiving/processing halibut, and non-trawl...

  5. An eddy-permitting, dynamically consistent adjoint-based assimilation system for the tropical Pacific: Hindcast experiments in 2000

    KAUST Repository

    Hoteit, Ibrahim; Cornuelle, B.; Heimbach, P.

    2010-01-01

    An eddy-permitting adjoint-based assimilation system has been implemented to estimate the state of the tropical Pacific Ocean. The system uses the Massachusetts Institute of Technology's general circulation model and its adjoint. The adjoint method

  6. Banking and back-loading emission permits

    International Nuclear Information System (INIS)

    Chaton, Corinne; Creti, Anna; Peluchon, Benoît

    2015-01-01

    In this article we focus on the so-called back-loading policy adopted by the European Commission to increase the carbon market price. This environmental measure consists of removing a share of the allowances allocated for a given period in order to reallocate some or all of them later on. To analyze the impact of the permits back-loading, we determine the CO 2 price equilibrium with and without the policy measure, considering not only the market for permits but also the output market of regulated sectors. We propose a two-period model, where the market for permits is perfectly competitive, and the output market can be either competitive or oligopolistic. First, we define the condition under which banking from one period to another is optimal. This condition, that is the absence of arbitrage opportunities (AOA), depends not only from the period initial allocation but also on production market fundamentals. When this condition is satisfied, the market for emission is shown intertemporally efficient. Second, we point out that the back-loading measure may create inefficiencies or leave unaffected the permits price, if it alters the AOA. -- Highlights: •Relationship between the market for permits and the output market of regulated sectors. •Analysis of CO 2 prices and banking. •Impact of a recent environmental policy measure (backloading) on CO 2 prices

  7. Hawaii Integrated Energy Assessment. Volume V. Rules, regulations, permits and policies affecting the development of alternate energy sources in Hawaii

    Energy Technology Data Exchange (ETDEWEB)

    1980-01-01

    A comprehensive presentaton of the major permits, regulations, rules, and controls which are likely to affect the development of alternate energy sources in Hawaii is presented. An overview of the permit process, showing the major categories and types of permits and controls for energy alternatives is presented. This is followed by a brief resume of current and projected changes designed to streamline the permit process. The permits, laws, regulations, and controls that are applicable to the development of energy alternatives in Hawaii are described. The alternate energy technologies affected, a description of the permit or control, and the requirements for conformance are presented for each applicable permit. Federal, state, and county permits and controls are covered. The individual energy technologies being considered as alternatives to the State's present dependence on imported fossil fuels are emphasized. The alternate energy sources covered are bioconversion, geothermal, ocean thermal, wind, solar (direct), and solid waste. For each energy alternative, the significant permits are summarized with a brief explanation of why they may be necessary. The framework of policy development at each of the levels of government with respect to the alternate energy sources is covered.

  8. Hanford facility dangerous waste permit application

    International Nuclear Information System (INIS)

    1991-01-01

    This document, Set 2, the Hanford Facility Dangerous Waste Part B Permit Application, consists of 15 chapters that address the content of the Part B checklists prepared by the Washington State Department of Ecology (Ecology 1987) and the US Environmental Protection Agency (40 CFR 270), with additional information requirements mandated by the Hazardous and Solid Waste Amendments of 1984 and revisions of WAC 173-303. For ease of reference, the Washington State Department of Ecology checklist section numbers, in brackets, follow the chapter headings and subheadings. This permit application contains ''umbrella- type'' documentation with overall application to the Hanford Facility. This documentation is broad in nature and applies to all TSD units that have final status under the Hanford Facility Permit

  9. 75 FR 19987 - Endangered and Threatened Species Permit Applications

    Science.gov (United States)

    2010-04-16

    ... applied for scientific research permits to conduct certain activities with endangered species under the...) within Arizona. Permit TE-178778 Applicant: Marks Lab of Aquatic Ecology, Flagstaff, Arizona. Applicant...

  10. Permit issued for expansion of the Gronau uranium enrichment plant

    International Nuclear Information System (INIS)

    2005-01-01

    Over the next few years, the Gronau Uranium Enrichment Plant (UAG) will be able to raise its capacity in steps from 1 800 tonnes to 4 500 tonnes SWU per annum. This development in steps depends on the extent to which demand on the world market can be turned into contracts for Urenco. After a procedure taking more than six years to complete, Urenco Deutschland GmbH was issued the required permit by the North Rhine-Westphalian State Ministry for Transport, Energy, and Planning on February 14 this year. The permit was preceded by the drafting and examination of two safety reports of several hundred pages each, and of over 1 000 detailed documents. The application documents were examined by a large number of expert consultants and public authorities from all over Germany acting on behalf of the nuclear licensing authority. Urenco Ltd. sells enrichment services worldwide, at present holding a share of approx. 19% of the world market for uranium separative work. Although this world market is not going to grow for a foreseeable period of time, Urenco is expanding its capacities. This is based on the latest centrifuge technology characterized by extremely low power consumption and high availability. It replaces diffusion technology, which currently holds a share of approx. 40% of the world market. (orig.)

  11. High Density Linkage Map Construction and Mapping of Yield Trait QTLs in Maize (Zea mays) Using the Genotyping-by-Sequencing (GBS) Technology

    Science.gov (United States)

    Su, Chengfu; Wang, Wei; Gong, Shunliang; Zuo, Jinghui; Li, Shujiang; Xu, Shizhong

    2017-01-01

    Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS. A total of 1,046,524,604 reads with an average of 5,258,918 reads per F2 individual were generated. This number of reads represents an approximately 0.36-fold coverage of the maize reference genome Zea_mays.AGPv3.29 for each F2 individual. A total of 68,882 raw SNPs were discovered in the F2 population, which, after stringent filtering, led to a total of 29,927 high quality SNPs. Comparative analysis using these physically mapped marker loci revealed a higher degree of synteny with the reference genome. The SNP genotype data were utilized to construct an intra-specific genetic linkage map of maize consisting of 3,305 bins on 10 linkage groups spanning 2,236.66 cM at an average distance of 0.68 cM between consecutive markers. From this map, we identified 28 QTLs associated with yield traits (100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, corn grains per row, ear weight, and grain weight per plant) using the composite interval mapping (CIM) method and 29 QTLs using the least absolute shrinkage selection operator (LASSO) method. QTLs identified by the CIM method account for 6.4% to 19.7% of the phenotypic variation. Small intervals of three QTLs (qCGR-1, qKW-2, and qGWP-4) contain several genes, including one gene (GRMZM2G139872) encoding the F-box protein, three genes (GRMZM2G180811, GRMZM5G828139, and GRMZM5G873194) encoding the WD40-repeat protein, and

  12. Permitting mixed waste treatment, storage and disposal facilities: A mixed bag

    International Nuclear Information System (INIS)

    Ranek, N.L.; Coalgate, J.L.

    1995-01-01

    The Federal Facility Compliance Act of 1992 (FFCAct) requires the U.S. Department of Energy (DOE) to make a comprehensive national inventory of its mixed wastes (i.e., wastes that contain both a hazardous component that meets the Resource Conservation and Recovery Act (RCRA) definition of hazardous waste and a radioactive component consisting of source, special nuclear, or byproduct material regulated under the Atomic Energy Act (AEA)), and of its mixed waste treatment technologies and facilities. It also requires each DOE facility that stores or generates mixed waste to develop a treatment plan that includes, in part, a schedule for constructing units to treat those wastes that can be treated using existing technologies. Inherent in constructing treatment units for mixed wastes is, of course, permitting. This paper identifies Federal regulatory program requirements that are likely to apply to new DOE mixed waste treatment units. The paper concentrates on showing how RCRA permitting requirements interrelate with the permitting or licensing requirements of such other laws as the Atomic Energy Act, the Clean Water Act, and the Clean Air Act. Documentation needed to support permit applications under these laws are compared with RCRA permit application documentation. National Environmental Policy Act (NEPA) documentation requirements are also addressed, and throughout the paper, suggestions are made for managing the permitting process

  13. 50 CFR 18.31 - Scientific research permits and public display permits.

    Science.gov (United States)

    2010-10-01

    ... the population stock and the marine ecosystem. In determining whether to issue a public display permit... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Scientific research permits and public..., DEPARTMENT OF THE INTERIOR (CONTINUED) TAKING, POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER...

  14. Permitting of Wind Energy Facilities: A Handbook

    Energy Technology Data Exchange (ETDEWEB)

    NWCC Siting Work Group

    2002-08-01

    This handbook has been written for individuals and groups involved in evaluating wind projects: decision-makers and agency staff at all levels of government, wind developers, interested parties and the public. Its purpose is to help stakeholders make permitting wind facility decisions in a manner which assures necessary environmental protection and responds to public needs.

  15. 27 CFR 19.157 - Operating permits.

    Science.gov (United States)

    2010-04-01

    ... OF THE TREASURY LIQUORS DISTILLED SPIRITS PLANTS Qualification of Distilled Spirits Plants § 19.157... file an application for registration under § 19.151 shall make application for and obtain an operating permit before commencing any of the following operations: (1) Distilling for industrial use. (2...

  16. 75 FR 54649 - Endangered Wildlife; Permits

    Science.gov (United States)

    2010-09-08

    ...-02997A Applicant: University of Hawaii, Hilo, Hawaii. The applicant requests a permit to take (capture...-listed Drosophila species on the island of Kauai in the State of Hawaii for the purpose of enhancing its... in the State of Hawaii: Astelia waialealae (painiu), Canavalia napaliensis (awikiwiki), Chamaesyce...

  17. 15 CFR 5.4 - Permits.

    Science.gov (United States)

    2010-01-01

    ... standards relating to appearance, safety, sanitation, maintenance, and efficiency of operation. Due regard... the Government and prospective patrons of the stand. (f) The permit shall describe the location of the stand proper and the location of any vending machines which are operated in conjunction with it. ...

  18. 9 CFR 93.802 - Import permit.

    Science.gov (United States)

    2010-01-01

    ... CONVEYANCE AND SHIPPING CONTAINERS Elephants, Hippopotami, Rhinoceroses, and Tapirs § 93.802 Import permit. (a) An elephant, hippopotamus, rhinoceros, or tapir shall not be imported into the United States... export an elephant, hippopotamus, rhinoceros, or tapir to the United States; (2) The name and address of...

  19. 19 CFR 12.107 - Importations permitted.

    Science.gov (United States)

    2010-04-01

    ... TREASURY SPECIAL CLASSES OF MERCHANDISE Pre-Columbian Monumental and Architectural Sculpture and Murals § 12.107 Importations permitted. Pre-Columbian monumental or architectural sculpture or mural for which... sculpture or mural, in a form acceptable to the Secretary, certifying that such exportation was not in...

  20. 50 CFR 648.4 - Vessel permits.

    Science.gov (United States)

    2010-10-01

    ... carrying passengers for hire. (8) Atlantic bluefish vessels. (i) Commercial. Any vessel of the United... lands Atlantic bluefish in or from the EEZ in excess of the recreational possession limit specified at § 648.164 must have been issued and carry on board a valid commercial bluefish vessel permit. (ii) Party...

  1. 40 CFR 70.5 - Permit applications.

    Science.gov (United States)

    2010-07-01

    ... establish. Where an existing part 70 permit would prohibit such construction or change in operation, the... information only if it is related to the proposed change. Information required under paragraph (c) of this... part shall state that, based on information and belief formed after reasonable inquiry, the statements...

  2. Tradable CO{sub 2} permits in Danish and European energy policy

    Energy Technology Data Exchange (ETDEWEB)

    Varming, S.; Vesterdal, M. [ELSAMPROJEKT A/S (Denmark); Boerre Eriksen, P. [Eltra I/S (Denmark); Grohnheit, P.E.; Nielsen, L. [RISOe (Denmark); Tinggaard Svendsen, G. [Handelshoejskolen i Aarhus (Denmark)

    2000-08-01

    This report presents the results of the project 'Tradable CO{sub 2} permits in Danish and European energy policy'. The project was financed by a grant from the Danish Energy Research Programme 1998 (Grant 1753/98-0002). The project was conducted in co-operation between Elsamprojekt A/S (project manager), Risoe National Laboratory, Aarhus School of Business and I/S Eltra. The three major objectives of the project were: To identify and analyse the economical and political issues that are relevant with regard to the construction of a tradable CO{sub 2} permit market as well as proposing a suitable design for a tradable CO{sub 2} permit market for the energy sector in the EU. Experience from the tradable S{sub O}2 permit market in the US is taken into consideration as well. To present an overview of price estimates of CO{sub 2} and greenhouse gas permits in different models as well as discussing the assumptions leading to the different outcomes. Furthermore, the special role of backstop technologies in relation to permit prices is analysed. To analyse the connection between CO{sub 2} permit prices and technology choice in the energy sector in the medium and longer term (i.e., 2010 and 2020) with a special emphasis on combined heat and power and renewables. In addition, the short-term effects on CO{sub 2} emissions and electricity trade of introducing tradable CO{sub 2} permit with limited coverage (i.e. a national system) as well as complete coverage (i.e. including all the countries) in the Nordic electricity system are analysed. (au)

  3. Tradable CO{sub 2} permits in Danish and European energy policy

    Energy Technology Data Exchange (ETDEWEB)

    Varming, S; Vesterdal, M [ELSAMPROJEKT A/S (Denmark); Boerre Eriksen, P [Eltra I/S (Denmark); Grohnheit, P E; Nielsen, L [RISOe (Denmark); Tinggaard Svendsen, G [Handelshoejskolen i Aarhus (Denmark)

    2000-08-01

    This report presents the results of the project 'Tradable CO{sub 2} permits in Danish and European energy policy'. The project was financed by a grant from the Danish Energy Research Programme 1998 (Grant 1753/98-0002). The project was conducted in co-operation between Elsamprojekt A/S (project manager), Risoe National Laboratory, Aarhus School of Business and I/S Eltra. The three major objectives of the project were: To identify and analyse the economical and political issues that are relevant with regard to the construction of a tradable CO{sub 2} permit market as well as proposing a suitable design for a tradable CO{sub 2} permit market for the energy sector in the EU. Experience from the tradable S{sub O}2 permit market in the US is taken into consideration as well. To present an overview of price estimates of CO{sub 2} and greenhouse gas permits in different models as well as discussing the assumptions leading to the different outcomes. Furthermore, the special role of backstop technologies in relation to permit prices is analysed. To analyse the connection between CO{sub 2} permit prices and technology choice in the energy sector in the medium and longer term (i.e., 2010 and 2020) with a special emphasis on combined heat and power and renewables. In addition, the short-term effects on CO{sub 2} emissions and electricity trade of introducing tradable CO{sub 2} permit with limited coverage (i.e. a national system) as well as complete coverage (i.e. including all the countries) in the Nordic electricity system are analysed. (au)

  4. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  5. 50 CFR 648.88 - Multispecies open access permit restrictions.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Multispecies open access permit... Management Measures for the NE Multispecies and Monkfish Fisheries § 648.88 Multispecies open access permit restrictions. (a) Handgear permit. A vessel issued a valid open access NE multispecies Handgear permit is...

