Sample records for accurate finished sequence

  1. Sequencing intractable DNA to close microbial genomes.

    PubMed

    Hurt, Richard A; Brown, Steven D; Podar, Mircea; Palumbo, Anthony V; Elias, Dwayne A

    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 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.

  2. A Hybrid Approach for the Automated Finishing of Bacterial Genomes

    PubMed Central

    Robins, William P.; Chin, Chen-Shan; Webster, Dale; Paxinos, Ellen; Hsu, David; Ashby, Meredith; Wang, Susana; Peluso, Paul; Sebra, Robert; Sorenson, Jon; Bullard, James; Yen, Jackie; Valdovino, Marie; Mollova, Emilia; Luong, Khai; Lin, Steven; LaMay, Brianna; Joshi, Amruta; Rowe, Lori; Frace, Michael; Tarr, Cheryl L.; Turnsek, Maryann; Davis, Brigid M; Kasarskis, Andrew; Mekalanos, John J.; Waldor, Matthew K.; Schadt, Eric E.

    2013-01-01

    Dramatic improvements in DNA sequencing technology have revolutionized our ability to characterize most genomic diversity. However, accurate resolution of large structural events has remained challenging due to the comparatively shorter read lengths of second-generation technologies. Emerging third-generation sequencing technologies, which yield markedly increased read length on rapid time scales and for low cost, have the potential to address assembly limitations. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at > 99.9% accuracy. Complex regions with clinically significant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 reference we obtain 14 and 8 scaffolds greater than 1kb, respectively, correcting several errors in the underlying source data. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. PMID:22750883

  3. Reducing assembly complexity of microbial genomes with single-molecule sequencing.

    PubMed

    Koren, Sergey; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; Harhay, Dayna M; Mcvey, Scott D; Radune, Diana; Bergman, Nicholas H; Phillippy, Adam M

    2013-01-01

    The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

  4. Automated Finishing with Autofinish

    PubMed Central

    Gordon, David; Desmarais, Cindy; Green, Phil

    2001-01-01

    Currently, the genome sequencing community is producing shotgun sequence data at a very high rate, but finishing (collecting additional directed sequence data to close gaps and improve the quality of the data) is not matching that rate. One reason for the difference is that shotgun sequencing is highly automated but finishing is not: Most finishing decisions, such as which directed reads to obtain and which specialized sequencing techniques to use, are made by people. If finishing rates are to increase to match shotgun sequencing rates, most finishing decisions also must be automated. The Autofinish computer program (which is part of the Consed computer software package) does this by automatically choosing finishing reads. Autofinish is able to suggest most finishing reads required for completion of each sequencing project, greatly reducing the amount of human attention needed. Autofinish sometimes completely finishes the project, with no human decisions required. It cannot solve the most complex problems, so we recommend that Autofinish be allowed to suggest reads for the first three rounds of finishing, and if the project still is not finished completely, a human finisher complete the work. We compared this Autofinish-Hybrid method of finishing against a human finisher in five different projects with a variety of shotgun depths by finishing each project twice—once with each method. This comparison shows that the Autofinish-Hybrid method saves many hours over a human finisher alone, while using roughly the same number and type of reads and closing gaps at roughly the same rate. Autofinish currently is in production use at several large sequencing centers. It is designed to be adaptable to the finishing strategy of the lab—it can finish using some or all of the following: resequencing reads, reverses, custom primer walks on either subclone templates or whole clone templates, PCR, or minilibraries. Autofinish has been used for finishing cDNA, genomic clones, and whole bacterial genomes (see http://www.phrap.org). PMID:11282977

  5. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

    PubMed

    Chin, Chen-Shan; Alexander, David H; Marks, Patrick; Klammer, Aaron A; Drake, James; Heiner, Cheryl; Clum, Alicia; Copeland, Alex; Huddleston, John; Eichler, Evan E; Turner, Stephen W; Korlach, Jonas

    2013-06-01

    We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.

  6. Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

    PubMed Central

    Li, Runsheng; Hsieh, Chia-Ling; Young, Amanda; Zhang, Zhihong; Ren, Xiaoliang; Zhao, Zhongying

    2015-01-01

    Most next-generation sequencing platforms permit acquisition of high-throughput DNA sequences, but the relatively short read length limits their use in genome assembly or finishing. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking. We evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans genome with no gap. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences prevents pre-assembly of long reads in the relevant genomic region. Second, the reads are able to reliably detect missing but not extra sequences in the C. elegans genome. Third, the reads of smaller size are more capable of recovering repetitive sequences than those of bigger size. Fourth, at least 40 Kbp missing genomic sequences are recovered in the C. elegans genome using the long reads. Finally, an N50 contig size of at least 86 Kbp can be achieved with 24×reads but with substantial mis-assembly errors, highlighting a need for novel assembly algorithm for the long reads. PMID:26039588

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

    PubMed Central

    Eastman, Alexander W.; Yuan, Ze-Chun

    2015-01-01

    Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects. PMID:25653642

  8. Finishing and Special Motifs: Lessons Learned from CRISPR Analysis Using Next-Generation Draft Sequences (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Campbell, Catherine

    2018-01-22

    Catherine Campbell on "Finishing and Special Motifs: Lessons learned from CRISPR analysis using next-generation draft sequences" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  9. Finishing and Special Motifs: Lessons Learned from CRISPR Analysis Using Next-Generation Draft Sequences (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Campbell, Catherine

    Catherine Campbell on "Finishing and Special Motifs: Lessons learned from CRISPR analysis using next-generation draft sequences" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  10. Nearly Finished Genomes Produced Using Gel Microdroplet Culturing (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fitzsimmons, Michael

    2012-06-01

    Michael Fitzsimmons from Los Alamos National Laboratory gives a talk titled "Nearly Finished Genomes Produced Using Gel Microdroplet Culturing" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  11. Nearly Finished Genomes Produced Using Gel Microdroplet Culturing (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Fitzsimmons, Michael

    2018-01-22

    Michael Fitzsimmons from Los Alamos National Laboratory gives a talk titled "Nearly Finished Genomes Produced Using Gel Microdroplet Culturing" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  12. Approaches for in silico finishing of microbial genome sequences

    PubMed Central

    Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

    2017-01-01

    Abstract The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing. PMID:28898352

  13. Approaches for in silico finishing of microbial genome sequences.

    PubMed

    Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

    The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.

  14. Finished Prokaryotic Genome Assemblies from a Low-cost Combination of Short and Long Reads (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yin, Shuangye

    2012-06-01

    Shuangye Yin on "Finished prokaryotic genome assemblies from a low-cost combination of short and long reads"; at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  15. Sequencing the Unrearranged Human Immunoglobin

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Warren, Rene

    2010-06-03

    Rene Warren from Canada's Michael Smith Genome Sciences Centre discusses sequencing and finishing the IgH heavy chain locus on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  16. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

    PubMed

    Utturkar, Sagar M; Klingeman, Dawn M; Hurt, Richard A; Brown, Steven D

    2017-01-01

    This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

  17. High Throughput Plasmid Sequencing with Illumina and CLC Bio (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Athavale, Ajay

    2018-01-04

    Ajay Athavale (Monsanto) presents "High Throughput Plasmid Sequencing with Illumina and CLC Bio" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  18. Single haplotype assembly of the human genome from a hydatidiform mole.

    PubMed

    Steinberg, Karyn Meltz; Schneider, Valerie A; Graves-Lindsay, Tina A; Fulton, Robert S; Agarwala, Richa; Huddleston, John; Shiryev, Sergey A; Morgulis, Aleksandr; Surti, Urvashi; Warren, Wesley C; Church, Deanna M; Eichler, Evan E; Wilson, Richard K

    2014-12-01

    A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly. © 2014 Steinberg et al.; Published by Cold Spring Harbor Laboratory Press.

  19. Single haplotype assembly of the human genome from a hydatidiform mole

    PubMed Central

    Steinberg, Karyn Meltz; Schneider, Valerie A.; Graves-Lindsay, Tina A.; Fulton, Robert S.; Agarwala, Richa; Huddleston, John; Shiryev, Sergey A.; Morgulis, Aleksandr; Surti, Urvashi; Warren, Wesley C.; Church, Deanna M.; Eichler, Evan E.; Wilson, Richard K.

    2014-01-01

    A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly. PMID:25373144

  20. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Buhay, Christian

    Christian Buhay from Baylor College of Medicine's Human Genome Sequencing Center discusses microbial genome finishing strategies on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  1. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.

    This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

  2. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

    DOE PAGES

    Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.; ...

    2017-07-18

    This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

  3. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

    PubMed Central

    Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Richard A.; Brown, Steven D.

    2017-01-01

    This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences. PMID:28769883

  4. New Technology Drafts: Production and Improvements

    ScienceCinema

    Lapidus, Alla

    2018-01-22

    Alla Lapidus, head of the DOE Joint Genome Institute's Finishing group, gives a talk on how the DOE JGI's microbial genome sequencing pipeline has been adapted to accommodate next generation sequencing platforms at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  5. Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Patel, Kamlesh D.

    2018-01-22

    Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  6. Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Patel, Kamlesh D.

    2012-06-01

    Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  7. Finishing Using Next Generation Technologies

    ScienceCinema

    Van Tonder, Andries

    2018-01-16

    Andries van Tonder of Wellcome Trust Sanger Institute discusses a pipeline for finishing genomes to the gold standard on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  8. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    McMahon, Ben

    2018-01-11

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  9. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McMahon, Ben

    2012-06-01

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  10. Introducing National Center for Genome Resources (NCGR) Informatics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Crow, John

    2018-01-22

    John Crow from the National Center for Genome Resources discusses his organization's informatics at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  11. Introducing National Center for Genome Resources (NCGR) Informatics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Crow, John

    2012-06-01

    John Crow from the National Center for Genome Resources discusses his organization's informatics at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  12. The PerkinElmer Omics Laboratory (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Smith, Todd

    2017-12-22

    Todd Smith of the PerkinElmer Omics Laboratory gives a talk about his lab and its work at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  13. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Sexton, David

    2018-01-22

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  14. The PerkinElmer Omics Laboratory (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smith, Todd

    2012-06-01

    Todd Smith of the PerkinElmer Omics Laboratory gives a talk about his lab and its work at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  15. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sexton, David

    2012-06-01

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  16. Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

    NASA Astrophysics Data System (ADS)

    Antonielli, Livio; Sessitsch, Angela

    2016-04-01

    Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

  17. [Complete genome sequencing and sequence analysis of BCG Tice].

    PubMed

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  18. PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lukjancenko, Oksana

    2012-06-01

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  19. PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Lukjancenko, Oksana

    2018-01-10

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  20. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Davenport, Karen

    Karen Davenport of Los Alamos National Laboratory discusses a high-throughput next generation genome finishing pipeline on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  1. Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes

    DOE PAGES

    Johnson, Shannon L.; Minogue, Timothy D.; Teshima, Hazuki; ...

    2015-01-15

    Bacillus cereus strain 03BB87, a blood culture isolate, originated in a 56-year-old male muller operator with a fatal case of pneumonia in 2003. Here we present the finished genome sequence of that pathogen, including a 5.46-Mb chromosome and two plasmids (209 and 52 Kb, respectively).

  2. Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Tremblay, Julien

    2018-01-22

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  3. Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tremblay, Julien

    2012-06-01

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  4. Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Peng, Ze

    2012-06-01

    Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  5. Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Peng, Ze

    2018-01-24

    Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  6. Use of Optical Mapping in Bacterial Genome Finishing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kumar, Dibyendu

    2010-06-03

    Dibyendu Kumar from the University of Florida discusses whole-genome optical mapping to help validate bacterial genome assemblies on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  7. Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

    PubMed Central

    Hillier, LaDeana W.; Zody, Michael C.; Goldstein, Steve; She, Xinwe; Bult, Carol J.; Agarwala, Richa; Cherry, Joshua L.; DiCuccio, Michael; Hlavina, Wratko; Kapustin, Yuri; Meric, Peter; Maglott, Donna; Birtle, Zoë; Marques, Ana C.; Graves, Tina; Zhou, Shiguo; Teague, Brian; Potamousis, Konstantinos; Churas, Christopher; Place, Michael; Herschleb, Jill; Runnheim, Ron; Forrest, Daniel; Amos-Landgraf, James; Schwartz, David C.; Cheng, Ze; Lindblad-Toh, Kerstin; Eichler, Evan E.; Ponting, Chris P.

    2009-01-01

    The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non–protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not. PMID:19468303

  8. Calibration and prediction of removal function in magnetorheological finishing.

    PubMed

    Dai, Yifan; Song, Ci; Peng, Xiaoqiang; Shi, Feng

    2010-01-20

    A calibrated and predictive model of the removal function has been established based on the analysis of a magnetorheological finishing (MRF) process. By introducing an efficiency coefficient of the removal function, the model can be used to calibrate the removal function in a MRF figuring process and to accurately predict the removal function of a workpiece to be polished whose material is different from the spot part. Its correctness and feasibility have been validated by simulations. Furthermore, applying this model to the MRF figuring experiments, the efficiency coefficient of the removal function can be identified accurately to make the MRF figuring process deterministic and controllable. Therefore, all the results indicate that the calibrated and predictive model of the removal function can improve the finishing determinacy and increase the model applicability in a MRF process.

  9. Superficial roughness on composite surface, composite-enamel and composite-dentin junctions after different finishing and polishing procedures. Part II: roughness with diamond finishing and differences between enamel composite vs body composite.

    PubMed

    Ferraris, Federico; Conti, Alessandro

    2014-01-01

    The following study asks three principle questions relative to composite finishing and composite polishing: 1) Will the superficial roughness of different restoration surfaces have different values, utilizing the same polishing system (multistep), after finishing with the tungsten carbide or diamond bur? 2) Under the same conditions of finishing and polishing sequences, will the composite surfaces (C), the composite-enamel (CE) and composite-dentin (CD) interfaces show different roughness values? 3) Will the surface roughness of composites of different translucency in the various phases of finishing and polishing, and on different interfaces, have different results? The null hypothesis is represented by the fact that there are no significant differences on roughness of composite restorations when polishing, after finishing with tungsten carbide or diamond burs. Furthermore, the null hypothesis is that there are no significant differences on roughness between polishing on composite surface, composite-enamel and composite-dentin interfaces, and finally there are no differences on roughness after finishing and polishing of two composite with different translucency. For the study, 56 class V cavities were prepared on extracted teeth. Restorations were done in nanofilled composite Filtek XTE (3M Espe) in a standard fashion, and then finished and polished. The 28 buccal cavities were restored on the surface with composite enamel and the 28 palatals with composite body. Finishing was done with fine toothing burs in tungsten carbide (16 blades) or fine grit diamond burs (46 μm), and made by the same manufacturer (Komet). The second phase of finishing was done with burs (with the same form as already mentioned) ultrafine toothing tungsten carbide (30 blades) or with extra and ultrafine grit diamond (25 and 8 μm). The polishing phase for both of the earlier sequences was done with the application of three rubber tips with decreasing abrasiveness and an application with a self-polishing brush. All measurements were taken from surfaces C, and interfaces CE and CD. Statistical analyses were carried out with c2 test (a = 0.05). 1) There were no relevant differences of surface roughness on the different surfaces if the polishing was done after finishing with tungsten carbide or diamond burs. 2) Keeping the same sequence of finishing and polishing, a difference was noticed between C, CE and CD, where the latter showed greater roughness. 3) Analyzing the data in all the phases of finishing and polishing on every interface, it can be concluded that the composite enamel and the composite body did not show different levels of superficial roughness. The clinical relevance could be resumed as follows: no difference after polishing, which is preceded by tungsten carbide or diamond finishing burs. The less favorable interface to be polished is CD, compared to CE and C. Considering two composites with different translucency, no difference on roughness after finishing and polishing were detected.

  10. NexGen Production – Sequencing and Analysis

    ScienceCinema

    Muzny, Donna

    2018-01-16

    Donna Muzny of the Baylor College of Medicine Human Genome Sequencing Center discusses next generation sequencing platforms and evaluating pipeline performance on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  11. Seal Technology in Gas Turbine Engines

    DTIC Science & Technology

    1978-08-01

    ambient temperatures and 427*C (800*F). 3. Application as a part of the normal manufacturing sequence without subsequent finishing operations...of demonstrable hardnless with sharp, cutting edges. 4. The coating must be applied to a finish dimmsion without subsequent processing. 5. Application...The JC1-Iii 3.4 coating had a surface finish of 11 V metre (425 mioroinches). Both materials appeared to be adequately rough for the proposed

  12. Ion Torren Semiconductor Sequencing Allows Rapid, Low Cost Sequencing of the Human Exome (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Jenkins, David

    2018-01-10

    David Jenkins on "Ion Torrent semiconductor sequencing allows rapid, low-cost sequencing of the human exome" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  13. Ion Torren Semiconductor Sequencing Allows Rapid, Low Cost Sequencing of the Human Exome (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jenkins, David

    David Jenkins on "Ion Torrent semiconductor sequencing allows rapid, low-cost sequencing of the human exome" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  14. GenePRIMP: Improving Microbial Gene Prediction Quality

    ScienceCinema

    Pati, Amrita

    2018-01-24

    Amrita Pati of the DOE Joint Genome Institute's Genome Biology group talks about a computational pipeline that evaluates the accuracy of gene models in genomes and metagenomes at different stages of finishing at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  15. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Daum, Chris

    Chris Daum of the DOE Joint Genome Institute discusses how the DOE JGI's Production Sequencing group optimizes the sequencer pipelines and assesses quality on the Production line on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  16. Finished genome assembly of warm spring isolate Francisella novicida DPG 3A-IS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Johnson, Shannon L.; Minogue, Timothy D.; Daligault, Hajnalka E.

    2015-09-17

    We sequenced the complete genome of Francisella novicida DPG 3A-IS to closed and finished status. This is a warm spring isolate recovered from Hobo Warm Spring (Utah, USA). The last assembly is available in NCBI under accession number CP012037.

  17. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

    PubMed

    Koren, Sergey; Phillippy, Adam M

    2015-02-01

    Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length. This has dramatically reduced sequencing cost, but resulted in fragmented assemblies, which negatively affect downstream analyses and hinder the creation of finished (gapless, high-quality) genomes. In contrast, emerging long-read sequencing technologies can now produce reads tens of kilobases in length, enabling the automated finishing of microbial genomes for under $1000. This promises to improve the quality of reference databases and facilitate new studies of chromosomal structure and variation. We present an overview of these new technologies and the methods used to assemble long reads into complete genomes. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Athavale, Ajay

    Ajay Athavale (Monsanto) presents "High Throughput Plasmid Sequencing with Illumina and CLC Bio" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  19. Engineered Polymerases Enable Novel Sequencing Applications (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Appel, Maryke

    2018-01-15

    Maryke Appel on "Engineered polymerases provide improved NGS library amplification and enable novel sequencing applications" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  20. Enhanced timing abilities in percussionists generalize to rhythms without a musical beat.

    PubMed

    Cameron, Daniel J; Grahn, Jessica A

    2014-01-01

    The ability to entrain movements to music is arguably universal, but it is unclear how specialized training may influence this. Previous research suggests that percussionists have superior temporal precision in perception and production tasks. Such superiority may be limited to temporal sequences that resemble real music or, alternatively, may generalize to musically implausible sequences. To test this, percussionists and nonpercussionists completed two tasks that used rhythmic sequences varying in musical plausibility. In the beat tapping task, participants tapped with the beat of a rhythmic sequence over 3 stages: finding the beat (as an initial sequence played), continuation of the beat (as a second sequence was introduced and played simultaneously), and switching to a second beat (the initial sequence finished, leaving only the second). The meters of the two sequences were either congruent or incongruent, as were their tempi (minimum inter-onset intervals). In the rhythm reproduction task, participants reproduced rhythms of four types, ranging from high to low musical plausibility: Metric simple rhythms induced a strong sense of the beat, metric complex rhythms induced a weaker sense of the beat, nonmetric rhythms had no beat, and jittered nonmetric rhythms also had no beat as well as low temporal predictability. For both tasks, percussionists performed more accurately than nonpercussionists. In addition, both groups were better with musically plausible than implausible conditions. Overall, the percussionists' superior abilities to entrain to, and reproduce, rhythms generalized to musically implausible sequences.

  1. Sequencing, Assembly and Analysis of Human Microbial Communities

    ScienceCinema

    Petrosino, Joe

    2018-02-02

    Joe Petrosino of Baylor College of Medicine discusses using next generation sequencing technologies to study human microbial communities associated with health and disease on June 4, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  2. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

    PubMed Central

    2013-01-01

    Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another. PMID:23870653

  3. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kumar, Dibyendu; Buhay, Christian; Van Tonder, Andries

    From left to right: Dibyendu Kumar of the University of Florida, Christian Buhay of Baylor College of Medicine, Andries van Tonder of Wellcome Sanger Trust Institute, Anna Montmayeur of the Broad Institute and Karen Davenport of Los Alamos National Laboratory at the Finishing forum on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  4. Sequencing Complex Genomic Regions

    ScienceCinema

    Eichler, Evan

    2018-02-12

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 1 of 2

  5. Defining Genome Project Standards in a New Era of Sequencing

    ScienceCinema

    Chain, Patrick

    2018-01-16

    Patrick Chain of the DOE Joint Genome Institute gives a talk on behalf of the International Genome Sequencing Standards Consortium on the need for intermediate genome classifications between "draft" and "finished".

  6. RapTOR: Automated Sequencing Library Preparation and Suppression for Rapid Pathogen Characterization (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Lane, Todd

    2018-05-18

    Todd Lane on "RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  7. Towards the Perfect Genome Sequence (Opening Keynote) (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Weinstock, George

    2018-04-30

    George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  8. A Rapid Whole Genome Sequencing and Analysis System Supporting Genomic Epidemiology (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    FitzGerald, Michael

    2012-06-01

    Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  9. En Route to the Clinic: Diagnostic Sequencing Applications Using the Ion Torrent (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Muzny, Donna

    2018-01-15

    Donna Muzny on "En route to the clinic: Diagnostic sequencing applications using the Ion Torrent" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  10. RapTOR: Automated Sequencing Library Preparation and Suppression for Rapid Pathogen Characterization (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lane, Todd

    2012-06-01

    Todd Lane on "RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  11. Towards the Perfect Genome Sequence (Opening Keynote) (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Weinstock, George

    2012-06-01

    George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  12. A Rapid Whole Genome Sequencing and Analysis System Supporting Genomic Epidemiology (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    FitzGerald, Michael

    2018-01-11

    Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  13. Sequencing Technologies Panel at SFAF

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Turner, Steve; Fiske, Haley; Knight, Jim

    2010-06-02

    From left to right: Steve Turner of Pacific Biosciences, Haley Fiske of Illumina, Jim Knight of Roche, Michael Rhodes of Life Technologies and Peter Vander Horn of Life Technologies' Single Molecule Sequencing group discuss new sequencing technologies and applications on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  14. Abrasive wear of resin composites as related to finishing and polishing procedures.

    PubMed

    Turssi, Cecilia P; Ferracane, Jack L; Serra, Mônica C

    2005-07-01

    Finishing and polishing procedures may cause topographical changes and introduce subsurface microcracks in dental composite restoratives. Since both of these effects may contribute toward the kinetics of wear, the purpose of this study was to assess and correlate the wear and surface roughness of minifilled and nanofilled composites finished and polished by different methods. Specimens (n=10) made of a minifilled and a nanofilled composite were finished and polished with one of the four sequences: (1) tungsten carbide burs plus Al(2)O(3)-impregnated brush (CbBr) or (2) tungsten carbide burs plus diamond-impregnated cup (CbCp), (3) diamond burs plus brush (DmBr) or (4) diamond burs plus cup (DmCp). As a control, abrasive papers were used. After surface roughness had been quantified, three-body abrasion was simulated using the OHSU wear machine. The wear facets were then scanned to measure wear depth and post-testing roughness. All sets of data were subjected to ANOVA and Tukey's tests (alpha=0.05). Pearson's correlation test was applied to check for the existence of a relationship between pre-testing roughness and wear. Significantly smoother surfaces were attained with the sequences CbBr and CbCp, whereas DmCp yielded the roughest surface. Regardless of the finishing/polishing technique, the nanofilled composite exhibited the lowest pre-testing roughness and wear. There was no correlation between the surface roughness achieved after finishing/polishing procedures and wear (p=0.3899). Nano-sized materials may have improved abrasive wear resistance over minifilled composites. The absence of correlation between wear and surface roughness produced by different finishing/polishing methods suggests that the latter negligibly influences material loss due to three-body abrasion.

  15. Apical extrusion of debris during the preparation of oval root canals: a comparative study between a full-sequence SAF system and a rotary file system supplemented by XP-endo finisher file.

    PubMed

    Kfir, Anda; Moza-Levi, Rotem; Herteanu, Moran; Weissman, Amir; Wigler, Ronald

    2018-03-01

    The purpose of this study was to assess the amount of apically extruded debris during the preparation of oval canals with either a rotary file system supplemented by the XP-endo Finisher file or a full-sequence self-adjusting file (SAF) system. Sixty mandibular incisors were randomly assigned to two groups: group A: stage 1-glide path preparation with Pre-SAF instruments. Stage 2-cleaning and shaping with SAF. Group B: stage 1-glide path preparation with ProGlider file. Stage 2-cleaning and shaping with ProTaper Next system. Stage 3-Final cleaning with XP-endo Finisher file. The debris extruded during each of the stages was collected, and the debris weights were compared between the groups and between the stages within the groups using t tests with a significance level set at P < 0.05. The complete procedure for group B resulted in significantly more extruded debris compared to group A. There was no significant difference between the stages in group A, while there was a significant difference between stage 2 and stages 1 and 3 in group B, but no significant difference between stages 1 and 3. Both instrumentation protocols resulted in extruded debris. Rotary file followed by XP-endo Finisher file extruded significantly more debris than a full-sequence SAF system. Each stage, in either procedure, had its own contribution to the extrusion of debris. Final preparation with XP-endo Finisher file contributes to the total amount of extruded debris, but the clinical relevance of the relative difference in the amount of apically extruded debris remains unclear.

  16. A new method to cluster genomes based on cumulative Fourier power spectrum.

    PubMed

    Dong, Rui; Zhu, Ziyue; Yin, Changchuan; He, Rong L; Yau, Stephen S-T

    2018-06-20

    Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences. Each sequence is translated into a vector in Euclidean space. Distances between the vectors can reflect the relationships between sequences. The mapping between the spectra and moment vector is one-to-one, which means that no information is lost in the power spectra during the calculation. We cluster and classify several datasets including Influenza A, primates, and human rhinovirus (HRV) datasets to build up the phylogenetic trees. Results show that the new proposed cumulative Fourier power spectrum is much faster and more accurately than MSA and another alignment-free method known as k-mer. The research provides us new insights in the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes. The computer programs of the cumulative Fourier power spectrum are available at GitHub (https://github.com/YaulabTsinghua/cumulative-Fourier-power-spectrum). Copyright © 2018. Published by Elsevier B.V.

  17. Analysis of Metagenomic Sequences: From Megabases to Terabases

    ScienceCinema

    Krypides, Nikos

    2018-05-04

    Nikos Krypides of the DOE Joint Genome Institute discusses metagenomics and the challenge of dealing with terabases of data on June 4, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  18. BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

    PubMed

    Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Folker; Schuster, Stephan C

    2005-04-01

    We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages. Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

  19. k-merSNP discovery: Software for alignment-and reference-free scalable SNP discovery, phylogenetics, and annotation for hundreds of microbial genomes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs or raw, unassembled reads. The method is fast to compute, finding SNPs and building a SNP phylogeny in minutes to hours, depending on the size and diversity of the input sequences. The SNP-based trees that result are consistent with known taxonomy and treesmore » determined in other studies. The approach we describe can handle many gigabases of sequence in a single run. The algorithm is based on k-mer analysis.« less

  20. One Bacterial Cell, One Complete Genome

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Woyke, Tanja; Tighe, Damon; Mavrommatis, Konstantinos

    2010-04-26

    While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated frommore » the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200?900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.« less

  1. Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

    PubMed

    Kisand, Veljo; Lettieri, Teresa

    2013-04-01

    De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.

  2. The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola

    USDA-ARS?s Scientific Manuscript database

    Repetitive sequence analysis has become an integral part of genome sequencing projects in addition to gene identification and annotation. Identification of repeats is important not only because it improves gene prediction, but also because of the role that repetitive sequences play in determining th...

  3. Draft versus finished sequence data for DNA and protein diagnostic signature development

    PubMed Central

    Gardner, Shea N.; Lam, Marisa W.; Smith, Jason R.; Torres, Clinton L.; Slezak, Tom R.

    2005-01-01

    Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors or NNs) to sequence. We use SAP to assess whether draft data are sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high-quality draft with error rates of 10−3–10−5 (∼8× coverage) of target organisms is suitable for DNA signature prediction. Low-quality draft with error rates of ∼1% (3× to 6× coverage) of target isolates is inadequate for DNA signature prediction, although low-quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high-quality draft of target and low-quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures. PMID:16243783

  4. Genome, Epigenome and RNA sequences of Monozygotic Twins Discordant for Multiple Sclerosis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Miller, Neil

    2010-06-02

    Neil Miller, Deputy Director of Software Engineering at the National Center for Genome Resources, discusses a monozygotic twin study on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  5. Genome, Epigenome and RNA sequences of Monozygotic Twins Discordant for Multiple Sclerosis

    ScienceCinema

    Miller, Neil

    2018-01-22

    Neil Miller, Deputy Director of Software Engineering at the National Center for Genome Resources, discusses a monozygotic twin study on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  6. Fulfilling the Promise of a Sequenced Human Genome – Part II

    ScienceCinema

    Green, Eric

    2018-02-02

    Eric Green, scientific director of the National Human Genome Research Institute (NHGRI), gives the opening keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM on May 27, 2009. Part 2 of 2

  7. Fulfilling the Promise of a Sequenced Human Genome – Part I

    ScienceCinema

    Green, Eric

    2018-02-02

    Eric Green, scientific director of the National Human Genome Research Institute (NHGRI), gives the opening keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM on May 27, 2009. Part 1 of 2

  8. Genome Improvement at JGI-HAGSC

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

    Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence.more » For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.« less

  9. Use of internal scintillator radioactivity to calibrate DOI function of a PET detector with a dual-ended-scintillator readout

    PubMed Central

    Bircher, Chad; Shao, Yiping

    2012-01-01

    Purpose: Positron emission tomography (PET) detectors that use a dual-ended-scintillator readout to measure depth-of-interaction (DOI) must have an accurate DOI function to provide the relationship between DOI and signal ratios to be used for detector calibration and recalibration. In a previous study, the authors used a novel and simple method to accurately and quickly measure DOI function by irradiating the detector with an external uniform flood source; however, as a practical concern, implementing external uniform flood sources in an assembled PET system is technically challenging and expensive. In the current study, therefore, the authors investigated whether the same method could be used to acquire DOI function from scintillator-generated (i.e., internal) radiation. The authors also developed a method for calibrating the energy scale necessary to select the events within the desired energy window. Methods: The authors measured the DOI function of a PET detector with lutetium yttrium orthosilicate (LYSO) scintillators. Radiation events originating from the scintillators’ internal Lu-176 beta decay were used to measure DOI functions which were then compared with those measured from both an external uniform flood source and an electronically collimated external point source. The authors conducted these studies with several scintillators of differing geometries (1.5 × 1.5 and 2.0 × 2.0 mm2 cross-section area and 20, 30, and 40 mm length) and various surface finishes (mirror-finishing, saw-cut rough, and other finishes in between), and in a prototype array. Results: All measured results using internal and external radiation sources showed excellent agreement in DOI function measurement. The mean difference among DOI values for all scintillators measured from internal and external radiation sources was less than 1.0 mm for different scintillator geometries and various surface finishes. Conclusions: The internal radioactivity of LYSO scintillators can be used to accurately measure DOI function in PET detectors, regardless of scintillator geometry or surface finish. Because an external radiation source is not needed, this method of DOI function measurement can be practically applied to individual PET detectors as well as assembled systems. PMID:22320787

  10. Use of internal scintillator radioactivity to calibrate DOI function of a PET detector with a dual-ended-scintillator readout.