  6. Renewable Energy Permitting Barriers in Hawaii: Experience from the Field

    Energy Technology Data Exchange (ETDEWEB)

    Busche, S.; Donnelly, C.; Atkins, D.; Fields, R.; Black, C.

    2013-03-01

    This white paper presents a summary of the solicited input from permitting agencies and renewable energy developers on the permitting process in Hawaii to provide stakeholders in Hawaii, particularly those involved in permitting, with information on current permitting barriers that renewable energy developers are experiencing.

  7. 40 CFR 144.51 - Conditions applicable to all permits.

    Science.gov (United States)

    2010-07-01

    ... PROGRAMS (CONTINUED) UNDERGROUND INJECTION CONTROL PROGRAM Permit Conditions § 144.51 Conditions applicable... permit. Any permit noncompliance constitutes a violation of the Safe Drinking Water Act and is grounds... denial of a permit renewal application; except that the permittee need not comply with the provisions of...

  8. 50 CFR 21.21 - Import and export permits.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Import and export permits. 21.21 Section... WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD PERMITS Specific Permit Provisions § 21.21 Import and export... must have a permit to import or export migratory birds, their parts, nests, or eggs. You must meet the...

  9. Should advertising by aesthetic surgeons be permitted?

    Directory of Open Access Journals (Sweden)

    Neeraj Nagpal

    2017-01-01

    Full Text Available Cosmetic, aesthetic and cutaneous surgical procedures require qualified specialists trained in the various procedures and competent to handle complications. However, it also requires huge investments in terms of infrastructure, trained staff and equipment. To be viable advertising is essential to any establishment which provides cosmetic and aesthetic procedures. Business men with deep pockets establish beauty chains which also provide these services and advertise heavily to sway public opinion in their favour. However, these saloons and spas lack basic medical facilities in terms of staff or equipment to handle any complication or medical emergency. To have a level playing field ethical advertising should be permitted to qualified aesthetic surgeons as is permitted in the US and UK by their respective organisations.

  10. Market Power in Laboratory Emission Permit Markets

    International Nuclear Information System (INIS)

    Godby, R.

    2002-01-01

    Many proposals suggesting the use of markets to control pollution assume markets will be competitive. When markets do not exhibit competitive characteristics, however, should they still be expected to result in efficiency improvement relative to traditional approaches? This paper employs experimental economic methods to examine the effect of market structure on the use of marketable emissions permits. Results indicate that in a market with one dominant firm and a number of fringe firms, strategic manipulation occurs repeatedly in the laboratory as predicted by market power models, undermining the allocative and dynamic efficiency benefits such markets offer. When firms compete in a downstream product market dominated by the same single firm, market efficiency can actually be reduced with the implementation of permit markets. Final market efficiencies reflect initial endowments and are influenced by competitive conditions elsewhere in the economy, indicating that policy-makers should carefully consider whether markets are appropriate in such circumstances

  11. PUREX Storage Tunnels dangerous waste permit application

    International Nuclear Information System (INIS)

    1991-12-01

    This report is part of a dangerous waste permit application for the storage of wastes from the Purex process at Hanford. Appendices are presented on the following: construction drawings; HSW-5638, specifications for disposal facility for failed equipment, Project CA-1513-A; HWS-8262, specification for Purex equipment disposal, Project CGC 964; storage tunnel checklist; classification of residual tank heels in Purex storage tunnels; emergency plan for Purex facility; training course descriptions; and the Purex storage tunnels engineering study

  12. Hanford Site air operating permit application

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-05-01

    The Clean Air Act Amendments of 1990, which amended the Federal Clean Air Act of 1977, required that the US Environmental Protection Agency develop a national Air Operating Permit Program, which in turn would require each state to develop an Air Operating Permit Program to identify all sources of ``regulated`` pollutants. Regulated pollutants include ``criteria`` pollutants (oxides of nitrogen, sulfur oxides, total suspended particulates, carbon monoxide, particulate matter greater than 10 micron, lead) plus 189 other ``Hazardous`` Air Pollutants. The Hanford Site, owned by the US Government and operated by the US Department of Energy, Richland Operations Office, is located in southcentral Washington State and covers 560 square miles of semi-arid shrub and grasslands located just north of the confluence of the Snake and Yakima Rivers with the Columbia River. This land, with restricted public access, provides a buffer for the smaller areas historically used for the production of nuclear materials, waste storage, and waste disposal. About 6 percent of the land area has been disturbed and is actively used. The Hanford Site Air Operating Permit Application consists of more than 1,100 sources and in excess of 300 emission points. Before January 1995, the maintenance and operations contractor and the environmental restoration contractor for the US Department of Energy completed an air emission inventory on the Hanford Site. The inventory has been entered into a database so that the sources and emission points can be tracked and updated information readily can be retrieved. The Hanford Site Air Operating Permit Application contains information current as of April 19, 1995.

  13. Hanford Site air operating permit application

    International Nuclear Information System (INIS)

    1995-05-01

    The Clean Air Act Amendments of 1990, which amended the Federal Clean Air Act of 1977, required that the US Environmental Protection Agency develop a national Air Operating Permit Program, which in turn would require each state to develop an Air Operating Permit Program to identify all sources of ''regulated'' pollutants. Regulated pollutants include ''criteria'' pollutants (oxides of nitrogen, sulfur oxides, total suspended particulates, carbon monoxide, particulate matter greater than 10 micron, lead) plus 189 other ''Hazardous'' Air Pollutants. The Hanford Site, owned by the US Government and operated by the US Department of Energy, Richland Operations Office, is located in southcentral Washington State and covers 560 square miles of semi-arid shrub and grasslands located just north of the confluence of the Snake and Yakima Rivers with the Columbia River. This land, with restricted public access, provides a buffer for the smaller areas historically used for the production of nuclear materials, waste storage, and waste disposal. About 6 percent of the land area has been disturbed and is actively used. The Hanford Site Air Operating Permit Application consists of more than 1,100 sources and in excess of 300 emission points. Before January 1995, the maintenance and operations contractor and the environmental restoration contractor for the US Department of Energy completed an air emission inventory on the Hanford Site. The inventory has been entered into a database so that the sources and emission points can be tracked and updated information readily can be retrieved. The Hanford Site Air Operating Permit Application contains information current as of April 19, 1995

  14. Grout Treatment Facility dangerous waste permit application

    International Nuclear Information System (INIS)

    1992-07-01

    The Grout Treatment Facility (GTF) is an existing treatment, storage, and/or disposal (TSD) unit located in the 200 East Area and the adjacent 600 Area of the Hanford Site. The GTF mixes dry cementitious solids with liquid mixed waste (containing both dangerous and radioactive constituents) produced by Hanford Site operations. The GTF consists of the following: The 241-AP-02D and 241-AP-04D waste pump pits and transfer piping; Dry Materials Facility (DMF); Grout Disposal Facility (GDF), consisting of the disposal vault and support and monitoring equipment; and Grout Processing Facility (GPF) and Westinghouse Hanford Company on the draft Hanford Facility Dangerous Waste Permit and may not be read to conflict with those comments. The Grout Treatment Facility Dangerous Waste Permit Application consists of both a Part A and a Part B permit application. An explanation of the Part A revisions associated with this TSD unit, including the current revision, is provided at the beginning of the Part A section. The Part B consists of 15 chapters addressing the organization and content of the Part B checklist prepared by the Washington State Department of Ecology (Ecology 1987). For ease of reference, the checklist section numbers, in brackets, follow chapter headings and subheadings

  15. 78 FR 52579 - SHINE Medical Technologies, Inc.

    Science.gov (United States)

    2013-08-23

    ... NUCLEAR REGULATORY COMMISSION [Docket No. 50-608; NRC-2013-0053] SHINE Medical Technologies, Inc... application for a construction permit, submitted by SHINE Medical Technologies, Inc. (SHINE). ADDRESSES... of a two-part application for a construction permit for a medical radioisotope production facility in...

  16. 78 FR 73897 - SHINE Medical Technologies, Inc.

    Science.gov (United States)

    2013-12-09

    ... NUCLEAR REGULATORY COMMISSION [Docket No. 50-608; NRC-2013-0053] SHINE Medical Technologies, Inc... construction permit, submitted by SHINE Medical Technologies, Inc. (SHINE) is acceptable for docketing... permit would allow SHINE to construct a medical radioisotope production facility in Janesville, Wisconsin...

  17. Genetic sequences derived from suppression subtractive ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-17

    Jun 17, 2008 ... their possible roles in Xanthomonas albilineans ... Technology, P. O. Box 1334, Durban 4000, Republic of South Africa. Accepted 4 ... Clones selected were sequenced (using a Perkin Elmer ABI PRISM Dye terminator cycle.

  18. Special Issue: Next Generation DNA Sequencing

    Directory of Open Access Journals (Sweden)

    Paul Richardson

    2010-10-01

    Full Text Available Next Generation Sequencing (NGS refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance. The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche, Illumina (formerly Solexa Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies and the Heliscope (Helicos Corporation. The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. [...

  19. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  20. Clinical applications of sequencing take center stage

    OpenAIRE

    Glusman, Gustavo

    2013-01-01

    A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013. This year's Advances in Genome Biology and Technology (AGBT) meeting reflected the current state of 'next generation' sequencing (NGS) technologies: significantly reduced competition and innovation, and a strong focus on standardization and application. Announcements of technological breakthroughs - a hallmark of previous AGBT meetings - were markedly absent, but existin...

  1. Massively parallel sequencing of forensic STRs

    DEFF Research Database (Denmark)

    Parson, Walther; Ballard, David; Budowle, Bruce

    2016-01-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

  2. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  3. Autonomously Generating Operations Sequences for a Mars Rover Using Artificial Intelligence-Based Planning

    Science.gov (United States)

    Sherwood, R.; Mutz, D.; Estlin, T.; Chien, S.; Backes, P.; Norris, J.; Tran, D.; Cooper, B.; Rabideau, G.; Mishkin, A.; Maxwell, S.

    2001-07-01

    This article discusses a proof-of-concept prototype for ground-based automatic generation of validated rover command sequences from high-level science and engineering activities. This prototype is based on ASPEN, the Automated Scheduling and Planning Environment. This artificial intelligence (AI)-based planning and scheduling system will automatically generate a command sequence that will execute within resource constraints and satisfy flight rules. An automated planning and scheduling system encodes rover design knowledge and uses search and reasoning techniques to automatically generate low-level command sequences while respecting rover operability constraints, science and engineering preferences, environmental predictions, and also adhering to hard temporal constraints. This prototype planning system has been field-tested using the Rocky 7 rover at JPL and will be field-tested on more complex rovers to prove its effectiveness before transferring the technology to flight operations for an upcoming NASA mission. Enabling goal-driven commanding of planetary rovers greatly reduces the requirements for highly skilled rover engineering personnel. This in turn greatly reduces mission operations costs. In addition, goal-driven commanding permits a faster response to changes in rover state (e.g., faults) or science discoveries by removing the time-consuming manual sequence validation process, allowing rapid "what-if" analyses, and thus reducing overall cycle times.

  4. E2FM: an encrypted and compressed full-text index for collections of genomic sequences.

    Science.gov (United States)

    Montecuollo, Ferdinando; Schmid, Giovannni; Tagliaferri, Roberto

    2017-09-15

    Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets-as those related to personalized medicine-require the compliance with regulations about the storage and processing of sensitive data. We have designed and carefully engineered E 2 FM -index, a new full-text index in minute space which was optimized for compressing and encrypting nucleotide sequence collections in FASTA format and for performing fast pattern-search queries. E 2 FM -index allows to build self-indexes which occupy till to 1/20 of the storage required by the input FASTA file, thus permitting to save about 95% of storage when indexing collections of highly similar sequences; moreover, it can exactly search the built indexes for patterns in times ranging from few milliseconds to a few hundreds milliseconds, depending on pattern length. Source code is available at https://github.com/montecuollo/E2FM . ferdinando.montecuollo@unicampania.it. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  5. Permit processes for nuclear power. International lessons

    International Nuclear Information System (INIS)

    Gaahlin, Emil; Nilsson, Isabelle; Pettersson, Maria; Soederholm, Patrik

    2010-01-01

    The overall objective of this report is to analyze and compare the legal permitting and planning process for (first and foremost) new nuclear power stations in a number of selected countries. In this way the report provides relevant knowledge that could form the basis for discussing the efficiency of various national licensing processes (include the Swedish one). The study builds heavily on the analysis of legal documents and regulations, and addresses both the formal requirements for licensing and territorial planning procedures as well as the issues of public participation and access to justice in the respective countries. In addition to this legal approach, however, we also adopt an investor's perspective on the legislation, i.e., an analysis of the legal rules can influence investment decisions in practice. Furthermore, the study relies largely on a synthesis of previous studies as well as interviews with researchers, electricity companies and government officials in Sweden and abroad. The countries that are compared include Sweden, Finland, France, Canada, Switzerland, Great Britain, USA and South Korea. These include those that currently invest in new nuclear power as well as those who have recently reformed their plant permitting processes. The analysis highlights important differences among the various countries, including issues such as the political influence on the licensing process, the allocation of political power between the national and local levels, means of interacting with regular citizens, and the overall transparency and predictability of the legislation. Some selected practical experiences of the current legislation are also presented. The report first provides a short background to the role and the status of nuclear power in the global energy system, and we then present a rather comprehensive comparison of the permitting processes in the above countries. Each country section comprises a short background, a presentation of the existing

  6. Adaptive Basis Selection for Exponential Family Smoothing Splines with Application in Joint Modeling of Multiple Sequencing Samples

    OpenAIRE

    Ma, Ping; Zhang, Nan; Huang, Jianhua Z.; Zhong, Wenxuan

    2017-01-01

    Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments in parallel. After the resulting sequences (short reads) are mapped to the genome, one gets a sequence of short read counts along the genome. Effective extraction of signals in these short read counts is the key to the success of sequencing technologies. No...

  7. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  9. SMITH: a LIMS for handling next-generation sequencing workflows.

    Science.gov (United States)

    Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

    2014-01-01

    Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available

  10. SMITH: a LIMS for handling next-generation sequencing workflows

    Science.gov (United States)

    2014-01-01

    Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). Methods SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. Results SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The

  11. Tradable permit allocations and sequential choice

    Energy Technology Data Exchange (ETDEWEB)

    MacKenzie, Ian A. [Centre for Economic Research, ETH Zuerich, Zurichbergstrasse 18, 8092 Zuerich (Switzerland)

    2011-01-15

    This paper investigates initial allocation choices in an international tradable pollution permit market. For two sovereign governments, we compare allocation choices that are either simultaneously or sequentially announced. We show sequential allocation announcements result in higher (lower) aggregate emissions when announcements are strategic substitutes (complements). Whether allocation announcements are strategic substitutes or complements depends on the relationship between the follower's damage function and governments' abatement costs. When the marginal damage function is relatively steep (flat), allocation announcements are strategic substitutes (complements). For quadratic abatement costs and damages, sequential announcements provide a higher level of aggregate emissions. (author)

  12. PSD Permit for the Marblehead Lime Company

    Science.gov (United States)

    This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

  13. Honda Permits to Install 1 Year Aggregation

    Science.gov (United States)

    This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

  14. 75 FR 27814 - Receipt of Applications for Permit

    Science.gov (United States)

    2010-05-18

    ... permit to export one female captive bred giant panda (Ailuropoda melanoleuca) born at the zoo in 2005 and... education. The permit numbers and animals are: 070854, Bimbo Jr.; 079868, Vickie; 079870, Jenny; 079871...

  15. 34 CFR 395.35 - Terms of permit.

    Science.gov (United States)

    2010-07-01

    ..., periodicals, publications, confections, tobacco products, foods, beverages, chances for any lottery authorized... PROPERTY Federal Property Management § 395.35 Terms of permit. Every permit shall describe the location of...

  16. 78 FR 27249 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2013-05-09

    ... purpose of enhancing the species' survival. Permit No. TE-99477A Applicant: Benjamin S. Wallace, Fairfield...-99473A Applicant: Joseph D. Henry, San Diego, California The applicant requests a permit to take (capture...

  17. 76 FR 35235 - Endangered and Threatened Species Permit Applications

    Science.gov (United States)

    2011-06-16

    ... chub (Gila intermedia), Gila topminnow (Poeciliopsis occidentalis occidentalis), humpback chub (Gila... intermedia) within Arizona. Permit TE-43777A Applicant: Sea Life US, LLC, Grapevine, Texas. Applicant...), and Gila chub (Gila intermedia) within Arizona. Permit TE-118414 Applicant: Cherokee Nation, Tahlequah...

  18. Storm water permitting for oil and gas facilities

    International Nuclear Information System (INIS)

    de Blanc, P.C.

    1991-01-01

    After several false starts, the US Environmental Protection Agency (EPA) published new federal storm water regulations in the November 16, 1990 Federal Register. These regulations identify facilities which must apply for a storm water permit and detail permit application requirements. The regulations appear at 40 CFR 122 Subpart B and became effective December 17, 1990. An outline of these regulations and their applicability to oil and gas facilities is presented. They are: facilities which require a storm water permit; types of storm water permits; permit application deadlines; permit application forms; facilities with existing storm water permits; storm water permit application data requirements; storm water sampling and analysis requirements; and EPA contacts for additional information

  19. Remediation General Permit (RGP) for Massachusetts & New Hampshire

    Science.gov (United States)

    Documents, links & contacts for the Notice of Availability of the National Pollutant Discharge Elimination System (NPDES) General Permit for Remediation Activity Discharges – the Remediation General Permit in MA (MAG910000) and NH (NHG910000).

  20. Next Generation DNA Sequencing and the Future of Genomic Medicine

    OpenAIRE

    Anderson, Matthew W.; Schrijver, Iris

    2010-01-01

    In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpreta...

  1. The Use of Transferable Permits in Transport Policy

    OpenAIRE

    Raux, Charles

    2004-01-01

    http://dx.doi.org/10.1016/j.trd.2004.01.001; International audience; This paper considers potential use of domestic transferable, or tradable, permit systems for the purposes of travel management, especially reducing environmental nuisances. The main arguments for and against the use of permits are analyzed. Secondly two case studies of existing permit systems are examined. The main conclusions are that tradable permits can address greenhouse gas and regional atmospheric pollutant emissions, ...

  2. Grout treatment facility dangerous waste permit application

    International Nuclear Information System (INIS)

    1988-01-01

    This section briefly describes the Hanford Site, provides a general description of the site operations and administration, provides an overview of the contents of this Grout Treatment Facility (GTF) Permit Application, and gives a list of acronyms and abbreviations used in the document. The decision was made to use the checklist as a locator reference instead of using the checklist section numbers as paragraph section numbers because several different types of waste management units, some of which are not addressed in the checklists, are part of the GTF. The GTF is a waste management unit within the Hanford Site facility. In May 1988, permit application was filed that identified the GTF as an existing facility. The GTF mixes dry cementitious solids with liquid mixed wastes (containing both dangerous and radioactive constituents) produced by Hanford Site operations. In addition to the design and operating features of the GTF that are intended to meet the requirements of dangerous waste regulations, many additional design and operating features are necessary to comply with radioactive waste management practices. The GTF design features and practices are intended to keep operational exposure to radionuclides and dangerous substances ''as low as reasonably achievable'' (ALARA) and to provide a disposal system that protects the environment for at least 10,000 yr. In some instances, ALARA practices present difficulties when complying with requirements of dangerous waste regulations

  3. Grout treatment facility dangerous waste permit application

    International Nuclear Information System (INIS)

    1988-01-01

    This section briefly describes the Hanford Site, provides a general description of the site operations and administration, provides an overview of the contents of this Grout Treatment Facility (GTF) Permit Application, and gives a list of acronyms and abbreviations used in the document. The decision was made to use the checklist as a locator reference instead of using the checklist section numbers as paragraph section numbers because several different types of waste management units, some of which are not addressed in the checklists, are part of the GTF. The GTF is a waste management unit within the Hanford Site facility. In May 1988, a permit application was filed that identified the GTF as an existing facility. The GTF mixes dry cementitious solids with liquid mixed wastes (containing both dangerous and radioactive constituents) produced by Hanford Site operations. In addition to the design and operating features of the GTF that are intended to meet the requirements of dangerous waste regulations, many additional design and operating features are necessary to comply with radioactive waste management practices. The GTF design features and practices are intended to keep operational exposure to radionuclides and dangerous substances ''as low as reasonably achievable'' (ALARA) and to provide a disposal system that protects the environment for at least 10,000 yr. In some instances, ALARA practices present difficulties when complying with requirements of dangerous waste regulations. This volume contains 2 appendices covering engineering drawings and operating procedures

  4. Are LMFBR permits unconstitutional. [German Feferal Republic

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, H; Ziegler, E

    1977-12-01

    The August 18, 1977 decision by the Muenster Higher Administrative Court to have the Federal Constitutional Court investigate the constitutionality of permits granted for fast breeder power plants has aroused much attention, both in the FRG and in other countries. This is the first time that the German Atomic Energy Act is being questioned with respect to the separation of powers between legislative and executive authorities and also with respect to the principle of a constitutional state. As a result of their analysis of the first information available about the court decision the authors have some doubts as to whether the views held by the court about the consequences of the development of fast breeder reactors and of the permit granted for the SNR 300 demonstration nuclear power station are essentially correct. In view of the wording of and the official comments on the incriminated Section 7 of the Atomic Energy Act and the large number of subsequent leading decisions by the Federal Diet about fast breeder reactors also the concern about the constitutionality of that reactor line appears to be unfounded.

  5. The run permit protection system for GTA

    International Nuclear Information System (INIS)

    Atkins, W.H.; Jones, R.G.

    1992-01-01

    A Run Permit system has been designed for the Ground Test Accelerator (GTA). The system implements mode-dependent software interlocks to ensure proper operation of the accelerator, enabling the ion source extractor and RF systems when proper conditions are met. The system is implemented using the GTA control system; thus all information available to the control system is also available for use in interlock logic. The logic is defined in terms of control system channels, which reflect accelerator parameters such as actuator positions, power supply values, temperatures, etc. A mode switch in the control room selects the accelerator operating mode, for example i njector only . The Run Permit software selects interlock logic as appropriate operating mode. This implementation easily accommodates logic changes as requirements evolve. To ensure reliable operation of a software-based system, a special circuit with a watch-dog timer is employed to produce the system's output signals. The software must periodically address the circuit, or the output signals are forced to a disabled state. For additional protection, there are self-test provisions for detecting and reacting to failures of the control system. (Author) 4 figs., ref

  6. Grout treatment facility dangerous waste permit application

    International Nuclear Information System (INIS)

    1988-01-01

    This section briefly describes the Hanford Site, provides a general description of the site operations and administration, provides an overview of the contents of this Grout Treatment Facility (GTF) Permit Application, and gives a list of acronyms and abbreviations used in the document. The decision was made to use the checklist as a locator reference instead of using the checklist section numbers as paragraph section numbers because several different types of waste management units, some of which are not addressed in the checklists, are part of the GTF. The GTF is a waste management unit within the Hanford Site facility. In May 1988, a permit application was filed that identified the GTF as an existing facility. The GTF mixes dry cementitious solids with liquid mixed wastes (containing both dangerous and radioactive constitutents) produced by Hanford Site operations. In addition to the design and operating features of the GTF that are intended to meet the requirements of dangerous waste regulations, many additional design and operating features are necessary to comply with radioactive waste management practices. The GTF design features and practices are intended to keep operational exposure to radionuclides and dangerous substances ''as low as reasonably achievable'' (ALARA) and to provide a disposal system that protects the environment for at least 10,000 yr. In some instances, ALARA practices present difficulties when complying with requirements of dangerous waste regulations. This volume contains 2 Appendices covering engineering drawings and operating procedures

  7. Grout Treatment Facility dangerous waste permit application

    International Nuclear Information System (INIS)

    1988-01-01

    This section briefly describes the Hanford Site, provides a general description of the site operations and administration, provides an overview of the contents of this Grout Treatment Facility (GTF) Permit Application, and gives a list of acronyms and abbreviations used in the document. The decision was made to use the checklist as a locator reference instead of using the checklist section numbers as paragraph section numbers because several different types of waste management units, some of which are not addressed in the checklists, are part of the GTF. The GTF is a waste management unit within the Hanford Site facility. In May 1988, a permit application was filed that identified the GTF as an existing facility. The GTF mixes dry cementitious solids with liquid wastes (containing both dangerous and radioactive constituents) produced by Hanford Site operations. In addition to the design and operating features of the GTF that are intended to meet the requirements of dangerous waste regulations, many additional design and operating features are necessary to comply with radioactive waste management practices. The GTF design features and practices are intended to keep operational exposure to radionuclides and dangerous substances ''as low as reasonably achievable'' (ALARA) and to provide a disposal system that protects the environment for at least 10,000 yr. In some instances, ALARA practices present difficulties when complying with requirements of dangerous waste regulations. This volume contains 14 Appendices. Topics include Engineering Drawings, Maps, Roads, Toxicity Testing, and Pilot-Scale Testing

  8. 76 FR 67650 - Migratory Bird Permits; Abatement Regulations

    Science.gov (United States)

    2011-11-02

    ... and suggestions on migratory bird permit regulations for a permit to use raptors (birds of prey) in abatement activities. Abatement means the use of trained raptors to flush, scare (haze), or take birds or... for a specific permit authorizing the use of raptors in abatement activities (76 FR 39368). The...

  9. 75 FR 20622 - Endangered Wildlife and Plants; Permits

    Science.gov (United States)

    2010-04-20

    .... Permit No. TE-02997A Applicant: University of Hawaii, Hilo, Hawaii. The applicant requests a permit to... scientific research including genetic, morphological and behavioral research on the island of Hawaii in the State of Hawaii for the purpose of enhancing its survival. The applicant also requests a permit to take...

  10. 25 CFR 211.56 - Geological and geophysical permits.

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Geological and geophysical permits. 211.56 Section 211.56... FOR MINERAL DEVELOPMENT Rents, Royalties, Cancellations and Appeals § 211.56 Geological and geophysical permits. Permits to conduct geological and geophysical operations on Indian lands which do not...

  11. 25 CFR 212.56 - Geological and geophysical permits.

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Geological and geophysical permits. 212.56 Section 212.56... FOR MINERAL DEVELOPMENT Rents, Royalties, Cancellations, and Appeals § 212.56 Geological and geophysical permits. (a) Permits to conduct geological and geophysical operations on Indian lands which do not...

  12. 40 CFR 270.65 - Research, development, and demonstration permits.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 26 2010-07-01 2010-07-01 false Research, development, and... Special Forms of Permits § 270.65 Research, development, and demonstration permits. (a) The Administrator may issue a research, development, and demonstration permit for any hazardous waste treatment facility...

  13. 40 CFR 52.2184 - Operating permits for minor sources.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 4 2010-07-01 2010-07-01 false Operating permits for minor sources. 52... permits for minor sources. Emission limitations and related provisions established in South Dakota minor... right to deem permit conditions not federally enforceable. Such a determination will be made according...

  14. 77 FR 34061 - Endangered Species; Issuance of Permits

    Science.gov (United States)

    2012-06-08

    ...-FF09A30000] Endangered Species; Issuance of Permits AGENCY: Fish and Wildlife Service, Interior. ACTION... following permits to conduct certain activities with endangered species. We issue these permits under the Endangered Species Act (ESA). ADDRESSES: Brenda Tapia, Division of Management Authority, U.S. Fish and...

  15. 78 FR 27255 - Endangered Species; Issuance of Permits

    Science.gov (United States)

    2013-05-09

    ...-FF09A30000] Endangered Species; Issuance of Permits AGENCY: Fish and Wildlife Service, Interior. ACTION... following permits to conduct certain activities with endangered species. We issue these permits under the Endangered Species Act (ESA). ADDRESSES: Brenda Tapia, Division of Management Authority, U.S. Fish and...