    PubMed

    Bircher, Chad; Shao, Yiping

    2012-02-01

    Positron emission tomography (PET) detectors that use a dual-ended-scintillator readout to measure depth-of-interaction (DOI) must have an accurate DOI function to provide the relationship between DOI and signal ratios to be used for detector calibration and recalibration. In a previous study, the authors used a novel and simple method to accurately and quickly measure DOI function by irradiating the detector with an external uniform flood source; however, as a practical concern, implementing external uniform flood sources in an assembled PET system is technically challenging and expensive. In the current study, therefore, the authors investigated whether the same method could be used to acquire DOI function from scintillator-generated (i.e., internal) radiation. The authors also developed a method for calibrating the energy scale necessary to select the events within the desired energy window. The authors measured the DOI function of a PET detector with lutetium yttrium orthosilicate (LYSO) scintillators. Radiation events originating from the scintillators' internal Lu-176 beta decay were used to measure DOI functions which were then compared with those measured from both an external uniform flood source and an electronically collimated external point source. The authors conducted these studies with several scintillators of differing geometries (1.5 × 1.5 and 2.0 × 2.0 mm(2) cross-section area and 20, 30, and 40 mm length) and various surface finishes (mirror-finishing, saw-cut rough, and other finishes in between), and in a prototype array. All measured results using internal and external radiation sources showed excellent agreement in DOI function measurement. The mean difference among DOI values for all scintillators measured from internal and external radiation sources was less than 1.0 mm for different scintillator geometries and various surface finishes. The internal radioactivity of LYSO scintillators can be used to accurately measure DOI function in PET detectors, regardless of scintillator geometry or surface finish. Because an external radiation source is not needed, this method of DOI function measurement can be practically applied to individual PET detectors as well as assembled systems.

  11. Use of internal scintillator radioactivity to calibrate DOI function of a PET detector with a dual-ended-scintillator readout

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bircher, Chad; Shao Yiping

    Purpose: Positron emission tomography (PET) detectors that use a dual-ended-scintillator readout to measure depth-of-interaction (DOI) must have an accurate DOI function to provide the relationship between DOI and signal ratios to be used for detector calibration and recalibration. In a previous study, the authors used a novel and simple method to accurately and quickly measure DOI function by irradiating the detector with an external uniform flood source; however, as a practical concern, implementing external uniform flood sources in an assembled PET system is technically challenging and expensive. In the current study, therefore, the authors investigated whether the same method couldmore » be used to acquire DOI function from scintillator-generated (i.e., internal) radiation. The authors also developed a method for calibrating the energy scale necessary to select the events within the desired energy window. Methods: The authors measured the DOI function of a PET detector with lutetium yttrium orthosilicate (LYSO) scintillators. Radiation events originating from the scintillators' internal Lu-176 beta decay were used to measure DOI functions which were then compared with those measured from both an external uniform flood source and an electronically collimated external point source. The authors conducted these studies with several scintillators of differing geometries (1.5 x 1.5 and 2.0 x 2.0 mm{sup 2} cross-section area and 20, 30, and 40 mm length) and various surface finishes (mirror-finishing, saw-cut rough, and other finishes in between), and in a prototype array. Results: All measured results using internal and external radiation sources showed excellent agreement in DOI function measurement. The mean difference among DOI values for all scintillators measured from internal and external radiation sources was less than 1.0 mm for different scintillator geometries and various surface finishes. Conclusions: The internal radioactivity of LYSO scintillators can be used to accurately measure DOI function in PET detectors, regardless of scintillator geometry or surface finish. Because an external radiation source is not needed, this method of DOI function measurement can be practically applied to individual PET detectors as well as assembled systems.« less

  12. Sustainable Design of EPA's Campus in Research Triangle Park, NC—Environmental Performance Specifications in Construction Contracts—Section 01450 Sequence of Finishes Installation

    EPA Pesticide Factsheets

    Learn more about the special construction scheduling/sequencing requirements and procedures necessary to assure achievement of designed Indoor Air Quality (IAQ) levels for the completed project required by the EPA IAQ Program.

  13. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gardner, Shea; Slezak, Tom

    With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs. The method is fast to compute, finding SNPs and building a SNP phylogeny in seconds to hours. We use it to identify thousands of putative SNPs from all publicly available Filoviridae, Poxviridae, foot-and-mouth disease virus, Bacillus, and Escherichia coli genomes and plasmids. Themore » SNP-based trees that result are consistent with known taxonomy and trees determined in other studies. The approach we describe can handle as input hundreds of gigabases of sequence in a single run. The algorithm is based on k-mer analysis using a suffix array, so we call it saSNP.« less

  14. Listening to Students and Faculty: The Value to Developmental Education Leaders

    ERIC Educational Resources Information Center

    Clifton, Connie J.

    2013-01-01

    Helping students complete developmental course sequences and graduate from college is one of the biggest challenges facing community college leaders and educators. The majority of entering students need one or more developmental courses yet most of these students never finish the developmental sequence. Colleges are continuously developing new…

  15. Final Report for LDRD Project 02-ERD-069: Discovering the Unknown Mechanism(s) of Virulence in a BW, Class A Select Agent

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chain, P; Garcia, E

    2003-02-06

    The goal of this proposed effort was to assess the difficulty in identifying and characterizing virulence candidate genes in an organism for which very limited data exists. This was accomplished by first addressing the finishing phase of draft-sequenced F. tularensis genomes and conducting comparative analyses to determine the coding potential of each genome; to discover the differences in genome structure and content, and to identify potential genes whose products may be involved in the F. tularensis virulence process. The project was divided into three parts: (1) Genome finishing: This part involves determining the order and orientation of the consensus sequencesmore » of contigs obtained from Phrap assemblies of random draft genomic sequences. This tedious process consists of linking contig ends using information embedded in each sequence file that relates the sequence to the original cloned insert. Since inserts are sequenced from both ends, we can establish a link between these paired-ends in different contigs and thus order and orient contigs. Since these genomes carry numerous copies of insertion sequences, these repeated elements ''confuse'' the Phrap assembly program. It is thus necessary to break these contigs apart at the repeated sequences and individually join the proper flanking regions using paired-end information, or using results of comparisons against a similar genome. Larger repeated elements such as the small subunit ribosomal RNA operon require verification with PCR. Tandem repeats require manual intervention and typically rely on single nucleotide polymorphisms to be resolved. Remaining gaps require PCR reactions and sequencing. Once the genomes have been ''closed'', low quality regions are addressed by resequencing reactions. (2) Genome analysis: The final consensus sequences are processed by combining the results of three gene modelers: Glimmer, Critica and Generation. The final gene models are submitted to a battery of homology searches and domain prediction programs in order to annotate them (e.g. BLAST, Pfam, TIGRfam, COG, KEGG, InterPro, TMhmm, SignalP). The genome structure is also assessed in terms of G+C content, GC bias (GC skew), and locations of repeated regions (e.g. IS elements) and phage-like genes. (3) Comparative genomics: The results of the various genome analyses are compared between the finished (or almost finished) genomes. Here, we have compared the F. tularensis genomes from the extremely lethal strain Schu4 (subsp. tularensis), the vaccine strain LVS (subsp. holartica), and strain UT01-4992 of the less virulent, opportunistic subsp. novicida. Regions present in the highly virulent strain that are absent from the other less virulent strains may provide insight into what factors are required for the high level of virulence.« less

  16. Legume Genome Initiative at the University of Oklahoma

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bruce A. Roe

    2004-02-27

    Consolidated Appropriations Resolution, 2003 Conference Report for the Department of Energy's Biological and Environmental Research (BER) program provided $481,000 for the Legume Genome Initiative at the University of Oklahoma. These funds were used to support our research that is aimed at determining the entire sequence of the gene rich regions of the genome of the legume, Medicago truncatula, by allowing us to obtain a greater degree of finished BAC sequences from the draft sequences we have already obtained through research funded by the Noble Foundation. During the funding period we increased the number of Medicago truncatula BACs with finished (Bermudamore » standard) sequences from 109 to 359, and the total number of BACs for which we collected sequence data from 584 to 842, 359 of which reached phase 2 (ordered and oriented contigs). We also sequenced a series of pooled BAC clones that cover additional euchromatic (gene rich) genomic regions. This work resulted in 6 refereed publications, see below. Genes whose sequence was determined during this study included multiple members of the plant disease resistance (R-gene) family as well as several genes involved in flavinoid biosynthesis, nitrogen fixation and plant-microbial symbosis. This work also served as a prelude to obtaining NSF funding for the international collaborative effort to complete the entire sequence of the Medicago truncatula genomic euchromatic regions using a BAC based approach.« less

  17. The Release 6 reference sequence of the Drosophila melanogaster genome

    DOE PAGES

    Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.; ...

    2015-01-14

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

  18. The Release 6 reference sequence of the Drosophila melanogaster genome

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

  19. GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

    PubMed

    Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

    2013-04-10

    Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. New Generation Sequencing Technology Panel at SFAF-Part II

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fiske, Haley; Turner, Steve; Rhodes, Michael

    2009-05-27

    From left to right: Haley Fiske of Illumina Inc., Steve Turner of Pacific Biosciences, Michael Rhodes of Applied Biosystems, Patrice Milos of Helicos Biosciences and Tim Harkins of Roche Diagnostics answer questions in a forum moderated by Bob Fulton at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  1. New Generation Sequencing Technology Panel at SFAF-Part I

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fiske, Haley; Turner, Steve; Rhodes, Michael

    2009-05-27

    From left to right: Haley Fiske of Illumina Inc., Steve Turner of Pacific Biosciences, Michael Rhodes of Applied Biosystems, Patrice Milos of Helicos Biosciences and Tim Harkins of Roche Diagnostics answer questions in a forum moderated by Bob Fulton at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

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

    PubMed

    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).

  3. Los Alamos National Laboratory Overview

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Neu, Mary

    Mary Neu, Associate Director for Chemistry, Life and Earth Sciences at Los Alamos National Laboratory, delivers opening remarks at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  4. Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms

    USDA-ARS?s Scientific Manuscript database

    Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica sub...

  5. Noncontiguous Finished Genome Sequence of Staphylococcus aureus KLT6, a Staphylococcal Enterotoxin B-Positive Strain Involved in a Food Poisoning Outbreak in Switzerland

    PubMed Central

    Tobes, Raquel; Manrique, Marina; Brozynska, Marta; Stephan, Roger; Pareja, Eduardo

    2013-01-01

    We present the first complete genome sequence of a Staphylococcus aureus strain assigned to clonal complex 12. The strain was isolated in a food poisoning outbreak due to contaminated potato salad in Switzerland in 2009, and it produces staphylococcal enterotoxin B. PMID:23704175

  6. Sequencing Centers Panel at SFAF

    ScienceCinema

    Schilkey, Faye; Ali, Johar; Grafham, Darren; Muzny, Donna; Fulton, Bob; Fitzgerald, Mike; Hostetler, Jessica; Daum, Chris

    2018-02-13

    From left to right: Faye Schilkey of NCGR, Johar Ali of OICR, Darren Grafham of Wellcome Trust Sanger Institute, Donna Muzny of the Baylor College of Medicine, Bob Fulton of Washington University, Mike Fitzgerald of the Broad Institute, Jessica Hostetler of the J. Craig Venter Institute and Chris Daum of the DOE Joint Genome Institute discuss sequencing technologies, applications and pipelines on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  7. Complete Genome Sequence of NEB 5-alpha, a Derivative of Escherichia coli K-12 DH5α.

    PubMed

    Anton, Brian P; Raleigh, Elisabeth A

    2016-11-10

    Escherichia coli K-12 DH5α is one of the most popular and widely available laboratory strains, but, surprisingly, no complete genome sequence has been publicly available. Here, we report the complete, finished sequence of NEB 5-alpha (DH5α fhuA2). It should serve as a useful reference for researchers working with DH5α. Copyright © 2016 Anton and Raleigh.

  8. Sequencing Centers Panel at SFAF

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schilkey, Faye; Ali, Johar; Grafham, Darren

    From left to right: Faye Schilkey of NCGR, Johar Ali of OICR, Darren Grafham of Wellcome Trust Sanger Institute, Donna Muzny of the Baylor College of Medicine, Bob Fulton of Washington University, Mike Fitzgerald of the Broad Institute, Jessica Hostetler of the J. Craig Venter Institute and Chris Daum of the DOE Joint Genome Institute discuss sequencing technologies, applications and pipelines on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  9. Distribution of Salmonella serovars in breeding, nursery, and grow-to-finish pigs, and risk factors for shedding in ten farrow-to-finish swine farms in Alberta and Saskatchewan.

    PubMed

    Wilkins, Wendy; Rajić, Andrijana; Waldner, Cheryl; McFall, Margaret; Chow, Eva; Muckle, Anne; Rosengren, Leigh

    2010-04-01

    The study objectives were to investigate Salmonella prevalence, serovar distribution, and risk factors for shedding in 10 purposively selected farrow-to-finish farms in Saskatchewan and Alberta. Pooled fecal samples from the breeding and grow-finish phases and individual fecal samples from breeding, nursery, and grow-finish pigs were cultured for Salmonella; serotyping of isolates was performed. Pig and pen characteristics were recorded for each pig and pen sampled.Overall, 407/1143 (36%) of samples were Salmonella positive; within-farm prevalence ranged from 1% to 79%. Sows, nursery, and grow-finish pigs accounted for 43%, 29%, and 28% of positive samples, respectively. More Salmonella were detected in pooled pen than individual pig samples (P < 0.001). Among 418 Salmonella isolates, there were 19 distinct serovars; the most common were S. Derby (28.5%), S. Typhimurium, var. Copenhagen (19.1%), S. Putten (11.8%), S. Infantis (6.8%), and S. Mbandaka (6.1%). Sows were more likely to shed Salmonella than nursery or grow-finisher (OR 2.9, P < 0.001) pigs. Pelleted feed (OR 8.2, P < 0.001) and nose-to-nose pig contact through pens (OR 2.2, P = 0.005) were associated with increased Salmonella prevalence. Significant differences in serovar distribution were detected among production phases. The use of pooled pen samples is recommended as a more efficient means for accurate evaluation of Salmonella status in different phases of pig production. The breeding herd might be an important source of Salmonella persistence within farrow-to-finish farms and should be targeted in control efforts. The latter might also apply to the use of pelleted feed, which remains the most consistently reported significant risk factor for Salmonella shedding in pigs.

  10. Alveolar-Membrane Diffusing Capacity Limits Performance in Boston Marathon Qualifiers

    PubMed Central

    Lavin, Kaleen M.; Straub, Allison M.; Uhranowsky, Kathleen A.; Smoliga, James M.; Zavorsky, Gerald S.

    2012-01-01

    Purpose (1) to examine the relation between pulmonary diffusing capacity and marathon finishing time, and (2), to evaluate the accuracy of pulmonary diffusing capacity for nitric oxide (DLNO) in predicting marathon finishing time relative to that of pulmonary diffusing capacity for carbon monoxide (DLCO). Methods 28 runners [18 males, age = 37 (SD 9) years, body mass = 70 (13) kg, height = 173 (9) cm, percent body fat = 17 (7) %] completed a test battery consisting of measurement of DLNO and DLCO at rest, and a graded exercise test to determine running economy and aerobic capacity prior to the 2011 Steamtown Marathon (Scranton, PA). One to three weeks later, all runners completed the marathon (range: 2∶22:38 to 4∶48:55). Linear regressions determined the relation between finishing time and a variety of anthropometric characteristics, resting lung function variables, and exercise parameters. Results In runners meeting Boston Marathon qualification standards, 74% of the variance in marathon finishing time was accounted for by differences in DLNO relative to body surface area (BSA) (SEE = 11.8 min, p<0.01); however, the relation between DLNO or DLCO to finishing time was non-significant in the non-qualifiers (p = 0.14 to 0.46). Whereas both DLCO and DLNO were predictive of finishing time for all finishers, DLNO showed a stronger relation (r2 = 0.30, SEE = 33.4 min, p<0.01) compared to DLCO when considering BSA. Conclusion DLNO is a performance-limiting factor in only Boston qualifiers. This suggests that alveolar-capillary membrane conductance is a limitation to performance in faster marathoners. Additionally, DLNO/BSA predicts marathon finishing time and aerobic capacity more accurately than DLCO. PMID:22984520

  11. 9 CFR 381.309 - Finished product inspection.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... alternative documented procedures for handling process deviations. (1) Incubation of shelf stable canned product—(i) Incubator. The establishment shall provide incubation facilities which include an accurate... the facility. The Program is responsible for the security of the incubator. (ii) Incubation...

  12. 9 CFR 381.309 - Finished product inspection.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... alternative documented procedures for handling process deviations. (1) Incubation of shelf stable canned product—(i) Incubator. The establishment shall provide incubation facilities which include an accurate... the facility. The Program is responsible for the security of the incubator. (ii) Incubation...

  13. 9 CFR 381.309 - Finished product inspection.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... alternative documented procedures for handling process deviations. (1) Incubation of shelf stable canned product—(i) Incubator. The establishment shall provide incubation facilities which include an accurate... the facility. The Program is responsible for the security of the incubator. (ii) Incubation...

  14. Electroformed screens with uniform hole size

    NASA Technical Reports Server (NTRS)

    Schaer, G. R.

    1968-01-01

    Efficient method electroforms fine-mesh nickel screens, or plagues, with uniform hole size and accurate spacing between holes. An electroformed nickel mandrel has nonconducting silicone rubber projections that duplicate the desired hole size and shape in the finished nickel screen.

  15. Kinetic model for the formation of acrylamide during the finish-frying of commercial french fries.

    PubMed

    Parker, Jane K; Balagiannis, Dimitrios P; Higley, Jeremy; Smith, Gordon; Wedzicha, Bronislaw L; Mottram, Donald S

    2012-09-12

    Acrylamide is formed from reducing sugars and asparagine during the preparation of French fries. The commercial preparation of French fries is a multistage process involving the preparation of frozen, par-fried potato strips for distribution to catering outlets, where they are finish-fried. The initial blanching, treatment in glucose solution, and par-frying steps are crucial because they determine the levels of precursors present at the beginning of the finish-frying process. To minimize the quantities of acrylamide in cooked fries, it is important to understand the impact of each stage on the formation of acrylamide. Acrylamide, amino acids, sugars, moisture, fat, and color were monitored at time intervals during the frying of potato strips that had been dipped in various concentrations of glucose and fructose during a typical pretreatment. A mathematical model based on the fundamental chemical reaction pathways of the finish-frying was developed, incorporating moisture and temperature gradients in the fries. This showed the contribution of both glucose and fructose to the generation of acrylamide and accurately predicted the acrylamide content of the final fries.

  16. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.

    PubMed

    Elkins, James G; Hamilton-Brehm, Scott D; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam L; Hauser, Loren; Kyrpides, Nikos C; Ivanova, Natalia N; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W

    2013-04-11

    Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments.

  17. The Opposing Forces that Shape Developmental Education: Assessment, Placement, and Progression at CUNY Community Colleges. CCRC Working Paper No. 36

    ERIC Educational Resources Information Center

    Jaggars, Shanna Smith; Hodara, Michelle

    2011-01-01

    The developmental education process, as it is typically implemented in colleges across the country, seems straightforward: underprepared students are assessed and placed into an appropriate developmental course sequence designed to prepare them for college-level work; once finished with the sequence, these students presumably then move on to…

  18. Postadjustment polishing of CAD-CAM ceramic with luminescence diamond gel.

    PubMed

    Finger, W J; Noack, M D

    2000-02-01

    (1) to investigate by SEM and profilometry the effectiveness of Luminescence diamond polishing gel on machinable ceramic after adjustment grinding with different grit diamond finishing burs, and (2) to define a simple, time-saving ceramic finishing and polishing technique for clinically satisfactory results. Discs, 3 mm thick, were cut from Vita Mark II CAD-CAM ceramic and ground to a uniform surface finish on 600 grit wet SiC paper. Five specimens in each of the seven groups below were finished unidirectionally by a sweeping mode with the following Two Striper MFS diamond burs: 1. MF1 (45 microm); 2. MF2 (25 microm); 3. MF3 (10 microm); 4. MF1 + MF2; 5. MF1 + MF3; 6. MF2 + MF3; 7. MF1 + MF2 + MF3. Then, Luminescence diamond polishing gel was dispensed on a mandrel-mounted felt applicator and applied at 10,000 rpm for 60 s, and after dipping in water for another 60-s sequence. Surface roughness was determined for each step with a stylus-fitted surface analyzer. On each specimen five parallel tracings (evaluation length 4.0 mm and cut-off length 0.8 mm) were made 1 mm apart. Ra and Rz values were recorded as roughness parameters. Data was subjected to one-way ANOVA and Tukey's multiple comparison test at a significance level of alpha = 0.05. One additional sample for each grinding and polishing step in each of the seven groups was produced for SEM analysis. Diamond polishing after MF1 finishing reduced Ra and Rz significantly from 1.75 to 0.79, and from 10.0 to 4.09 microm, respectively, whereas the Ra and Rz reduction after MF3 finishing and diamond polishing were from 0.64 to 0.49 and from 4.31 to 1.81 microm. The polished surface roughness of specimens prefinished with MF2 or MF3 burs alone or as the final step after preceding grinding with coarser grits was not significantly different. The average Ra and Rz values were 0.42 microm and 1.73 microm. SEM photographs confirmed the uniformity of the surface finish in these groups. The second polishing sequence did not significantly improve the smoothness obtained with the first cycle.

  19. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lapidus, Alla L.

    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 ofmore » 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.« less

  20. ALLPATHS: Assembling Large Genomes with Short Illumina Reads

    ScienceCinema

    Gnerre, Sante

    2018-02-06

    Sante Gnerre from the Broad Institute speaks on the challenge of developing high quality assemblies of large genomes using short reads at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  1. Genomics at the Ontario Institute for Cancer Research

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ali, Johar

    Johar Ali of the Ontario Institute for Cancer Research discusses genomics and next-gen applications at the OICR on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  2. Multisurface fixture permits easy grinding of tool bit angles

    NASA Technical Reports Server (NTRS)

    Jones, C. R.

    1966-01-01

    Multisurface fixture with a tool holder permits accurate grinding and finishing of right and left hand single point threading tools. All angles are ground by changing the fixture position to rest at various references angles without removing the tool from the holder.

  3. Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites▿

    PubMed Central

    Song, Ju Yeon; Jeong, Haeyoung; Yu, Dong Su; Fischbach, Michael A.; Park, Hong-Seog; Kim, Jae Jong; Seo, Jeong-Sun; Jensen, Susan E.; Oh, Tae Kwang; Lee, Kye Joon; Kim, Jihyun F.

    2010-01-01

    Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics. PMID:20889745

  4. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T

    PubMed Central

    Hamilton-Brehm, Scott D.; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W.; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren; Kyrpides, Nikos C.; Ivanova, Natalia N.; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W.

    2013-01-01

    Thermodesulfobacterium geofontis OPF15T (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments. PMID:23580711

  5. Complete genome sequence of Yersinia ruckeri str. CSF007-82, etiologic agent of enteric redmouth disease in salmonid fish

    USDA-ARS?s Scientific Manuscript database

    We present the complete, closed and finished chromosomal and extra-chromosomal genome sequences of Y. ruckeri strain CSF007-82, etiologic agent of enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a G+C content of 47.5% and encodes 3,530 predicted CDS, 7 ribosomal opero...

  6. Data Management Requirements for the Rapid Identification and Character of Unknown Genomic Samples

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rosenzweig, Nicole

    2010-06-02

    Nicole Rosenzweig of OptiMetrics discusses the development of informatics infrastructure for studying bacterial pathogens on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  7. DNA capture elements for rapid detection and identification of biological agents

    NASA Astrophysics Data System (ADS)

    Kiel, Johnathan L.; Parker, Jill E.; Holwitt, Eric A.; Vivekananda, Jeeva

    2004-08-01

    DNA capture elements (DCEs; aptamers) are artificial DNA sequences, from a random pool of sequences, selected for their specific binding to potential biological warfare agents. These sequences were selected by an affinity method using filters to which the target agent was attached and the DNA isolated and amplified by polymerase chain reaction (PCR) in an iterative, increasingly stringent, process. Reporter molecules were attached to the finished sequences. To date, we have made DCEs to Bacillus anthracis spores, Shiga toxin, Venezuelan Equine Encephalitis (VEE) virus, and Francisella tularensis. These DCEs have demonstrated specificity and sensitivity equal to or better than antibody.

  8. Implementing genomic medicine in pathology.

    PubMed

    Williams, Eli S; Hegde, Madhuri

    2013-07-01

    The finished sequence of the Human Genome Project, published 50 years after Watson and Crick's seminal paper on the structure of DNA, pushed human genetics into the public eye and ushered in the genomic era. A significant, if overlooked, aspect of the race to complete the genome was the technology that propelled scientists to the finish line. DNA sequencing technologies have become more standardized, automated, and capable of higher throughput. This technology has continued to grow at an astounding rate in the decade since the Human Genome Project was completed. Today, massively parallel sequencing, or next-generation sequencing (NGS), allows the detection of genetic variants across the entire genome. This ability has led to the identification of new causes of disease and is changing the way we categorize, treat, and manage disease. NGS approaches such as whole-exome sequencing and whole-genome sequencing are rapidly becoming an affordable genetic testing strategy for the clinical laboratory. One test can now provide vast amounts of health information pertaining not only to the disease of interest, but information that may also predict adult-onset disease, reveal carrier status for a rare disease and predict drug responsiveness. The issue of what to do with these incidental findings, along with questions pertaining to NGS testing strategies, data interpretation and storage, and applying genetic testing results into patient care, remains without a clear answer. This review will explore these issues and others relevant to the implementation of NGS in the clinical laboratory.

  9. Experimental Reservoirs of Human Pathogens: The Vibrio Cholerae Paradigm (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Colwell, Rita

    2018-05-14

    Rita Colwell on "Experimental Reservoirs of Human Pathogens: The Vibrio cholerae paradigm" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  10. Grepping Life: A New Paradigm for Analyzing Metagenomic Data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Berendzen, Joel

    2010-06-04

    Joel Berendzen of Los Alamos National Laboratory discusses a phylogenetic method based on answering the question "What Would Google Do?" on June 4, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  11. Experimental Reservoirs of Human Pathogens: The Vibrio Cholerae Paradigm (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Colwell, Rita

    Rita Colwell on "Experimental Reservoirs of Human Pathogens: The Vibrio cholerae paradigm" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  12. Process Development for Automated Solar Cell and Module Production. Task 4: Automated Array Assembly

    NASA Technical Reports Server (NTRS)

    1979-01-01

    A baseline sequence for the manufacture of solar cell modules was specified. Starting with silicon wafers, the process goes through damage etching, texture etching, junction formation, plasma edge etch, aluminum back surface field formation, and screen printed metallization to produce finished solar cells. The cells were then series connected on a ribbon and bonded into a finished glass tedlar module. A number of steps required additional developmental effort to verify technical and economic feasibility. These steps include texture etching, plasma edge etch, aluminum back surface field formation, array layup and interconnect, and module edge sealing and framing.

  13. Sharpening ball-nose mill cutters

    NASA Technical Reports Server (NTRS)

    Burch, C. F.

    1977-01-01

    Economical attachment allows faster, more precise grinding. Vibrationless and rigid relation between grinding wheel and cutter allows for extremely high finish and accurate grinding. Leveling device levels flutes with respect to toolholder rotation that generates ball-nose radius. Constant relief around entire profile of cutting edge produces longer tool life.

  14. Analysis of cutting force signals by wavelet packet transform for surface roughness monitoring in CNC turning

    NASA Astrophysics Data System (ADS)

    García Plaza, E.; Núñez López, P. J.

    2018-01-01

    On-line monitoring of surface finish in machining processes has proven to be a substantial advancement over traditional post-process quality control techniques by reducing inspection times and costs and by avoiding the manufacture of defective products. This study applied techniques for processing cutting force signals based on the wavelet packet transform (WPT) method for the monitoring of surface finish in computer numerical control (CNC) turning operations. The behaviour of 40 mother wavelets was analysed using three techniques: global packet analysis (G-WPT), and the application of two packet reduction criteria: maximum energy (E-WPT) and maximum entropy (SE-WPT). The optimum signal decomposition level (Lj) was determined to eliminate noise and to obtain information correlated to surface finish. The results obtained with the G-WPT method provided an in-depth analysis of cutting force signals, and frequency ranges and signal characteristics were correlated to surface finish with excellent results in the accuracy and reliability of the predictive models. The radial and tangential cutting force components at low frequency provided most of the information for the monitoring of surface finish. The E-WPT and SE-WPT packet reduction criteria substantially reduced signal processing time, but at the expense of discarding packets with relevant information, which impoverished the results. The G-WPT method was observed to be an ideal procedure for processing cutting force signals applied to the real-time monitoring of surface finish, and was estimated to be highly accurate and reliable at a low analytical-computational cost.

  15. Finished Genome Sequence of Escherichia coli K-12 Strain HMS174 (ATCC 47011).

    PubMed

    Mairhofer, Juergen; Krempl, Peter M; Thallinger, Gerhard G; Striedner, Gerald

    2014-11-20

    Escherichia coli strain K-12 substrain HMS174 is an engineered descendant of the E. coli K-12 wild-type strain. Like its ancestor, it is an important organism in biotechnological research and is used in fermentation processes for heterologous protein production. Here, we report the complete genome sequence of E. coli HMS174 (ATCC 47011). Copyright © 2014 Mairhofer et al.

  16. Complete Genome Sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700▿

    PubMed Central

    Di Bonaventura, Maria Pia; DeSalle, Rob; Pop, Mihai; Nagarajan, Niranjan; Figurski, David H.; Fine, Daniel H.; Kaplan, Jeffrey B.; Planet, Paul J.

    2009-01-01

    We report the finished and annotated genome sequence of Aggregatibacter aphrophilus strain NJ8700, a strain isolated from the oral flora of a healthy individual, and discuss characteristics that may affect its dual roles in human health and disease. This strain has a rough appearance, and its genome contains genes encoding a type VI secretion system and several factors that may participate in host colonization. PMID:19447908

  17. Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay.

    PubMed

    Heredia, Nicholas J

    2018-01-01

    Digital PCR is a valuable tool to quantify next-generation sequencing (NGS) libraries precisely and accurately. Accurately quantifying NGS libraries enable accurate loading of the libraries on to the sequencer and thus improve sequencing performance by reducing under and overloading error. Accurate quantification also benefits users by enabling uniform loading of indexed/barcoded libraries which in turn greatly improves sequencing uniformity of the indexed/barcoded samples. The advantages gained by employing the Droplet Digital PCR (ddPCR™) library QC assay includes the precise and accurate quantification in addition to size quality assessment, enabling users to QC their sequencing libraries with confidence.