  16. 78 FR 56922 - Endangered Species; Issuance of Permits

    Science.gov (United States)

    2013-09-16

    ...-FF09A30000] Endangered Species; Issuance of Permits AGENCY: Fish and Wildlife Service, Interior. ACTION... following permits to conduct certain activities with endangered species. We issue these permits under the Endangered Species Act (ESA). ADDRESSES: Brenda Tapia, Division of Management Authority, U.S. Fish and...

  17. 76 FR 40338 - Marine Mammals; Photography Permit No. 16360

    Science.gov (United States)

    2011-07-08

    ... Mammals; Photography Permit No. 16360 AGENCY: National Marine Fisheries Service (NMFS), National Oceanic... photography of cetaceans off Hawaii. ADDRESSES: The permit and related documents are available for review upon... photography on 12 cetacean species had been submitted by the above-named applicant. The requested permit has...

  18. 78 FR 24305 - Actions on Special Permit Applications

    Science.gov (United States)

    2013-04-24

    ... special permit Lincoln, NE. to authorize an alternative fire protection system. 11624-M Clean Harbors 49... Special Permit Applications AGENCY: Pipeline and Hazardous Materials Safety Administration (PHMSA), DOT. ACTION: Notice of actions on Special Permit Applications. SUMMARY: In accordance with the procedures...

  19. 40 CFR 96.323 - CAIR permit contents and term.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false CAIR permit contents and term. 96.323 Section 96.323 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... the permitting authority, as necessary to facilitate coordination of the renewal of the CAIR permit...

  20. 21 CFR 1312.23 - Issuance of export permit.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Issuance of export permit. 1312.23 Section 1312.23... CONTROLLED SUBSTANCES Exportation of Controlled Substances § 1312.23 Issuance of export permit. (a) The... regulation in § 1312.30 of this part be exported only pursuant to the issuance of an export permit. The...

  1. 50 CFR 20.64 - Foreign export permits.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Foreign export permits. 20.64 Section 20... WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Importations § 20.64 Foreign export permits. No... such birds are accompanied by export permits, tags, or other documentation required by applicable...

  2. 21 CFR 1312.22 - Application for export permit.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Application for export permit. 1312.22 Section... EXPORTATION OF CONTROLLED SUBSTANCES Exportation of Controlled Substances § 1312.22 Application for export permit. (a) An application for a permit to export controlled substances shall be made on DEA Form 161...

  3. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  4. Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

    2013-01-01

    to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

  5. 15 CFR 971.423 - Best available technology.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Best available technology. 971.423... technology. The Administrator will require in all activities under new permits, and wherever practicable in activities under existing permits, the use of the best available technologies for the protection of safety...

  6. 75 FR 47583 - Application to Rescind Presidential Permit; Joint Application for Presidential Permit; British...

    Science.gov (United States)

    2010-08-06

    ... Presidential Permit No. PP-22, as amended, to BC Hydro. The application requested that the Department of Energy... the transmission of electric energy between the United States and a foreign country is prohibited in... law pursuant to British Columbia's Clean Energy Act. Since restructuring of the electric power...

  7. 21 CFR 108.12 - Manufacturing, processing, or packing without a permit, or in violation of a permit.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Manufacturing, processing, or packing without a permit, or in violation of a permit. 108.12 Section 108.12 Food and Drugs FOOD AND DRUG ADMINISTRATION... General Provisions § 108.12 Manufacturing, processing, or packing without a permit, or in violation of a...

  8. Regulatory Review of Early Site Permit Applications

    International Nuclear Information System (INIS)

    Scott, Michael L.

    2004-01-01

    The U.S. Nuclear Regulatory Commission (NRC) has received and is reviewing three applications for early site permits (ESPs). The ESP process allows early resolution of site-related issues affecting possible construction and operation of a new nuclear power plant. The nuclear industry views a successful and predictable ESP process as an important step in assessing whether to seek authorization to construct and operate a new generation of nuclear power reactors in the United States. Because consideration of ESP applications is a first-of-a-kind activity, a number of issues have emerged prior to and during the reviews of the first three applications. Issues have included the need for design information at the ESP stage, accident analyses, quality assurance, and seismic analyses. The NRC has been working to resolve identified issues to support a Commission decision on whether to issue an ESP approximately 33-37 months after receipt of each ESP application. (authors)

  9. Requirements for permitting a mixed waste incinerator

    International Nuclear Information System (INIS)

    Trichon, M.; Feldman, J.; Serne, J.C.

    1990-01-01

    The consideration, design, selection and operation of any incinerator depends primarily on characteristic quality (ultimate and proximate analyses) and quantity to the waste to be incinerated. In the case of burning any combination of mixed hazardous, biomedical and radioactive low level waste, specific federal and generic state environmental regulatory requirements are outlined. Combustion chamber temperature and waste residence time requirements will provide the rest of the envelope for consideration. Performance requirements must be balanced between the effects of time and temperature on destruction of the organic waste and the vaporization and possible emission of the inorganic waste components (e.g., toxic metals, radioactive inorganics) as operating conditions and emission levels will be set in state and federal regulatory permits. To this end the complete characterization of the subject waste stream must be determined if an accurate assessment of incineration effectiveness and impact are to be performed

  10. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  11. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  12. Hanford Site Solid Waste Landfill permit application

    International Nuclear Information System (INIS)

    1991-01-01

    Daily activities at the Hanford Site generate sanitary solid waste (nonhazardous and nonradioactive) that is transported to and permanently disposed of at the Hanford Site Solid Waste Landfill. This permit application describes the manner in which the solid Waste Landfill will be operated under Washington State Department of Ecology Minimum Functional Standards for Solid Waste Handling, Washington Administrative Code 173-304. The solid Waste Landfill is owned by the US Department of Energy -- Richland Operations Office and is used for disposal of solid waste generated at the US Department of Energy Hanford Site. The jurisdictional health department's permit application form for the Solid Waste Landfill is provided in Chapter 1.0. Chapter 2.0 provides a description of the Hanford Site and the Solid Waste Landfill and reviews applicable locational, general facility, and landfilling standards. Chapter 3.0 discusses the characteristics and quantity of the waste disposed of in the Solid Waste Landfill. Chapter 4.0 reviews the regional and site geology and hydrology and the groundwater and vadose zone quality beneath the landfill. Chapters 5.0, 6.0, and 7.0 contain the plan of operation, closure plan, and postclosure plan, respectively. The plan of operation describes the routine operation and maintenance of the Solid Waste Landfill, the environmental monitoring program, and the safety and emergency plans. Chapter 5.0 also addresses the operational cover, environmental controls, personnel requirements, inspections, recordkeeping, reporting, and site security. The postclosure plan describes requirements for final cover maintenance and environmental monitoring equipment following final closure. Chapter 8.0 discusses the integration of closure and postclosure activities between the Solid Waste Landfill and adjacent Nonradioactive Dangerous Waste Landfill. 76 refs., 48 figs, 15 tabs

  13. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  14. ENVIRONMENTAL PERMITTING IN ETHIOPIA: NO RESTRAINT ON ...

    African Journals Online (AJOL)

    power, such that potentially polluting businesses cannot open or continue to operate ... For a historical overview of international cooperation to solve environmental problem .... The Green Revolution is the movement of technological advances.

  15. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  16. Sequencing Intractable DNA to Close Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  17. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  18. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  19. The contribution of next generation sequencing to epilepsy genetics

    DEFF Research Database (Denmark)

    Møller, Rikke S.; Dahl, Hans A.; Helbig, Ingo

    2015-01-01

    During the last decade, next generation sequencing technologies such as targeted gene panels, whole exome sequencing and whole genome sequencing have led to an explosion of gene identifications in monogenic epilepsies including both familial epilepsies and severe epilepsies, often referred to as ...

  20. From Genome Sequence to Taxonomy - A Skeptic’s View

    DEFF Research Database (Denmark)

    Özen, Asli Ismihan; Vesth, Tammi Camilla; Ussery, David

    2012-01-01

    The relative ease of sequencing bacterial genomes has resulted in thousands of sequenced bacterial genomes available in the public databases. This same technology now allows for using the entire genome sequence as an identifier for an organism. There are many methods available which attempt to us...

  1. Coping with EPA's new petroleum industry storm water permits

    International Nuclear Information System (INIS)

    Veal, S.C.; Whitescarver, J.P.

    1994-01-01

    The United States Environmental Protection Agency has just released for public comment its so-called multi-sector industry specific storm water permit. This permit -- developed in response to the 730 group storm water permit applications submitted in 1992 to EPA -- proposes the establishment of specific runoff sampling and facility design requirements for at least two petroleum industry sectors. This proposed permit establishes specific conditions for the oil and gas extraction section (SIC group 13) and for lubricant manufacturers (SIC 2992). Permit conditions are also established for allied industrial sectors such as the chemical, transportation and asphalt materials industries. By most standards, the proposed permit is much tougher than EPA's baseline general permit for storm water discharges which was released in September of 1992. For example, under the proposal, most industries are required to perform periodic storm water sampling. EPA has also established storm water effluent and performance standards for several industrial categories. This paper will discuss the petroleum industry specific conditions of the new permit. The paper will also discuss the results of the industry-wide storm water sampling efforts undertaken by more than 300 oil patch facilities across the country. In particular, sampling results will be discussed in the context to the permit conditions proposed by EPA. The paper will also discuss strategies for dealing with the new permits

  2. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  3. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  4. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  5. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  6. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  7. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  8. PUREX Storage Tunnels dangerous waste permit application

    International Nuclear Information System (INIS)

    1991-12-01

    The PUREX Storage Tunnels are a mixed waste storage unit consisting of two underground railroad tunnels: Tunnel Number 1 designated 218-E-14 and Tunnel Number 2 designated 218-E-15. The two tunnels are connected by rail to the PUREX Plant and combine to provide storage space for 48 railroad cars (railcars). The PUREX Storage Tunnels provide a long-term storage location for equipment removed from the PUREX Plant. Transfers into the PUREX Storage Tunnels are made on an as-needed basis. Radioactively contaminated equipment is loaded on railcars and remotely transferred by rail into the PUREX Storage Tunnels. Railcars act as both a transport means and a storage platform for equipment placed into the tunnels. This report consists of part A and part B. Part A reports on amounts and locations of the mixed water. Part B permit application consists of the following: Facility Description and General Provisions; Waste Characteristics; Process Information; Groundwater Monitoring; Procedures to Prevent Hazards; Contingency Plan; Personnel Training; Exposure Information Report

  9. Moral concerns on tradable pollution permits in international environmental agreements

    Energy Technology Data Exchange (ETDEWEB)

    Eyckmans, Johan [Hogeschool-Universiteit Brussel - HUB, Stormstraat 2, B-1000 Brussels (Belgium); Katholieke Universiteit Leuven, Centrum voor Economische Studien Naamsestraat 69, 3000 Leuven (Belgium); Kverndokk, Snorre [Ragnar Frisch Centre for Economic Research, Gaustadalleen 21, 0349 Oslo (Norway)

    2010-07-15

    We investigate how moral concerns about permit trading affect an endogenous pollution permit trading equilibrium, where governments choose non-cooperatively the amount of permits they allocate to domestic industries. Politicians may feel reluctant to allow permit trading and/or may prefer that abatement is undertaken domestically because of moral concerns. This will have an effect on the initial permit allocations, and, therefore, on global emissions. The impact on global emissions depends on the precise formulation of the moral concerns, but under reasonable assumptions, we show that global emissions may increase. Thus, doing what is perceived as good does not always yield the desired outcome. However, this can be offset by restrictions on permit trading when governments have moral concerns about this trade. (author)

  10. Moral concerns on tradable pollution permits in international environmental agreements

    International Nuclear Information System (INIS)

    Eyckmans, Johan; Kverndokk, Snorre

    2010-01-01

    We investigate how moral concerns about permit trading affect an endogenous pollution permit trading equilibrium, where governments choose non-cooperatively the amount of permits they allocate to domestic industries. Politicians may feel reluctant to allow permit trading and/or may prefer that abatement is undertaken domestically because of moral concerns. This will have an effect on the initial permit allocations, and, therefore, on global emissions. The impact on global emissions depends on the precise formulation of the moral concerns, but under reasonable assumptions, we show that global emissions may increase. Thus, doing what is perceived as good does not always yield the desired outcome. However, this can be offset by restrictions on permit trading when governments have moral concerns about this trade. (author)

  11. Next-generation sequencing for genetic testing of familial colorectal cancer syndromes.

    Science.gov (United States)

    Simbolo, Michele; Mafficini, Andrea; Agostini, Marco; Pedrazzani, Corrado; Bedin, Chiara; Urso, Emanuele D; Nitti, Donato; Turri, Giona; Scardoni, Maria; Fassan, Matteo; Scarpa, Aldo

    2015-01-01

    Genetic screening in families with high risk to develop colorectal cancer (CRC) prevents incurable disease and permits personalized therapeutic and follow-up strategies. The advancement of next-generation sequencing (NGS) technologies has revolutionized the throughput of DNA sequencing. A series of 16 probands for either familial adenomatous polyposis (FAP; 8 cases) or hereditary nonpolyposis colorectal cancer (HNPCC; 8 cases) were investigated for intragenic mutations in five CRC familial syndromes-associated genes (APC, MUTYH, MLH1, MSH2, MSH6) applying both a custom multigene Ion AmpliSeq NGS panel and conventional Sanger sequencing. Fourteen pathogenic variants were detected in 13/16 FAP/HNPCC probands (81.3 %); one FAP proband presented two co-existing pathogenic variants, one in APC and one in MUTYH. Thirteen of these 14 pathogenic variants were detected by both NGS and Sanger, while one MSH2 mutation (L280FfsX3) was identified only by Sanger sequencing. This is due to a limitation of the NGS approach in resolving sequences close or within homopolymeric stretches of DNA. To evaluate the performance of our NGS custom panel we assessed its capability to resolve the DNA sequences corresponding to 2225 pathogenic variants reported in the COSMIC database for APC, MUTYH, MLH1, MSH2, MSH6. Our NGS custom panel resolves the sequences where 2108 (94.7 %) of these variants occur. The remaining 117 mutations reside inside or in close proximity to homopolymer stretches; of these 27 (1.2 %) are imprecisely identified by the software but can be resolved by visual inspection of the region, while the remaining 90 variants (4.0 %) are blind spots. In summary, our custom panel would miss 4 % (90/2225) of pathogenic variants that would need a small set of Sanger sequencing reactions to be solved. The multiplex NGS approach has the advantage of analyzing multiple genes in multiple samples simultaneously, requiring only a reduced number of Sanger sequences to resolve

  12. Applying Next Generation Sequencing to Skeletal Development and Disease

    OpenAIRE

    Bowen, Margot Elizabeth

    2013-01-01

    Next Generation Sequencing (NGS) technologies have dramatically increased the throughput and lowered the cost of DNA sequencing. In this thesis, I apply these technologies to unresolved questions in skeletal development and disease. Firstly, I use targeted re-sequencing of genomic DNA to identify the genetic cause of the cartilage tumor syndrome, metachondromatosis (MC). I show that the majority of MC patients carry heterozygous loss-of-function mutations in the PTPN11 gene, which encodes a p...

  13. Issues in third party attacks on SMCRA permits. [USA - Indiana

    Energy Technology Data Exchange (ETDEWEB)

    Kelley, G.D. Jr. (Ice Miller Donadio Ryan, Indianapolis, IN (USA))

    1990-01-01

    Legal issues which have occurred in third party attacks on SMCRA (Surface Mining Control and Reclamation Act) permit, mainly in Indiana, are discussed. Problems that can occur with the interrelationship of common law nuisance/injunction actions, the permit process, enforcement proceedings and collateral estoppel from administrative agency action, as well as finality issues in the permit process as related to other provisions of SMCRA. 37 refs.

  14. Liquid effluent retention facility dangerous waste permit application

    International Nuclear Information System (INIS)

    1991-06-01

    This appendix to the Liquid Effluent Retention Facility Dangerous Waste Permit Application contains pumps, piping, leak detection systems, geomembranes, leachate collection systems, earthworks and floating cover systems

  15. Proposed Issuance of NPDES Permit for NTUA Kayenta WWTF

    Science.gov (United States)

    Public Notice of proposed Issuance of National Pollutant Discharge Elimination System Permit (NPDES No. NN0020281) for Navajo Tribal Utility Authority (“NTUA”) Kayenta Wastewater Treatment Facility.

  16. Tradeable emission permits in Dutch environmental policy. A utopia?

    International Nuclear Information System (INIS)

    Schuurman, S.J.

    1997-01-01

    Because of the lack of experience with permits in the Netherlands, and in view of the similarities between various other tradeable permit systems, the functioning of Dutch systems of tradeable fish, milk and manure quotas is discussed. Evaluation of these systems is based on criteria of effectiveness, target-group efficiency and government efficiency. These systems of tradeable permits appear to constitute a successful addition to the Dutch policy of direct regulation. Considering this, and the favorable American experience with the Emissions Trading Program, tradeable emission permits deserve a chance to be implemented in Dutch environmental policy. The question remains, however, whether the Dutch government is ready for such a step. 28 refs

  17. 75 FR 66123 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2010-10-27

    ... enhancing their survival. Permit No. TE-24582A Applicant: Russell C. Croel, Folsom, California. The..., Contra Costa, Fresno, Glenn, Kings, Merced, Placer, Sacramento, San Joaquin, Shasta, Solano, Stanislaus...

  18. 78 FR 9067 - Receipt of Applications for Endangered Species Permits

    Science.gov (United States)

    2013-02-07

    ... County, Alabama. Permit Application Number: TE-91366A Applicant: Dr. Paul Stewart, Troy, Alabama...: TE-91373A Applicant: Jonathan Miller, Troy, Alabama. Applicant requests authorization to take...

  19. Industrial Fuel Gas Demonstration Plant Program: environmental permit compliance plan

    Energy Technology Data Exchange (ETDEWEB)

    Bodamer, Jr., James W.; Bocchino, Robert M.

    1979-11-01

    This Environmental Permit Compliance Plan is intended to assist the Memphis Light, Gas and Water Division in acquiring the necessary environmental permits for their proposed Industrial Fuel Gas Demonstration Plant in a time frame consistent with the construction schedule. Permits included are those required for installation and/or operation of gaseous, liquid and solid waste sources and disposal areas. Only those permits presently established by final regulations are described. The compliance plan describes procedures for obtaining each permit from identified federal, state and local agencies. The information needed for the permit application is presented, and the stepwise procedure to follow when filing the permit application is described. Information given in this plan was obtained by reviewing applicable laws and regulations and from telephone conversations with agency personnel on the federal, state and local levels. This Plan also presents a recommended schedule for beginning the work necessary to obtain the required environmental permits in order to begin dredging operations in October, 1980 and construction of the plant in September, 1981. Activity for several key permits should begin as soon as possible.

  20. Guide to Permitting Hydrogen Motor Fuel Dispensing Facilities

    Energy Technology Data Exchange (ETDEWEB)

    Rivkin, Carl [National Renewable Energy Lab. (NREL), Golden, CO (United States); Buttner, William [National Renewable Energy Lab. (NREL), Golden, CO (United States); Burgess, Robert [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-03-28

    The purpose of this guide is to assist project developers, permitting officials, code enforcement officials, and other parties involved in developing permit applications and approving the implementation of hydrogen motor fuel dispensing facilities. The guide facilitates the identification of the elements to be addressed in the permitting of a project as it progresses through the approval process; the specific requirements associated with those elements; and the applicable (or potentially applicable) codes and standards by which to determine whether the specific requirements have been met. The guide attempts to identify all applicable codes and standards relevant to the permitting requirements.

  1. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    OpenAIRE

    Arabi E. keshk

    2014-01-01

    The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between se...

  2. Complete Genome Sequence of Ikoma Lyssavirus

    OpenAIRE

    Marston, Denise A.; Ellis, Richard J.; Horton, Daniel L.; Kuzmin, Ivan V.; Wise, Emma L.; McElhinney, Lorraine M.; Banyard, Ashley C.; Ngeleja, Chanasa; Keyyu, Julius; Cleaveland, Sarah; Lembo, Tiziana; Rupprecht, Charles E.; Fooks, Anthony R.

    2012-01-01

    Lyssaviruses (family Rhabdoviridae) constitute one of the most important groups of viral zoonoses globally. All lyssaviruses cause the disease rabies, an acute progressive encephalitis for which, once symptoms occur, there is no effective cure. Currently available vaccines are highly protective against the predominantly circulating lyssavirus species. Using next-generation sequencing technologies, we have obtained the whole-genome sequence for a novel lyssavirus, Ikoma lyssavirus (IKOV), isol...

  3. Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

    Science.gov (United States)

    Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

    2014-02-01

    Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

  4. Quantitative phenotyping via deep barcode sequencing.

    Science.gov (United States)

    Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

    2009-10-01

    Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

  5. A case for permitting altruistic surrogacy.

    Science.gov (United States)

    Baker, B M

    1996-01-01

    Canada's Royal Commission on New Reproductive Technologies rejects all forms of surrogacy arrangement under the rubric of objecting to commercial surrogacy. Noncommercial surrogacy arrangements, however, can be defended against the commission's objections. They can be viewed as cases of giving a benefit or service to another in a way that expresses benevolence, and establishes a relationship between surrogates and prospective 'social' parents that allows mutual understanding and reciprocal personal interaction between them.

  6. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  7. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  8. Hazardous waste incinerator permitting in Texas from inception to operation

    International Nuclear Information System (INIS)

    Simms, M.D.; McDonnell, R.G. III

    1991-01-01

    The regulatory permitting process for hazardous waste incinerators i a long and arduous proposition requiring a well-developed overall strategy. In Texas, RCRA permits for the operation of hazardous waste incinerator facilities are issued through the federally delegated Texas Water Commission (TWC). While the TWC has primacy in the issuance of RCRA permits for hazardous waste incinerators, the Texas Air Control Board (TACB) provides a significant portion of the Part B application review and provides much of the permit language. In addition to dealing with regulatory agencies, RCRA permitting provides by significant public involvement. Often the lack of public support becomes a major roadblock for an incinerator project. In order to establish an effective strategy which addresses the concerns of regulatory agencies and the public, it is important to have an understanding of the steps involved in obtaining a permit. A permit applicant seeking to construct a new hazardous waste incinerator can expect to go through a preapplication meeting with government regulators, a site selection process, file an application, respond to calls for additional technical information from both the TACB and the TWC, defend the application in a hearing, have a recommendation from a TWC hearing examiner and, finally, receive a determination from the TWC's Commissioners. Presuming a favorable response from the Commission, the permittee will be granted a trial burn permit and may proceed with the construction, certification and execution of a trial burn at the facility. Subsequent to publication of the trial burn results and approval by the TWC, the permittee will possess an operational hazardous waste incinerator permit. The paper describes the major steps required to receive an operational permit for a hazardous waste incinerator in the State of Texas. Important issues involved in each step will be discussed including insights gained from recent incinerator permitting efforts

  9. Cooperative Emissions Trading Game: International Permit Market Dominated by Buyers.

    Science.gov (United States)

    Honjo, Keita

    2015-01-01

    Rapid reduction of anthropogenic greenhouse gas emissions is required to mitigate disastrous impacts of climate change. The Kyoto Protocol introduced international emissions trading (IET) to accelerate the reduction of carbon dioxide (CO2) emissions. The IET controls CO2 emissions through the allocation of marketable emission permits to sovereign countries. The costs for acquiring additional permits provide buyers with an incentive to reduce their CO2 emissions. However, permit price has declined to a low level during the first commitment period (CP1). The downward trend in permit price is attributed to deficiencies of the Kyoto Protocol: weak compliance enforcement, the generous allocation of permits to transition economies (hot air), and the withdrawal of the US. These deficiencies created a buyer's market dominated by price-making buyers. In this paper, I develop a coalitional game of the IET, and demonstrate that permit buyers have dominant bargaining power. In my model, called cooperative emissions trading (CET) game, a buyer purchases permits from sellers only if the buyer forms a coalition with the sellers. Permit price is determined by bargaining among the coalition members. I evaluated the demand-side and supply-side bargaining power (DBP and SBP) using Shapley value, and obtained the following results: (1) Permit price is given by the product of the buyer's willingness-to-pay and the SBP (= 1 - DBP). (2) The DBP is greater than or equal to the SBP. These results indicate that buyers can suppress permit price to low levels through bargaining. The deficiencies of the Kyoto Protocol enhance the DBP, and contribute to the demand-side dominance in the international permit market.

  10. Complying with the Kyoto Protocol under uncertainty: Taxes or tradable permits?

    International Nuclear Information System (INIS)

    Quirion, Philippe

    2010-01-01

    The Kyoto Protocol allocates tradable emission allowances (AAUs) to developed countries, but they are free to choose a set of policy instruments to comply with these targets. We compare two different policy instruments: a tax and purely domestic tradable permits, for the European Union, the US and Japan. Information on abatement costs and international permit price is imperfect and stems from nine global economic models. For a country party to the Protocol, the benefit of emission reduction is that it can sell more or has to buy less AAUs. We show that in this context, permits entail a slightly lower expected cost than a tax for the US and Japan, whereas both instruments yield an almost equal outcome for Europe. Applying Weitzman's framework (Prices vs. quantities, RES, 1974) in this context, we show the importance of the positive correlation between costs and benefits: technology shocks that lead to low abatement costs in one country generally lead to low abatement costs in other countries too, thereby leading to a low international permit price in the true-up period.

  11. Offshore Wind Energy Permitting: A Survey of U.S. Project Developers

    Energy Technology Data Exchange (ETDEWEB)

    Van Cleve, Frances B.; Copping, Andrea E.

    2010-11-30

    The U.S. Department of Energy (DOE) has adopted a goal to generate 20% of the nation’s electricity from wind power by 2030. Achieving this “20% Wind Scenario” in 2030 requires acceleration of the current rate of wind project development. Offshore wind resources contribute substantially to the nation’s wind resource, yet to date no offshore wind turbines have been installed in the U.S. Progress developing offshore wind projects has been slowed by technological challenges, uncertainties about impacts to the marine environment, siting and permitting challenges, and viewshed concerns. To address challenges associated with siting and permitting, Pacific Northwest National Laboratory (PNNL) surveyed offshore wind project developers about siting and project development processes, their experience with the environmental permitting process, and the role of coastal and marine spatial planning (CMSP) in development of the offshore wind industry. Based on the responses to survey questions, we identify several priority recommendations to support offshore wind development. Recommendations also include considerations for developing supporting industries in the U.S. and how to use Coastal and Marine Spatial Planning (CMSP) to appropriately consider ocean energy among existing ocean uses. In this report, we summarize findings, discuss the implications, and suggest actions to improve the permitting and siting process.

  12. Cleaner Technology in Denmark - support measures and regulatory efforts

    DEFF Research Database (Denmark)

    Jørgensen, Ulrik

    2005-01-01

    Danish cleaner technology support policies have been successful in fostering innovations that reduce the invironmental impact of products and production. But the lack of enforcement support for cleaner technology in environmental permits has limited the overall impact....

  13. Waste Feed Delivery Environmental Permits and Approvals Plan

    Energy Technology Data Exchange (ETDEWEB)

    TOLLEFSON, K.S.

    2000-01-18

    This plan describes the environmental permits approvals, and other requirements that may affect establishment of a waste feed delivery system for the Hanford Site's River Protection Project. This plan identifies and screens environmental standards for potential applicability, outlines alternatives for satisfying applicable standards, and describes preferred permitting and approval approaches.

  14. Quantifying the CO{sub 2} permit price sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Gruell, Georg; Kiesel, Ruediger [Duisburg-Essen Univ., Essen (Germany). Inst. of Energy Trading and Financial Services

    2012-06-15

    Equilibrium models have been widely used in the literature with the aim of showing theoretical properties of emissions trading schemes. This paper applies equilibrium models to empirically study permit prices and to quantify the permit price sensitivity. In particular, we demonstrate that emission trading schemes both with and without banking are inherently prone to price jumps. (orig.)

  15. 36 CFR 228.54 - Single entry sales or permits.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Single entry sales or permits... MINERALS Disposal of Mineral Materials General Provisions § 228.54 Single entry sales or permits. The... plan which describes operating procedures and reclamation measures, unless the requirement is waived by...