  18. NGS for the Masses: Empowering Biologists to Improve Bioinformatics Productivity ( 7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Qaadri, Kashef [Biomatters Inc., San Francisco, CA (United States)

    2018-05-21

    Kashef Qaadri on "NGS for the Masses: Empowering biologists to improve bioinformatic productivity" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  19. NGS for the Masses: Empowering Biologists to Improve Bioinformatics Productivity ( 7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Qaadri, Kashef

    2012-06-01

    Kashef Qaadri on "NGS for the Masses: Empowering biologists to improve bioinformatic productivity" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  20. Literature and patent analysis of the cloning and identification of human functional genes in China.

    PubMed

    Xia, Yan; Tang, LiSha; Yao, Lei; Wan, Bo; Yang, XianMei; Yu, Long

    2012-03-01

    The Human Genome Project was launched at the end of the 1980s. Since then, the cloning and identification of functional genes has been a major focus of research across the world. In China too, the potentially profound impact of such studies on the life sciences and on human health was realized, and relevant studies were initiated in the 1990s. To advance China's involvement in the Human Genome Project, in the mid-1990s, Committee of Experts in Biology from National High Technology Research and Development Program of China (863 Program) proposed the "two 1%" goal. This goal envisaged China contributing 1% of the total sequencing work, and cloning and identifying 1% of the total human functional genes. Over the past 20 years, tremendous achievement has been accomplished by Chinese scientists. It is well known that scientists in China finished the 1% of sequencing work of the Human Genome Project, whereas, there is no comprehensive report about "whether China had finished cloning and identifying 1% of human functional genes". In the present study, the GenBank database at the National Center of Biotechnology Information, the PubMed search tool, and the patent database of the State Intellectual Property Office, China, were used to retrieve entries based on two screening standards: (i) Were the newly cloned and identified genes first reported by Chinese scientists? (ii) Were the Chinese scientists awarded the gene sequence patent? Entries were retrieved from the databases up to the cut-off date of 30 June 2011 and the obtained data were analyzed further. The results showed that 589 new human functional genes were first reported by Chinese scientists and 159 gene sequences were patented (http://gene.fudan.sh.cn/introduction/database/chinagene/chinagene.html). This study systematically summarizes China's contributions to human functional genomics research and answers the question "has China finished cloning and identifying 1% of human functional genes?" in the affirmative.

  1. Finished Genome Sequence of the Laboratory Strain Escherichia coli K-12 RV308 (ATCC 31608).

    PubMed

    Krempl, Peter M; Mairhofer, Juergen; Striedner, Gerald; Thallinger, Gerhard G

    2014-11-20

    Escherichia coli strain K-12 substrain RV308 is an engineered descendant of the K-12 wild-type strain. Like its ancestor, it is an important organism in biotechnological research and is heavily used for the expression of single-chain variable fragments. Here, we report the complete genome sequence of E. coli K-12 RV308 (ATCC 31608). Copyright © 2014 Krempl et al.

  2. Gingival Retraction Methods for Fabrication of Fixed Partial Denture: Literature Review

    PubMed Central

    S, Safari; Ma, Vossoghi Sheshkalani; Mi, Vossoghi Sheshkalani; F, Hoseini Ghavam; M, Hamedi

    2016-01-01

    Fixed dental prosthesis success requires appropriate impression taking of the prepared finish line. This is critical in either tooth supported fixed prosthesis (crown and bridge) or implant supported fixed prosthesis (solid abutment). If the prepared finish line is adjacent to the gingival sulcus, gingival retraction techniques should be used to decrease the marginal discrepancy among the restoration and the prepared abutment. Accurate marginal positioning of the restoration in the prepared finish line of the abutment is required for therapeutic, preventive and aesthetic purposes. In this article, conventional and modern methods of gingival retraction in the fixed tooth supported prosthesis and fixed implant supported prosthesis are expressed. PubMed and Google Scholar databases were searched manually for studies on gingival tissue managements prior to impression making in fixed dental prosthesis since 1975. Conclusions were extracted and summarized. Keywords were impression making, gingival retraction, cordless retraction, and implant. Gingival retraction techniques can be classified as mechanical, chemical or surgical. In this article, different gingival management techniques are discussed. PMID:28959744

  3. Gingival Retraction Methods for Fabrication of Fixed Partial Denture: Literature Review.

    PubMed

    S, Safari; Ma, Vossoghi Sheshkalani; Mi, Vossoghi Sheshkalani; F, Hoseini Ghavam; M, Hamedi

    2016-06-01

    Fixed dental prosthesis success requires appropriate impression taking of the prepared finish line. This is critical in either tooth supported fixed prosthesis (crown and bridge) or implant supported fixed prosthesis (solid abutment). If the prepared finish line is adjacent to the gingival sulcus, gingival retraction techniques should be used to decrease the marginal discrepancy among the restoration and the prepared abutment. Accurate marginal positioning of the restoration in the prepared finish line of the abutment is required for therapeutic, preventive and aesthetic purposes. In this article, conventional and modern methods of gingival retraction in the fixed tooth supported prosthesis and fixed implant supported prosthesis are expressed. PubMed and Google Scholar databases were searched manually for studies on gingival tissue managements prior to impression making in fixed dental prosthesis since 1975. Conclusions were extracted and summarized. Keywords were impression making, gingival retraction, cordless retraction, and implant. Gingival retraction techniques can be classified as mechanical, chemical or surgical. In this article, different gingival management techniques are discussed.

  4. Complex Microbial Communities: We’re not in Kansas Anymore

    ScienceCinema

    Fraser-Liggett, Claire M.

    2018-05-08

    Claire Fraser-Liggett, Director of the Institute for Genome Sciences and professor at the University of Maryland School of Medicine, gives the June 2, 2010 keynote at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  5. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Johnson, Shannon L.; Minogue, Timothy D.; Teshima, Hazuki

    Bacillus cereus strain 03BB87, a blood culture isolate, originated in a 56-year-old male muller operator with a fatal case of pneumonia in 2003. Here we present the finished genome sequence of that pathogen, including a 5.46-Mb chromosome and two plasmids (209 and 52 Kb, respectively).

  6. Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina citri) (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Saha, Surya

    Surya Saha on "Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina citri)" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  7. Advances in High-Throughput Speed, Low-Latency Communication for Embedded Instrumentation (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Jordan, Scott

    2018-01-24

    Scott Jordan on "Advances in high-throughput speed, low-latency communication for embedded instrumentation" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  8. Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina citri) (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Saha, Surya [Cornell University

    2017-12-09

    Surya Saha on "Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina citri)" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  9. Temperature dependence of the pulse-duration memory effect in NbSe3

    NASA Astrophysics Data System (ADS)

    Jones, T. C.; Simpson, C. R., Jr.; Clayhold, J. A.; McCarten, J. P.

    2000-04-01

    The temperature dependence of the oscillatory response of the 59 K charge-density wave in NbSe3 to a sequence of repetitive current pulses was investigated. For 52 K>T>45 K the learned behavior commonly referred to as the pulse-duration memory effect (PDME) is very evident; after training the voltage oscillation always finishes the pulse at a minimum. At lower temperatures the PDME changes qualitatively. In nonswitching samples the voltage oscillation always finishes the pulse increasing. In switching samples there is a conduction delay which becomes fixed after training, but no learning of the duration of the pulse.

  10. Ultra-smooth finishing of aspheric surfaces using CAST technology

    NASA Astrophysics Data System (ADS)

    Kong, John; Young, Kevin

    2014-06-01

    Growing applications for astronomical ground-based adaptive systems and air-born telescope systems demand complex optical surface designs combined with ultra-smooth finishing. The use of more sophisticated and accurate optics, especially aspheric ones, allows for shorter optical trains with smaller sizes and a reduced number of components. This in turn reduces fabrication and alignment time and costs. These aspheric components include the following: steep surfaces with large aspheric departures; more complex surface feature designs like stand-alone off-axis-parabola (OAP) and free form optics that combine surface complexity with a requirement for ultra-high smoothness, as well as special optic materials such as lightweight silicon carbide (SiC) for air-born systems. Various fabrication technologies for finishing ultra-smooth aspheric surfaces are progressing to meet these growing and demanding challenges, especially Magnetorheological Finishing (MRF) and ion-milling. These methods have demonstrated some good success as well as a certain level of limitations. Amongst them, computer-controlled asphere surface-finishing technology (CAST), developed by Precision Asphere Inc. (PAI), plays an important role in a cost effective manufacturing environment and has successfully delivered numerous products for the applications mentioned above. One of the most recent successes is the Gemini Planet Imager (GPI), the world's most powerful planet-hunting instrument, with critical aspheric components (seven OAPs and free form optics) made using CAST technology. GPI showed off its first images in a press release on January 7, 2014 . This paper reviews features of today's technologies in handling the ultra-smooth aspheric optics, especially the capabilities of CAST on these challenging products. As examples, three groups of aspheres deployed in astronomical optics systems, both polished and finished using CAST, will be discussed in detail.

  11. Phytophthora capsici - Loss of Heterozygosity (LOH): A Widespread Mechanism for Rapid Adaptation (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Mudge, Joanne

    2018-01-15

    Joanne Mudge on "Phytophthora capsici - Loss of Heterozygosity (LOH): A Widespread Mechanism for Rapid Mutation" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  12. Unusual Gene Order and Organization of the Sea Urchin Hox Cluster

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cameron, R A; Rowen, L; Nesbitt, R

    2005-10-11

    The highly consistent gene order and axial colinear expression patterns found in vertebrate hox gene clusters are less well conserved across the rest of bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3 gene is Hox5. (The gene order is :more » 5-Hox1, 2, 3, 11/13c, 11/13b, 11/13a, 9/10, 8, 7, 6, 5 - 3). The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.« less

  13. Unusual Gene Order and Organization of the Sea Urchin HoxCluster

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Richardson, Paul M.; Lucas, Susan; Cameron, R. Andrew

    2005-05-10

    The highly consistent gene order and axial colinear expression patterns found in vertebrate hox gene clusters are less well conserved across the rest of bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3' gene is Hox5. (The gene order is :more » 5'-Hox1,2, 3, 11/13c, 11/13b, '11/13a, 9/10, 8, 7, 6, 5 - 3)'. The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.« less

  14. Management characteristics of cow-calf, stocker, and finishing operations in the Northern Plains and Midwest Regions of the United States

    USDA-ARS?s Scientific Manuscript database

    Comprehensive region-specific data that accurately characterize cattle production practices are being collected to support a national life cycle assessment (LCA) of U.S. beef. The present study reports production information obtained via voluntary surveys and visits in two of seven demarcated region...

  15. Error analysis of numerical gravitational waveforms from coalescing binary black holes

    NASA Astrophysics Data System (ADS)

    Fong, Heather; Chu, Tony; Kumar, Prayush; Pfeiffer, Harald; Boyle, Michael; Hemberger, Daniel; Kidder, Lawrence; Scheel, Mark; Szilagyi, Bela; SXS Collaboration

    2016-03-01

    The Advanced Laser Interferometer Gravitational-wave Observatory (Advanced LIGO) has finished a successful first observation run and will commence its second run this summer. Detection of compact object binaries utilizes matched-filtering, which requires a vast collection of highly accurate gravitational waveforms. This talk will present a set of about 100 new aligned-spin binary black hole simulations. I will discuss their properties, including a detailed error analysis, which demonstrates that the numerical waveforms are sufficiently accurate for gravitational wave detection purposes, as well as for parameter estimation purposes.

  16. Ultra-low roughness magneto-rheological finishing for EUV mask substrates

    NASA Astrophysics Data System (ADS)

    Dumas, Paul; Jenkins, Richard; McFee, Chuck; Kadaksham, Arun J.; Balachandran, Dave K.; Teki, Ranganath

    2013-09-01

    EUV mask substrates, made of titania-doped fused silica, ideally require sub-Angstrom surface roughness, sub-30 nm flatness, and no bumps/pits larger than 1 nm in height/depth. To achieve the above specifications, substrates must undergo iterative global and local polishing processes. Magnetorheological finishing (MRF) is a local polishing technique which can accurately and deterministically correct substrate figure, but typically results in a higher surface roughness than the current requirements for EUV substrates. We describe a new super-fine MRF® polishing fluid whichis able to meet both flatness and roughness specifications for EUV mask blanks. This eases the burden on the subsequent global polishing process by decreasing the polishing time, and hence the defectivity and extent of figure distortion.

  17. Effect of Binder and Mold parameters on Collapsibility and Surface Finish of Gray Cast Iron No-bake Sand Molds

    NASA Astrophysics Data System (ADS)

    Srinivasulu Reddy, K.; Venkata Reddy, Vajrala; Mandava, Ravi Kumar

    2017-08-01

    Chemically bonded no-bake molds and cores have good mechanical properties and produce dimensionally accurate castings compared to green sand molds. Poor collapsibility property of CO2 hardened sodium silicate bonded sand mold and phenolic urethane no-bake (PUN) binder system, made the reclamation of the sands more important. In the present work fine silica sand is mixed with phenolic urethane no-bake binder and the sand sets in a very short time within few minutes. In this paper it is focused on optimizing the process parameters of PUN binder based sand castings for better collapsibility and surface finish of gray cast iron using Taguchi design. The findings were successfully verified through experiments.

  18. Genome assemblies for 11 Yersinia pestis strains isolated in the Caucasus region

    DOE PAGES

    Zhgenti, Ekaterine; Johnson, Shannon L.; Davenport, Karen W.; ...

    2015-09-17

    Yersinia pestis, the causative agent of plague, is endemic to the Caucasus region but few reference strain genome sequences from that region are available. We present the improved draft or finished assembled genomes from 11 strains isolated in the nation of Georgia and surrounding countries.

  19. A Common Framework for Multiple Sources of Bacterial Annotation

    ScienceCinema

    White, Owen

    2018-05-03

    Owen White, professor of epidemiology and preventive medicine at the University of Maryland School of Medicine and a researcher at the University of Maryland Institute for Genome Sciences, gives the May 29, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  20. Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer (7th Annual SFAF Meeting, 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Copeland, Alex

    2012-06-01

    Alex Copeland on "Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  1. Non-contiguous finished genome sequence of Ornithobacterium rhinotracheale strain H06-030791

    USDA-ARS?s Scientific Manuscript database

    The Gram-negative pleomorphic rod-shaped bacterium Ornithobacterium rhinotracheale (O. rhinotracheale) is a cause of pneumonia and airsacculitis in poultry. It is a member of the family Flavobacteriaceae of the phylum Bacteroidetes. O. rhinotracheale strain H06-030791 was isolated from the lung of...

  2. Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Copeland, Alex [DOE JGI

    2017-12-09

    Alex Copeland on "Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  3. Different phylogenomic approaches to resolve the evolutionary relationships among model fish species.

    PubMed

    Negrisolo, Enrico; Kuhl, Heiner; Forcato, Claudio; Vitulo, Nicola; Reinhardt, Richard; Patarnello, Tomaso; Bargelloni, Luca

    2010-12-01

    Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect to the choice of alignment methodology applied to noncoding parts of the genomic region under study. This may limit the use of intergenic/noncoding sequences in phylogenomics until more robust alignment algorithms are developed.

  4. Materials Database Development for Ballistic Impact Modeling

    NASA Technical Reports Server (NTRS)

    Pereira, J. Michael

    2007-01-01

    A set of experimental data is being generated under the Fundamental Aeronautics Program Supersonics project to help create and validate accurate computational impact models of jet engine impact events. The data generated will include material property data generated at a range of different strain rates, from 1x10(exp -4)/sec to 5x10(exp 4)/sec, over a range of temperatures. In addition, carefully instrumented ballistic impact tests will be conducted on flat plates and curved structures to provide material and structural response information to help validate the computational models. The material property data and the ballistic impact data will be generated using materials from the same lot, as far as possible. It was found in preliminary testing that the surface finish of test specimens has an effect on measured high strain rate tension response of AL2024. Both the maximum stress and maximum elongation are greater on specimens with a smoother finish. This report gives an overview of the testing that is being conducted and presents results of preliminary testing of the surface finish study.

  5. Effect of bamboo vinegar powder as an antibiotic alternative on the digesta bacteria communities of finishing pigs.

    PubMed

    Qu, Huan; Huang, Yanjie; Shi, Yinghao; Liu, Ying; Wu, Shenglong; Bao, Wenbin

    2018-05-18

    This study investigated the use for bamboo vinegar powder as an antibiotic alternative in the diet of growing-finishing pigs by examining their digestive bacterial communities. Forty-five Duroc × Landrace × Yorkshire growing-finishing pigs were randomly allocated to five diet groups: 0%,0.5%, 1.0%, or 1.5% bamboo vinegar levels and antibiotics. After 37 days, the digesta in duodenum of four pigs from each treatment were analyzed for their bacterial community compositions using 16S rRNA gene sequencing. Addition of 1.5% bamboo vinegar powder had the most similar effect on the intestinal microflora to that of antibiotics, indicating its potential to promote the growth and development of finishing pigs. We also found the 1.5% bamboo vinegar powder group to have an increased abundance of Firmicute/Bacteroidetes compared with the other bamboo vinegar powder groups, which may enhance the ability of the host to absorb food energy and store more body fat. Additionally, the effects of bamboo vinegar powder on promoting the abundances of Lactobacillus and Thalassospira and on inhibiting Streptococcus and Prevotella growth revealed it may play an important role in animal production. Moreover, functional predictions of microbes via PICRUSt indicated that feed supplemented with 1.5% bamboo vinegar powder could promote many vital metabolic pathways.

  6. Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant.

    PubMed

    Hou, Luanfeng; Zhou, Qin; Wu, Qingping; Gu, Qihui; Sun, Ming; Zhang, Jumei

    2018-06-01

    To gain insight into the bacterial dynamics present in drinking water treatment (DWT) systems, the microbial community and activity in a full-scale DWT plant (DWTP) in Guangzhou, South China, were investigated using Illumina Hiseq sequencing analyses combined with cultivation-based techniques during the wet and dry seasons. Illumina sequencing analysis of 16S rRNA genes revealed a large shift in the proportion of Actinobacteria, Proteobacteria and Firmicutes during the treatment process, with the proportion of Actinobacteria decreased sharply, whereas that of Proteobacteria and Firmicutes increased and predominated in treated water. Both microbial activity and bacterial diversity during the treatment process showed obvious spatial variation, with higher levels observed during the dry season and lower levels during the wet season. Clustering analysis and principal component analysis indicated dramatic shifts in the bacterial community after chlorination, suggesting that chlorination was highly effective at influencing the bacterial community. The bacterial community structure of finished water primarily comprised Pseudomonas, Citrobacter, and Acinetobacter, and interestingly showed high similarity to biofilms on granular activated carbon. Additionally, the abundance of bacterial communities was relatively stable in finished water and did not change with the season. A large number of unique operational taxonomic units were shared during treatment steps, indicating the presence of a diverse core microbiome throughout the treatment process. Opportunistic pathogens, including Pseudomonas, Acinetobacter, Citrobacter, Mycobacterium, Salmonella, Staphylococcus, Legionella, Streptococcus and Enterococcus, were detected in water including finished water, suggesting a potential threat to drinking-water safety. We also detected bacteria isolated from each treatment step using the pure-culture method. In particular, two isolates, identified as Mycobacterium sp. and Blastococcus sp., which belong to the phylum Actinobacteria, were obtained from finished water during the dry season. Together, these results provided evidence of spatial and temporal variations in DWTPs and contributed to the beneficial manipulation of the drinking water microbiome. Copyright © 2017. Published by Elsevier B.V.

  7. Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems.

    PubMed

    Brooks, John P; Adeli, Ardeshir; McLaughlin, Michael R

    2014-06-15

    The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future "downstream" implications from both an environmental and public health perspective. Published by Elsevier Ltd.

  8. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

    PubMed Central

    2014-01-01

    Background Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. Results A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a phophoenolpyruvate synthase) and substrate utilization pathway (mannose and aromatics utilization) that might explain phenotypic differences between C. autoethanogenum and C. ljungdahlii. Conclusions Single molecule sequencing will be increasingly used to produce finished microbial genomes. The complete genome will facilitate comparative genomics and functional genomics and support future comparisons between Clostridia and studies that examine the evolution of plasmids, bacteriophage and CRISPR systems. PMID:24655715

  9. Comparative genomic analysis of single-molecule sequencing and hybrid approaches for finishing the Clostridium autoethanogenum JA1-1 strain DSM 10061 genome

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Brown, Steven D; Nagaraju, Shilpa; Utturkar, Sagar M

    Background Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. Results A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G +more » C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a phophoenolpyruvate synthase) and substrate utilization pathway (mannose and aromatics utilization) that might explain phenotypic differences between C. autoethanogenum and C. ljungdahlii. Conclusions Single molecule sequencing will be increasingly used to produce finished microbial genomes. The complete genome will facilitate comparative genomics and functional genomics and support future comparisons between Clostridia and studies that examine the evolution of plasmids, bacteriophage and CRISPR systems.« less

  10. ABACAS: algorithm-based automatic contiguation of assembled sequences

    PubMed Central

    Assefa, Samuel; Keane, Thomas M.; Otto, Thomas D.; Newbold, Chris; Berriman, Matthew

    2009-01-01

    Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk PMID:19497936

  11. Association between the genetic similarity of the open reading frame 5 sequence of Porcine reproductive and respiratory syndrome virus and the similarity in clinical signs of Porcine reproductive and respiratory syndrome in Ontario swine herds.

    PubMed

    Rosendal, Thomas; Dewey, Cate; Friendship, Robert; Wootton, Sarah; Young, Beth; Poljak, Zvonimir

    2014-10-01

    A study of Ontario swine farms positive for Porcine reproductive and respiratory syndrome virus (PRRSV) tested the association between genetic similarity of the virus and similarity of clinical signs reported by the herd owner. Herds were included if a positive result of polymerase chain reaction for PRRSV at the Animal Health Laboratory at the University of Guelph, Guelph, Ontario, was found between September 2004 and August 2007. Nucleotide-sequence similarity and clinical similarity, as determined from a telephone survey, were calculated for all pairs of herds. The Mantel test indicated that clinical similarity and sequence similarity were weakly correlated for most clinical signs. The generalized additive model indicated that virus homology with 2 vaccine viruses affected the association between sequence similarity and clinical similarity. When the data for herds with vaccine-like virus were removed from the dataset there was a significant association between virus similarity and similarity of the reported presence of abortion, stillbirth, preweaning mortality, and sow/boar mortality. Ownership similarity was also found to be associated with virus similarity and with similarity of the reported presence of sows being off-feed, nursery respiratory disease, nursery mortality, finisher respiratory disease, and finisher mortality. These results indicate that clinical signs of PRRS are associated with PRRSV genotype and that herd ownership is associated with both of these.

  12. Association between the genetic similarity of the open reading frame 5 sequence of Porcine reproductive and respiratory syndrome virus and the similarity in clinical signs of Porcine reproductive and respiratory syndrome in Ontario swine herds

    PubMed Central

    Rosendal, Thomas; Dewey, Cate; Friendship, Robert; Wootton, Sarah; Young, Beth; Poljak, Zvonimir

    2014-01-01

    A study of Ontario swine farms positive for Porcine reproductive and respiratory syndrome virus (PRRSV) tested the association between genetic similarity of the virus and similarity of clinical signs reported by the herd owner. Herds were included if a positive result of polymerase chain reaction for PRRSV at the Animal Health Laboratory at the University of Guelph, Guelph, Ontario, was found between September 2004 and August 2007. Nucleotide-sequence similarity and clinical similarity, as determined from a telephone survey, were calculated for all pairs of herds. The Mantel test indicated that clinical similarity and sequence similarity were weakly correlated for most clinical signs. The generalized additive model indicated that virus homology with 2 vaccine viruses affected the association between sequence similarity and clinical similarity. When the data for herds with vaccine-like virus were removed from the dataset there was a significant association between virus similarity and similarity of the reported presence of abortion, stillbirth, preweaning mortality, and sow/boar mortality. Ownership similarity was also found to be associated with virus similarity and with similarity of the reported presence of sows being off-feed, nursery respiratory disease, nursery mortality, finisher respiratory disease, and finisher mortality. These results indicate that clinical signs of PRRS are associated with PRRSV genotype and that herd ownership is associated with both of these. PMID:25355993

  13. Finishing Genomes with Limited Resources: Lessons from an Ensemble of Microbial Genomes

    DTIC Science & Technology

    2010-01-01

    proteobacteria from the Pasteurellaceae family that is strongly implicated as a causative agent of infective endo- carditis [6]. It can also be found as an...Sequence of Aggregatibacter (Haemophilus) aphrophilus NJB700. J Bacrerio/2009, 191(14):4693-4694. 6. Khairat 0: Endocarditis due to a new species of

  14. Students' Network Integration as a Predictor of Persistence in Introductory Physics Courses

    ERIC Educational Resources Information Center

    Zwolak, Justyna P.; Dou, Remy; Williams, Eric A.; Brewe, Eric

    2017-01-01

    Increasing student retention (successfully finishing a particular course) and persistence (continuing through a sequence of courses or the major area of study) is currently a major challenge for universities. While students' academic and social integration into an institution seems to be vital for student retention, research into the effect of…

  15. Hierarchical Scaffolding With Bambus

    PubMed Central

    Pop, Mihai; Kosack, Daniel S.; Salzberg, Steven L.

    2004-01-01

    The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced. We thus developed a general-purpose scaffolder, called Bambus, which affords users significant flexibility in controlling the scaffolding parameters. Bambus was used recently to scaffold the low-coverage draft dog genome data. Most significantly, Bambus enables the use of linking data other than that inferred from mate-pair information. For example, the sequence of a completed genome can be used to guide the scaffolding of a related organism. We present several applications of Bambus: support for finishing, comparative genomics, analysis of the haplotype structure of genomes, and scaffolding of a mammalian genome at low coverage. Bambus is available as an open-source package from our Web site. PMID:14707177

  16. Hierarchical scaffolding with Bambus.

    PubMed

    Pop, Mihai; Kosack, Daniel S; Salzberg, Steven L

    2004-01-01

    The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced. We thus developed a general-purpose scaffolder, called Bambus, which affords users significant flexibility in controlling the scaffolding parameters. Bambus was used recently to scaffold the low-coverage draft dog genome data. Most significantly, Bambus enables the use of linking data other than that inferred from mate-pair information. For example, the sequence of a completed genome can be used to guide the scaffolding of a related organism. We present several applications of Bambus: support for finishing, comparative genomics, analysis of the haplotype structure of genomes, and scaffolding of a mammalian genome at low coverage. Bambus is available as an open-source package from our Web site.

  17. A Force-Controllable Macro-Micro Manipulator and its Application to Medical Robotics

    NASA Technical Reports Server (NTRS)

    Marzwell, Neville I.; Uecker, Darrin R.; Wang, Yulun

    1993-01-01

    This paper describes an 8-degrees-of-freedom macro-micro robot. This robot is capable of performing tasks that require accurate force control, such as polishing, finishing, grinding, deburring, and cleaning. The design of the macro-micro mechanism, the control algorithms, and the hardware/sofware implemtation of the algotithms are described in this paper. Initial experimental results are reported.

  18. Comparison of calculated and experimentally determined SID of CP and AA in complex diets differing in AA contents for grower finisher pigs.

    PubMed

    Büsing, K; Berk, A; Müller, S; Kieckhäven, S; Krüger, K; Zeyner, A

    2017-10-01

    In practice, the content of standardized ileal digestible AA in complex feeds for pigs is calculated on the basis of tabulated values for individual feedstuffs. It comes into question, however, whether this truly reflects an accurate content based upon the estimate made for the individual feedstuffs. The objective of this study was to compare standardized ileal digestibility (SID) of crude protein (CP) and selected AA in complex feeds for grower and finisher pigs either calculated or experimentally determined. Six diets with increasing AA levels were prepared for grower (BW from 30 to 70 kg) and finisher (BW from 70 to 120 kg) feed. Crystalline L-lys, DL-met and L-thr were added to both diets, L-trp and L-val only to the grower feed. SID of both CP and AA was calculated from feed tables and experimentally determined in six adult minipigs (MINILEWE) with ileorectal anastomosis. With increasing AA levels, experimentally determined SID of supplemented AA increased (p < 0.05), but SID of CP (p ≥ 0.05) was not affected. In both grower and finisher feed, calculated and experimentally determined SID of CP, Met, Cys, Trp, Ile and Tyr differed by more than 2% units, but those of Lys and His only in the finisher feed. Yet this effect was not directly consistent. The margin of error following estimation of SID of AA via tabulated values for individual feedstuffs, however, seems to be acceptable for practical use. Journal of Animal Physiology and Animal Nutrition © 2017 Blackwell Verlag GmbH.

  19. Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.

    PubMed Central

    Roux, Véronique; Million, Matthieu; Robert, Catherine; Magne, Alix; Raoult, Didier

    2013-01-01

    Oceanobacillus massiliensis strain N’DiopT sp. nov. is the type strain of O. massiliensis sp. nov., a new species within the genus Oceanobacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. O. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,532,675 bp long genome contains 3,519 protein-coding genes and 72 RNA genes, including between 6 and 8 rRNA operons. PMID:24976893

  20. Computional algorithm for lifetime exposure to antimicrobials in pigs using register data-The LEA algorithm.

    PubMed

    Birkegård, Anna Camilla; Andersen, Vibe Dalhoff; Halasa, Tariq; Jensen, Vibeke Frøkjær; Toft, Nils; Vigre, Håkan

    2017-10-01

    Accurate and detailed data on antimicrobial exposure in pig production are essential when studying the association between antimicrobial exposure and antimicrobial resistance. Due to difficulties in obtaining primary data on antimicrobial exposure in a large number of farms, there is a need for a robust and valid method to estimate the exposure using register data. An approach that estimates the antimicrobial exposure in every rearing period during the lifetime of a pig using register data was developed into a computational algorithm. In this approach data from national registers on antimicrobial purchases, movements of pigs and farm demographics registered at farm level are used. The algorithm traces batches of pigs retrospectively from slaughter to the farm(s) that housed the pigs during their finisher, weaner, and piglet period. Subsequently, the algorithm estimates the antimicrobial exposure as the number of Animal Defined Daily Doses for treatment of one kg pig in each of the rearing periods. Thus, the antimicrobial purchase data at farm level are translated into antimicrobial exposure estimates at batch level. A batch of pigs is defined here as pigs sent to slaughter at the same day from the same farm. In this study we present, validate, and optimise a computational algorithm that calculate the lifetime exposure of antimicrobials for slaughter pigs. The algorithm was evaluated by comparing the computed estimates to data on antimicrobial usage from farm records in 15 farm units. We found a good positive correlation between the two estimates. The algorithm was run for Danish slaughter pigs sent to slaughter in January to March 2015 from farms with more than 200 finishers to estimate the proportion of farms that it was applicable for. In the final process, the algorithm was successfully run for batches of pigs originating from 3026 farms with finisher units (77% of the initial population). This number can be increased if more accurate register data can be obtained. The algorithm provides a systematic and repeatable approach to estimating the antimicrobial exposure throughout the rearing period, independent of rearing site for finisher batches, as a lifetime exposure measurement. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. [Factors of the rapid startup for nitrosation in sequencing batch reactor].

    PubMed

    Li, Dong; Tao, Xiao-Xiao; Li, Zhan; Wang, Jun-An; Zhang, Jie

    2011-08-01

    The approach and factors for realizing the rapid startup of nitrosation were researched at the low level of dissolved oxygen (DO) in sequencing batch reactor (SBR). The main parameters of the reactor were controlled as follows: DO were 0.15-0.40 mg/L, pH values kept from 7.52 to 8.30, temperature maintained at 22.3-27.1 degrees C, and time of aeration was 8 hours. The purpose of rapid startup for nitrosation was achieved after 57 cycles (36 d) with the alternative influent of high and low ammonium wastewater (the mean values were 245.28 mg/L and 58.08 mg/L respectively) in a SBR, and the nitrosation rate was even 100%. Factors of accumulation of nitrite were investigated and the effects of DO and pH were analyzed during the startup for nitrosation. The results showed that it could improve the efficiency of nitrosation when DO concentration was increased appropriately. The activity of nitrite oxidizing bacteria (NOB) was recovered gradually when DO was higher than 0.72 mg/L. The key factor of controlling nitrosation reaction was the concentration of free ammonia (FA), while the final factor was the concentration of DO. pH was a desired controlling parameter to show the end of nitrification in a SBR cycle, while DO concentration did not indicate the finishing of SBR nitrification accurately because it increased rapidly before ammonia nitrogen was oxidized absolutely.