  16. Waste Feed Delivery Environmental Permits and Approvals Plan

    International Nuclear Information System (INIS)

    TOLLEFSON, K.S.

    2000-01-01

    This plan describes the environmental permits approvals, and other requirements that may affect establishment of a waste feed delivery system for the Hanford Site's River Protection Project. This plan identifies and screens environmental standards for potential applicability, outlines alternatives for satisfying applicable standards, and describes preferred permitting and approval approaches

  17. 46 CFR 78.40-10 - No smoking permitted.

    Science.gov (United States)

    2010-10-01

    ... § 78.40-10 No smoking permitted. (a) The master shall have appropriate “No Smoking” signs posted and shall take all necessary precautions to prevent smoking or carrying of lighted or smoldering cigars... 46 Shipping 3 2010-10-01 2010-10-01 false No smoking permitted. 78.40-10 Section 78.40-10 Shipping...

  18. 77 FR 74507 - Endangered Species; Marine Mammals; Issuance of Permits

    Science.gov (United States)

    2012-12-14

    ... not operate to the disadvantage of the endangered species, and (3) the granted permit would be.... Zoological Park. 2012. 82880A Big Game Studio 77 FR 54604; September 5, October 17, 2012. 2012. 83520A Donald...; fax (703) 358-2280. Brenda Tapia, Program Analyst/Data Administrator, Branch of Permits, Division of...

  19. 76 FR 39368 - Migratory Bird Permits; Abatement Regulations

    Science.gov (United States)

    2011-07-06

    ... promulgating migratory bird permit regulations for a permit to use raptors (birds of prey) in abatement activities. Abatement means the use of trained raptors to flush, scare (haze), or take birds or other...). Background In response to public interest in the use of trained raptors to haze (scare) depredating and other...

  20. Wilderness Management... A Computerized System for Summarizing Permit Information

    Science.gov (United States)

    Gary H. Elsner

    1972-01-01

    Permits were first needed for visits to wilderness areas in California during summer 1971. A computerized system for analyzing these permits and summarizing information from them has been developed. It produces four types of summary tables: point-of-origin of visitors; daily variation in total number of persons present; variations in group size; and variations in...

  1. 19 CFR 12.99 - Procedures for permitted entry.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Procedures for permitted entry. 12.99 Section 12.99 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY SPECIAL CLASSES OF MERCHANDISE Switchblade Knives § 12.99 Procedures for permitted entry...

  2. 76 FR 74070 - Endangered and Threatened Species; Permits

    Science.gov (United States)

    2011-11-30

    ... Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq.). Dated: November 21, 2011. Lynn M. Lewis...-FF03E00000] Endangered and Threatened Species; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION... permits to conduct certain activities with endangered species under the authority of the Endangered...

  3. 78 FR 9415 - Endangered and Threatened Species; Permits

    Science.gov (United States)

    2013-02-08

    ...). Authority: The authority for this notice is the Endangered Species Act of 1973, as amended (16 U.S.C. 1531...-FF03E00000] Endangered and Threatened Species; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION... permits to conduct certain activities with endangered species under the authority of the Endangered...

  4. 78 FR 57410 - Endangered Species; Issuance of Permits

    Science.gov (United States)

    2013-09-18

    ... permits to conduct certain activities with endangered species under the authority of the Endangered Species Act, as amended (Act). ADDRESSES: Endangered Species Program Manager, Ecological Services, U.S...-FF01E00000] Endangered Species; Issuance of Permits AGENCY: Fish and Wildlife Service, Interior. ACTION...

  5. 75 FR 45650 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2010-08-03

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R6-ES-2010-N149; 60120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permits. SUMMARY: We announce our receipt of an application to...

  6. 76 FR 8374 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2011-02-14

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R6-ES-2011-N021; 60120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permits. SUMMARY: We announce our receipt of applications to...

  7. 75 FR 28278 - Endangered Wildlife and Plants; Permits

    Science.gov (United States)

    2010-05-20

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R1-ES-2010-N092; 10120-1113-0000-F5] Endangered Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of availability of permit applications; request for comments. SUMMARY: In accordance with the requirements of the...

  8. 76 FR 33334 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2011-06-08

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R6-ES-2011-N112; 60120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permits. SUMMARY: We announce our receipt of applications to...

  9. 75 FR 52012 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2010-08-24

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R6-ES-2010-N181; 60120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permits. SUMMARY: We announce our receipt of applications to...

  10. 75 FR 5101 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2010-02-01

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R6-ES-2010-N010; 60120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permits. SUMMARY: We announce our receipt of applications to...

  11. 76 FR 18576 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2011-04-04

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R6-ES-2011-N056; 60120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permits. SUMMARY: We announce our receipt of applications to...

  12. 76 FR 10063 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2011-02-23

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R6-ES-2011-N026; 60120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permits. SUMMARY: We announce our receipt of applications to...

  13. 75 FR 27361 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2010-05-14

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R6-ES-2010-N095; 60120-1113-0000-D2] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permits. SUMMARY: We announce our receipt of applications to...

  14. 75 FR 20621 - Endangered and Threatened Wildlife and Plants; Permits

    Science.gov (United States)

    2010-04-20

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R3-ES-2009-N0054]; [30120-1113-0000-F6] Endangered and Threatened Wildlife and Plants; Permits AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of availability of permit applications; request for comments. SUMMARY: We, the U.S. Fish and...

  15. 43 CFR 13.4 - Terms of permit.

    Science.gov (United States)

    2010-10-01

    ... § 13.4 Terms of permit. Every permit shall describe the location of the vending facilities and shall be... Interior bureau or office for each location. The head of the Interior bureau or office may require... efficiency as may be prescribed by the head of the Interior bureau or office. Such standards shall conform...

  16. 50 CFR 300.182 - HMS international trade permit.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false HMS international trade permit. 300.182... FISHERIES REGULATIONS International Trade Documentation and Tracking Programs for Highly Migratory Species § 300.182 HMS international trade permit. (a) General. An importer, entering for consumption fish or...

  17. Permits for coal-fired power plants under scrutiny

    International Nuclear Information System (INIS)

    Hoekstra, B.

    2011-01-01

    The attorney-general of the European Court of Justice offered advice to the European Judge on the prejudicial questions of the Department of Administrative Law of the Council of State in the framework of appeal cases against environmental permits of three planned power plants in the Netherlands. The advice may have large consequences for these permits. [nl

  18. 77 FR 49483 - Actions on Special Permit Applications

    Science.gov (United States)

    2012-08-16

    ... modify the special permit Town, South Africa. 178.277(b)(1). to increase the water capacity from 17000... prevent leakage during transportation. (mode 1). 15667-N Volga Dnepr--UNIQUE AIR 49 CFR 172.101 Column To...). NEW SPECIAL PERMIT WITHDRAWN 15494-N Johnson Controls Battery 49 CFR 173.159 To authorize the Group...

  19. 76 FR 6490 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2011-02-04

    ... permit to take (trap, seine, capture, handle, fin clip, release, collect, transport, and captive breed... requests a permit to take (capture, handle, collect, transport, and kill) the Lost River sucker (Deltistes... Service, invite the public to comment on the following applications to conduct certain activities with...

  20. 48 CFR 52.247-2 - Permits, Authorities, or Franchises.

    Science.gov (United States)

    2010-10-01

    ... Franchises. 52.247-2 Section 52.247-2 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION....247-2 Permits, Authorities, or Franchises. As prescribed in 47.207-1(a), insert the following clause: Permits, Authorities, or Franchises (JAN 1997) (a) The offeror does □, does not □, hold authorization from...

  1. 75 FR 4136 - Pipeline Safety: Request To Modify Special Permit

    Science.gov (United States)

    2010-01-26

    ... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket No. PHMSA-2009-0377] Pipeline Safety: Request To Modify Special Permit AGENCY: Pipeline and Hazardous... coating on its gas pipeline. DATES: Submit any comments regarding this special permit modification request...

  2. 76 FR 11853 - Pipeline Safety: Request for Special Permit

    Science.gov (United States)

    2011-03-03

    ... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket No. PHMSA-2011-0027] Pipeline Safety: Request for Special Permit AGENCY: Pipeline and Hazardous Materials... a 24-inch mainline natural gas pipeline, 595 feet in length. The first segment of the special permit...

  3. 29 CFR 1910.146 - Permit-required confined spaces.

    Science.gov (United States)

    2010-07-01

    ... any failure of hazard control or monitoring equipment) or event internal or external to the permit... could be trapped or asphyxiated by inwardly converging walls or by a floor which slopes downward and... complying with the permit space requirements that apply to all employers, each contractor who is retained to...

  4. 75 FR 52965 - Endangered and Threatened Species Permit Applications

    Science.gov (United States)

    2010-08-30

    ... appointment only, during normal business hours at the U.S. Fish and Wildlife Service, 500 Gold Ave., SW., Room... permit for research and recovery purposes to conduct presence/absence surveys for American burying beetle...., Round Rock, Texas. Applicant requests an amendment to a current permit for research and recovery...

  5. 50 CFR 21.27 - Special purpose permits.

    Science.gov (United States)

    2010-10-01

    ... certification required by part 13 and makes a sufficient showing of benefit to the migratory bird resource..., salvage, otherwise acquire, transport, or possess migratory birds, their parts, nests, or eggs for any... WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD PERMITS Specific Permit Provisions § 21.27 Special purpose...

  6. 9 CFR 73.10 - Permitted dips; substances allowed.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Permitted dips; substances allowed. 73.10 Section 73.10 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT... flowers of sulphur or sulphur flour to 100 gallons of water; or a specifically permitted proprietary brand...

  7. 77 FR 54604 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2012-09-05

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and... applicant requests a permit to export sport hunted trophies of one male addax (Addax nasomaculatus), one.... Applicant: John Fry, Carson City, NV; PRT-82592A The applicant requests a permit to import a sport-hunted...

  8. 78 FR 76171 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2013-12-16

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and...: Geoffrey Ridder; Utopia, TX; PRT-00030B The applicant requests a permit to export the sport-hunted trophy... period. Multiple Applicants The following applicants each request a permit to import the sport- hunted...

  9. 40 CFR 68.85 - Hot work permit.

    Science.gov (United States)

    2010-07-01

    ... Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CHEMICAL ACCIDENT PREVENTION PROVISIONS Program 3 Prevention Program § 68.85 Hot work permit. (a) The owner or operator shall issue a hot work permit for hot work operations conducted on or near a covered process. (b...

  10. 40 CFR 123.25 - Requirements for permitting.

    Science.gov (United States)

    2010-07-01

    ... MS4, may I share the responsibility to implement the minimum control measures with other entities... held prior to issuing any permit while reducing the amount of advance notice of such a hearing. State... individual, including the Director, who has or shares authority to approve all or portions of permits either...

  11. 29 CFR 2.12 - Audiovisual coverage permitted.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Audiovisual coverage permitted. 2.12 Section 2.12 Labor Office of the Secretary of Labor GENERAL REGULATIONS Audiovisual Coverage of Administrative Hearings § 2.12 Audiovisual coverage permitted. The following are the types of hearings where the Department...

  12. 76 FR 63322 - Endangered and Threatened Species Permit Applications

    Science.gov (United States)

    2011-10-12

    ... from Helianthus paradoxus (Pecos sunflower) from plants in Texas. Permit TE-829761 Applicant: Bureau of... for endangered plant species, and 50 CFR 17.72 for threatened plant species. Applications Available...: Texas A & M University, Galveston, Texas. Applicant requests a new permit for husbandry and holding of...

  13. 75 FR 67765 - Endangered and Threatened Species Permit Applications

    Science.gov (United States)

    2010-11-03

    ... collect leaf tissue and seeds from the following endangered plants: South Texas ambrosia (Ambrosia... transportation, at the Miller Park Zoo. Permit TE-24625A Applicant: Wendy Leonard, San Antonio, Texas. Applicant...-cheeked warbler (Dendroica chrysoparia) and black-capped vireo (Vireo atricapilla) within Texas. Permit TE...

  14. 78 FR 14110 - Emergency Issuance of Endangered Species Permit

    Science.gov (United States)

    2013-03-04

    ... issued an endangered species permit to address emergency veterinary care for an injured green sea turtle...] Emergency Issuance of Endangered Species Permit AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice... endangered and threatened species under section 10(a)(1)(A) of the Endangered Species Act of 1973, as amended...

  15. 21 CFR 1312.13 - Issuance of import permit.

    Science.gov (United States)

    2010-04-01

    ... drug listed in Schedule III, IV, or V if he finds: (1) That the substance is crude opium, poppy straw... shall render it void and of no effect. Permits are not transferable. Each copy of the permit shall have... the Act (21 U.S.C. 952(a)(1) or (a)(2)(A)), the importation of approved narcotic raw material (opium...

  16. 23 CFR 650.807 - Bridges requiring a USCG permit.

    Science.gov (United States)

    2010-04-01

    ... engineering, social, economic and environmental benefit and impacts. (e) The HA shall consider hydraulic... permit. (a) The USCG has the responsibility (1) to determine whether a USCG permit is required for the... the USCG to be involved throughout the environmental review process in accordance with 23 CFR part 771...

  17. 78 FR 12776 - Endangered and Threatened Species Permit Applications

    Science.gov (United States)

    2013-02-25

    ... and recovery purposes to conduct pollination on 36 individual adult Arizona hedgehog cactus.... Permit TE-43777A Applicant: Sea Life US, LLC, Grapevine, Texas. Applicant requests an amendment to a... Aquarium, Grapevine, Texas. Permit TE-92366A Applicant: Kimley-Horn and Associates, Inc., Dallas, Texas...

  18. 75 FR 53708 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2010-09-01

    ...] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice... endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also requires that we...

  19. 78 FR 57650 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2013-09-19

    ...-FF08E00000] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior... with endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also...

  20. 77 FR 12611 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2012-03-01

    ...-FF08E00000] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior... with endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also...

  1. 75 FR 69699 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2010-11-15

    ...] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice... endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also requires that we...

  2. 75 FR 79387 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2010-12-20

    ...] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice... endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also requires that we...

  3. 76 FR 14424 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2011-03-16

    ...] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice... endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also requires that we...

  4. 77 FR 5045 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2012-02-01

    ...-FF08E00000] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior... certain activities with endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity...