  2. The End Justifies the Means, but Only in the Middle

    ERIC Educational Resources Information Center

    Toure-Tillery, Maferima; Fishbach, Ayelet

    2012-01-01

    Achieving goals often requires the completion of sequential actions, such as finishing a series of assignments to pass a class. In the course of pursuing such goals, people can decide how closely to follow their personal standards for each action. We propose that actions at the beginning and end of a sequence appear more diagnostic of the…

  3. Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20T)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pati, Amrita; Gronow, Sabine; Lu, Megan

    2011-01-01

    Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes andmore » is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

  4. Detection of Anti-Hepatitis B Virus Drug Resistance Mutations Based on Multicolor Melting Curve Analysis.

    PubMed

    Mou, Yi; Athar, Muhammad Ammar; Wu, Yuzhen; Xu, Ye; Wu, Jianhua; Xu, Zhenxing; Hayder, Zulfiqar; Khan, Saeed; Idrees, Muhammad; Nasir, Muhammad Israr; Liao, Yiqun; Li, Qingge

    2016-11-01

    Detection of anti-hepatitis B virus (HBV) drug resistance mutations is critical for therapeutic decisions for chronic hepatitis B virus infection. We describe a real-time PCR-based assay using multicolor melting curve analysis (MMCA) that could accurately detect 24 HBV nucleotide mutations at 10 amino acid positions in the reverse transcriptase region of the HBV polymerase gene. The two-reaction assay had a limit of detection of 5 copies per reaction and could detect a minor mutant population (5% of the total population) with the reverse transcriptase M204V amino acid mutation in the presence of the major wild-type population when the overall concentration was 10 4 copies/μl. The assay could be finished within 3 h, and the cost of materials for each sample was less than $10. Clinical validation studies using three groups of samples from both nucleos(t)ide analog-treated and -untreated patients showed that the results for 99.3% (840/846) of the samples and 99.9% (8,454/8,460) of the amino acids were concordant with those of Sanger sequencing of the PCR amplicon from the HBV reverse transcriptase region (PCR Sanger sequencing). HBV DNA in six samples with mixed infections consisting of minor mutant subpopulations was undetected by the PCR Sanger sequencing method but was detected by MMCA, and the results were confirmed by coamplification at a lower denaturation temperature-PCR Sanger sequencing. Among the treated patients, 48.6% (103/212) harbored viruses that displayed lamivudine monoresistance, adefovir monoresistance, entecavir resistance, or lamivudine and adefovir resistance. Among the untreated patients, the Chinese group had more mutation-containing samples than did the Pakistani group (3.3% versus 0.56%). Because of its accuracy, rapidness, wide-range coverage, and cost-effectiveness, the real-time PCR assay could be a robust tool for the detection if anti-HBV drug resistance mutations in resource-limited countries. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  5. Fundamental Bounds for Sequence Reconstruction from Nanopore Sequencers.

    PubMed

    Magner, Abram; Duda, Jarosław; Szpankowski, Wojciech; Grama, Ananth

    2016-06-01

    Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: (i) for given indel error characteristics and rate, what is the probability of accurate reconstruction as a function of sequence length; (ii) using replicated extrusion (the process of passing a DNA strand through the nanopore), what is the number of replicas needed to accurately reconstruct the true sequence with high probability? Our results provide a number of important insights: (i) the probability of accurate reconstruction of a sequence from a single sample in the presence of indel errors tends quickly (i.e., exponentially) to zero as the length of the sequence increases; and (ii) replicated extrusion is an effective technique for accurate reconstruction. We show that for typical distributions of indel errors, the required number of replicas is a slow function (polylogarithmic) of sequence length - implying that through replicated extrusion, we can sequence large reads using nanopore sequencers. Moreover, we show that in certain cases, the required number of replicas can be related to information-theoretic parameters of the indel error distributions.

  6. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Degenhardt, R.; PFH, Private University of Applied Sciences Goettingen, Composite Engineering Campus Stade; Araujo, F. C. de

    European aircraft industry demands for reduced development and operating costs. Structural weight reduction by exploitation of structural reserves in composite aerospace structures contributes to this aim, however, it requires accurate and experimentally validated stability analysis of real structures under realistic loading conditions. This paper presents different advances from the area of computational stability analysis of composite aerospace structures which contribute to that field. For stringer stiffened panels main results of the finished EU project COCOMAT are given. It investigated the exploitation of reserves in primary fibre composite fuselage structures through an accurate and reliable simulation of postbuckling and collapse. Formore » unstiffened cylindrical composite shells a proposal for a new design method is presented.« less

  7. Traffic Video Image Segmentation Model Based on Bayesian and Spatio-Temporal Markov Random Field

    NASA Astrophysics Data System (ADS)

    Zhou, Jun; Bao, Xu; Li, Dawei; Yin, Yongwen

    2017-10-01

    Traffic video image is a kind of dynamic image and its background and foreground is changed at any time, which results in the occlusion. In this case, using the general method is more difficult to get accurate image segmentation. A segmentation algorithm based on Bayesian and Spatio-Temporal Markov Random Field is put forward, which respectively build the energy function model of observation field and label field to motion sequence image with Markov property, then according to Bayesian' rule, use the interaction of label field and observation field, that is the relationship of label field’s prior probability and observation field’s likelihood probability, get the maximum posterior probability of label field’s estimation parameter, use the ICM model to extract the motion object, consequently the process of segmentation is finished. Finally, the segmentation methods of ST - MRF and the Bayesian combined with ST - MRF were analyzed. Experimental results: the segmentation time in Bayesian combined with ST-MRF algorithm is shorter than in ST-MRF, and the computing workload is small, especially in the heavy traffic dynamic scenes the method also can achieve better segmentation effect.

  8. Section Curve Reconstruction and Mean-Camber Curve Extraction of a Point-Sampled Blade Surface

    PubMed Central

    Li, Wen-long; Xie, He; Li, Qi-dong; Zhou, Li-ping; Yin, Zhou-ping

    2014-01-01

    The blade is one of the most critical parts of an aviation engine, and a small change in the blade geometry may significantly affect the dynamics performance of the aviation engine. Rapid advancements in 3D scanning techniques have enabled the inspection of the blade shape using a dense and accurate point cloud. This paper proposes a new method to achieving two common tasks in blade inspection: section curve reconstruction and mean-camber curve extraction with the representation of a point cloud. The mathematical morphology is expanded and applied to restrain the effect of the measuring defects and generate an ordered sequence of 2D measured points in the section plane. Then, the energy and distance are minimized to iteratively smoothen the measured points, approximate the section curve and extract the mean-camber curve. In addition, a turbine blade is machined and scanned to observe the curvature variation, energy variation and approximation error, which demonstrates the availability of the proposed method. The proposed method is simple to implement and can be applied in aviation casting-blade finish inspection, large forging-blade allowance inspection and visual-guided robot grinding localization. PMID:25551467

  9. Section curve reconstruction and mean-camber curve extraction of a point-sampled blade surface.

    PubMed

    Li, Wen-long; Xie, He; Li, Qi-dong; Zhou, Li-ping; Yin, Zhou-ping

    2014-01-01

    The blade is one of the most critical parts of an aviation engine, and a small change in the blade geometry may significantly affect the dynamics performance of the aviation engine. Rapid advancements in 3D scanning techniques have enabled the inspection of the blade shape using a dense and accurate point cloud. This paper proposes a new method to achieving two common tasks in blade inspection: section curve reconstruction and mean-camber curve extraction with the representation of a point cloud. The mathematical morphology is expanded and applied to restrain the effect of the measuring defects and generate an ordered sequence of 2D measured points in the section plane. Then, the energy and distance are minimized to iteratively smoothen the measured points, approximate the section curve and extract the mean-camber curve. In addition, a turbine blade is machined and scanned to observe the curvature variation, energy variation and approximation error, which demonstrates the availability of the proposed method. The proposed method is simple to implement and can be applied in aviation casting-blade finish inspection, large forging-blade allowance inspection and visual-guided robot grinding localization.

  10. SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

    PubMed

    Mariano, Diego C B; Pereira, Felipe L; Aguiar, Edgar L; Oliveira, Letícia C; Benevides, Leandro; Guimarães, Luís C; Folador, Edson L; Sousa, Thiago J; Ghosh, Preetam; Barh, Debmalya; Figueiredo, Henrique C P; Silva, Artur; Ramos, Rommel T J; Azevedo, Vasco A C

    2016-12-15

    The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .

  11. Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome

    PubMed Central

    Lim, Alex; Dimalanta, Eileen T.; Potamousis, Konstantinos D.; Yen, Galex; Apodoca, Jennifer; Tao, Chunhong; Lin, Jieyi; Qi, Rong; Skiadas, John; Ramanathan, Arvind; Perna, Nicole T.; Plunkett, Guy; Burland, Valerie; Mau, Bob; Hackett, Jeremiah; Blattner, Frederick R.; Anantharaman, Thomas S.; Mishra, Bhubaneswar; Schwartz, David C.

    2001-01-01

    We have constructed NheI and XhoI optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies. PMID:11544203

  12. Sequence Grazing of Perennial and Annual Cool-Season Grasses to Extend the Grazing Season for Stocker Calves

    USDA-ARS?s Scientific Manuscript database

    Grazing of cool-season grasses by beef calves before entry into the feedlot for finishing is an important component of the US beef production system. The length of time in the feedlot and the quantity of feed grain required to reach market BW would be reduced if more BW was gained during the grazing...

  13. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).

    PubMed

    Chang, Yun-Juan; Land, Miriam; Hauser, Loren; Chertkov, Olga; Del Rio, Tijana Glavina; Nolan, Matt; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Mavromatis, Konstantinos; Liolios, Konstantinos; Brettin, Thomas; Fiebig, Anne; Rohde, Manfred; Abt, Birte; Göker, Markus; Detter, John C; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla

    2011-10-15

    Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; Armougom, Fabrice; Mishra, Ajay Kumar; Nguyen, Thi-Tien; Raoult, Didier; Fournier, Pierre-Edouard

    2012-01-01

    Alistipes timonensis strain JC136T sp. nov. is the type strain of A. timonensis sp. nov., a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. A. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,497,779 bp long genome (one chromosome but no plasmid) contains 2,742 protein-coding and 50 RNA genes, including three rRNA genes. PMID:23408657

  15. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; Elkarkouri, Khalid; Rivet, Romain; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes. PMID:24019984

  16. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

    PubMed Central

    Coyne, Robert S; Thiagarajan, Mathangi; Jones, Kristie M; Wortman, Jennifer R; Tallon, Luke J; Haas, Brian J; Cassidy-Hanley, Donna M; Wiley, Emily A; Smith, Joshua J; Collins, Kathleen; Lee, Suzanne R; Couvillion, Mary T; Liu, Yifan; Garg, Jyoti; Pearlman, Ronald E; Hamilton, Eileen P; Orias, Eduardo; Eisen, Jonathan A; Methé, Barbara A

    2008-01-01

    Background Tetrahymena thermophila, a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic macronucleus (MAC). The recent draft MAC genome assembly revealed low sequence repetitiveness, a result of the epigenetic removal of invasive DNA elements found only in the MIC genome. Such low repetitiveness makes complete closure of the MAC genome a feasible goal, which to achieve would require standard closure methods as well as removal of minor MIC contamination of the MAC genome assembly. Highly accurate preliminary annotation of Tetrahymena's coding potential was hindered by the lack of both comparative genomic sequence information from close relatives and significant amounts of cDNA evidence, thus limiting the value of the genomic information and also leaving unanswered certain questions, such as the frequency of alternative splicing. Results We addressed the problem of MIC contamination using comparative genomic hybridization with purified MIC and MAC DNA probes against a whole genome oligonucleotide microarray, allowing the identification of 763 genome scaffolds likely to contain MIC-limited DNA sequences. We also employed standard genome closure methods to essentially finish over 60% of the MAC genome. For the improvement of annotation, we have sequenced and analyzed over 60,000 verified EST reads from a variety of cellular growth and development conditions. Using this EST evidence, a combination of automated and manual reannotation efforts led to updates that affect 16% of the current protein-coding gene models. By comparing EST abundance, many genes showing apparent differential expression between these conditions were identified. Rare instances of alternative splicing and uses of the non-standard amino acid selenocysteine were also identified. Conclusion We report here significant progress in genome closure and reannotation of Tetrahymena thermophila. Our experience to date suggests that complete closure of the MAC genome is attainable. Using the new EST evidence, automated and manual curation has resulted in substantial improvements to the over 24,000 gene models, which will be valuable to researchers studying this model organism as well as for comparative genomics purposes. PMID:19036158

  17. Sequence Data for Clostridium autoethanogenum using Three Generations of Sequencing Technologies

    DOE PAGES

    Utturkar, Sagar M.; Klingeman, Dawn Marie; Bruno-Barcena, José M.; ...

    2015-04-14

    During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequencemore » datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.« less

  18. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

    PubMed Central

    Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.; Hugenholtz, Philip; Tyson, Gene W.

    2015-01-01

    Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. PMID:25977477

  19. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

    PubMed

    Parks, Donovan H; Imelfort, Michael; Skennerton, Connor T; Hugenholtz, Philip; Tyson, Gene W

    2015-07-01

    Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. © 2015 Parks et al.; Published by Cold Spring Harbor Laboratory Press.

  20. Using structure to explore the sequence alignment space of remote homologs.

    PubMed

    Kuziemko, Andrew; Honig, Barry; Petrey, Donald

    2011-10-01

    Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  1. Qualitative and quantitative evaluation of human dental enamel after bracket debonding: a noncontact three-dimensional optical profilometry analysis.

    PubMed

    Ferreira, Fabiano G; Nouer, Darcy F; Silva, Nelson P; Garbui, Ivana U; Correr-Sobrinho, Lourenço; Nouer, Paulo R A

    2014-09-01

    The aim of this study was to undertake a qualitative and quantitative evaluation of changes on enamel surfaces after debonding of brackets followed by finishing procedures, using a high-resolution three-dimensional optical profiler and to investigate the accuracy of the technique. The labial surfaces of 36 extracted upper central incisors were examined. Before bonding, the enamel surfaces were subjected to profilometry, recording four amplitude parameters. Brackets were then bonded using two types of light-cured orthodontic adhesive: composite resin and resin-modified glass ionomer cement. Finishing was performed by three different methods: pumice on a rubber cup, fine and ultrafine aluminum oxide discs, and microfine diamond cups followed by silicon carbide brushes. The samples were subsequently re-analyzed by profilometry. Wilcoxon signed-rank test, Kruskal-Wallis test (p < 0.05) and a posteriori Mann-Whitney U test with Bonferroni correction (p < 0.0167) revealed a significant reduction of enamel roughness when diamond cups followed by silicon carbide brushes were used to finish surfaces that had remnants of resin-modified glass ionomer adhesive and when pumice was used to finish surfaces that had traces of composite resin. Enamel loss was minimal. The 3D optical profilometry technique was able to provide accurate qualitative and quantitative assessment of changes on the enamel surface after debonding. Morphological changes in the topography of dental surfaces, especially if related to enamel loss and roughness, are of considerable clinical importance. The quantitative evaluation method used herein enables a more comprehensive understanding of the effects of orthodontic bonding on teeth.

  2. Optical testing using the transport-of-intensity equation.

    PubMed

    Dorrer, C; Zuegel, J D

    2007-06-11

    The transport-of-intensity equation links the intensity and phase of an optical source to the longitudinal variation of its intensity in the presence of Fresnel diffraction. This equation can be used to provide a simple, accurate spatial-phase measurement for optical testing of flat surfaces. The properties of this approach are derived. The experimental demonstration is performed by quantifying the surface variations induced by the magnetorheological finishing process on laser rods.

  3. An efficient approach to BAC based assembly of complex genomes.

    PubMed

    Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; Batley, Jacqueline; Šimková, Hana; Doležel, Jaroslav; Edwards, David

    2016-01-01

    There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.

  4. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

    PubMed

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

    2015-05-01

    We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

  5. Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov.

    PubMed Central

    Ramasamy, Dhamodaran; Dubourg, Gregory; Robert, Catherine; Caputo, Aurelia; Papazian, Laurent; Raoult, Didier; Fournier, Pierre-Edouard

    2014-01-01

    Enorma timonensis strain GD5T sp. nov., is the type strain of E. timonensis sp. nov., a new member of the genus Enorma within the family Coriobacteriaceae. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old woman hospitalized for 3 months in an intensive care unit. E. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060 protein-coding and 52 RNA genes, including 4 rRNA genes. PMID:25197477

  6. Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov.

    PubMed Central

    Mishra, Ajay Kumar; Hugon, Perrine; Lagier, Jean-Christophe; Nguyen, Thi-Thien; Robert, Catherine; Couderc, Carine; Raoult, Didier

    2013-01-01

    Peptoniphilus obesi strain ph1T sp. nov., is the type strain of P. obesi sp. nov., a new species within the genus Peptoniphilus. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. P. obesi strain ph1T is a Gram-positive, obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,774,150 bp long genome (1 chromosome but no plasmid) contains 1,689 protein-coding and 29 RNA genes, including 5 rRNA genes. PMID:24019985

  7. RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

    PubMed Central

    Wright, Imogen A.; Travers, Simon A.

    2014-01-01

    The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

  8. A Broken Immigration System: Two Vital Remedies Before Policy Reform

    DTIC Science & Technology

    2012-03-16

    the applicant may well have finished most of his or her working life before arriving in the United States,” which does nothing to serve American...5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Jennifer L. Duval 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7...impact and importance of immigrants to the United States, there is “a widespread and accurate perception that the immigration system is not working

  9. Experimental Measurement of the Static Coefficient of Friction at the Ti-Ti Taper Connection in Total Hip Arthroplasty.

    PubMed

    Bitter, T; Khan, I; Marriott, T; Schreurs, B W; Verdonschot, N; Janssen, D

    2016-03-01

    The modular taper junction in total hip replacements has been implicated as a possible source of wear. The finite-element (FE) method can be used to study the wear potential at the taper junction. For such simulations it is important to implement representative contact parameters, in order to achieve accurate results. One of the main parameters in FE simulations is the coefficient of friction. However, in current literature, there is quite a wide spread in coefficient of friction values (0.15 - 0.8), which has a significant effect on the outcome of the FE simulations. Therefore, to obtain more accurate results, one should use a coefficient of friction that is determined for the specific material couple being analyzed. In this study, the static coefficient of friction was determined for two types of titanium-on-titanium stem-adaptor couples, using actual cut-outs of the final implants, to ensure that the coefficient of friction was determined consistently for the actual implant material and surface finish characteristics. Two types of tapers were examined, Biomet type-1 and 12/14, where type-1 has a polished surface finish and the 12/14 is a microgrooved system. We found static coefficients of friction of 0.19 and 0.29 for the 12/14 and type-1 stem-adaptor couples, respectively.

  10. PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites.

    PubMed

    Schwach, Frank; Bushell, Ellen; Gomes, Ana Rita; Anar, Burcu; Girling, Gareth; Herd, Colin; Rayner, Julian C; Billker, Oliver

    2015-01-01

    The Plasmodium Genetic Modification (PlasmoGEM) database (http://plasmogem.sanger.ac.uk) provides access to a resource of modular, versatile and adaptable vectors for genome modification of Plasmodium spp. parasites. PlasmoGEM currently consists of >2000 plasmids designed to modify the genome of Plasmodium berghei, a malaria parasite of rodents, which can be requested by non-profit research organisations free of charge. PlasmoGEM vectors are designed with long homology arms for efficient genome integration and carry gene specific barcodes to identify individual mutants. They can be used for a wide array of applications, including protein localisation, gene interaction studies and high-throughput genetic screens. The vector production pipeline is supported by a custom software suite that automates both the vector design process and quality control by full-length sequencing of the finished vectors. The PlasmoGEM web interface allows users to search a database of finished knock-out and gene tagging vectors, view details of their designs, download vector sequence in different formats and view available quality control data as well as suggested genotyping strategies. We also make gDNA library clones and intermediate vectors available for researchers to produce vectors for themselves. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Proteolytic enzyme engineering: a tool for wool.

    PubMed

    Araújo, Rita; Silva, Carla; Machado, Raul; Casal, Margarida; Cunha, António M; Rodriguez-Cabello, José Carlos; Cavaco-Paulo, Artur

    2009-06-08

    One of the goals of protein engineering is to tailor the structure of enzymes to optimize industrial bioprocesses. In the present work, we present the construction of a novel high molecular weight subtilisin, based on the fusion of the DNA sequences coding for Bacillus subtilis prosubtilisin E and for an elastin-like polymer (ELP). The resulting fusion protein was biologically produced in Escherichia coli , purified and used for wool finishing assays. When compared to the commercial protease Esperase, the recombinant subtilisinE-VPAVG(220) activity was restricted to the cuticle of wool, allowing a significant reduction of pilling, weight loss and tensile strength loss of wool fibers. Here we report, for the first time, the microbial production of a functionalized high molecular weight protease for controlled enzymatic hydrolysis of wool surface. This original process overcomes the unrestrained diffusion and extended fiber damage which are the major obstacles for the use of proteases for wool finishing applications.

  12. Identification and genomic characterization of a novel porcine parvovirus (PPV6) in China.

    PubMed

    Ni, Jianqiang; Qiao, Caixia; Han, Xue; Han, Tao; Kang, Wenhua; Zi, Zhanchao; Cao, Zhen; Zhai, Xinyan; Cai, Xuepeng

    2014-12-02

    Parvoviruses are classified into two subfamilies based on their host range: the Parvovirinae, which infect vertebrates, and the Densovirinae, which mainly infect insects and other arthropods. In recent years, a number of novel parvoviruses belonging to the subfamily Parvovirinae have been identified from various animal species and humans, including human parvovirus 4 (PARV4), porcine hokovirus, ovine partetravirus, porcine parvovirus 4 (PPV4), and porcine parvovirus 5 (PPV5). Using sequence-independent single primer amplification (SISPA), a novel parvovirus within the subfamily Parvovirinae that was distinct from any known parvoviruses was identified and five full-length genome sequences were determined and analyzed. A novel porcine parvovirus, provisionally named PPV6, was initially identified from aborted pig fetuses in China. Retrospective studies revealed the prevalence of PPV6 in aborted pig fetuses and piglets(50% and 75%, respectively) was apparently higher than that in finishing pigs and sows (15.6% and 3.8% respectively). Furthermore, the prevalence of PPV6 in finishing pig was similar in affected and unaffected farms (i.e. 16.7% vs. 13.6%-21.7%). This finding indicates that animal age, perhaps due to increased innate immune resistance, strongly influences the level of PPV6 viremia. Complete genome sequencing and multiple alignments have shown that the nearly full-length genome sequences were approximately 6,100 nucleotides in length and shared 20.5%-42.6% DNA sequence identity with other members of the Parvovirinae subfamily. Phylogenetic analysis showed that PPV6 was significantly distinct from other known parvoviruses and was most closely related to PPV4. Our findings and review of published parvovirus sequences suggested that a novel porcine parvovirus is currently circulating in China and might be classified into the novel genus Copiparvovirus within the subfamily Parvovirinae. However, the clinical manifestations of PPV6 are still unknown in that the prevalence of PPV6 was similar between healthy pigs and sick pigs in a retrospective epidemiological study. The identification of PPV6 within the subfamily Parvovirinae provides further insight into the viral and genetic diversity of parvoviruses.

  13. Ultraaccurate genome sequencing and haplotyping of single human cells.

    PubMed

    Chu, Wai Keung; Edge, Peter; Lee, Ho Suk; Bansal, Vikas; Bafna, Vineet; Huang, Xiaohua; Zhang, Kun

    2017-11-21

    Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10 -8 and average 500-kb-long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7 Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs. Copyright © 2017 the Author(s). Published by PNAS.

  14. Human Genome Sequencing in Health and Disease

    PubMed Central

    Gonzaga-Jauregui, Claudia; Lupski, James R.; Gibbs, Richard A.

    2013-01-01

    Following the “finished,” euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges. PMID:22248320

  15. The Effect of Various Finish Line Configurations on the Marginal Seal and Occlusal Discrepancy of Cast Full Crowns After Cementation - An In-vitro Study.

    PubMed

    Nemane, Vaishali; Akulwar, Ravikumar Suryakanth; Meshram, Suresh

    2015-08-01

    The marginal fit of crowns is of clinical importance. It is found that marginal and occlusal discrepancies are commonly increased following cementation. The resistance of cementing materials is a factor that prevents cast restorations from being correctly seated. Different finish lines behave differently in facilitating the escape of the cement. When the escape path of the cement decreases, the crown fails to seat further. This study was planned with an aim to evaluate the effect of various finish lines on the marginal seal and occlusal seat of full crown preparations. Six stainless steel metal dies were machined to simulate molar crown preparations. The diameter was 10 mm and height was 6mm. The occlusal surface was kept flat and a small circular dimple was machined for reorientation of the wax pattern and metal copings, margins of various designs were machined accurately. The margins prepared were Group A- 90(0)C shoulder, Group B- Rounded shoulder, Group C- 45 degree sloped shoulder, Group D- Chamfer, Group E- Long chamfer, Group F- Feather edge. Full cast metal crowns of base metal alloy were fabricated over the metal dies. Zinc phosphate luting cement was used for the cementation. After twenty four hours, the cemented crown and die assembly were embedded in clear acrylic resin so as to hold the assembly together while sectioning. Twenty four hours later, all the samples were sectioned sagitally. The sectioned halves were focused under a stereomicroscope and the cement spaces were measured to the nearest micron. The cement thickness was measured at two points on the occlusal surface and one at each margin. Significant differences were observed in the occlusal seat and marginal seal of all the finish line configurations. The rounded shoulder had the best occlusal seat, followed by 90(0)C shoulder. The occlusal seat and marginal seal afforded by the shoulder finish lines were similar whereas there was a vast difference in the seating and sealing of long chamfer and feather edged preparations. They showed the worst occlusal seat. It was found that the finish lines like shoulder preparations which exhibit poor sealing prior to complete cementation allow good seating whereas margins which seal earlier do not allow escape of cement and hence do not seat completely.

  16. The Effect of Various Finish Line Configurations on the Marginal Seal and Occlusal Discrepancy of Cast Full Crowns After Cementation - An In-vitro Study

    PubMed Central

    Nemane, Vaishali; Meshram, Suresh

    2015-01-01

    Background The marginal fit of crowns is of clinical importance. It is found that marginal and occlusal discrepancies are commonly increased following cementation. The resistance of cementing materials is a factor that prevents cast restorations from being correctly seated. Different finish lines behave differently in facilitating the escape of the cement. When the escape path of the cement decreases, the crown fails to seat further. Materials and Methods This study was planned with an aim to evaluate the effect of various finish lines on the marginal seal and occlusal seat of full crown preparations. Six stainless steel metal dies were machined to simulate molar crown preparations. The diameter was 10 mm and height was 6mm. The occlusal surface was kept flat and a small circular dimple was machined for reorientation of the wax pattern and metal copings, margins of various designs were machined accurately. The margins prepared were Group A- 900C shoulder, Group B- Rounded shoulder, Group C- 45 degree sloped shoulder, Group D- Chamfer, Group E- Long chamfer, Group F- Feather edge. Full cast metal crowns of base metal alloy were fabricated over the metal dies. Zinc phosphate luting cement was used for the cementation. After twenty four hours, the cemented crown and die assembly were embedded in clear acrylic resin so as to hold the assembly together while sectioning. Twenty four hours later, all the samples were sectioned sagitally. The sectioned halves were focused under a stereomicroscope and the cement spaces were measured to the nearest micron. The cement thickness was measured at two points on the occlusal surface and one at each margin. Results Significant differences were observed in the occlusal seat and marginal seal of all the finish line configurations. The rounded shoulder had the best occlusal seat, followed by 900C shoulder. The occlusal seat and marginal seal afforded by the shoulder finish lines were similar whereas there was a vast difference in the seating and sealing of long chamfer and feather edged preparations. They showed the worst occlusal seat. Conclusion It was found that the finish lines like shoulder preparations which exhibit poor sealing prior to complete cementation allow good seating whereas margins which seal earlier do not allow escape of cement and hence do not seat completely. PMID:26436039

  17. RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.

    PubMed

    Wright, Imogen A; Travers, Simon A

    2014-07-01

    The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Impact of asymmetric martensite and austenite nucleation and growth behavior on the phase stability and hysteresis of freestanding shape-memory nanoparticles

    NASA Astrophysics Data System (ADS)

    Ko, Won-Seok; Grabowski, Blazej; Neugebauer, Jörg

    2018-03-01

    Martensitic transformations in nanoscaled shape-memory alloys exhibit characteristic features absent for the bulk counterparts. Detailed understanding is required for applications in micro- and nanoelectromechanical systems, and experimental limitations render atomistic simulation an important complementary approach. Using a recently developed, accurate potential we investigate the phase transformation in freestanding Ni-Ti shape-memory nanoparticles with molecular-dynamics simulations. The results confirm that the decrease in the transformation temperature with decreasing particle size is correlated with an overstabilization of the austenitic surface energy over the martensitic surface energy. However, a detailed atomistic analysis of the nucleation and growth behavior reveals an unexpected difference in the mechanisms determining the austenite finish and martensite start temperature. While the austenite finish temperature is directly affected by a contribution of the surface energy difference, the martensite start temperature is mostly affected by the transformation strain, contrary to general expectations. This insight not only explains the reduced transformation temperature but also the reduced thermal hysteresis in freestanding nanoparticles.

  19. Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers

    PubMed Central

    Niu, Yuhong; Meng, Qingxiang; Li, Shengli; Ren, Liping; Zhou, Bo; Schonewille, Thomas; Zhou, Zhenming

    2016-01-01

    This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p < 0.001); however, the bacterial community composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or archaeal community composition of finishing steers. PMID:27258373

  20. Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers.

    PubMed

    Niu, Yuhong; Meng, Qingxiang; Li, Shengli; Ren, Liping; Zhou, Bo; Schonewille, Thomas; Zhou, Zhenming

    2016-01-01

    This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p < 0.001); however, the bacterial community composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or archaeal community composition of finishing steers.

  1. Final progress report, Construction of a genome-wide highly characterized clone resource for genome sequencing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nierman, William C.

    At TIGR, the human Bacterial Artificial Chromosome (BAC) end sequencing and trimming were with an overall sequencing success rate of 65%. CalTech human BAC libraries A, B, C and D as well as Roswell Park Cancer Institute's library RPCI-11 were used. To date, we have generated >300,000 end sequences from >186,000 human BAC clones with an average read length {approx}460 bp for a total of 141 Mb covering {approx}4.7% of the genome. Over sixty percent of the clones have BAC end sequences (BESs) from both ends representing over five-fold coverage of the genome by the paired-end clones. The average phredmore » Q20 length is {approx}400 bp. This high accuracy makes our BESs match the human finished sequences with an average identity of 99% and a match length of 450 bp, and a frequency of one match per 12.8 kb contig sequence. Our sample tracking has ensured a clone tracking accuracy of >90%, which gives researchers a high confidence in (1) retrieving the right clone from the BA C libraries based on the sequence matches; and (2) building a minimum tiling path of sequence-ready clones across the genome and genome assembly scaffolds.« less

  2. How to achieve more accurate comparisons in organ donation activity: time to effectiveness indicators.

    PubMed

    Deulofeu, R; Bodí, M A; Twose, J; López, P

    2010-06-01

    We are used to comparisons of activity using donation or transplantation population (pmp) rates between regions or countries, without a further evaluation of the process. But crude pmp rates do not clearly reflect real transplantation capacity, because organ procurement does not finish with the donation step; it is also necessary to know the utilization of the obtained organs. The objective of this study was to present methods and indicators deemed necessary to evaluate the effectiveness of the process. We have proposed the use of simple definitions and indicators to more accurately measure and compare the effectiveness of the total organ procurement process. To illustrate the use and performance of these indicators, we have presented the donation and transplantation activity in Catalonia from 2002 to 2007.

  3. Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

    PubMed

    Wymant, Chris; Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe

    2018-01-01

    Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.

  4. The evolution of vertebrate Toll-like receptors

    USGS Publications Warehouse

    Roach, J.C.; Glusman, G.; Rowen, L.; Kaur, A.; Purcell, M.K.; Smith, K.D.; Hood, L.E.; Aderem, A.

    2005-01-01

    The complete sequences of Takifugu Toll-like receptor (TLR) loci and gene predictions from many draft genomes enable comprehensive molecular phylogenetic analysis. Strong selective pressure for recognition of and response to pathogen-associated molecular patterns has maintained a largely unchanging TLR recognition in all vertebrates. There are six major families of vertebrate TLRs. This repertoire is distinct from that of invertebrates. TLRs within a family recognize a general class of pathogen-associated molecular patterns. Most vertebrates have exactly one gene ortholog for each TLR family. The family including TLR1 has more species-specific adaptations than other families. A major family including TLR11 is represented in humans only by a pseudogene. Coincidental evolution plays a minor role in TLR evolution. The sequencing phase of this study produced finished genomic sequences for the 12 Takifugu rubripes TLRs. In addition, we have produced > 70 gene models, including sequences from the opossum, chicken, frog, dog, sea urchin, and sea squirt. ?? 2005 by The National Academy of Sciences of the USA.

  5. Template-based protein structure modeling using the RaptorX web server.

    PubMed

    Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo

    2012-07-19

    A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world.

  6. Template-based protein structure modeling using the RaptorX web server

    PubMed Central

    Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo

    2016-01-01

    A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world. PMID:22814390

  7. DNA barcode data accurately assign higher spider taxa

    PubMed Central

    Coddington, Jonathan A.; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina

    2016-01-01

    The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades. PMID:27547527

  8. Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls.

    PubMed

    Zhou, Zhenming; Meng, Qingxiang; Li, Shengli; Jiang, Lan; Wu, Hao

    2017-08-01

    In this study, we evaluated the effects of urea-supplemented diets on the ruminal bacterial and archaeal communities of finishing bulls using sequencing technology. Eighteen bulls were fed a total mixed ration based on maize silage and concentrate (40:60) and randomly allocated to one of three experimental diets: a basal diet with no urea (UC, 0%), a basal diet supplemented with low urea levels (UL, 0.8% dry matter (DM) basis), and a basal diet supplemented with high urea levels (UH, 2% DM basis). All treatments were iso-nitrogenous (14% crude protein, DM basis) and iso-metabolic energetic (ME = 11.3 MJ/kg, DM basis). After a 12-week feeding trial, DNA was isolated from ruminal samples and used for 16S rRNA gene amplicon sequencing. For bacteria, the most abundant phyla were Firmicutes (44.47%) and Bacteroidetes (41.83%), and the dominant genera were Prevotella (13.17%), Succiniclasticum (4.24%), Butyrivibrio (2.36%), and Ruminococcus (1.93%). Urea supplementation had no effect on most phyla (P > 0.05), while there was a decreasing tendency in phylum TM7 with increasing urea levels (P = 0.0914). Compared to UC, UH had lower abundance of genera Butyrivibrio and Coprococcus (P = 0.0092 and P = 0.0222, respectively). For archaea, the most abundant phylum was Euryarchaeota (99.81% of the sequence reads), and the most abundant genus was Methanobrevibacter (90.87% of the sequence reads). UH increased the abundance of genus Methanobrevibacter and Methanobacterium (P = 0.0299 and P = 0.0007, respectively) and decreased the abundance of vadinCA11 (P = 0.0151). These findings suggest that urea-supplemented diets were associated with a shift in archaeal biodiversity and changes in the bacterial community in the rumen.

  9. Artificial Intelligence and Robotics.

    DTIC Science & Technology

    1984-02-01

    assertibly, seam welding and surface finishing, have clearly revealed the inabilities of current robots. Research prototypes have explored the use of...oriletats SysCtes fhat sae iuch representaios iay’n riot be ca al~esr todn solt ion givn roemes Teeaifch userr a complete ear pronsldurens and...rangle of1 possible (sequences of) *(4411pli:4444 4140 \\ -s. that r( ima rarlteed to achieve the goal, llotwitlhst and ing errors. lProt:4hli1)"i~ bv fh

  10. Using Maximum Entropy to Find Patterns in Genomes

    NASA Astrophysics Data System (ADS)

    Liu, Sophia; Hockenberry, Adam; Lancichinetti, Andrea; Jewett, Michael; Amaral, Luis

    The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. To accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. This approach can also be easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes. National Institute of General Medical Science, Northwestern University Presidential Fellowship, National Science Foundation, David and Lucile Packard Foundation, Camille Dreyfus Teacher Scholar Award.

  11. Deep Sequencing to Identify the Causes of Viral Encephalitis

    PubMed Central

    Chan, Benjamin K.; Wilson, Theodore; Fischer, Kael F.; Kriesel, John D.

    2014-01-01

    Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue. PMID:24699691

  12. Rapid Identification of Sequences for Orphan Enzymes to Power Accurate Protein Annotation

    PubMed Central

    Ojha, Sunil; Watson, Douglas S.; Bomar, Martha G.; Galande, Amit K.; Shearer, Alexander G.

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the “back catalog” of enzymology – “orphan enzymes,” those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme “back catalog” is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology’s “back catalog” another powerful tool to drive accurate genome annotation. PMID:24386392

  13. Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

    PubMed

    Ramkissoon, Kevin R; Miller, Jennifer K; Ojha, Sunil; Watson, Douglas S; Bomar, Martha G; Galande, Amit K; Shearer, Alexander G

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

  14. Chondromalacia patellae: an in vitro study. Comparison of MR criteria with histologic and macroscopic findings.

    PubMed

    van Leersum, M; Schweitzer, M E; Gannon, F; Finkel, G; Vinitski, S; Mitchell, D G

    1996-11-01

    To develop MR criteria for grades of chondromalacia patellae and to assess the accuracy of these grades. Fat-suppressed T2-weighted double-echo, fat-suppressed T2-weighted fast spin echo, fat-suppressed T1-weighted, and gradient echo sequences were performed at 1.5 T for the evaluation of chondromalacia. A total of 1000 MR, 200 histologic, and 200 surface locations were graded for chondromalacia and statistically compared. Compared with gross inspection as well as with histology the most accurate sequences were fat-suppressed T2-weighted conventional spin echo and fat suppressed T2-weighted fast spin echo, although the T1-weighted and proton density images also correlated well. The most accurate MR criteria applied to the severe grades of chondromalacia, with less accurate results for lesser grades. This study demonstrates that fat-suppressed routine T2-weighted and fast spin echo T2-weighted sequences seem to be more accurate than proton density, T1-weighted, and gradient echo sequences in grading chondromalacia. Good histologic and macroscopic correlation was seen in more severe grades of chondromalacia, but problems remain for the early grades in all sequences studied.

  15. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

    PubMed Central

    Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A.; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M.; Kyrpides, Nikos C.

    2012-01-01

    The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11 472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond. PMID:22135293

  16. Haemonchus contortus: Genome Structure, Organization and Comparative Genomics.

    PubMed

    Laing, R; Martinelli, A; Tracey, A; Holroyd, N; Gilleard, J S; Cotton, J A

    2016-01-01

    One of the first genome sequencing projects for a parasitic nematode was that for Haemonchus contortus. The open access data from the Wellcome Trust Sanger Institute provided a valuable early resource for the research community, particularly for the identification of specific genes and genetic markers. Later, a second sequencing project was initiated by the University of Melbourne, and the two draft genome sequences for H. contortus were published back-to-back in 2013. There is a pressing need for long-range genomic information for genetic mapping, population genetics and functional genomic studies, so we are continuing to improve the Wellcome Trust Sanger Institute assembly to provide a finished reference genome for H. contortus. This review describes this process, compares the H. contortus genome assemblies with draft genomes from other members of the strongylid group and discusses future directions for parasite genomics using the H. contortus model. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.

    PubMed

    Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M; Kyrpides, Nikos C

    2012-01-01

    The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11,472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond.

  18. Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.

    PubMed

    Gardiner, Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall, Anthony

    2014-12-01

    Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. © 2014 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

  19. GFinisher: a new strategy to refine and finish bacterial genome assemblies

    NASA Astrophysics Data System (ADS)

    Guizelini, Dieval; Raittz, Roberto T.; Cruz, Leonardo M.; Souza, Emanuel M.; Steffens, Maria B. R.; Pedrosa, Fabio O.

    2016-10-01

    Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.

  20. GFinisher: a new strategy to refine and finish bacterial genome assemblies.

    PubMed

    Guizelini, Dieval; Raittz, Roberto T; Cruz, Leonardo M; Souza, Emanuel M; Steffens, Maria B R; Pedrosa, Fabio O

    2016-10-10

    Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.

  1. Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.

    PubMed Central

    Padmanabhan, Roshan; Dubourg, Gregory; Nguyen, Thi-Thien; Couderc, Carine; Rossi-Tamisier, Morgane; Caputo, Aurelia; Raoult, Didier; Fournier, Pierre-Edouard

    2014-01-01

    Collinsella massiliensis strain GD3T is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon. PMID:25197489

  2. Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.

    PubMed

    Padmanabhan, Roshan; Dubourg, Gregory; Nguyen, Thi-Thien; Couderc, Carine; Rossi-Tamisier, Morgane; Caputo, Aurelia; Raoult, Didier; Fournier, Pierre-Edouard

    2014-06-15

    Collinsella massiliensis strain GD3(T) is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon.

  3. The FlyBase database of the Drosophila genome projects and community literature

    PubMed Central

    2003-01-01

    FlyBase (http://flybase.bio.indiana.edu/) provides an integrated view of the fundamental genomic and genetic data on the major genetic model Drosophila melanogaster and related species. FlyBase has primary responsibility for the continual reannotation of the D. melanogaster genome. The ultimate goal of the reannotation effort is to decorate the euchromatic sequence of the genome with as much biological information as is available from the community and from the major genome project centers. A complete revision of the annotations of the now-finished euchromatic genomic sequence has been completed. There are many points of entry to the genome within FlyBase, most notably through maps, gene products and ontologies, structured phenotypic and gene expression data, and anatomy. PMID:12519974

  4. Aozan: an automated post-sequencing data-processing pipeline.

    PubMed

    Perrin, Sandrine; Firmo, Cyril; Lemoine, Sophie; Le Crom, Stéphane; Jourdren, Laurent

    2017-07-15

    Data management and quality control of output from Illumina sequencers is a disk space- and time-consuming task. Thus, we developed Aozan to automatically handle data transfer, demultiplexing, conversion and quality control once a run has finished. This software greatly improves run data management and the monitoring of run statistics via automatic emails and HTML web reports. Aozan is implemented in Java and Python, supported on Linux systems, and distributed under the GPLv3 License at: http://www.outils.genomique.biologie.ens.fr/aozan/ . Aozan source code is available on GitHub: https://github.com/GenomicParisCentre/aozan . aozan@biologie.ens.fr. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  5. Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.

    PubMed

    Reid-Bayliss, Kate S; Loeb, Lawrence A

    2017-08-29

    Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.

  6. Experimentally Derived Beta Corrections to Accurately Model the Fatigue Crack Growth Behavior at Cold Expanded Holes in 2024-T351 Aluminum Alloys

    DTIC Science & Technology

    2008-08-01

    was attached to the upper grip and the runout was checked as the lower grip was rotated. The maximum runout was recorded as 0.021 inch. Due to the...difficulties with adjusting the Interlaken test frame, this runout value was noted but considered acceptable. 2.3 Fatigue Testing Procedures...easier to polish the specimen to a mirror finish. The polishing of the specimen was performed using an electric Dremel with a polishing wheel attached

  7. NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.

    PubMed

    Liu, Sophia S; Hockenberry, Adam J; Lancichinetti, Andrea; Jewett, Michael C; Amaral, Luís A N

    2016-11-01

    The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. In order to accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. While many tools have been developed to create random nucleotide sequences, protein coding sequences are subject to a unique set of constraints that complicates the process of generating appropriate null models. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content for the purpose of hypothesis testing. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content, which we have developed into a python package. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. Furthermore, this approach can easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes as well as more effective engineering of biological systems.

  8. A macro-micro robot for precise force applications

    NASA Technical Reports Server (NTRS)

    Marzwell, Neville I.; Wang, Yulun

    1993-01-01

    This paper describes an 8 degree-of-freedom macro-micro robot capable of performing tasks which require accurate force control. Applications such as polishing, finishing, grinding, deburring, and cleaning are a few examples of tasks which need this capability. Currently these tasks are either performed manually or with dedicated machinery because of the lack of a flexible and cost effective tool, such as a programmable force-controlled robot. The basic design and control of the macro-micro robot is described in this paper. A modular high-performance multiprocessor control system was designed to provide sufficient compute power for executing advanced control methods. An 8 degree of freedom macro-micro mechanism was constructed to enable accurate tip forces. Control algorithms based on the impedance control method were derived, coded, and load balanced for maximum execution speed on the multiprocessor system.

  9. The limits of protein sequence comparison?

    PubMed Central

    Pearson, William R; Sierk, Michael L

    2010-01-01

    Modern sequence alignment algorithms are used routinely to identify homologous proteins, proteins that share a common ancestor. Homologous proteins always share similar structures and often have similar functions. Over the past 20 years, sequence comparison has become both more sensitive, largely because of profile-based methods, and more reliable, because of more accurate statistical estimates. As sequence and structure databases become larger, and comparison methods become more powerful, reliable statistical estimates will become even more important for distinguishing similarities that are due to homology from those that are due to analogy (convergence). The newest sequence alignment methods are more sensitive than older methods, but more accurate statistical estimates are needed for their full power to be realized. PMID:15919194

  10. Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca).

    PubMed

    Zheng, Yang; Cai, Jing; Li, JianWen; Li, Bo; Lin, Runmao; Tian, Feng; Wang, XiaoLing; Wang, Jun

    2010-01-01

    A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

  11. Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding.

    PubMed

    Ma, Eddie Y T; Ratnasingham, Sujeevan; Kremer, Stefan C

    2018-01-01

    This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label. KB must also rate the replacement with quality value of in the additional read. Corrections are only available during system training. Developing the system, nearly 850,000 N-labels are obtained from Barcode of Life Datasystems, the premier database of genetic markers called DNA Barcodes. Increasing the number of correct bases improves reference sequence reliability, increases sequence identification accuracy, and assures analysis correctness. Keeping with barcoding standards, our system maintains an error rate of percent. Our system only applies corrections when it estimates low rate of error. Tested on this data, our automation selects and recovers: 79 percent of N-labels from COI (animal barcode); 80 percent from matK and rbcL (plant barcodes); and 58 percent from non-protein-coding sequences (across eukaryotes).

  12. Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

    PubMed Central

    Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

    2018-01-01

    Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver. PMID:29876136

  13. Stent manufacturing using cobalt chromium molybdenum (CoCrMo) by selective laser melting technology

    NASA Astrophysics Data System (ADS)

    Omar, Mohd Asnawi; Baharudin, BT-HT; Sulaiman, S.

    2017-12-01

    This paper reviews the capabilities of additive manufacturing (AM) technology and the use of Cobalt super alloy stent fabrication by looking at the dimensional accuracy and mechanical properties of the stent. Current conventional process exhibit many processes which affect the supply chain, costing, and post processing. By alternatively switching to AM, the step of production can be minimized and thus customization of stent can be carried out according to patients need. The proposed methodology is a perfect choice as surgeons need to have an accurate size during stent implantation. It also is able to reduce time-to-market delivery in a matter of hours and from days. The suggested stent model was taken from the third party vendor and flow optimization was carried out using Materialise Magics TM software. By using SLM125TM printer, the printing parameters such as Energy Density (DE), Laser Power (PL), Scanning Speed (SS) and Hatching Distance (DH) was used to print the stent. The properties of the finished product, such as strength, surface finish and orientation was investigated.

  14. Advancing three-dimensional MEMS by complimentary laser micro manufacturing

    NASA Astrophysics Data System (ADS)

    Palmer, Jeremy A.; Williams, John D.; Lemp, Tom; Lehecka, Tom M.; Medina, Francisco; Wicker, Ryan B.

    2006-01-01

    This paper describes improvements that enable engineers to create three-dimensional MEMS in a variety of materials. It also provides a means for selectively adding three-dimensional, high aspect ratio features to pre-existing PMMA micro molds for subsequent LIGA processing. This complimentary method involves in situ construction of three-dimensional micro molds in a stand-alone configuration or directly adjacent to features formed by x-ray lithography. Three-dimensional micro molds are created by micro stereolithography (MSL), an additive rapid prototyping technology. Alternatively, three-dimensional features may be added by direct femtosecond laser micro machining. Parameters for optimal femtosecond laser micro machining of PMMA at 800 nanometers are presented. The technical discussion also includes strategies for enhancements in the context of material selection and post-process surface finish. This approach may lead to practical, cost-effective 3-D MEMS with the surface finish and throughput advantages of x-ray lithography. Accurate three-dimensional metal microstructures are demonstrated. Challenges remain in process planning for micro stereolithography and development of buried features following femtosecond laser micro machining.

  15. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

    PubMed

    Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

    2012-01-01

    Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor model is uninformative in the worst possible sense. For all inputs, all trees optimize the likelihood score. Second, we show that a greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree can produce very poor alignments and trees. Therefore, the excellent performance of SATé-II and SATé-I is not because ML is used as an optimization criterion for choosing the best tree/alignment pair but rather due to the particular divide-and-conquer realignment techniques employed.

  16. Arbitrarily accurate twin composite π -pulse sequences

    NASA Astrophysics Data System (ADS)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

    We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

  17. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    PubMed

    Kelly, Steven; Maini, Philip K

    2013-01-01

    The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  18. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Meier-Kolthoff, Jan P.; Lu, Megan; Huntemann, Marcel

    Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyanmore » blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).« less

  19. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055T)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Huntemann, Marcel; Stackebrandt, Erko; Held, Brittany

    2013-01-01

    Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell enve- lope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is as- sociated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the firstmore » genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the Ge- nomic Encyclopedia of Bacteria and Archaea project.« less

  20. A paper-based device for double-stranded DNA detection with Zif268

    NASA Astrophysics Data System (ADS)

    Zhang, Daohong

    2017-05-01

    Here, a small analytical device was fabricated on both nitrocellulose membrane and filter paper, for the detection of biotinylated double-stranded DNA (dsDNA) from 1 nM. Zif268 was utilized for capturing the target DNA, which was a zinc finger protein that recognized only a dsDNA with specific sequence. Therefore, this detection platform could be utilized for PCR result detection, with the well-designed primers (interpolate both biotin and Zif268 binding sequence). The result of the assay could be recorded by a camera-phone, and analyzed with software. The whole assay finished within 1 hour. Due to the easy fabrication, operation and disposal of this device, this method can be employed in point-of-care detection or on-site monitoring.

  1. Genomic sequence of the xylose fermenting, insect-inhabitingyeast, Pichia stipitis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jeffries, Thomas W.; Grigoriev, Igor; Grimwood, Jane

    2007-06-25

    Xylose is a major constituent of angiosperm lignocellulose,so its fermentation is important for bioconversion to fuels andchemicals. Pichia stipitis is the best-studied native xylose fermentingyeast. Genes from P. stipitis have been used to engineer xylosemetabolism in Saccharomycescerevisiae, and the regulation of the P.stipitis genome offers insights into the mechanisms of xylose metabolismin yeasts. We have sequenced, assembled and finished the genome ofP.stipitis. As such, it is one of only a handful of completely finishedeukaryotic organisms undergoing analysis and manual curation. Thesequence has revealed aspects of genome organization, numerous genes forbiocoversion, preliminary insights into regulation of central metabolicpathways, numerous examples ofmore » co-localized genes with related functions,and evidence of how P. stipitis manages to achieve redox balance whilegrowing on xylose under microaerobic conditions.« less

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

    PubMed

    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.

  3. 40 CFR 63.5335 - How do I determine the actual HAP loss?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... and the mass fraction of HAP in each solvent/finish. (1) Measure Finish as Applied. Use a finish... and the mass fraction of HAP in each applied finish. Figure 1 of this subpart shows an example log for... each finish applied to the leather; (iii) Mass fraction of HAP in each applied finish; (iv) Date of the...

  4. 40 CFR 63.5335 - How do I determine the actual HAP loss?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... and the mass fraction of HAP in each solvent/finish. (1) Measure Finish as Applied. Use a finish... and the mass fraction of HAP in each applied finish. Figure 1 of this subpart shows an example log for... each finish applied to the leather; (iii) Mass fraction of HAP in each applied finish; (iv) Date of the...

  5. 40 CFR 63.5335 - How do I determine the actual HAP loss?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... and the mass fraction of HAP in each solvent/finish. (1) Measure Finish as Applied. Use a finish... and the mass fraction of HAP in each applied finish. Figure 1 of this subpart shows an example log for... each finish applied to the leather; (iii) Mass fraction of HAP in each applied finish; (iv) Date of the...

  6. 40 CFR Figure 1 to Subpart Tttt of... - Example Logs for Recording Leather Finish Use and HAP Content

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Finishing Operations Part 63, Subpt. TTTT, Fig. 1 Figure 1 to Subpart TTTT of Part 63—Example Logs for Recording Leather Finish Use and HAP Content Month:______Year:______ Finish Inventory Log Finish type Finish usage(pounds) HAP Content(mass fraction) Date and time Operator's name Product process operation Monthly...

  7. Read clouds uncover variation in complex regions of the human genome

    PubMed Central

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E.; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-01-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies. PMID:26286554

  8. A segmentation method for lung nodule image sequences based on superpixels and density-based spatial clustering of applications with noise

    PubMed Central

    Zhang, Wei; Zhang, Xiaolong; Qiang, Yan; Tian, Qi; Tang, Xiaoxian

    2017-01-01

    The fast and accurate segmentation of lung nodule image sequences is the basis of subsequent processing and diagnostic analyses. However, previous research investigating nodule segmentation algorithms cannot entirely segment cavitary nodules, and the segmentation of juxta-vascular nodules is inaccurate and inefficient. To solve these problems, we propose a new method for the segmentation of lung nodule image sequences based on superpixels and density-based spatial clustering of applications with noise (DBSCAN). First, our method uses three-dimensional computed tomography image features of the average intensity projection combined with multi-scale dot enhancement for preprocessing. Hexagonal clustering and morphological optimized sequential linear iterative clustering (HMSLIC) for sequence image oversegmentation is then proposed to obtain superpixel blocks. The adaptive weight coefficient is then constructed to calculate the distance required between superpixels to achieve precise lung nodules positioning and to obtain the subsequent clustering starting block. Moreover, by fitting the distance and detecting the change in slope, an accurate clustering threshold is obtained. Thereafter, a fast DBSCAN superpixel sequence clustering algorithm, which is optimized by the strategy of only clustering the lung nodules and adaptive threshold, is then used to obtain lung nodule mask sequences. Finally, the lung nodule image sequences are obtained. The experimental results show that our method rapidly, completely and accurately segments various types of lung nodule image sequences. PMID:28880916

  9. Accurate phylogenetic classification of DNA fragments based onsequence composition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis

    2006-05-01

    Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequencemore » characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.« less

  10. Finishing bacterial genome assemblies with Mix.

    PubMed

    Soueidan, Hayssam; Maurier, Florence; Groppi, Alexis; Sirand-Pugnet, Pascal; Tardy, Florence; Citti, Christine; Dupuy, Virginie; Nikolski, Macha

    2013-01-01

    Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions produce draft assemblies that often require a resource intensive finishing phase. In this paper we address these two aspects by developing Mix , a tool that mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length. We evaluate the performance of Mix on bacterial NGS data from the GAGE-B study and apply it to newly sequenced Mycoplasma genomes. Resulting final assemblies demonstrate a significant improvement in the overall assembly quality. In particular, Mix is consistent by providing better overall quality results even when the choice is guided solely by standard assembly statistics, as is the case for de novo projects. Mix is implemented in Python and is available at https://github.com/cbib/MIX, novel data for our Mycoplasma study is available at http://services.cbib.u-bordeaux2.fr/mix/.

  11. Bacterial community of biofilms developed under different water supply conditions in a distribution system.

    PubMed

    Sun, Huifang; Shi, Baoyou; Bai, Yaohui; Wang, Dongsheng

    2014-02-15

    In order to understand the bacterial community characteristics of biofilms developed under different finished water supply histories in drinking water distribution systems (DWDS), biofilm samples on different type of iron corrosion scales in a real DWDS were collected and systematically investigated using 454 pyrosequencing of 16S rRNA gene. The richness and diversity estimators showed that biofilms formed in DWDS transporting finished groundwater (GW) had the lowest level of bacterial diversity. From phylum to genus level, the dominant bacterial groups found in the biofilms under finished surface water (SW) and GW conditions were distinct. Proteobacteria was the dominant group in all biofilm samples (in the range of 40%-97%), but was relatively higher in biofilms with GW. The relative abundance of Firmicutes in biofilms with SW (28%-35%) was significantly higher (p<0.01) than that in biofilms with GW (0.5%-2.88%). Statistical analysis (Spearman's rank) revealed that alkalinity and chemical oxygen demand (CODMn) positively correlated with the relative abundance of Proteobacteria and Firmicutes, respectively. The abundance of sequences affiliated to iron-reducing bacteria (mainly Bacillus) and iron-oxidizing bacteria (mainly Acidovorax) were relatively higher in biofilms with SW, which might contribute to the formation of much thicker or tubercle-formed corrosion scales under SW supply condition. Several potential opportunistic pathogens, such as Burkholderia fungorum, Mycobacterium neoaurum, Mycobacterium frederiksbergense were detected in the biofilms. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers.

    PubMed

    Li, Yan; Meng, Qingxiang; Zhou, Bo; Zhou, Zhenming

    2017-04-21

    Here, we aimed to investigate the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers. To this end, the steers were reared on a standard TMR diet, standard diet containing EML, and standard diet containing SMFP. The protein and energy levels of all the diets were similar. Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene and quantitative real-time PCR were used to analyze and detect the fecal bacterial community. Most of the sequences were assigned to Firmicutes (56.67%) and Bacteroidetes (35.90%), followed by Proteobacteria (1.87%), Verrucomicrobia (1.80%) and Tenericutes (1.37%). The predominant genera were 5-7 N15 (5.91%), CF231 (2.49%), Oscillospira (2.33%), Paludibacter (1.23%) and Akkermansia (1.11%). No significant differences were observed in the numbers of Firmicutes (p = 0.28), Bacteroidetes (p = 0.63), Proteobacteria (p = 0.46), Verrucomicrobia (p = 0.17), and Tenericutes (p = 0.75) populations between the treatment groups. At the genus level, genera classified with high abundance (more than 0.1%) belonged primarily to Bacteroidetes and Firmicutes. Furthermore, no differences were observed at the genus level: 5-7 N15, CF231, Oscillospira, Paludibacter, and Akkermansia (p > 0.05 in all cases), except that rc4-4 was lower in the CON and SMFP groups than in the EML group (p = 0.02). There were no significant differences in the richness estimate and diversity indices between the groups (p > 0.16), and the different diets did not significantly influence most selected fecal bacterial species (p > 0.06), except for Ruminococcus albus, which was higher in the EML group (p < 0.01) and Streptococcus bovis, which was lower in the CON group (p < 0.01) relative to the other groups. In conclusion, diets supplemented with EML and SMFP have little influence on the fecal bacterial community composition in finishing steers.

  13. Carcass quality and meat tenderness of Hawaii pasture-finished cattle and Hawaii-originated, mainland feedlot-finished cattle.

    PubMed

    Kim, Yong Soo; Fukumoto, Glen Kazumi; Kim, Sunae

    2012-10-01

    The objective of this study was to compare the carcass quality and meat tenderness of Hawaii cattle finished on subtropical pasture with those of mainland US feedlot-finished cattle that were shipped from Hawaii after weaning. Rib-eye steak samples were collected from 30 feedlot-finished cattle harvested at a slaughter house in Washington State, USA and from 13 subtropical pasture-finished cattle harvested at a local slaughter house in Hawaii, then shipped to meat science laboratory at the University of Hawaii, Manoa. Samples were aged for 2 weeks at 4°C and frozen for later proximate analysis and meat tenderness measurement. Feedlot-finished cattle had significantly heavier carcass weight (353 vs 290 kg) and thicker backfat (13.5 vs 6.6 mm), but no significant difference was observed in rib-eye area between the two groups. Marbling score (Small) and United States Department of Agriculture quality grade (Choice) of the pasture-finished beef were not significantly (P < 0.05) different from those of feedlot-finished beef. The shear force value of pasture-finished beef (5.18 kg) was not statistically different (P < 0.05) from that of feedlot-finished beef (4.40 kg). In conclusion, results of this study suggest that Hawaii cattle finished on subtropical pasture produced as tender beef as mainland feedlot-finished cattle with less intramuscular fat.

  14. Integration of Sustainment Management Systems (SMS) with the Army Installation Status Report for Infrastructure (ISR-I)

    DTIC Science & Technology

    2011-09-01

    Interior Wall Finishes Element: Walls Type: CMU Block, Drywall , Other Criteria: Green, Amber, Red Section Name: Administrative Space This linkage...1 EA C20 Staircases C2010 Stair Construction Stairwells Landings and Treads N/A 50 SF C30 Interior Finishes C3010 Wall Finishes Admin...Areas N/A N/A 100 SF C30 Interior Finishes C3010 Wall Finishes Corridors N/A N/A 100 SF C30 Interior Finishes C3010 Wall Finishes Lobby N/A N/A

  15. Lung Sliding Identification Is Less Accurate in the Left Hemithorax.

    PubMed

    Piette, Eric; Daoust, Raoul; Lambert, Jean; Denault, André

    2017-02-01

    The aim of our study was to compare the accuracy of lung sliding identification for the left and right hemithoraxes, using prerecorded short US sequences, in a group of physicians with mixed clinical and US training. A total of 140 US sequences of a complete respiratory cycle were recorded in the operating room. Each sequence was divided in two, yielding 140 sequences of present lung sliding and 140 sequences of absent lung sliding. Of these 280 sequences, 40 were randomly repeated to assess intraobserver variability, for a total of 320 sequences. Descriptive data, the mean accuracy of each participant, as well as the rate of correct answers for each of the original 280 sequences were tabulated and compared for different subgroups of clinical and US training. A video with examples of present and absent lung sliding and a lung pulse was shown before testing. Two sessions were planned to facilitate the participation of 75 clinicians. In the first group, the rate of accurate lung sliding identification was lower in the left hemithorax than in the right (67.0% [interquartile range (IQR), 43.0-83.0] versus 80.0% [IQR, 57.0-95.0]; P < .001). In the second group, the rate of accurate lung sliding identification was also lower in the left hemithorax than in the right (76.3% [IQR, 42.9-90.9] versus 88.7% [IQR, 63.1-96.9]; P = .001). Mean accuracy rates were 67.5% (95% confidence interval, 65.7-69.4) in the first group and 73.1% (95% confidence interval, 70.7-75.5) in the second (P < .001). Lung sliding identification seems less accurate in the left hemithorax when using a short US examination. This study was done on recorded US sequences and should be repeated in a live clinical situation to confirm our results. © 2016 by the American Institute of Ultrasound in Medicine.