  5. 78 FR 16703 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2013-03-18

    ...-FF08E00000] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior... with endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also...

  6. 76 FR 70160 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2011-11-10

    ...] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice... endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also requires that we...

  7. 78 FR 55287 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2013-09-10

    ...-FF08E00000] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior... with endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also...

  8. 76 FR 20004 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2011-04-11

    ...] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice... endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also requires that we...

  9. 75 FR 20857 - Endangered Species Recovery Permit Applications

    Science.gov (United States)

    2010-04-21

    ...] Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice... endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such activity. The Act also requires that we...

  10. 40 CFR 76.9 - Permit application and compliance plans.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Permit application and compliance plans. 76.9 Section 76.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.9 Permit application and...

  11. 40 CFR 97.223 - CAIR permit contents and term.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false CAIR permit contents and term. 97.223 Section 97.223 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... facilitate coordination of the renewal of the CAIR permit with issuance, revision, or renewal of the CAIR SO2...

  12. 40 CFR 96.223 - CAIR permit contents and term.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false CAIR permit contents and term. 96.223 Section 96.223 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... necessary to facilitate coordination of the renewal of the CAIR permit with issuance, revision, or renewal...

  13. 40 CFR 96.123 - CAIR permit contents and term.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false CAIR permit contents and term. 96.123 Section 96.123 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... necessary to facilitate coordination of the renewal of the CAIR permit with issuance, revision, or renewal...

  14. 40 CFR 97.123 - CAIR permit contents and term.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false CAIR permit contents and term. 97.123 Section 97.123 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... facilitate coordination of the renewal of the CAIR permit with issuance, revision, or renewal of the CAIR NOX...

  15. 40 CFR 97.323 - CAIR permit contents and term.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false CAIR permit contents and term. 97.323 Section 97.323 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... authority, as necessary to facilitate coordination of the renewal of the CAIR permit with issuance, revision...

  16. 27 CFR 555.45 - Original license or permit.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 3 2010-04-01 2010-04-01 false Original license or permit. 555.45 Section 555.45 Alcohol, Tobacco Products, and Firearms BUREAU OF ALCOHOL, TOBACCO, FIREARMS... Original license or permit. (a) Licenses issued prior to May 24, 2003. Any person who intends to engage in...

  17. 25 CFR 166.223 - Can I use a permit as collateral for a loan?

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Can I use a permit as collateral for a loan? 166.223... PERMITS Permit Requirements Permit (leasehold) Mortgage § 166.223 Can I use a permit as collateral for a loan? We may approve a permit containing a provision that authorizes the permittee to encumber the...

  18. Bridge technology report

    CERN Document Server

    2013-01-01

    Please note this is a Short Discount publication. As LANs have proliferated, new technologies and system concepts have come to the fore. One of the key issues is how to interconnect networks. One means of interconnection is to use a 'bridge'. Other competing technologies are repeaters, routers, and gateways. Bridges permit traffic isolation, connect network segments together and operate at the MAC layer. Further, because they operate at the MAC layer, they can handle a variety of protocols such as TCP/IP, SNA, and X.25. This report focuses on the specific technology of bridging two netw

  19. Waste water pilot plant research, development, and demonstration permit application

    International Nuclear Information System (INIS)

    1993-03-01

    This permit application has been prepared to obtain a research, development, and demonstration permit to perform pilot-scale treatability testing on the 242-A Evaporator process condensate waste water effluent stream. It provides the management framework, and controls all the testing conducted in the waste water pilot plant using dangerous waste. It also provides a waste acceptance envelope (upper limits for selected constituents) and details the safety and environmental protection requirements for waste water pilot plant testing. This permit application describes the overall approach to testing and the various components or requirements that are common to all tests. This permit application has been prepared at a sufficient level of detail to establish permit conditions for all waste water pilot plant tests to be conducted

  20. Air quality permits in Texas and New Mexico

    International Nuclear Information System (INIS)

    Fusselman, D.K.; Hofmann, J.E.

    1991-01-01

    Permitting gas processing equipment ranges from fairly simple procedures under the Texas Air Control Board (TACB) Standard Exemption List and the New Mexico Environmental Improvement Division (NMEID) Registration Regulations to an extremely complicated procedure requiring a federal Prevention of Significant Deterioration (PSD) and/or non-attainment review. The following topics relating to obtaining air permits for gas plants will be addressed in this paper: Type of permit/exemption necessary for construction, Specific permit/exemption requirements, New Source Performance Standards (NSPS) Subparts KKK, LLL, GG, K, Ka and Kb, Potential effects of the Federal Clean Air Act Amendments (FCAA). This paper only addresses specific permitting concerns and requirements that apply to the natural gas production industry. The same requirements apply to other industries, with possible additional requirements of National Emission Standards for Hazardous Air Pollutants (NESHAP), NSPS other than Subparts KKK, LLL, GG, K, Ka and Kb, and non-attainment review for pollutants other than ozone

  1. Permissible state permit/fee systems for radioactive materials transportation

    International Nuclear Information System (INIS)

    Friel, L.

    1987-01-01

    Many state permit/fee systems for radioactive materials transportation have been ruled inconsistent with federal law invalidated by the courts. As the date for repository operation, and its associated transportation, draws near, more states can be expected to adopt permit/fee systems. Examination of the U.S. Department of Transportation's advisory rulings and federal court cases on previous permit/fee systems gives general guidance on the type of permit/fee systems most likely to withstand challenges. Such a system would: have a simplified permit application with minimal information requirements; address a federally-defined class of hazardous or radioactive materials; allow access to all shipments conducted in compliance with federal law; charge a fee reasonably related to the costs imposed on the state by the transportation; and minimize the potential for re-directing shipments to other jurisdictions

  2. Source Taxation of Technological Services in Finnish Tax Treaties

    OpenAIRE

    Kiviranta, Tuomas

    2016-01-01

    In this study, I analyze the various means of source taxation of technological and other services permitted by Finnish double taxation conventions and the future of source taxation of technological and other services. I attempt to shed light on the various means of source taxation of technological services permitted by Finnish tax treaties and by tax treaties also more generally. I analyze 1) the taxation of technological services in the source country as the profits of a permanent establishm...

  3. Regulatory barriers to hazardous waste technology innovation

    International Nuclear Information System (INIS)

    Kuusinen, T.L.; Siegel, M.R.

    1991-02-01

    The primary federal regulatory programs that influence the development of new technology for hazardous waste are the Resource Conservation and Recovery Act (RCRA) and the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA, also commonly known as Superfund). Two important aspects of RCRA that can create barriers to hazardous waste technology innovation are technology-based waste pre-treatment standards and a cumbersome permitting program. By choosing a technology-based approach to the RCRA land disposal restrictions program, the US Environmental Protection Agency (EPA) has simultaneously created tremendous demand for the technologies specified in its regulations, while at the same time significantly reduced incentives for technology innovation that might have otherwise existed. Also, the RCRA hazardous waste permitting process can take years and cost hundreds of thousands of dollars. The natural tendency of permit writers to be cautious of unproven (i.e., innovative) technology also can create a barrier to deployment of new technologies. EPA has created several permitting innovations, however, to attempt to mitigate this latter barrier. Understanding the constraints of these permitting innovations can be important to the success of hazardous waste technology development programs. 3 refs

  4. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  5. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  6. 7 CFR 330.203 - Action on applications for permits to move plant pests; form of and conditions in permits.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 5 2010-01-01 2010-01-01 false Action on applications for permits to move plant pests... PEST REGULATIONS; GENERAL; PLANT PESTS; SOIL, STONE, AND QUARRY PRODUCTS; GARBAGE Movement of Plant Pests § 330.203 Action on applications for permits to move plant pests; form of and conditions in...

  7. 78 FR 6817 - Clean Air Act Operating Permit Program; Petition for Objection to State Operating Permit for...

    Science.gov (United States)

    2013-01-31

    ... Wisconsin Public Service Corporation--JP Pulliam Plant. Pursuant to section 505(b)(2) of the Act, a... ENVIRONMENTAL PROTECTION AGENCY [FRL 9774-6] Clean Air Act Operating Permit Program; Petition for Objection to State Operating Permit for Wisconsin Public Service Corporation--JP Pulliam Plant AGENCY...

  8. 75 FR 22400 - Clean Air Act Operating Permit Program; Petition To Object to Title V Permit for Wheelabrator...

    Science.gov (United States)

    2010-04-28

    ... ENVIROMENTAL PROTECTION AGENCY [FRL-9142-6] Clean Air Act Operating Permit Program; Petition To Object to Title V Permit for Wheelabrator Baltimore, L.P., Baltimore City, MD AGENCY: Environmental Protection Agency (EPA). ACTION: Notice of final action. SUMMARY: Pursuant to section 505(b)(2) of the Clean...

  9. 76 FR 53452 - Clean Air Act Operating Permit Program; Response to Petition To Reopen the 2001 Title V Permit...

    Science.gov (United States)

    2011-08-26

    ... ENVIROMENTAL PROTECTION AGENCY [FRL-9457-3 ] Clean Air Act Operating Permit Program; Response to Petition To Reopen the 2001 Title V Permit for Reliant Portland Generating Station, Upper Mount Bethel Township, Northampton County, PA AGENCY: Environmental Protection Agency (EPA). ACTION: Notice of action...

  10. 75 FR 75463 - Clean Air Act Operating Permit Program; Petition To Object to Title V Permit for Luke Paper...

    Science.gov (United States)

    2010-12-03

    ... ENVIROMENTAL PROTECTION AGENCY [FRL-9234-9] Clean Air Act Operating Permit Program; Petition To Object to Title V Permit for Luke Paper Company, Luke, MD AGENCY: Environmental Protection Agency (EPA). ACTION: Notice of final action. SUMMARY: Pursuant to section 505(b)(2) of the Clean Air Act (CAA), the...

  11. Genetic counselors' views and experiences with the clinical integration of genome sequencing.

    Science.gov (United States)

    Machini, Kalotina; Douglas, Jessica; Braxton, Alicia; Tsipis, Judith; Kramer, Kate

    2014-08-01

    In recent years, new sequencing technologies known as next generation sequencing (NGS) have provided scientists the ability to rapidly sequence all known coding as well as non-coding sequences in the human genome. As the two emerging approaches, whole exome (WES) and whole genome (WGS) sequencing, have started to be integrated in the clinical arena, we sought to survey health care professionals who are likely to be involved in the implementation process now and/or in the future (e.g., genetic counselors, geneticists and nurse practitioners). Two hundred twenty-one genetic counselors- one third of whom currently offer WES/WGS-participated in an anonymous online survey. The aims of the survey were first, to identify barriers to the implementation of WES/WGS, as perceived by survey participants; second, to provide the first systematic report of current practices regarding the integration of WES/WGS in clinic and/or research across the US and Canada and to illuminate the roles and challenges of genetic counselors participating in this process; and third to evaluate the impact of WES/WGS on patient care. Our results showed that genetic counseling practices with respect to WES/WGS are consistent with the criteria set forth in the ACMG 2012 policy statement, which highlights indications for testing, reporting, and pre/post test considerations. Our respondents described challenges related to offering WES/WGS, which included billing issues, the duration and content of the consent process, result interpretation and disclosure of incidental findings and variants of unknown significance. In addition, respondents indicated that specialty area (i.e., prenatal and cancer), lack of clinical utility of WES/WGS and concerns about interpretation of test results were factors that prevented them from offering this technology to patients. Finally, study participants identified the aspects of their professional training which have been most beneficial in aiding with the integration of

  12. Hanford Facility Dangerous Waste Permit Application, 222-S Laboratory Complex

    International Nuclear Information System (INIS)

    WILLIAMS, J.F.

    2000-01-01

    The Hanford Facility Dangerous Waste Permit Application is considered to be a single application organized into a General Information Portion (document number DOE/RL-91-28) and a Unit-Specific Portion. The scope of the Unit-Specific Portion is limited to Part B permit application documentation submitted for individual, operating treatment, storage, and/or disposal units, such as the 222-S Laboratory Complex (this document, DOE/RL-91-27). Both the General Information and Unit-Specific portions of the Hanford Facility Dangerous Waste Permit Application address the content of the Part B permit application guidance prepared by the Washington State Department of Ecology (Ecology 1987 and 1996) and the U.S. Environmental Protection Agency (40 Code of Federal Regulations 270), with additional information needs defined by the Hazardous and Solid Waste Amendments and revisions of Washington Administrative Code 173-303. For ease of reference, the Washington State Department of Ecology alpha-numeric section identifiers from the permit application guidance documentation (Ecology 1996) follow, in brackets, the chapter headings and subheadings. Documentation contained in the General Information Portion is broader in nature and could be used by multiple treatment, storage, and/or disposal units (e.g., the glossary provided in the General Information Portion). Wherever appropriate, the 222-S Laboratory Complex permit application documentation makes cross-reference to the General Information Portion, rather than duplicating text. Information provided in this 222-S Laboratory Complex permit application documentation is current as of August 2000

  13. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  14. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  15. Emission Permits trade between the Nordic and Baltic Countries

    Energy Technology Data Exchange (ETDEWEB)

    Alm, Leif Kristian

    2000-05-01

    A bottom-up technology oriented model of the energy systems in the Nordic and Baltic countries have been constructed and used for analysing an optimal set of energy and emission trading within the region. The model used is MARKAL, which has been developed within the IEA-ETSAP. The analyses are based on national emission levels agreed on in the Kyoto protocol (and the following burden sharing negotiations within the European Union), and with an additional strengthening after 2010. Only energy related CO{sub 2} emissions are explicitly considered. Nuclear power in Sweden is assumed to be phased out. The results show that especially Norway and Sweden have large abatement costs when acting alone, whale the Baltic countries will probably not need to take domestic actions due to the Kyoto protocol if they act alone, as the restructuring of their economies in the beginning of the 1990ties cut emissions (and their economies) dramatically. It is shown that emission trading among the Nordic and Baltic countries can reduce abatement costs among the Nordic countries significantly, possibly down to a level equivalent to a world market (Annex I) permit price. Extending the Nordic common electricity market to Balticum will have minor influence on overall energy system costs. There is no pronounced direction for net electricity flow between the Nordic and Baltic countries. High marginal costs during peak hours in Balticum indicate that imports of Nordic hydro power during peak-hours could be a cost-effective option. This possibility could be implemented with a subsea AC/DC connection between Sweden and Latvia. It is politically viable to develop more hydropower in Norway, this country will be the major electricity exporter in the region, while Sweden will be the main importer. Changing scenario assumptions, i.e. no more Norwegian hydropower, but life extension of Swedish nuclear power, could change this picture. (author)

  16. Project W-314 phase I environmental permits and approvals plan

    International Nuclear Information System (INIS)

    TOLLEFSON, K.S.