  16. The Finish Line.

    ERIC Educational Resources Information Center

    Cohen, Andrew

    1998-01-01

    Details what is expected in a good floor finish for athletic facilities, and explores the different categories of finishes and their content within the context of environmental regulation and manufacturing standards. Also discusses urethane finishings, the debate over using waterbased finishes, and the influence of regulatory control that may…

  17. The potential of three different PCR-related approaches for the authentication of mixtures of herbal substances and finished herbal medicinal products.

    PubMed

    Doganay-Knapp, Kirsten; Orland, Annika; König, Gabriele M; Knöss, Werner

    2018-04-01

    Herbal substances and preparations thereof play an important role in healthcare systems worldwide. Due to the variety of these products regarding origin, composition and processing procedures, appropriate methodologies for quality assessment need to be considered. A majority of herbal substances is administered as multicomponent mixtures, especially in the field of Traditional Chinese Medicine and ayurvedic medicine, but also in finished medicinal products. Quality assessment of complex mixtures of herbal substances with conventional methods is challenging. Thus, emphasis of the present work was directed on the development of complementary methods to elucidate the composition of mixtures of herbal substances and finished herbal medicinal products. An indispensable prerequisite for the safe and effective use of herbal medicines is the unequivocal authentication of the medicinal plants used therein. In this context, we investigated the potential of three different PCR-related methods in the characterization and authentication of herbal substances. A multiplex PCR assay and a quantitative PCR (qPCR) assay were established to analyze defined mixtures of the herbal substances Quercus cortex, Juglandis folium, Aristolochiae herba, Matricariae flos and Salviae miltiorrhizae radix et rhizoma and a finished herbal medicinal product. Furthermore, a standard cloning approach using universal primers targeting the ITS region was established in order to allow the investigation of herbal mixtures with unknown content. The cloning approach had some limitations regarding the detection/recovery of the components in defined mixtures of herbal substances, but the complementary use of two sets of universal primer pairs increased the detection of components out of the mixture. While the multiplex PCR did not retrace all components in the defined mixtures of herbal substances, the established qPCR resulted in simultaneous and specific detection of the five target sequences in all defined mixtures. These data indicate that for authentication purposes, complementary PCR-related methods are highly recommendable for the analysis of herbal mixtures in parallel. Copyright © 2018 Elsevier GmbH. All rights reserved.

  18. Physiological Effects of Touching Coated Wood.

    PubMed

    Ikei, Harumi; Song, Chorong; Miyazaki, Yoshifumi

    2017-07-13

    This study examined the physiological effects of touching wood with various coating with the palm of the hand on brain activity and autonomic nervous activity. Participants were 18 female university students (mean age, 21.7 ± 1.6 years). As an indicator of brain activity, oxyhemoglobin concentrations were measured in the left and right prefrontal cortices using near-infrared time-resolved spectroscopy. Heart rate variability (HRV) and heart rate were used as indicators of autonomic nervous activity. The high-frequency (HF) component of HRV, which reflects parasympathetic nervous activity, and the low-frequency (LF)/HF ratio, which reflects sympathetic nervous activity, were measured. Plates of uncoated, oil-finished, vitreous-finished, urethane-finished, and mirror-finished white oak wood were used as tactile stimuli. After sitting at rest with their eyes closed for 60 s, participants touched the stimuli with their palm for 90 s each. The results indicated that tactile stimulation with uncoated wood calmed prefrontal cortex activity (vs. urethane finish and mirror finish), increased parasympathetic nervous activity (vs. vitreous finish, urethane finish, and mirror finish), and decreased heart rate (vs. mirror finish), demonstrating a physiological relaxation effect. Further, tactile stimulation with oil- and vitreous-finished wood calmed left prefrontal cortex activity and decreased heart rate relative to mirror-finished wood.

  19. Physiological Effects of Touching Coated Wood

    PubMed Central

    2017-01-01

    This study examined the physiological effects of touching wood with various coating with the palm of the hand on brain activity and autonomic nervous activity. Participants were 18 female university students (mean age, 21.7 ± 1.6 years). As an indicator of brain activity, oxyhemoglobin concentrations were measured in the left and right prefrontal cortices using near-infrared time-resolved spectroscopy. Heart rate variability (HRV) and heart rate were used as indicators of autonomic nervous activity. The high-frequency (HF) component of HRV, which reflects parasympathetic nervous activity, and the low-frequency (LF)/HF ratio, which reflects sympathetic nervous activity, were measured. Plates of uncoated, oil-finished, vitreous-finished, urethane-finished, and mirror-finished white oak wood were used as tactile stimuli. After sitting at rest with their eyes closed for 60 s, participants touched the stimuli with their palm for 90 s each. The results indicated that tactile stimulation with uncoated wood calmed prefrontal cortex activity (vs. urethane finish and mirror finish), increased parasympathetic nervous activity (vs. vitreous finish, urethane finish, and mirror finish), and decreased heart rate (vs. mirror finish), demonstrating a physiological relaxation effect. Further, tactile stimulation with oil- and vitreous-finished wood calmed left prefrontal cortex activity and decreased heart rate relative to mirror-finished wood. PMID:28703777

  20. Advantages of utilizing DMD based rapid manufacturing systems in mass customization applications

    NASA Astrophysics Data System (ADS)

    El-Siblani, A.

    2010-02-01

    The Use of DMD based Rapid Manufacturing Systems has proven to be very advantageous in the production of highly accurate plastic based components for use in mass customization market such as hearing aids, and dental markets. The voxelization process currently afforded with the DLP technology eliminates any layering effect associated with all existing additive Rapid Manufacturing technologies. The smooth accurate surfaces produced in an additive process utilizing DLP technology, through the voxelization approach, allow for the production of custom finished products. The implementation of DLP technology in rapid prototyping and rapid manufacturing systems allow for the usage of highly viscous photopolymer based liquid and paste composites for rapid manufacturing that could not be used in any other additive process prior to implementation of DLP technology in RP and RM systems. It also allowed for the greater throughput in production without sacrificing quality and accuracy.

  1. Design and realization of test system for testing parallelism and jumpiness of optical axis of photoelectric equipment

    NASA Astrophysics Data System (ADS)

    Shi, Sheng-bing; Chen, Zhen-xing; Qin, Shao-gang; Song, Chun-yan; Jiang, Yun-hong

    2014-09-01

    With the development of science and technology, photoelectric equipment comprises visible system, infrared system, laser system and so on, integration, information and complication are higher than past. Parallelism and jumpiness of optical axis are important performance of photoelectric equipment,directly affect aim, ranging, orientation and so on. Jumpiness of optical axis directly affect hit precision of accurate point damage weapon, but we lack the facility which is used for testing this performance. In this paper, test system which is used fo testing parallelism and jumpiness of optical axis is devised, accurate aim isn't necessary and data processing are digital in the course of testing parallelism, it can finish directly testing parallelism of multi-axes, aim axis and laser emission axis, parallelism of laser emission axis and laser receiving axis and first acuualizes jumpiness of optical axis of optical sighting device, it's a universal test system.

  2. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

    DOE PAGES

    Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J.; ...

    2017-06-12

    We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster withmore » potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.« less

  3. Structural characterization of the thermally tolerant pectin methylesterase purified from citrus sinensis fruit and its gene sequence.

    PubMed

    Savary, Brett J; Vasu, Prasanna; Cameron, Randall G; McCollum, T Gregory; Nuñez, Alberto

    2013-12-26

    Despite the longstanding importance of the thermally tolerant pectin methylesterase (TT-PME) activity in citrus juice processing and product quality, the unequivocal identification of the protein and its corresponding gene has remained elusive. TT-PME was purified from sweet orange [ Citrus sinensis (L.) Osbeck] finisher pulp (8.0 mg/1.3 kg tissue) with an improved purification scheme that provided 20-fold increased enzyme yield over previous results. Structural characterization of electrophoretically pure TT-PME by MALDI-TOF MS determined molecular masses of approximately 47900 and 53000 Da for two principal glycoisoforms. De novo sequences generated from tryptic peptides by MALDI-TOF/TOF MS matched multiple anonymous Citrus EST cDNA accessions. The complete tt-pme cDNA (1710 base pair) was cloned from a fruit mRNA library using RT- and RLM-RACE PCR. Citrus TT-PME is a novel isoform that showed higher sequence identity with the multiply glycosylated kiwifruit PME than to previously described Citrus thermally labile PME isoforms.

  4. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J.

    We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster withmore » potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.« less

  5. Complete genome sequence of Paenibacillus riograndensis SBR5(T), a Gram-positive diazotrophic rhizobacterium.

    PubMed

    Brito, Luciana Fernandes; Bach, Evelise; Kalinowski, Jörn; Rückert, Christian; Wibberg, Daniel; Passaglia, Luciane M; Wendisch, Volker F

    2015-08-10

    Paenibacillus riograndensis is a Gram-positive rhizobacterium which exhibits plant growth promoting activities. It was isolated from the rhizosphere of wheat grown in the state of Rio Grande do Sul, Brazil. Here we announce the complete genome sequence of P. riograndensis strain SBR5(T). The genome of P. riograndensis SBR5(T) consists of a circular chromosome of 7,893,056bps. The genome was finished and fully annotated, containing 6705 protein coding genes, 87 tRNAs and 27 rRNAs. The knowledge of the complete genome helped to explain why P. riograndensis SBR5(T) can grow with the carbon sources arabinose and mannitol, but not myo-inositol, and to explain physiological features such as biotin auxotrophy and antibiotic resistances. The genome sequence will be valuable for functional genomics and ecological studies as well as for application of P. riograndensis SBR5(T) as plant growth-promoting rhizobacterium. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Methodologic European external quality assurance for DNA sequencing: the EQUALseq program.

    PubMed

    Ahmad-Nejad, Parviz; Dorn-Beineke, Alexandra; Pfeiffer, Ulrike; Brade, Joachim; Geilenkeuser, Wolf-Jochen; Ramsden, Simon; Pazzagli, Mario; Neumaier, Michael

    2006-04-01

    DNA sequencing is a key technique in molecular diagnostics, but to date no comprehensive methodologic external quality assessment (EQA) programs have been instituted. Between 2003 and 2005, the European Union funded, as specific support actions, the EQUAL initiative to develop methodologic EQA schemes for genotyping (EQUALqual), quantitative PCR (EQUALquant), and sequencing (EQUALseq). Here we report on the results of the EQUALseq program. The participating laboratories received a 4-sample set comprising 2 DNA plasmids, a PCR product, and a finished sequencing reaction to be analyzed. Data and information from detailed questionnaires were uploaded online and evaluated by use of a scoring system for technical skills and proficiency of data interpretation. Sixty laboratories from 21 European countries registered, and 43 participants (72%) returned data and samples. Capillary electrophoresis was the predominant platform (n = 39; 91%). The median contiguous correct sequence stretch was 527 nucleotides with considerable variation in quality of both primary data and data evaluation. The association between laboratory performance and the number of sequencing assays/year was statistically significant (P <0.05). Interestingly, more than 30% of participants neither added comments to their data nor made efforts to identify the gene sequences or mutational positions. Considerable variations exist even in a highly standardized methodology such as DNA sequencing. Methodologic EQAs are appropriate tools to uncover strengths and weaknesses in both technique and proficiency, and our results emphasize the need for mandatory EQAs. The results of EQUALseq should help improve the overall quality of molecular genetics findings obtained by DNA sequencing.

  7. Enantioselective synthesis of α-oxy amides via Umpolung amide synthesis.

    PubMed

    Leighty, Matthew W; Shen, Bo; Johnston, Jeffrey N

    2012-09-19

    α-Oxy amides are prepared through enantioselective synthesis using a sequence beginning with a Henry addition of bromonitromethane to aldehydes and finishing with Umpolung Amide Synthesis (UmAS). Key to high enantioselection is the finding that ortho-iodo benzoic acid salts of the chiral copper(II) bis(oxazoline) catalyst deliver both diastereomers of the Henry adduct with high enantiomeric excess, homochiral at the oxygen-bearing carbon. Overall, this approach to α-oxy amides provides an innovative complement to alternatives that focus almost entirely on the enantioselective synthesis of α-oxy carboxylic acids.

  8. BAIT: Organizing genomes and mapping rearrangements in single cells.

    PubMed

    Hills, Mark; O'Neill, Kieran; Falconer, Ester; Brinkman, Ryan; Lansdorp, Peter M

    2013-01-01

    Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, identifying approximately 21 Mb of incorrectly oriented fragments and placing over half (2.6 Mb) of the orphan fragments in mm10/GRCm38. BAIT also stratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. BAIT is available at http://sourceforge.net/projects/bait/.

  9. GenColors: annotation and comparative genomics of prokaryotes made easy.

    PubMed

    Romualdi, Alessandro; Felder, Marius; Rose, Dominic; Gausmann, Ulrike; Schilhabel, Markus; Glöckner, Gernot; Platzer, Matthias; Sühnel, Jürgen

    2007-01-01

    GenColors (gencolors.fli-leibniz.de) is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. A variety of export/import filters manages an effective data flow from sequence assembly and manipulation programs (e.g., GAP4) to GenColors and back as well as to standard GenBank file(s). The genome comparison tools include best bidirectional hits, gene conservation, syntenies, and gene core sets. Precomputed UniProt matches allow annotation and analysis in an effective manner. In addition to these analysis options, base-specific quality data (coverage and confidence) can also be handled if available. The GenColors system can be used both for annotation purposes in ongoing genome projects and as an analysis tool for finished genomes. GenColors comes in two types, as dedicated genome browsers and as the Jena Prokaryotic Genome Viewer (JPGV). Dedicated genome browsers contain genomic information on a set of related genomes and offer a large number of options for genome comparison. The system has been efficiently used in the genomic sequencing of Borrelia garinii and is currently applied to various ongoing genome projects on Borrelia, Legionella, Escherichia, and Pseudomonas genomes. One of these dedicated browsers, the Spirochetes Genome Browser (sgb.fli-leibniz.de) with Borrelia, Leptospira, and Treponema genomes, is freely accessible. The others will be released after finalization of the corresponding genome projects. JPGV (jpgv.fli-leibniz.de) offers information on almost all finished bacterial genomes, as compared to the dedicated browsers with reduced genome comparison functionality, however. As of January 2006, this viewer includes 632 genomic elements (e.g., chromosomes and plasmids) of 293 species. The system provides versatile quick and advanced search options for all currently known prokaryotic genomes and generates circular and linear genome plots. Gene information sheets contain basic gene information, database search options, and links to external databases. GenColors is also available on request for local installation.

  10. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

    PubMed Central

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong

    2015-01-01

    Abstract We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate—slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory. PMID:25549288

  11. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

    PubMed Central

    Camargo, Anamaria A.; Samaia, Helena P. B.; Dias-Neto, Emmanuel; Simão, Daniel F.; Migotto, Italo A.; Briones, Marcelo R. S.; Costa, Fernando F.; Aparecida Nagai, Maria; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; Sonati, Maria de Fátima; Tajara, Eloiza H.; Valentini, Sandro R.; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Arnaldi, Liliane A. T.; de Assis, Angela M.; Bengtson, Mário Henrique; Bergamo, Nadia Aparecida; Bombonato, Vanessa; de Camargo, Maria E. R.; Canevari, Renata A.; Carraro, Dirce M.; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Corrêa, Rosana F. R.; Costa, Maria Cristina R.; Curcio, Cyntia; Hokama, Paula O. M.; Ferreira, Ari J. S.; Furuzawa, Gilberto K.; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Krieger, José E.; Leite, Luciana C. C.; Majumder, Paromita; Marins, Mozart; Marques, Everaldo R.; Melo, Analy S. A.; Melo, Monica; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana G.; Prevedel, Aline C.; Rahal, Paula; Rainho, Claudia A.; Reis, Eduardo M. R.; Ribeiro, Marcelo L.; da Rós, Nancy; de Sá, Renata G.; Sales, Magaly M.; Sant'anna, Simone Cristina; dos Santos, Mariana L.; da Silva, Aline M.; da Silva, Neusa P.; Silva, Wilson A.; da Silveira, Rosana A.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Soares, Fernando; Moreira, Eloisa S.; Nunes, Diana N.; Correa, Ricardo G.; Zalcberg, Heloisa; Carvalho, Alex F.; Reis, Luis F. L.; Brentani, Ricardo R.; Simpson, Andrew J. G.; de Souza, Sandro J.

    2001-01-01

    Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription–PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning. PMID:11593022

  12. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome.

    PubMed

    Camargo, A A; Samaia, H P; Dias-Neto, E; Simão, D F; Migotto, I A; Briones, M R; Costa, F F; Nagai, M A; Verjovski-Almeida, S; Zago, M A; Andrade, L E; Carrer, H; El-Dorry, H F; Espreafico, E M; Habr-Gama, A; Giannella-Neto, D; Goldman, G H; Gruber, A; Hackel, C; Kimura, E T; Maciel, R M; Marie, S K; Martins, E A; Nobrega, M P; Paco-Larson, M L; Pardini, M I; Pereira, G G; Pesquero, J B; Rodrigues, V; Rogatto, S R; da Silva, I D; Sogayar, M C; Sonati, M F; Tajara, E H; Valentini, S R; Alberto, F L; Amaral, M E; Aneas, I; Arnaldi, L A; de Assis, A M; Bengtson, M H; Bergamo, N A; Bombonato, V; de Camargo, M E; Canevari, R A; Carraro, D M; Cerutti, J M; Correa, M L; Correa, R F; Costa, M C; Curcio, C; Hokama, P O; Ferreira, A J; Furuzawa, G K; Gushiken, T; Ho, P L; Kimura, E; Krieger, J E; Leite, L C; Majumder, P; Marins, M; Marques, E R; Melo, A S; Melo, M B; Mestriner, C A; Miracca, E C; Miranda, D C; Nascimento, A L; Nobrega, F G; Ojopi, E P; Pandolfi, J R; Pessoa, L G; Prevedel, A C; Rahal, P; Rainho, C A; Reis, E M; Ribeiro, M L; da Ros, N; de Sa, R G; Sales, M M; Sant'anna, S C; dos Santos, M L; da Silva, A M; da Silva, N P; Silva, W A; da Silveira, R A; Sousa, J F; Stecconi, D; Tsukumo, F; Valente, V; Soares, F; Moreira, E S; Nunes, D N; Correa, R G; Zalcberg, H; Carvalho, A F; Reis, L F; Brentani, R R; Simpson, A J; de Souza, S J; Melo, M

    2001-10-09

    Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

  13. Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens

    PubMed Central

    Ojha, Sohita; Pummill, Jeff F.; Koon, Joseph A.; Wideman, Robert F.; Rhoads, Douglas D.

    2015-01-01

    Lameness in broiler chickens is a significant animal welfare and financial issue. Lameness can be enhanced by rearing young broilers on wire flooring. We have identified Staphylococcus agnetis as significantly involved in bacterial chondronecrosis with osteomyelitis (BCO) in proximal tibia and femorae, leading to lameness in broiler chickens in the wire floor system. Administration of S. agnetis in water induces lameness. Previously reported in some cases of cattle mastitis, this is the first report of this poorly described pathogen in chickens. We used long and short read next generation sequencing to assemble single finished contigs for the genome and a large plasmid from the chicken pathogen. Comparison of the S. agnetis genome to those of other pathogenic Staphylococci shows that S.agnetis contains a distinct repertoire of virulence determinants. Additionally, the S. agnetis genome has several regions that differ substantially from the genomes of other pathogenic Staphylococci. Comparison of our finished genome to a recent draft genome for a cattle mastitis isolate suggests that future investigations focus on the evolutionary epidemiology of this emerging pathogen of domestic animals. PMID:26606420

  14. [The statistical analysis for the use of the 55,787 finished resin teeth].

    PubMed

    Wu, Shu-hong; Yu, Hai-yang; Wang, Lu; Xu, Ling; Xiao, Zhi-li

    2010-08-01

    To analyze the use situation of finished resin teeth for the different location, and to provide reference for manufacturers of finished resin teeth and all the buyers. To analyze the use situation of finished resin teeth in the Dental Laboratory of the Affiliated Hospital of Stomatology of Chongqing Medical University from January 2006 to December 2008 by using statistic methods. During the use of 55,787 finished resin teeth, the study found some rules. (1) The top use of finished resin teeth was D6 with the percentage of 5.31%, and the lowest use of finished resin teeth was D3 with the percentage of 1.94%. (2) Except the maxillary canines and the mandibular lateral incisors, there was no significant difference between the usage of other same name finished resin teeth (P > 0.05). (3) Among all finished resin teeth, the usage of section B exceeded section A, and the usage of maxillary finished resin teeth exceeded mandibular finished resin teeth (P < 0.05). (4) The use of the complete denture and single complete denture was about 1/3 of the total usage of finished resin teeth. (5) Except the use situation of complete denture and single complete denture, the frequency of simultaneously using mandibular left and right central incisors was the most with the percentage of 81.46%, for the frequency of simultaneously using maxillary left and right canines was 43.26% of the total, which was the lowest. There is significant difference in the use frequency of finished resin teeth for different location. For such reason, the manufacturers should produce finished resin teeth pro rata as well as the buyers for their purchase.

  15. Simple chained guide trees give high-quality protein multiple sequence alignments

    PubMed Central

    Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

    2014-01-01

    Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495

  16. Predicting DNA hybridization kinetics from sequence

    NASA Astrophysics Data System (ADS)

    Zhang, Jinny X.; Fang, John Z.; Duan, Wei; Wu, Lucia R.; Zhang, Angela W.; Dalchau, Neil; Yordanov, Boyan; Petersen, Rasmus; Phillips, Andrew; Zhang, David Yu

    2018-01-01

    Hybridization is a key molecular process in biology and biotechnology, but so far there is no predictive model for accurately determining hybridization rate constants based on sequence information. Here, we report a weighted neighbour voting (WNV) prediction algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants. To construct this algorithm we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (36 nt sub-sequences of the CYCS and VEGF genes) at temperatures ranging from 28 to 55 °C. Automated feature selection and weighting optimization resulted in a final six-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 3 with ∼91% accuracy, based on leave-one-out cross-validation. Accurate prediction of hybridization kinetics allows the design of efficient probe sequences for genomics research.

  17. Read clouds uncover variation in complex regions of the human genome.

    PubMed

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-10-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies. © 2015 Bishara et al.; Published by Cold Spring Harbor Laboratory Press.

  18. Case Report: Application of whole exome sequencing for accurate diagnosis of rare syndromes of mineralocorticoid excess

    PubMed Central

    Narayanan, Ranjit; Karuthedath Vellarikkal, Shamsudheen; Jayarajan, Rijith; Verma, Ankit; Dixit, Vishal; Scaria, Vinod; Sivasubbu, Sridhar

    2017-01-01

    Syndromes of mineralocorticoid excess (SME) are closely related clinical manifestations occurring within a specific set of diseases. Overlapping clinical manifestations of such syndromes often create a dilemma in accurate diagnosis, which is crucial for disease surveillance and management especially in rare genetic disorders. Here we demonstrate the use of whole exome sequencing (WES) for accurate diagnosis of rare SME and report that p.R337C variation in the HSD11B2 gene causes progressive apparent mineralocorticoid excess (AME) syndrome in a South Indian family of Mappila origin. PMID:29067160

  19. 9 CFR 381.309 - Finished product inspection.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Finished product inspection. (a) Finished product inspections must be handled according to: (1) A HACCP.... (b)-(c) [Reserved] (d) Procedures for finished product inspections where the HACCP plan for thermally...

  20. 40 CFR 63.5335 - How do I determine the actual HAP loss?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... to the leather; (iii) Mass fraction of HAP in each applied finish; (iv) Date of the recorded entry... recorded finish usage by the corresponding mass fraction of HAP in the finish. The result is the HAP loss... the pounds of each recorded finish usage by the corresponding mass fraction of HAP in the finish. The...

  1. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.

    PubMed

    van Baren, Marijke J; Bachy, Charles; Reistetter, Emily Nahas; Purvine, Samuel O; Grimwood, Jane; Sudek, Sebastian; Yu, Hang; Poirier, Camille; Deerinck, Thomas J; Kuo, Alan; Grigoriev, Igor V; Wong, Chee-Hong; Smith, Richard D; Callister, Stephen J; Wei, Chia-Lin; Schmutz, Jeremy; Worden, Alexandra Z

    2016-03-31

    Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages. Extensive differences in gene loss and architecture between related prasinophytes underscore their divergence. PG biosynthesis genes from the cyanobacterial endosymbiont that became the plastid, have been selectively retained in multiple plants and algae, implying a biological function. Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution.

  2. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

    PubMed Central

    Ben M'Barek, Sarrah; Dhillon, Braham; Wittenberg, Alexander H. J.; Crane, Charles F.; Hane, James K.; Foster, Andrew J.; Van der Lee, Theo A. J.; Grimwood, Jane; Aerts, Andrea; Antoniw, John; Bailey, Andy; Bluhm, Burt; Bowler, Judith; Bristow, Jim; van der Burgt, Ate; Canto-Canché, Blondy; Churchill, Alice C. L.; Conde-Ferràez, Laura; Cools, Hans J.; Coutinho, Pedro M.; Csukai, Michael; Dehal, Paramvir; De Wit, Pierre; Donzelli, Bruno; van de Geest, Henri C.; van Ham, Roeland C. H. J.; Hammond-Kosack, Kim E.; Henrissat, Bernard; Kilian, Andrzej; Kobayashi, Adilson K.; Koopmann, Edda; Kourmpetis, Yiannis; Kuzniar, Arnold; Lindquist, Erika; Lombard, Vincent; Maliepaard, Chris; Martins, Natalia; Mehrabi, Rahim; Nap, Jan P. H.; Ponomarenko, Alisa; Rudd, Jason J.; Salamov, Asaf; Schmutz, Jeremy; Schouten, Henk J.; Shapiro, Harris; Stergiopoulos, Ioannis; Torriani, Stefano F. F.; Tu, Hank; de Vries, Ronald P.; Waalwijk, Cees; Ware, Sarah B.; Wiebenga, Ad; Zwiers, Lute-Harm; Oliver, Richard P.

    2011-01-01

    The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed “mesosynteny” is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors. PMID:21695235

  3. rpoB Gene Sequencing for Identification of Corynebacterium Species

    PubMed Central

    Khamis, Atieh; Raoult, Didier; La Scola, Bernard

    2004-01-01

    The genus Corynebacterium is a heterogeneous group of species comprising human and animal pathogens and environmental bacteria. It is defined on the basis of several phenotypic characters and the results of DNA-DNA relatedness and, more recently, 16S rRNA gene sequencing. However, the 16S rRNA gene is not polymorphic enough to ensure reliable phylogenetic studies and needs to be completely sequenced for accurate identification. The almost complete rpoB sequences of 56 Corynebacterium species were determined by both PCR and genome walking methods. In all cases the percent similarities between different species were lower than those observed by 16S rRNA gene sequencing, even for those species with degrees of high similarity. Several clusters supported by high bootstrap values were identified. In order to propose a method for strain identification which does not require sequencing of the complete rpoB sequence (approximately 3,500 bp), we identified an area with a high degree of polymorphism, bordered by conserved sequences that can be used as universal primers for PCR amplification and sequencing. The sequence of this fragment (434 to 452 bp) allows accurate species identification and may be used in the future for routine sequence-based identification of Corynebacterium species. PMID:15364970

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

    PubMed Central

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

    2014-01-01

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

  5. Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.

    PubMed

    Kuroshu, Reginaldo M; Watanabe, Junichi; Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka; Kasahara, Masahiro

    2010-05-07

    Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only approximately US$3 per clone, demonstrating a significant advantage over previous approaches.

  6. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

    PubMed

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

    2009-07-01

    The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

  7. An atomic-scale and high efficiency finishing method of zirconia ceramics by using magnetorheological finishing

    NASA Astrophysics Data System (ADS)

    Luo, Hu; Guo, Meijian; Yin, Shaohui; Chen, Fengjun; Huang, Shuai; Lu, Ange; Guo, Yuanfan

    2018-06-01

    Zirconia ceramics is a valuable crucial material for fabricating functional components applied in aerospace, biology, precision machinery, military industry and other fields. However, the properties of its high brittleness and high hardness could seriously reduce its finishing efficiency and surface quality by conventional processing technology. In this work, we present a high efficiency and high-quality finishing process by using magnetorheological finishing (MRF), which employs the permanent magnetic yoke with straight air gap as excitation unit. The sub-nanoscale surface roughness and damage free surface can be obtained after magnetorheological finishing. The XRD results and SEM morphologies confirmed that the mechanical shear removal with ductile modes are the dominant material removal mechanism for the magnetorheological finishing of zirconia ceramic. With the developed experimental apparatus, the effects of workpiece speed, trough speed and work gap on material removal rate and surface roughness were systematically investigated. Zirconia ceramics finished to ultra-smooth surface with surface roughness less than Ra 1 nm was repeatedly achieved during the parametric experiments. Additionally, the highest material removal rate exceeded 1 mg/min when using diamond as an abrasive particle. Magnetorheological finishing promises to be an adaptable and efficient method for zirconia ceramics finishing.

  8. Development of Multi-functional Properties on Cotton Fabric by In Situ Application of TiO2 and ZnO Nanoparticles

    NASA Astrophysics Data System (ADS)

    Butola, B. S.; Garg, Aayush; Garg, Aman; Chauhan, Indu

    2018-06-01

    Cotton fabrics functionalized with different combinations of TiO2 and ZnO were evaluated for multifunctional properties including UV protection, antimicrobial and self-cleaning. The ZnO nanoparticles synthesized using sol gel method were applied on cotton fabric by pad-dry-cure method and TiO2 was deposited in situ. The deposition of both TiO2 and ZnO was examined and confirmed by SEM and EDX analysis. Application of both metal oxides resulted in good improvement in UV protection of treated fabrics. The fabrics which were finished with combination of both Zinc and Titanium oxides, showed UPF rating of 50+ as compared to UPF rating of untreated cotton, which was only 5. The same fabrics also showed higher self-cleaning extent as compared to untreated cotton fabric. It was found that the sequence of application of ZnO and TiO2 affected the antimicrobial activity of the finished fabric and also the durability. When application of TiO2 was followed by ZnO, the combination resulted in development of excellent antimicrobial property against Escherichia coli ( 99% colony reduction) which was retained after 10 wash cycles. However, when application of ZnO nanoparticles was followed by application of TiO2, the improvement in antimicrobial activity was found to be moderate ( 48% colony reduction) and had poor wash durability. Hence, the specific sequence of application of these metals oxides can be utilized for obtaining good durability of the multifunctional properties on cotton fabric.