    1999-01-01

    This document describes the range of environmental actions, including required permits and other agency approvals, for Project W-314 activities in the Hanford Site's Tank Waste Remediation System. This document outlines alternative approaches to satisfying applicable environmental standards, and describes selected strategies for acquiring permits and other approvals needed for waste feed delivery to proceed. This document also includes estimated costs and schedule to obtain the required permits and approvals based on the selected strategy. It also provides estimated costs for environmental support during design and construction based on the preliminary project schedule provided

  17. Permitting plan for project W-236B, initial pretreatment module

    International Nuclear Information System (INIS)

    Tollefson, K.S.

    1995-01-01

    The Tank Waste Remediation System pretreatment process mission is to separate high-level and low-level waste fractions. A comprehensive review of environmental regulations has indicated that several environmental reviews, permits, and approvals are required before construction and operation of the facility. This revised document provides a summary of permit application data requirements, alternative strategies for permit completion and approval, as well as the probability of success for each alternative for the Initial Pretreatment Module resulting from recent revisions to the Tri-Party Agreement

  18. Political and Economic Scope for Permit Markets in Europe

    DEFF Research Database (Denmark)

    Svendsen, Gert Tinggaard

    1999-01-01

    (organized polluters) due to the possibility of a free, initial distribution (grand-fathering). As such, a mix of green taxes (in relation to non-organized interests) and grandfathered permit markets (in relation to organized interests) should be considered in the search for cost-effective and politically...... of permit markets in the US. Therefore, the policy recommendation for e.g. CO2 reduction in Europe is to apply taxation in relation to large and non-organized groups only, such as households and the transportation sector. A permit market, on the other hand, is politically more attrac-tive to the industry...

  19. Enforcing Transferable Permit Systems in the Presence of Market Power

    International Nuclear Information System (INIS)

    Chavez, C.A.; Stanlund, J.K.

    2003-01-01

    We derive an enforcement strategy for a transferable permit system in the presence of market power that achieves complete compliance in a cost-effective manner. We show that the presence of a firm with market influence makes designing an enforcement strategy more difficult than enforcing a perfectly competitive system. We also re-consider the suggestion that a firm with market influence should be allocated permits so that it chooses to not participate in the permit market. When enforcement and its costs are taken into account, that suggestion does not hold except in a very special case

  20. Genome sequencing for obstetricians & gynaecologists | Kent ...

    African Journals Online (AJOL)

    The medical profession has been waiting for a decade to be invigorated by the sequencing of the human genome, arguably the greatest scientific project ever. The technology has been spectacular but the results of the project have yielded more unexpected results than definitive answers – many about the very nature of our ...

  1. Oxford Nanopore MinION Sequencing and Genome Assembly

    Directory of Open Access Journals (Sweden)

    Hengyun Lu

    2016-10-01

    Full Text Available The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS technology. The third-generation sequencing (TGS technology, led by Pacific Biosciences (PacBio, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT. MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.

  2. JVM: Java Visual Mapping tool for next generation sequencing read.

    Science.gov (United States)

    Yang, Ye; Liu, Juan

    2015-01-01

    We developed a program JVM (Java Visual Mapping) for mapping next generation sequencing read to reference sequence. The program is implemented in Java and is designed to deal with millions of short read generated by sequence alignment using the Illumina sequencing technology. It employs seed index strategy and octal encoding operations for sequence alignments. JVM is useful for DNA-Seq, RNA-Seq when dealing with single-end resequencing. JVM is a desktop application, which supports reads capacity from 1 MB to 10 GB.

  3. The International Nucleotide Sequence Database Collaboration.

    Science.gov (United States)

    Cochrane, Guy; Karsch-Mizrachi, Ilene; Nakamura, Yasukazu

    2011-01-01

    Under the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org), globally comprehensive public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data formats and conventions that enable consistent data submission to their databases and support regular data exchange around the globe. Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core foundation for the global bioinformatics data infrastructure. While growth in sequence data volumes comes no longer as a surprise to INSDC partners, the uptake of next-generation sequencing technology by mainstream science that we have witnessed in recent years brings a step-change to growth, necessarily making a clear mark on INSDC strategy. In this article, we introduce the INSDC, outline data growth patterns and comment on the challenges of increased growth.

  4. Aplikace logistických technologií Just-in-Time a Just-in-Sequence ve společnosti Robert Bosch spol. s r.o.

    OpenAIRE

    ŠTEFKOVÁ, Iveta

    2009-01-01

    This work is mostly oriented to define theory and application of principle Just in Time ( JIT ), Just in Sequence (JIS ) and related methods in Robert Bosch Ltd.Part goals are define theoretical basis of JIT and JIS from knowledge of Czech and foreign literature and detailed analysis of particular methods. Each method is well evaluated with all its pros and cons. Further observations engaged method of Kanban, Heijunka, MRPI, MRPII, which are close related to JIT and JIS. This work precisely d...

  5. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  6. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  7. Resource Conservation and Recovery Act: Part B, Permit application

    International Nuclear Information System (INIS)

    1992-03-01

    This report contains information related to the permit application for the WIPP facility. Information is presented on solid waste management; personnel safety; emergency plans; site characterization; applicable regulations; decommissioning; and ground water monitoring requirements

  8. Storm Water General Permit 3 for Rock and Asphalt

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — General permit #3 for storm water discharges associated with industrial activity for Asphalt Plants, Concrete Batch Plants, Rock Crushing Plants and Construction...

  9. 77 FR 49453 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2012-08-16

    ... citations to, and analyses of, the applicable laws and regulations. We will not consider or include in our... period. Applicant: Alexandria Rosati, Cambridge, MA; PRT-72061A The applicant requests a permit to...

  10. 75 FR 34766 - Receipt of Applications for Permit

    Science.gov (United States)

    2010-06-18

    ... permit to export one female captive bred giant panda (Ailuropoda melanoleuca) born at the zoo in 2007and.... Applicant: United States Department of Agriculture/Animal and Plant Health Inspection Service/Wildlife...

  11. 50 CFR 25.55 - Refuge admission permits.

    Science.gov (United States)

    2010-10-01

    ...-specific permits, at Fish and Wildlife Service Regional and Washington, DC Offices, and at other locations....55 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR... the holder on the front. ...

  12. Oversize/overweight vehicle unified permitting process (UPP) : phase I.

    Science.gov (United States)

    2017-08-01

    Multiple jurisdictions within Minnesota process oversize/overweight (OSOW) permits for the movement of freight on state roadways, county roads, and municipal and township streets. Movement of freight has increased in recent years to help support econ...

  13. Oversize/overweight permitting practices review : phase II.

    Science.gov (United States)

    2013-02-01

    This study explores a more detailed analysis of the permitting process in the Mid-Atlantic Region and : delves into operational practice, and theory and history of the practice among states. The states : practices examined in greater detail include C...

  14. Hydroelectric Generating Facilities General Permit (HYDROGP) for Massachusetts & New Hampshire

    Science.gov (United States)

    Documents, links & contacts for the Notice of Availability of the Final NPDES General Permits (HYDROGP) for Discharges at Hydroelectric Generating Facilities in Massachusetts (MAG360000) and New Hampshire (NHG360000) and Tribal Lands in the State of MA.

  15. 36 CFR 296.10 - Suspension and revocation of permits.

    Science.gov (United States)

    2010-07-01

    ... AGRICULTURE PROTECTION OF ARCHAEOLOGICAL RESOURCES: UNIFORM REGULATIONS § 296.10 Suspension and revocation of... correct the situation which led to suspension of the permit. (b) Suspension or revocation for management...

  16. 78 FR 75369 - Endangered and Threatened Species Permit Applications

    Science.gov (United States)

    2013-12-11

    ... into the wild in Oklahoma. Permit TE-833851 Applicant: City of Austin Watershed Protection Department... reddelli) Black-capped vireo (Vireo atricapilla) Bone Cave harvestman (Texella reyesi) Braken Bat Cave...

  17. Storm Water General Permit 1 for Industrial Facilities

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — General permit #1 for storm water discharges associated with industrial facilities in Iowa for the National Pollutant Discharge Elimination System (NPDES) program.

  18. 48 CFR 52.236-7 - Permits and Responsibilities.

    Science.gov (United States)

    2010-10-01

    ... obtaining any necessary licenses and permits, and for complying with any Federal, State, and municipal laws... negligence. The Contractor shall also be responsible for all materials delivered and work performed until...

  19. NPDES Permit for Crow Nation Water Treatment Plants in Montana

    Science.gov (United States)

    Under NPDES permit MT-0030538, the U.S. Bureau of Indian Affairs is authorized to discharge from the Crow Agency water treatment plants via the wastewater treatment facility located in Bighorn County, Montana to the Little Bighorn River.

  20. 75 FR 30428 - Receipt of Applications for Permit

    Science.gov (United States)

    2010-06-01

    ... (Oreonax flavicauda) from Peru for the purpose of enhancement of the species through scientific research... be conducted under the remainder of the 5-year period of the permit. Applicant: Natural History...

  1. RHIC beam permit and quench detection communications system

    International Nuclear Information System (INIS)

    Conkling, C.R. Jr.

    1997-01-01

    A beam permit module has been developed to concentrate RHIC, subsystem sensor outputs, permit beam, and initiate emergency shutdowns. The modules accept inputs from the vacuum, cryogenic, power supply, beam loss, and superconducting magnet quench detection systems. Modules are located at equipment locations around the RHIC ring. The modules are connected by three fiberoptic communications links; a beam permit link, and two magnet power supply interlock links. During operation, carrier presence allows beam. If a RHIC subsystem detects a fault, the beam permit carrier terminates - initiating a beam dump. If the fault was a superconducting magnet quench, a power supply interlock carrier terminates - initiating an emergency magnet power dump. In addition, the master module triggers an event to cause remote sensors to log and hold data at the time-of-failure

  2. Resource Conservation and Recovery Act Part B permit application

    International Nuclear Information System (INIS)

    1992-01-01

    This permit application (Vol. 7) for the WIPP facility contains appendices related to the following information: Ground water protection; personnel; solid waste management; and memorandums concerning environmental protection standards

  3. 77 FR 3493 - Endangered Species Receipt of Applications for Permit

    Science.gov (United States)

    2012-01-24

    ..., Moseley, VA; PRT-57466A. The applicant requests a permit to import 6 female captive-born cheetahs (Acinonyx jubatus jubatus) from De Wildt Cheetah Breeding Centre, De Wildt, South Africa for the purpose of...

  4. 9 CFR 72.13 - Permitted dips and procedures.

    Science.gov (United States)

    2010-01-01

    ... proprietary brands of permitted dips—as well the use of compressed air, vat management techniques, and other... maintained and that under actual field conditions the dipping of cattle with a solution of definite strength...

  5. 76 FR 27660 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2011-05-12

    ... decisions are: (1) Those supported by quantitative information or studies; and (2) Those that include... applicant requests a permit to import a sport-hunted trophy of one male bontebok (Damaliscus pygargus...

  6. 76 FR 20705 - Endangered Species Receipt of Applications for Permit

    Science.gov (United States)

    2011-04-13

    ... quantitative information or studies; and (2) Those that include citations to, and analyses of, the applicable.... Multiple Applicants The following applicants each request a permit to import the sport- hunted trophy of...

  7. 78 FR 59052 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2013-09-25

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and.... Multiple Applicants The following applicants each request a permit to import the sport- hunted trophy of...

  8. 78 FR 45954 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2013-07-30

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and... Applicants The following applicants each request a permit to import the sport- hunted trophy of one male...

  9. 76 FR 52965 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2011-08-24

    ... quantitative information or studies; and (2) Those that include citations to, and analyses of, the applicable... permit to import the sport- hunted trophy of one male bontebok (Damaliscus pygargus pygargus) culled from...

  10. 75 FR 63196 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2010-10-14

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and... a permit to import a sport-hunted trophy of one male bontebok (Damaliscus pygargus pygargus) culled...

  11. 75 FR 76022 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2010-12-07

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and... public display. Multiple Applicants The following applicants each request a permit to import the sport...

  12. 76 FR 39432 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2011-07-06

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and.... Multiple Applicants (New Applications) The following applicants each request a permit to import the sport...

  13. 78 FR 112 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2013-01-02

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and... applicants each request a permit to import the sport- hunted trophy of one male bontebok (Damaliscus pygargus...

  14. 78 FR 62647 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2013-10-22

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and... permit to import the sport- hunted trophy of one male bontebok (Damaliscus pygargus pygargus) culled from...

  15. 77 FR 72882 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2012-12-06

    ...) Those supported by quantitative information or studies; and (2) Those that include citations to, and... following applicants each request a permit to import the sport- hunted trophy of one male bontebok...

  16. 75 FR 41235 - Receipt of Applications for Permit

    Science.gov (United States)

    2010-07-15

    ... quantitative information or studies; and (2) Those that include citations to, and analyses of, the applicable... the species. Multiple Applicants The following applicants each request a permit to import the sport...

  17. 78 FR 21627 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2013-04-11

    ... decisions are: (1) Those supported by quantitative information or studies; and (2) Those that include... Tapiridae Applicant: Michael Tomb, Jackson, LA; PRT-01602B The applicant requests a permit to import a sport...

  18. 75 FR 44986 - Receipt of Applications for Permit

    Science.gov (United States)

    2010-07-30

    ... quantitative information or studies; and (2) Those that include citations to, and analyses of, the applicable... requests a permit to import a sport-hunted trophy of one male bontebok (Damaliscus pygargus pygargus...

  19. 76 FR 51051 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2011-08-17

    ... quantitative information or studies; and (2) Those that include citations to, and analyses of, the applicable... request a permit to import the sport- hunted trophy of one male bontebok (Damaliscus pygargus pygargus...

  20. 76 FR 32223 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2011-06-03

    ... studies; and (2) Those that include citations to, and analyses of, the applicable laws and regulations. We... Applicants The following applicants each request a permit to import the sport- hunted trophy of one male...