  9. Development of Multi-functional Properties on Cotton Fabric by In Situ Application of TiO2 and ZnO Nanoparticles

    NASA Astrophysics Data System (ADS)

    Butola, B. S.; Garg, Aayush; Garg, Aman; Chauhan, Indu

    2018-05-01

    Cotton fabrics functionalized with different combinations of TiO2 and ZnO were evaluated for multifunctional properties including UV protection, antimicrobial and self-cleaning. The ZnO nanoparticles synthesized using sol gel method were applied on cotton fabric by pad-dry-cure method and TiO2 was deposited in situ. The deposition of both TiO2 and ZnO was examined and confirmed by SEM and EDX analysis. Application of both metal oxides resulted in good improvement in UV protection of treated fabrics. The fabrics which were finished with combination of both Zinc and Titanium oxides, showed UPF rating of 50+ as compared to UPF rating of untreated cotton, which was only 5. The same fabrics also showed higher self-cleaning extent as compared to untreated cotton fabric. It was found that the sequence of application of ZnO and TiO2 affected the antimicrobial activity of the finished fabric and also the durability. When application of TiO2 was followed by ZnO, the combination resulted in development of excellent antimicrobial property against Escherichia coli ( 99% colony reduction) which was retained after 10 wash cycles. However, when application of ZnO nanoparticles was followed by application of TiO2, the improvement in antimicrobial activity was found to be moderate ( 48% colony reduction) and had poor wash durability. Hence, the specific sequence of application of these metals oxides can be utilized for obtaining good durability of the multifunctional properties on cotton fabric.

  10. Assessing Analytical Similarity of Proposed Amgen Biosimilar ABP 501 to Adalimumab.

    PubMed

    Liu, Jennifer; Eris, Tamer; Li, Cynthia; Cao, Shawn; Kuhns, Scott

    2016-08-01

    ABP 501 is being developed as a biosimilar to adalimumab. Comprehensive comparative analytical characterization studies have been conducted and completed. The objective of this study was to assess analytical similarity between ABP 501 and two adalimumab reference products (RPs), licensed by the United States Food and Drug Administration (adalimumab [US]) and authorized by the European Union (adalimumab [EU]), using state-of-the-art analytical methods. Comprehensive analytical characterization incorporating orthogonal analytical techniques was used to compare products. Physicochemical property comparisons comprised the primary structure related to amino acid sequence and post-translational modifications including glycans; higher-order structure; primary biological properties mediated by target and receptor binding; product-related substances and impurities; host-cell impurities; general properties of the finished drug product, including strength and formulation; subvisible and submicron particles and aggregates; and forced thermal degradation. ABP 501 had the same amino acid sequence and similar post-translational modification profiles compared with adalimumab RPs. Primary structure, higher-order structure, and biological activities were similar for the three products. Product-related size and charge variants and aggregate and particle levels were also similar. ABP 501 had very low residual host-cell protein and DNA. The finished ABP 501 drug product has the same strength with regard to protein concentration and fill volume as adalimumab RPs. ABP 501 and the RPs had a similar stability profile both in normal storage and thermal stress conditions. Based on the comprehensive analytical similarity assessment, ABP 501 was found to be similar to adalimumab with respect to physicochemical and biological properties.

  11. Contribution of Primordial Binary Evolution to the Two Blue-straggler Sequences in Globular Cluster M30

    NASA Astrophysics Data System (ADS)

    Jiang, Dengkai; Chen, Xuefei; Li, Lifang; Han, Zhanwen

    2017-11-01

    Two blue-straggler sequences discovered in globular cluster M30 provide a strong constraint on the formation mechanisms of blue stragglers. We study the formation of blue-straggler binaries through binary evolution, and find that binary evolution can contribute to the blue stragglers in both of the sequences. Whether a blue-straggler is located in the blue sequence or red sequence depends on the contribution of the mass donor to the total luminosity of the binary, which is generally observed as a single star in globular clusters. The blue stragglers in the blue sequence have a cool white dwarf companion, while the majority (˜60%) of the objects in the red sequence are binaries that are still experiencing mass transfer. However, there are also some objects for which the donors have just finished the mass transfer (the stripped-core stars, ˜10%) or the blue stragglers (the accretors) have evolved away from the blue sequence (˜30%). Meanwhile, W UMa contact binaries found in both sequences may be explained by various mass ratios, that is, W UMa contact binaries in the red sequence have two components with comparable masses (e.g., mass ratio q ˜ 0.3-1.0), while those in the blue sequence have low mass ratios (e.g., q< 0.3). However, the fraction of the blue sequence in M30 cannot be reproduced by binary population synthesis if we assumed the initial parameters of a binary sample to be the same as those of the field. This possibly indicates that dynamical effects on binary systems are very important in globular clusters.

  12. Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis.

    PubMed

    Jakupciak, John P; Wells, Jeffrey M; Karalus, Richard J; Pawlowski, David R; Lin, Jeffrey S; Feldman, Andrew B

    2013-01-01

    Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.

  13. Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis

    PubMed Central

    Jakupciak, John P.; Wells, Jeffrey M.; Karalus, Richard J.; Pawlowski, David R.; Lin, Jeffrey S.; Feldman, Andrew B.

    2013-01-01

    Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations. PMID:24455204

  14. Finishing Techniques for Silicon Nitride Bearings

    DTIC Science & Technology

    1976-03-01

    finishing procedures. Rolling contact fatigue lives of silicon nitride with selected smoother finishes tested at 800 ksi Hertz stress were an order...grinding. Rolling contact fatigue lives of silicon nitride with selected smoother finishes tested at 800 ksi Hertz stress were an order of magnitude...lives of silicon nitride with selected smoother finishes tested at 800 ksi Hertz stress were an order of magnitude longer than those

  15. High-Quality Genome Sequence of the Highly Resistant Bacterium Staphylococcus haemolyticus, Isolated from a Neonatal Bloodstream Infection.

    PubMed

    Hosseinkhani, Farideh; Emaneini, Mohammad; van Leeuwen, Willem

    2017-07-20

    Using Illumina HiSeq and PacBio technologies, we sequenced the genome of the multidrug-resistant bacterium Staphylococcus haemolyticus , originating from a bloodstream infection in a neonate. The sequence data can be used as an accurate reference sequence. Copyright © 2017 Hosseinkhani et al.

  16. Heart rate variability and short duration spaceflight: relationship to post-flight orthostatic intolerance

    PubMed Central

    Blaber, Andrew P; Bondar, Roberta L; Kassam, Mahmood S

    2004-01-01

    Background Upon return from space many astronauts experience symptoms of orthostatic intolerance. Research has implicated altered autonomic cardiovascular regulation due to spaceflight with further evidence to suggest that there might be pre-flight autonomic indicators of post-flight orthostatic intolerance. We used heart rate variability (HRV) to determine whether autonomic regulation of the heart in astronauts who did or did not experience post-flight orthostatic intolerance was different pre-flight and/or was differentially affected by short duration (8 – 16 days) spaceflight. HRV data from ten-minute stand tests collected from the 29 astronauts 10 days pre-flight, on landing day and three days post-flight were analysed using coarse graining spectral analysis. From the total power (PTOT), the harmonic component was extracted and divided into high (PHI: >0.15 Hz) and low (PLO: = 0.15 Hz) frequency power regions. Given the distribution of autonomic nervous system activity with frequency at the sinus node, PHI/PTOT was used as an indicator of parasympathetic activity; PLO/PTOT as an indicator of sympathetic activity; and, PLO/PHI as an estimate of sympathovagal balance. Results Twenty-one astronauts were classified as finishers, and eight as non-finishers, based on their ability to remain standing for 10 minutes on landing day. Pre-flight, non-finishers had a higher supine PHI/PTOT than finishers. Supine PHI/PTOT was the same pre-flight and on landing day in the finishers; whereas, in the non-finishers it was reduced. The ratio PLO/PHI was lower in non-finishers compared to finishers and was unaffected by spaceflight. Pre-flight, both finishers and non-finishers had similar supine values of PLO/PTOT, which increased from supine to stand. Following spaceflight, only the finishers had an increase in PLO/PTOT from supine to stand. Conclusions Both finishers and non-finishers had an increase in sympathetic activity with stand on pre-flight, yet only finishers retained this response on landing day. Non-finishers also had lower sympathovagal balance and higher pre-flight supine parasympathetic activity than finishers. These results suggest pre-flight autonomic status and post-flight impairment in autonomic control of the heart may contribute to orthostatic intolerance. The mechanism by which higher pre-flight parasympathetic activity might contribute to post-flight orthostatic intolerance is not understood and requires further investigation. PMID:15113425

  17. Rapid and accurate pyrosequencing of angiosperm plastid genomes

    PubMed Central

    Moore, Michael J; Dhingra, Amit; Soltis, Pamela S; Shaw, Regina; Farmerie, William G; Folta, Kevin M; Soltis, Douglas E

    2006-01-01

    Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20) System (454 Life Sciences Corporation), to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae) and Platanus occidentalis (Platanaceae). Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy observed in the GS 20 plastid genome sequence was generated for a significant reduction in time and cost over traditional shotgun-based genome sequencing techniques, although with approximately half the coverage of previously reported GS 20 de novo genome sequence. The GS 20 should be broadly applicable to angiosperm plastid genome sequencing, and therefore promises to expand the scale of plant genetic and phylogenetic research dramatically. PMID:16934154

  18. Mind the gap; seven reasons to close fragmented genome assemblies.

    PubMed

    Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

    2016-05-01

    Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow.

    PubMed

    Suryawanshi, Gajendra W; Xu, Song; Xie, Yiming; Chou, Tom; Kim, Namshin; Chen, Irvin S Y; Kim, Sanggu

    2017-06-14

    Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral gene therapy studies, IS assays, in combination with next-generation sequencing, have been used as a cell-tracking tool to characterize clonal stem cell populations sharing the same IS. For the accurate comparison of repopulating stem cell clones within and across different samples, the detection sensitivity, data reproducibility, and high-throughput capacity of the assay are among the most important assay qualities. This work provides a detailed protocol and data analysis workflow for bidirectional IS analysis. The bidirectional assay can simultaneously sequence both upstream and downstream vector-host junctions. Compared to conventional unidirectional IS sequencing approaches, the bidirectional approach significantly improves IS detection rates and the characterization of integration events at both ends of the target DNA. The data analysis pipeline described here accurately identifies and enumerates identical IS sequences through multiple steps of comparison that map IS sequences onto the reference genome and determine sequencing errors. Using an optimized assay procedure, we have recently published the detailed repopulation patterns of thousands of Hematopoietic Stem Cell (HSC) clones following transplant in rhesus macaques, demonstrating for the first time the precise time point of HSC repopulation and the functional heterogeneity of HSCs in the primate system. The following protocol describes the step-by-step experimental procedure and data analysis workflow that accurately identifies and quantifies identical IS sequences.

  20. Best of both worlds : clear exterior finishes : in search of finishes that protect wood without hiding its natural beauty

    Treesearch

    Tom Daniels; Marc Hirsch; Ken McClelland; Alan Ross; Sam Williams

    2000-01-01

    In recent years, a number of clear wood finishes have been developed that protect wood while accentuating its natural beauty. The focus of this publication is on those finishes having little visible pigment. In some cases, the pigments are included but are finely ground to create a coating that is transparent to visible light. Most natural clear wood finishes are...

  1. Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Krishnakumar, Raga; Sinha, Anupama; Bird, Sara W.

    Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed themore » quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.« less

  2. Single Nucleobase Identification Using Biophysical Signatures from Nanoelectronic Quantum Tunneling.

    PubMed

    Korshoj, Lee E; Afsari, Sepideh; Khan, Sajida; Chatterjee, Anushree; Nagpal, Prashant

    2017-03-01

    Nanoelectronic DNA sequencing can provide an important alternative to sequencing-by-synthesis by reducing sample preparation time, cost, and complexity as a high-throughput next-generation technique with accurate single-molecule identification. However, sample noise and signature overlap continue to prevent high-resolution and accurate sequencing results. Probing the molecular orbitals of chemically distinct DNA nucleobases offers a path for facile sequence identification, but molecular entropy (from nucleotide conformations) makes such identification difficult when relying only on the energies of lowest-unoccupied and highest-occupied molecular orbitals (LUMO and HOMO). Here, nine biophysical parameters are developed to better characterize molecular orbitals of individual nucleobases, intended for single-molecule DNA sequencing using quantum tunneling of charges. For this analysis, theoretical models for quantum tunneling are combined with transition voltage spectroscopy to obtain measurable parameters unique to the molecule within an electronic junction. Scanning tunneling spectroscopy is then used to measure these nine biophysical parameters for DNA nucleotides, and a modified machine learning algorithm identified nucleobases. The new parameters significantly improve base calling over merely using LUMO and HOMO frontier orbital energies. Furthermore, high accuracies for identifying DNA nucleobases were observed at different pH conditions. These results have significant implications for developing a robust and accurate high-throughput nanoelectronic DNA sequencing technique. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

    DOE PAGES

    Krishnakumar, Raga; Sinha, Anupama; Bird, Sara W.; ...

    2018-02-16

    Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed themore » quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.« less

  4. POLLUTION PREVENTION IN THE METAL FINISHING INDUSTRY

    EPA Science Inventory

    A broad overview of the metal finishing processes in pollution prevention. The volume of hazardous/toxic waste streams produced from metal finishing operations is significant. It is common for product surfaces to undergo more than 10 finishing steps. The elimination of any of ...

  5. Simulation of Magnetic Field Assisted Finishing (MFAF) Process Utilizing Smart MR Polishing Tool

    NASA Astrophysics Data System (ADS)

    Barman, Anwesa; Das, Manas

    2017-02-01

    Magnetic field assisted finishing process is an advanced finishing process. This process is capable of producing nanometer level surface finish. In this process magnetic field is applied to control the finishing forces using magnetorheological polishing medium. In the current study, permanent magnet is used to provide the required magnetic field in the finishing zone. The working gap between the workpiece and the magnet is filled with MR fluid which is used as the polishing brush to remove surface undulations from the top surface of the workpiece. In this paper, the distribution of magnetic flux density on the workpiece surface and behaviour of MR polishing medium during finishing are analyzed using commercial finite element packages (Ansys Maxwell® and Comsol®). The role of magnetic force in the indentation of abrasive particles on the workpiece surface is studied. A two-dimensional simulation study of the steady, laminar, and incompressible MR fluid flow behaviour during finishing process is carried out. The material removal and surface roughness modelling of the finishing process are also presented. The indentation force by a single active abrasive particle on the workpiece surface is modelled during simulation. The velocity profile of MR fluid with and without application of magnetic field is plotted. It shows non-Newtonian property without application of magnetic field. After that the total material displacement due to one abrasive particle is plotted. The simulated roughness profile is in a good agreement with the experimental results. The conducted study will help in understanding the fluid behavior and the mechanism of finishing during finishing process. Also, the modelling and simulation of the process will help in achieving better finishing performance.

  6. Percent recoveries of anthropogenic organic compounds with and without the addition of ascorbic acid to preserve finished-water samples containing free chlorine, 2004-10

    USGS Publications Warehouse

    Valder, Joshua F.; Delzer, Gregory C.; Bender, David A.; Price, Curtis V.

    2011-01-01

    This report presents finished-water matrix-spike recoveries of 270 anthropogenic organic compounds with and without the addition of ascorbic acid to preserve water samples containing free chlorine. Percent recoveries were calculated using analytical results from a study conducted during 2004-10 for the National Water-Quality Assessment (NAWQA) Program of the U.S. Geological Survey (USGS). The study was intended to characterize the effect of quenching on finished-water matrix-spike recoveries and to better understand the potential oxidation and transformation of 270 anthropogenic organic compounds. The anthropogenic organic compounds studied include those on analytical schedules 1433, 2003, 2033, 2060, 2020, and 4024 of the USGS National Water Quality Laboratory. Three types of samples were collected from 34 NAWQA locations across the Nation: (1) quenched finished-water samples (not spiked), (2) quenched finished-water matrix-spike samples, and (3) nonquenched finished-water matrix-spike samples. Percent recoveries of anthropogenic organic compounds in quenched and nonquenched finished-water matrix-spike samples are presented. Comparisons of percent recoveries between quenched and nonquenched spiked samples can be used to show how quenching affects finished-water samples. A maximum of 18 surface-water and 34 groundwater quenched finished-water matrix-spike samples paired with nonquenched finished-water matrix-spike samples were analyzed. Percent recoveries for the study are presented in two ways: (1) finished-water matrix-spike samples supplied by surface-water or groundwater, and (2) by use (or source) group category for surface-water and groundwater supplies. Graphical representations of percent recoveries for the quenched and nonquenched finished-water matrix-spike samples also are presented.

  7. Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

    USDA-ARS?s Scientific Manuscript database

    We report the development of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal is to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identify unknown entomopathogenic fungi...

  8. Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

    PubMed

    Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter

    2015-01-01

    To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

  9. Genotype x environment interactions for fatty acid profiles in Bos indicus and Bos taurus finished on pasture or grain.

    PubMed

    Bressan, M C; Rossato, L V; Rodrigues, E C; Alves, S P; Bessa, R J B; Ramos, E M; Gama, L T

    2011-01-01

    A study was conducted to characterize lipid profiles in the M. longissimus thoracis of commercial Brazilian beef and to assess how those profiles are influenced by finishing system, genetic group, and their interaction. Intramuscular fat (IMF) and fatty acid (FA) profiles were determined in 160 bulls of the Bos taurus (n = 75) and Bos indicus (n = 85) genetic groups, finished on pasture (n = 46) or with grain supplementation (n = 114) and slaughtered in a commercial abattoir. Finishing system had a major impact on the deposition of IMF, as well as on the concentration of SFA, PUFA, and their ratio, but genetic groups showed important differences in the ability to convert SFA into cis-9 MUFA and to convert 16:0 into 18:0. When compared with pasture-finished animals, those finished with grain had greater content of IMF and SFA (P < 0.01), similar amounts of MUFA (P > 0.05), and about one-half the amount of PUFA (P < 0.01). Except for MUFA, differences in FA profiles among finishing systems were mostly mediated through their effect on IMF, even though the relationship of IMF with groups of FA differed among finishing systems. Under grain finishing, B. taurus had less SFA and greater MUFA than B. indicus (P < 0.01), but no differences were observed in PUFA (P > 0.05). With pasture-finishing, no differences were observed among the 2 genetic groups in SFA and MUFA (P > 0.05), but PUFA were decreased in B. taurus (P < 0.01). When genetic groups were compared in grain-finishing, B. taurus had a decreased ability for elongation and B. indicus had a decreased aptitude for desaturation of FA. On the other hand, with pasture-finishing a greater deposition of intermediate FA from ruminal biohydrogenation was observed in B. indicus than in B. taurus. Overall, FA profiles were affected more by finishing system in B. indicus than in B. taurus.

  10. Effects of delayed finishing/polishing on surface roughness, hardness and gloss of tooth-coloured restorative materials.

    PubMed

    Yazici, A Ruya; Tuncer, Duygu; Antonson, Sibel; Onen, Alev; Kilinc, Evren

    2010-01-01

    The aim of this study was to investigate the effect of delayed finishing/polishing on the surface roughness, hardness and gloss of tooth-coloured restorative materials. Four different tooth-coloured restoratives: a flowable resin composite- Tetric Flow, a hybrid resin composite- Venus, a nanohybrid resin composite- Grandio, and a polyacid modified resin composite- Dyract Extra were used. 30 specimens were made for each material and randomly assigned into three groups. The first group was finished/polished immediately and the second group was finished/polished after 24 hours. The remaining 10 specimens served as control. The surface roughness of each sample was recorded using a laser profilometer. Gloss measurements were performed using a small-area glossmeter. Vickers microhardness measurements were performed from three locations on each specimen surface under 100g load and 10s dwell time. Data for surface roughness and hardness were analyzed by Kruskal Wallis test and data for gloss were subjected to one-way ANOVA and Tukey test (P <.05). The smoothest surfaces were obtained under Mylar strip for all materials. While there were no significant differences in surface roughness of immediate and delayed finished/polished Dyract Extra samples, immediately finished/polished Venus and Grandio samples showed significantly higher roughness than the delayed polished samples (P <.05). In Tetric Flow samples, immediately finishing/polishing provided smoother surface than delayed finishing/polishing (P <.05). The highest gloss values were recorded under Mylar strip for all materials. While delayed finishing/polishing resulted in a significantly higher gloss compared to immediate finishing/polishing in Venus samples (P <.05), no differences were observed between delayed or immediate finishing/polishing for the other materials (P>.05). The lowest hardness values were found under Mylar strip. Delayed finishing/polishing significantly increased the hardness of all materials. The effect of delayed finishing/polishing on surface roughness, gloss and hardness appears to be material dependent.

  11. 27 CFR 19.601 - Finished products records.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Finished products records. (a) Bottling and packaging. A proprietor must maintain daily transaction records and a daily summary record of the kind and quantity of finished products bottled or packaged within... daily records of the disposition of finished products from the processing account at the distilled...

  12. Enantioselective Synthesis of α-Oxy Amides via Umpolung Amide Synthesis

    PubMed Central

    Leighty, Matthew W.; Shen, Bo

    2012-01-01

    α-Oxy amides are prepared through enantioselective synthesis using a sequence beginning with a Henry addition of bromonitromethane to aldehydes, and finishing with Umpolung Amide Synthesis (UmAS). Key to high enantioselection is the finding that ortho-iodo benzoic acid salts of the chiral copper(II) bis(oxazoline) catalyst deliver both diastereomers of the Henry adduct with high enantiomeric excess, homochiral at the oxygen-bearing carbon. Overall, this approach to α-oxy amides provides an innovative complement to alternatives that focus almost entirely on the enantioselective synthesis of α-oxy carboxylic acids. PMID:22967461

  13. Facilitated sequence counting and assembly by template mutagenesis

    PubMed Central

    Levy, Dan; Wigler, Michael

    2014-01-01

    Presently, inferring the long-range structure of the DNA templates is limited by short read lengths. Accurate template counts suffer from distortions occurring during PCR amplification. We explore the utility of introducing random mutations in identical or nearly identical templates to create distinguishable patterns that are inherited during subsequent copying. We simulate the applications of this process under assumptions of error-free sequencing and perfect mapping, using cytosine deamination as a model for mutation. The simulations demonstrate that within readily achievable conditions of nucleotide conversion and sequence coverage, we can accurately count the number of otherwise identical molecules as well as connect variants separated by long spans of identical sequence. We discuss many potential applications, such as transcript profiling, isoform assembly, haplotype phasing, and de novo genome assembly. PMID:25313059

  14. [Comparative analysis of 3D data visibility of the prepared tooth finishing line on a synthetic jaw model, captured by international scanners in a laboratory conditions].

    PubMed

    Ryakhovskiy, A N; Kostyukova, V V

    The aim of the study was to compare accuracy of digital impression's finishing line and the zone under it taken by different intraoral scanning systems. Parameters of comparison were: different level of the finishing line to the gingiva and width of sulcus after retraction. For this purpose two synthetic jaw models with prepared teeth were scanned using intraoral scanning systems: 3D Progress (MHT S.P.A., IT - MHT Optic Research AG, CH); True Definition (3M ESPE, USA); Trios (3Shape A/S, DNK); CEREC AC Bluecam, CEREC Omnicam (Sirona Dental System GmbH, DE); Planscan (Planmeca, FIN) (each n=10). Reference-scanning was done by ATOS Core (GOM mbH, DE). The resulting digital impressions were superimposed with the master-scan. The lowest measured deviations (trueness) for intraoral scanners, where the finishing line was 0.5 mm above gingiva were with scanner True Definition - 18.8±6.63 (on the finishing line) and 51.0±14.33 µm (0.3 mm under the finishing line). In conditions where finishing line was on the same level with gingiva, scanner Trios showed the best results: 17.0±3.96 and 52.7±6.52 µm. When the finishing line was 0.5 mm under gingiva, none of the testing scanners could visualize the zone 0.3 mm lower the finishing line. The best results for accuracy o the finishing line in that circumstances showed Trios: 15.1±5.05 µm. The optimum visualization of the finishing line and the zone under it was reached when the sulcus was 0.3 mm after retraction. Thus, the best accuracy was obtained with Trios: 10.3±2.69 (on the finishing line) and 57.2±13.58 µm (0.3 mm under finishing line). The results show that intraoral scanners also provide enough accuracy for indicating finishing line and the zone under it in different conditions of preparation and gingiva retraction. However, not all of the testing scanners can properly indicate finishing line and the zone under it when shoulder is below gingiva and the width of sulcus is less than 0.2 mm.

  15. Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease.

    PubMed

    Bartram, Jack; Mountjoy, Edward; Brooks, Tony; Hancock, Jeremy; Williamson, Helen; Wright, Gary; Moppett, John; Goulden, Nick; Hubank, Mike

    2016-07-01

    High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. Here we examine the Ig heavy-chain gene HTS on the Illumina MiSeq platform for MRD. We identify errors associated with multiplexing that could potentially impact the accuracy of MRD analysis. We optimize a strategy that combines high-purity, sequence-optimized oligonucleotides, dual indexing, and an error-aware demultiplexing approach to minimize errors and maximize sensitivity. We present a probability-based, demultiplexing pipeline Error-Aware Demultiplexer that is suitable for all MiSeq strategies and accurately assigns samples to the correct identifier without excessive loss of data. Finally, using controls quantified by digital PCR, we show that HTS-MRD can accurately detect as few as 1 in 10(6) copies of specific leukemic MRD. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  16. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)

    PubMed Central

    Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

    2015-01-01

    The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. PMID:25362073

  17. School Building Finishing and Economy. The School Building Economy Series, No. 6.

    ERIC Educational Resources Information Center

    Connecticut State Dept. of Education, Hartford.

    Materials, elements, and methods of economical school construction are illustrated through explanatory outlines and accompany photographs and diagrams. Finishing elements covered include--(1) finished floorings, (2) ceilings and acoustical finishes, (3) carpentry and millwork, (4) chalkboards and tackboards, (5) toilet partitions, (6) finishing…

  18. Surface texture of resin-modified glass ionomer cements: effects of finishing/polishing time.

    PubMed

    Yap, A U J; Ong, S B; Yap, W Y; Tan, W S; Yeo, J C

    2002-01-01

    This study compared the surface texture of resin-modified glass ionomer cements after immediate and delayed finishing with different finishing/polishing systems. Class V preparations were made on the buccal and lingual/palatal surfaces of 64 freshly extracted teeth. The cavities on each tooth were restored with Fuji II LC (GC) and Photac-Fil Quick (3M-ESPE) according to manufacturers' instructions. Immediately after light-polymerization, gross finishing was done with 8-fluted tungsten carbide burs. The teeth were then randomly divided into four groups of 16 teeth. Half of the teeth in each group were finished immediately, while the remaining half were finished after one-week storage in distilled water at 37 degrees C. The following finishing/polishing systems were employed: (a) Robot Carbides; (b) Super-Snap system; (c) OneGloss and (d) CompoSite Polishers. The mean surface roughness (microm; n=8) in vertical (RaV) and horizontal (RaH) axis was measured using a profilometer. Data was subjected to ANOVA/Scheffe's tests and Independent Samples t-test at significance level 0.05. Ra values were generally lower in both vertical and horizontal axis with delayed finishing/polishing. Although significant differences in RaV and RaH values were observed among several systems with immediate finishing/polishing, only one (Fuji II LC: RaH - Super-Snap < Robot Carbides) was observed with delayed finishing.

  19. Asymmetry of Responsiveness in Client-Centered Therapy

    ERIC Educational Resources Information Center

    Shapiro, David A.

    1977-01-01

    Each utterance of a psychotherapy session conducted by Carl Rogers was transcribed on a separate card. Fifteen undergraduate subjects reconstituted client-therapist sequences more accurately than therapist-client sequences. (Author)

  20. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

    PubMed

    Swain, Martin T; Tsai, Isheng J; Assefa, Samual A; Newbold, Chris; Berriman, Matthew; Otto, Thomas D

    2012-06-07

    Genome projects now produce draft assemblies within weeks owing to advanced high-throughput sequencing technologies. For milestone projects such as Escherichia coli or Homo sapiens, teams of scientists were employed to manually curate and finish these genomes to a high standard. Nowadays, this is not feasible for most projects, and the quality of genomes is generally of a much lower standard. This protocol describes software (PAGIT) that is used to improve the quality of draft genomes. It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes (if available) in order to improve scaffolding and generating annotations. The protocol is most accessible for bacterial and small eukaryotic genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms. Applying PAGIT to an E. coli assembly takes ∼24 h: it doubles the average contig size and annotates over 4,300 gene models.

  1. DOE Office of Scientific and Technical Information (OSTI.GOV)

    V.T. Krivoshein; A.V. Makarov

    The sequence of pushing coke ovens is one of the most important aspects of battery operation. The sequence must satisfy a number of technical and process conditions: (1) achieve maximum heating-wall life by avoiding destructive expansion pressure in freshly charged ovens and during pushing of the finished coke; (2) ensure uniform brickwork temperature and prevent overheating by compensating for the high thermal flux in freshly charged ovens due to accumulated heat in adjacent ovens that are in the second half of the coking cycle; (3) ensure the most favorable working conditions and safety for operating personnel; (4) provide additional opportunitiesmore » for repair personnel to perform various types of work, such as replacing coke-machine rails, without interrupting coal production; (5) perform the maximum number of coke-machine operations simultaneously: pushing, charging, and cleaning doors, frames, and standpipe elbows; and (6) reduce electricity consumption by minimizing idle travel of coke machines.« less

  2. The Sequence and Analysis of Duplication Rich Human Chromosome 16

    DOE R&D Accomplishments Database

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-01-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  3. 77 FR 12227 - Long Term 2 Enhanced Surface Water Treatment Rule: Uncovered Finished Water Reservoirs; Public...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-29

    ... Water Treatment Rule: Uncovered Finished Water Reservoirs; Public Meeting AGENCY: Environmental... review of the uncovered finished water reservoir requirement in the Long Term 2 Enhanced Surface Water... uncovered finished water reservoir requirement and the agency's Six Year Review process. EPA also plans to...

  4. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL... POINT SOURCE CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet finish-sides subcategory. The provisions of this subpart are applicable to process wastewater...

  5. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL... CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet finish-sides subcategory. The provisions of this subpart are applicable to process wastewater discharges...

  6. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL... POINT SOURCE CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet finish-sides subcategory. The provisions of this subpart are applicable to process wastewater...

  7. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... retan-wet finish-sides subcategory. 425.40 Section 425.40 Protection of Environment ENVIRONMENTAL... POINT SOURCE CATEGORY Retan-Wet Finish-Sides Subcategory § 425.40 Applicability; description of the retan-wet finish-sides subcategory. The provisions of this subpart are applicable to process wastewater...

  8. Characterization of M40J Desized and Finished Fibers

    NASA Technical Reports Server (NTRS)

    Allred, Ronald E.; Gosau, Jan-M.; Shin, E. Eugene; McCorkle, Linda; O'Malley, Michelle; Sutter, James K.; Wheeler, Don

    1990-01-01

    A viewgraph presentation on desized and finished M40J carbon fibers shown. The topics include: 1) Program Goals and Prior Year Results Summary; 2) Continuous Desizing and Finishing System Development; 3) Characterizzation of Desized and Finished M40J Carbon Fibers and 4) Conclusions and Future Work.

  9. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Finished beer. 25.231... OF THE TREASURY LIQUORS BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  10. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Finished beer. 25.231... OF THE TREASURY ALCOHOL BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  11. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Finished beer. 25.231... OF THE TREASURY LIQUORS BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  12. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Finished beer. 25.231... OF THE TREASURY ALCOHOL BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  13. 76 FR 79221 - Penske Logistics, LLC, Customer Service Department General Motors and Tier Finished Goods...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-21

    ..., Customer Service Department General Motors and Tier Finished Goods/Finished Goods Division; a Subsidiary of... Manpower El Paso, TX; Amended Certification Regarding Eligibility To Apply for Worker Adjustment Assistance... should read Penske Logistics, LLC, Customer Service Department, General Motors and Tier Finished Goods...

  14. DEVELOPING A CAPE-OPEN COMPLIANT METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (CO-MFFP2T)

    EPA Science Inventory

    The USEPA is developing a Computer Aided Process Engineering (CAPE) software tool for the metal finishing industry that helps users design efficient metal finishing processes that are less polluting to the environment. Metal finishing process lines can be simulated and evaluated...

  15. 27 CFR 25.231 - Finished beer.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Finished beer. 25.231... OF THE TREASURY LIQUORS BEER Beer Purchased From Another Brewer § 25.231 Finished beer. (a) A brewer may obtain beer in barrels and kegs, finished and ready for sale from another brewer. The purchasing...

  16. Cost-Effective Sequencing of Full-Length cDNA Clones Powered by a De Novo-Reference Hybrid Assembly

    PubMed Central

    Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka

    2010-01-01

    Background Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. Methodology We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ∼800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. Conclusions The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only ∼US$3 per clone, demonstrating a significant advantage over previous approaches. PMID:20479877

  17. Optical mapping and its potential for large-scale sequencing projects.

    PubMed

    Aston, C; Mishra, B; Schwartz, D C

    1999-07-01

    Physical mapping has been rediscovered as an important component of large-scale sequencing projects. Restriction maps provide landmark sequences at defined intervals, and high-resolution restriction maps can be assembled from ensembles of single molecules by optical means. Such optical maps can be constructed from both large-insert clones and genomic DNA, and are used as a scaffold for accurately aligning sequence contigs generated by shotgun sequencing.

  18. DNA Damage and Oxidative Stress in Dyskeratosis Congenita: Analysis of Pathways and Therapeutic Stategies Using CPISPR and iPSC Model Systems

    DTIC Science & Technology

    2017-06-01

    Milestone Achieved: HRPO/ACURO Approval 6 Finished Major Task 2 CRISPR knockout/RNAseq Viral infection/prep 3-6 CRISPR KO virus library prep...finished; RNA-Seq: ~75% Cell manipulation 3-6 CRISPR KO virus infection: 50%; Single cDNA infections: finished Bioinformatics 1 CRISPR KO library...characterization 1-3 Finished Update: production of iPSC clones harboring DC mutations generated by CRISPR : Design 1 Finished Update: production of

  19. Energy use in pig production: an examination of current Iowa systems.

    PubMed

    Lammers, P J; Kenealy, M D; Kliebenstein, J B; Harmon, J D; Helmers, M J; Honeyman, M S

    2012-03-01

    This paper compares energy use for different pig production systems in Iowa, a leader in US swine production. Pig production systems include not only the growth and performance of the pigs, but also the supporting infrastructure of pig production. This supporting infrastructure includes swine housing, facility management, feedstuff provision, swine diets, and manure management. Six different facility type × diet formulation × cropping sequence scenarios were modeled and compared. The baseline system examined produces 15,600 pigs annually using confinement facilities and a corn-soybean cropping sequence. Diet formulations for the baseline system were corn-soybean meal diets that included the synthetic AA l-lysine and exogenous phytase. The baseline system represents the majority of current US pork production in the Upper Midwest, where most US swine are produced. This system was found to require 744.6 MJ per 136-kg market pig. An alternative system that uses bedded hoop barns for grow-finish pigs and gestating sows would require 3% less (720.8 MJ) energy per 136-kg market pig. When swine production systems were assessed, diet type and feed ingredient processing were the major influences on energy use, accounting for 61 and 79% of total energy in conventional and hoop barn-based systems, respectively. Improving feed efficiency and better matching the diet formulation with the thermal environment and genetic potential are thus key aspects of reducing energy use by pig production, particularly in a hoop barn-based system. The most energy-intensive aspect of provisioning pig feed is the production of synthetic N for crop production; thus, effectively recycling manure nutrients to cropland is another important avenue for future research. Almost 25% of energy use by a conventional farrow-to-finish pig production system is attributable to operation of the swine buildings. Developing strategies to minimize energy use for heating and ventilation of swine buildings while maintaining pig comfort and performance is a third critical area for future research. The hoop barn-based alternative uses 64% less energy to operate buildings but requires bedding and 2.4% more feed. Current Iowa pig production systems use energy differently but result in similar total energy use. Compared with 1975, current farrow-to-finish systems in Iowa require 80% less energy to produce live market pigs.

  20. Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries.

    PubMed

    Lu, Fu-Hao; McKenzie, Neil; Kettleborough, George; Heavens, Darren; Clark, Matthew D; Bevan, Michael W

    2018-05-01

    The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors are important for optimising future sequencing and assembly approaches and for comparative genomics. Here we use a Fosill 38-kb jumping library to assess medium and longer-range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent Bacterial Artificial Chromosome (BAC)-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a 3-fold increase in N50 values. Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient, and cost-effective methods.

  1. Determination of locust bean gum and guar gum by polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Meyer, K; Rosa, C; Hischenhuber, C; Meyer, R

    2001-01-01

    A polymerase chain reaction (PCR) was developed to differentiate the thickening agents locust bean gum (LBG) and the cheaper guar gum in finished food products. Universal primers for amplification of the intergenic spacer region between trnL 3' (UAA) exon and trnF (GAA) gene in the chloroplast (cp) genome and subsequent restriction analysis were applied to differentiate guar gum and LBG. The presence of <5% (w/w) guar gum powder added to LBG powder was detectable. Based on data obtained from sequencing this intergenic spacer region, a second PCR method for the specific detection of guar gum DNA was also developed. This assay detected guar gum powder in LBG in amounts as low as 1% (w/w). Both methods successfully detected guar gum and/or LBG in ice cream stabilizers and in foodstuffs, such as dairy products, ice cream, dry seasoning mixes, a finished roasting sauce, and a fruit jelly product, but not in products with highly degraded DNA, such as tomato ketchup and sterilized chocolate cream. Both methods detected guar gum and LBG in ice cream and fresh cheese at levels <0.1%.

  2. Reconnaissance of Young M Dwarfs: Locating the Elusive Majority of Nearby Moving Groups

    NASA Astrophysics Data System (ADS)

    Bowler, Brendan; Liu, Michael; Riaz, Basmah; Gizis, John; Shkolnik, Evgenya

    2014-02-01

    With ages between ~8-120 Myr and distances ≲80 pc, young moving group members make excellent targets for detailed studies of pre-main sequence evolution and exoplanet imaging surveys. We propose to finish a low-resolution spectroscopic program started in 2013B to confirm our sample of ~1300 X-ray-selected active M dwarfs, about one-third of which are expected to be members of young moving groups. Our larger program consists of three parts: an initial reconnaissance phase of low-resolution spectroscopy to vet unlikely association members, radial velocity observations to confirm group membership, and deep adaptive optics imaging to study the architecture and demographics of giant planets around low-mass stars. Our observations in 2014A will finish the phase of low-resolution spectroscopy covering the second half of the sky. We will also exploit our rich sample to study the evolution of chromospheric and coronal activity in low-mass stars with unprecedented precision. Altogether, this program will roughly double the population of M dwarfs in young moving groups, providing new targets for a broad range of star and planet formation studies in the near-future.

  3. Mycofier: a new machine learning-based classifier for fungal ITS sequences.

    PubMed

    Delgado-Serrano, Luisa; Restrepo, Silvia; Bustos, Jose Ricardo; Zambrano, Maria Mercedes; Anzola, Juan Manuel

    2016-08-11

    The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignment-free classification tool for fungal ITS1 sequences for large environmental surveys. This study describes the development of a machine learning-based classifier for the taxonomical assignment of fungal ITS1 sequences at the genus level. A fungal ITS1 sequence database was built using curated data. Training and test sets were generated from it. A Naïve Bayesian classifier was built using features from the primary sequence with an accuracy of 87 % in the classification at the genus level. The final model was based on a Naïve Bayes algorithm using ITS1 sequences from 510 fungal genera. This classifier, denoted as Mycofier, provides similar classification accuracy compared to BLASTN, but the database used for the classification contains curated data and the tool, independent of alignment, is more efficient and contributes to the field, given the lack of an accurate classification tool for large data from fungal ITS1 sequences. The software and source code for Mycofier are freely available at https://github.com/ldelgado-serrano/mycofier.git .

  4. Estimation Accuracy on Execution Time of Run-Time Tasks in a Heterogeneous Distributed Environment.

    PubMed

    Liu, Qi; Cai, Weidong; Jin, Dandan; Shen, Jian; Fu, Zhangjie; Liu, Xiaodong; Linge, Nigel

    2016-08-30

    Distributed Computing has achieved tremendous development since cloud computing was proposed in 2006, and played a vital role promoting rapid growth of data collecting and analysis models, e.g., Internet of things, Cyber-Physical Systems, Big Data Analytics, etc. Hadoop has become a data convergence platform for sensor networks. As one of the core components, MapReduce facilitates allocating, processing and mining of collected large-scale data, where speculative execution strategies help solve straggler problems. However, there is still no efficient solution for accurate estimation on execution time of run-time tasks, which can affect task allocation and distribution in MapReduce. In this paper, task execution data have been collected and employed for the estimation. A two-phase regression (TPR) method is proposed to predict the finishing time of each task accurately. Detailed data of each task have drawn interests with detailed analysis report being made. According to the results, the prediction accuracy of concurrent tasks' execution time can be improved, in particular for some regular jobs.

  5. 24 CFR 200.946 - Building product standards and certification program for exterior finish and insulation systems...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Glass Fiber Reinforcing Mesh for Use in Exterior Insulation and Finish Systems (EIFS), Class PB. (xv... certification program for exterior finish and insulation systems, use of Materials Bulletin UM 101. 200.946... product standards and certification program for exterior finish and insulation systems, use of Materials...

  6. 24 CFR 200.946 - Building product standards and certification program for exterior finish and insulation systems...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Glass Fiber Reinforcing Mesh for Use in Exterior Insulation and Finish Systems (EIFS), Class PB. (xv... certification program for exterior finish and insulation systems, use of Materials Bulletin UM 101. 200.946... product standards and certification program for exterior finish and insulation systems, use of Materials...

  7. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

    PubMed Central

    2017-01-01

    Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package. PMID:29107980

  8. Provenance of the oil in par-fried French fries after finish frying.

    PubMed

    Al-Khusaibi, Mohammed; Gordon, Michael H; Lovegrove, Julie A; Niranjan, Keshavan

    2012-01-01

    Frozen par-fried French fries are finish-fried either by using the same type of oil used for par frying, or a different type. The nutritive quality of the final oil contained in the product depends on the relative amounts and the fatty acid (FA) composition of the oils used for par frying and finish frying. With the aim of understanding the provenance of the oil in the final product, par-fried French fries-either purchased ready or prepared in the laboratory-were finish fried in oils different from the ones used for par frying. The moisture content, oil content, and FA compositions of the par-fried and finish-fried products were experimentally determined, and the relative amounts of each of the oils present in the final product were calculated using the FAs as markers and undertaking a mass balance on each component FA. The results demonstrate that 89% to 93% of the total oil in the final product originates from the finish-frying step. The study also shows that a significant proportion of the oil absorbed during par frying is expelled from the product during finish frying. Further, the expulsion of par-frying oil was found to occur in the early stages of the finish-frying step. Experiments involving different combinations of par-frying and finish-frying oils showed that the relative proportions of the 2 oils did not depend on the individual fatty acid profiles. This study concludes that any positive health benefits of using an oil having a favorable FA profile for par frying, can potentially be lost, if the oil used for finish frying has a less favorable composition. This paper estimates the relative amounts of oil in French fries that have been fried in 2 stages-a par-frying step and a finish-frying step-which is commonly practiced in food service establishments as well as homes. The 2 key conclusions are: (1) nearly 90% of the oil content of the final product is the one used for finish frying; that is, a processor may use very good oil for par frying but if the oil used for finish frying is inferior, its effect will dominate. (2) The paper also shows that a significant proportion of the oil used by the processor gets expelled during finish frying. © 2011 Institute of Food Technologists®

  9. Implementing targeted region capture sequencing for the clinical detection of Alagille syndrome: An efficient and cost‑effective method.

    PubMed

    Huang, Tianhong; Yang, Guilin; Dang, Xiao; Ao, Feijian; Li, Jiankang; He, Yizhou; Tang, Qiyuan; He, Qing

    2017-11-01

    Alagille syndrome (AGS) is a highly variable, autosomal dominant disease that affects multiple structures including the liver, heart, eyes, bones and face. Targeted region capture sequencing focuses on a panel of known pathogenic genes and provides a rapid, cost‑effective and accurate method for molecular diagnosis. In a Chinese family, this method was used on the proband and Sanger sequencing was applied to validate the candidate mutation. A de novo heterozygous mutation (c.3254_3255insT p.Leu1085PhefsX24) of the jagged 1 gene was identified as the potential disease‑causing gene mutation. In conclusion, the present study suggested that target region capture sequencing is an efficient, reliable and accurate approach for the clinical diagnosis of AGS. Furthermore, these results expand on the understanding of the pathogenesis of AGS.

  10. LLNL Genomic Assessment: Viral and Bacterial Sequencing Needs for TMTI, Tier 1 Report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Slezak, T; Borucki, M; Lenhoff, R

    2009-09-29

    The Lawrence Livermore National Lab Bioinformatics group has recently taken on a role in DTRA's Transformation Medical Technologies Initiative (TMTI). The high-level goal of TMTI is to accelerate the development of broad-spectrum countermeasures. To achieve those goals, TMTI has a near term need to obtain more sequence information across a large range of pathogens, near neighbors, and across a broad geographical and host range. Our role in this project is to research available sequence data for the organisms of interest and identify critical microbial sequence and knowledge gaps that need to be filled to meet TMTI objectives. This effort includes:more » (1) assessing current genomic sequence for each agent including phylogenetic and geographical diversity, host range, date of isolation range, virulence, sequence availability of key near neighbors, and other characteristics; (2) identifying Subject Matter Experts (SME's) and potential holders of isolate collections, contacting appropriate SME's with known expertise and isolate collections to obtain information on isolate availability and specific recommendations; (3) identifying sequence as well as knowledge gaps (eg virulence, host range, and antibiotic resistance determinants); (4) providing specific recommendations as to the most valuable strains to be placed on the DTRA sequencing queue. We acknowledge that criteria for prioritization of isolates for sequencing falls into two categories aligning with priority queues 1 and 2 as described in the summary. (Priority queue 0 relates to DTRA operational isolates whose availability is not predictable in advance.) 1. Selection of isolates that appear to have likelihood to provide information on virulence and antibiotic resistance. This will include sequence of known virulent strains. Particularly valuable would be virulent strains that have genetically similar yet avirulent, or non human transmissible, counterparts that can be used for comparison to help identify key virulence or host range genes. This approach will provide information that can be used by structural biologists to help develop therapeutics and vaccines. We have pointed out such high priority strains of which we are aware, and note that if any such isolates should be discovered, they will rise to the top priority. We anticipate difficulty locating samples with unusual resistance phenotypes, in particular. Sequencing strategies for isolates in queue 1 should aim for as complete finishing status as possible, since high-quality initial annotation (gene-calling) will be necessary for the follow-on protein structure analyses contributing to countermeasure development. Queue 2 for sequencing determination will be more dynamic than queue 1, and samples will be added to it as they become available to the TMTI program. 2. Selection of isolates that will provide broader information about diversity and phylogenetics and aid in specific detection as well as forensics. This approach focuses on sequencing of isolates that will provide better resolution of variants that are (or were) circulating in nature. The finishing strategy for queue 2 does not require complete closing with annotation. This queue is more static, as there is considerable phylogenetic data, and in this report we have sought to reveal gaps and make suggestions to fill them given existing sequence data and strain information. In this report we identify current sequencing gaps in both priority queue categories. Note that this is most applicable to the bacterial pathogens, as most viruses are by default in queue 1. The Phase I focus of this project is on viral hemorrhagic fever viruses and Category A bacterial agents as defined to us by TMTI. We have carried out individual analyses on each species of interest, and these are included as chapters in this report. Viruses and bacteria are biologically very distinct from each other and require different methods of analysis and criteria for sequencing prioritization. Therefore, we will describe our methods, analyses and conclusions separately for each category.« less

  11. A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2.

    PubMed

    Li, Jianli; Dai, Hongzheng; Feng, Yanming; Tang, Jia; Chen, Stella; Tian, Xia; Gorman, Elizabeth; Schmitt, Eric S; Hansen, Terah A A; Wang, Jing; Plon, Sharon E; Zhang, Victor Wei; Wong, Lee-Jun C

    2015-09-01

    Germline mutations in the DNA mismatch repair gene PMS2 underlie the cancer susceptibility syndrome, Lynch syndrome. However, accurate molecular testing of PMS2 is complicated by a large number of highly homologous sequences. To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2. Exonic deletions (E2 to E9, E5 to E9, E8, E10, E14, and E1 to E15), duplications (E11 to E12), and a nonsense mutation, p.S22*, were identified. Traditional multiplex ligation-dependent probe amplification and Sanger sequencing approaches cannot differentiate the origin of the exonic deletions in the 3' region when PMS2 and PMS2CL share identical sequences as a result of gene conversion. Our approach allows unambiguous identification of mutations in the active gene with a straightforward long-range-PCR/NGS method. Breakpoint analysis of multiple samples revealed that recurrent exon 14 deletions are mediated by homologous Alu sequences. Our comprehensive approach provides a reliable tool for accurate molecular analysis of genes containing multiple copies of highly homologous sequences and should improve PMS2 molecular analysis for patients with Lynch syndrome. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  12. The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization.

    PubMed

    Unemo, Magnus; Golparian, Daniel; Sánchez-Busó, Leonor; Grad, Yonatan; Jacobsson, Susanne; Ohnishi, Makoto; Lahra, Monica M; Limnios, Athena; Sikora, Aleksandra E; Wi, Teodora; Harris, Simon R

    2016-11-01

    Gonorrhoea and MDR Neisseria gonorrhoeae remain public health concerns globally. Enhanced, quality-assured, gonococcal antimicrobial resistance (AMR) surveillance is essential worldwide. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) was relaunched in 2009. We describe the phenotypic, genetic and reference genome characteristics of the 2016 WHO gonococcal reference strains intended for quality assurance in the WHO global GASP, other GASPs, diagnostics and research worldwide. The 2016 WHO reference strains (n = 14) constitute the eight 2008 WHO reference strains and six novel strains. The novel strains represent low-level to high-level cephalosporin resistance, high-level azithromycin resistance and a porA mutant. All strains were comprehensively characterized for antibiogram (n = 23), serovar, prolyliminopeptidase, plasmid types, molecular AMR determinants, N. gonorrhoeae multiantigen sequence typing STs and MLST STs. Complete reference genomes were produced using single-molecule PacBio sequencing. The reference strains represented all available phenotypes, susceptible and resistant, to antimicrobials previously and currently used or considered for future use in gonorrhoea treatment. All corresponding resistance genotypes and molecular epidemiological types were described. Fully characterized, annotated and finished references genomes (n = 14) were presented. The 2016 WHO gonococcal reference strains are intended for internal and external quality assurance and quality control in laboratory investigations, particularly in the WHO global GASP and other GASPs, but also in phenotypic (e.g. culture, species determination) and molecular diagnostics, molecular AMR detection, molecular epidemiology and as fully characterized, annotated and finished reference genomes in WGS analysis, transcriptomics, proteomics and other molecular technologies and data analysis. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. A Dual-Mode Large-Arrayed CMOS ISFET Sensor for Accurate and High-Throughput pH Sensing in Biomedical Diagnosis.

    PubMed

    Huang, Xiwei; Yu, Hao; Liu, Xu; Jiang, Yu; Yan, Mei; Wu, Dongping

    2015-09-01

    The existing ISFET-based DNA sequencing detects hydrogen ions released during the polymerization of DNA strands on microbeads, which are scattered into microwell array above the ISFET sensor with unknown distribution. However, false pH detection happens at empty microwells due to crosstalk from neighboring microbeads. In this paper, a dual-mode CMOS ISFET sensor is proposed to have accurate pH detection toward DNA sequencing. Dual-mode sensing, optical and chemical modes, is realized by integrating a CMOS image sensor (CIS) with ISFET pH sensor, and is fabricated in a standard 0.18-μm CIS process. With accurate determination of microbead physical locations with CIS pixel by contact imaging, the dual-mode sensor can correlate local pH for one DNA slice at one location-determined microbead, which can result in improved pH detection accuracy. Moreover, toward a high-throughput DNA sequencing, a correlated-double-sampling readout that supports large array for both modes is deployed to reduce pixel-to-pixel nonuniformity such as threshold voltage mismatch. The proposed CMOS dual-mode sensor is experimentally examined to show a well correlated pH map and optical image for microbeads with a pH sensitivity of 26.2 mV/pH, a fixed pattern noise (FPN) reduction from 4% to 0.3%, and a readout speed of 1200 frames/s. A dual-mode CMOS ISFET sensor with suppressed FPN for accurate large-arrayed pH sensing is proposed and demonstrated with state-of-the-art measured results toward accurate and high-throughput DNA sequencing. The developed dual-mode CMOS ISFET sensor has great potential for future personal genome diagnostics with high accuracy and low cost.

  14. 40 CFR 63.1347 - Standards for raw and finish mills.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 11 2010-07-01 2010-07-01 true Standards for raw and finish mills. 63... and Operating Limits § 63.1347 Standards for raw and finish mills. The owner or operator of each new or existing raw mill or finish mill at a facility which is a major source subject to the provisions...

  15. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 31 2012-07-01 2012-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Pulp, Chrome Tan, Retan-Wet Finish Subcategory § 425.10 Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory. The provisions of this subpart are...

  16. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 31 2013-07-01 2013-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Pulp, Chrome Tan, Retan-Wet Finish Subcategory § 425.10 Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory. The provisions of this subpart are...

  17. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 31 2012-07-01 2012-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Save, Chrome Tan, Retan-Wet Finish Subcategory § 425.20 Applicability; description of the hair save, chrome tan, retan-wet finish subcategory. The provisions of this subpart are...

  18. 40 CFR 425.10 - Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 30 2014-07-01 2014-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Pulp, Chrome Tan, Retan-Wet Finish Subcategory § 425.10 Applicability; description of the hair pulp, chrome tan, retan-wet finishing subcategory. The provisions of this subpart are...

  19. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 30 2014-07-01 2014-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Save, Chrome Tan, Retan-Wet Finish Subcategory § 425.20 Applicability; description of the hair save, chrome tan, retan-wet finish subcategory. The provisions of this subpart are...

  20. 40 CFR 425.20 - Applicability; description of the hair save, chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 31 2013-07-01 2013-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Save, Chrome Tan, Retan-Wet Finish Subcategory § 425.20 Applicability; description of the hair save, chrome tan, retan-wet finish subcategory. The provisions of this subpart are...

  1. Protecting wood decks from biodegradation and weathering : evaluation of deck finish systems

    Treesearch

    J. J. Morrell; P. F. Schneider; R. Sam Williams

    2001-01-01

    Mildew resistance, water repellency, and overall finish appearance were evaluated for 32 deck finishes on western redcedar (Thuja plicata D. Donn.) and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) after 12, 21, and 39 months of outdoor exposure in western Oregon. The finishes were either solvent-borne or waterborne; were ei- ther clear, tinted, or lightly...

  2. Calibrating genomic and allelic coverage bias in single-cell sequencing.

    PubMed

    Zhang, Cheng-Zhong; Adalsteinsson, Viktor A; Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L; Meyerson, Matthew; Love, J Christopher

    2015-04-16

    Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.

  3. Calibrating genomic and allelic coverage bias in single-cell sequencing

    PubMed Central

    Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L.; Meyerson, Matthew; Love, J. Christopher

    2016-01-01

    Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1–10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (~0.1 ×) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples. PMID:25879913

  4. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

    PubMed

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-05-01

    Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  5. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

    PubMed Central

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-01-01

    Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

  6. Structure and Evolution of Chlorate Reduction Composite Transposons

    PubMed Central

    Clark, Iain C.; Melnyk, Ryan A.; Engelbrektson, Anna; Coates, John D.

    2013-01-01

    ABSTRACT The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration. PMID:23919996

  7. Complete genome sequence and analysis of the industrial Saccharomyces cerevisiae strain N85 used in Chinese rice wine production.

    PubMed

    Zhang, Weiping; Li, Yudong; Chen, Yiwang; Xu, Sha; Du, Guocheng; Shi, Huidong; Zhou, Jingwen; Chen, Jian

    2018-02-05

    Chinese rice wine is a popular traditional alcoholic beverage in China, while its brewing processes have rarely been explored. We herein report the first gapless, near-finished genome sequence of the yeast strain Saccharomyces cerevisiae N85 for Chinese rice wine production. Several assembly methods were used to integrate Pacific Bioscience (PacBio) and Illumina sequencing data to achieve high-quality genome sequencing of the strain. The genome encodes more than 6,000 predicted proteins, and 238 long non-coding RNAs, which are validated by RNA-sequencing data. Moreover, our annotation predicts 171 novel genes that are not present in the reference S288c genome. We also identified 65,902 single nucleotide polymorphisms and small indels, many of which are located within genic regions. Dozens of larger copy-number variations and translocations were detected, mainly enriched in the subtelomeres, suggesting these regions may be related to genomic evolution. This study will serve as a milestone in studying of Chinese rice wine and related beverages in China and in other countries. It will help to develop more scientific and modern fermentation processes of Chinese rice wine, and explore metabolism pathways of desired and harmful components in Chinese rice wine to improve its taste and nutritional value. © The Author(s) 2018. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  8. A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD.

    PubMed

    Wilson, Mandy L; Hertzberg, Russell; Adam, Laura; Peccoud, Jean

    2011-01-01

    GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing genetic sequences. GenoCAD provides a graphical interface that allows users to design sequences consistent with formalized design strategies specific to a domain, organization, or project. Design strategies include limited sets of user-defined parts and rules indicating how these parts are to be combined in genetic constructs. In addition to reducing design time to minutes, GenoCAD improves the quality and reliability of the finished sequence by ensuring that the designs follow established rules of sequence construction. GenoCAD.org is a publicly available instance of GenoCAD that can be found at www.genocad.org. The source code and latest build are available from SourceForge to allow advanced users to install and customize GenoCAD for their unique needs. This chapter focuses primarily on how the GenoCAD tools can be used to organize genetic parts into customized personal libraries, then how these libraries can be used to design sequences. In addition, GenoCAD's parts management system and search capabilities are described in detail. Instructions are provided for installing a local instance of GenoCAD on a server. Some of the future enhancements of this rapidly evolving suite of applications are briefly described. Copyright © 2011 Elsevier Inc. All rights reserved.

  9. Abernathy's Lap

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A lap in this instance is not a midriff but a tool for presision.polishing and grinding. During the Saturn V moonbooster program, Marshall Space Flight Center found a need for a better lap. The need arose from the exquisitely precise tolerances required for parts of the launch vehicle's guidance,and control system. So William J. Abernathy, a former Marshall employee, built a better lap; he invented a method for charging aluminum lap plates with diamond powder, then hard-anodizing them. The resulting lap produces a high polish on materials ranging from the softest aluminum to the hardest ceramics. It operates faster, wears longer and requires less reworking. Abernathy got NASA's permission to obtain a personal patent and he formed the one-man Abernathy Laps Co. in Huntsville, which produces a variety of laps. One of Abernathy's customers is Bell Aerospace Textron, Buffalo, which uses the laps to finish polish delicate instrument parts produced for NASA's Viking and other space programs. Says a Bell official: "Time needed (with the Abernathy lap) is a fraction of that required by conventional methods. The result is extremely accurate flatness and surface finish." Abernathy is providing laps for other manufacturing applications and for preparation of metallurgical specimens. The business is small but steady, and Abernathy plans expansion into other markets.

  10. CNC water-jet machining and cutting center

    NASA Astrophysics Data System (ADS)

    Bartlett, D. C.

    1991-09-01

    Computer Numerical Control (CNC) water-jet machining was investigated to determine the potential applications and cost-effectiveness that would result by establishing this capability in the engineering shops of Allied-Signal Inc., Kansas City Division (KCD). Both conductive and nonconductive samples were machined at KCD on conventional machining equipment (a three-axis conversational programmed mill and a wire electrical discharge machine) and on two current-technology water-jet machines at outside vendors. These samples were then inspected, photographed, and evaluated. The current-technology water-jet machines were not as accurate as the conventional equipment. The resolution of the water-jet equipment was only +/- 0.005 inch, as compared to +/- 0.0002 inch for the conventional equipment. The principal use for CNC water-jet machining would be as follows: Contouring to near finished shape those items made from 300 and 400 series stainless steels, titanium, Inconel, aluminum, glass, or any material whose fabrication tolerance is less than the machine resolution of +/- 0.005 inch; and contouring to finished shape those items made from Kevlar, rubber, fiberglass, foam, aluminum, or any material whose fabrication specifications allow the use of a machine with +/- 0.005 inch tolerance. Additional applications are possible because there is minimal force generated on the material being cut and because the water-jet cuts without generating dust.

  11. Design and Feasibility Testing of the truth FinishIt Tobacco Countermarketing Brand Equity Scale.

    PubMed

    Evans, W Douglas; Rath, Jessica; Pitzer, Lindsay; Hair, Elizabeth C; Snider, Jeremy; Cantrell, Jennifer; Vallone, Donna

    2016-07-01

    The original truth campaign was a branded, national smoking prevention mass media effort focused on at-risk youth ages 12-17. Today the truth brand focuses on the goal of finishing tobacco (truth FinishIt). There have been significant changes in the tobacco control landscape, leading FinishIt to focus on 15- to 21-year-olds. The present article reports on formative research and media monitoring data collected to pilot test a new truth FinishIt brand equity scale. The goals of this study were to (a) content analyze truth FinishIt mass media ads, (b) assess truth's social media and followers' perceptions of truth's digital brand identity, and (c) develop and feasibility test a new version of the truth FinishIt brand equity scale using data from an existing Truth Initiative media monitoring study. Through factor analysis, we identified a brand equity scale, as in previous research, consisting of 4 main constructs: brand loyalty, leadership/satisfaction, personality, and awareness. Targeted truth attitudes and beliefs about social perceptions, acceptability, and industry-related beliefs were regressed on the higher order factor and each of the 4 individual brand equity factors. Ordinary least squares regression models generally showed associations in the expected directions (positive for anti-tobacco and negative for pro-tobacco) between targeted attitudes/beliefs and truth FinishIt brand equity. This study succeeded in developing and validating a new truth FinishIt brand equity scale. The scale may be a valuable metric for future campaign evaluation. Future studies should examine the effects of truth FinishIt brand equity on tobacco use behavioral outcomes over time.

  12. Ancestry estimation and control of population stratification for sequence-based association studies.

    PubMed

    Wang, Chaolong; Zhan, Xiaowei; Bragg-Gresham, Jennifer; Kang, Hyun Min; Stambolian, Dwight; Chew, Emily Y; Branham, Kari E; Heckenlively, John; Fulton, Robert; Wilson, Richard K; Mardis, Elaine R; Lin, Xihong; Swaroop, Anand; Zöllner, Sebastian; Abecasis, Gonçalo R

    2014-04-01

    Estimating individual ancestry is important in genetic association studies where population structure leads to false positive signals, although assigning ancestry remains challenging with targeted sequence data. We propose a new method for the accurate estimation of individual genetic ancestry, based on direct analysis of off-target sequence reads, and implement our method in the publicly available LASER software. We validate the method using simulated and empirical data and show that the method can accurately infer worldwide continental ancestry when used with sequencing data sets with whole-genome shotgun coverage as low as 0.001×. For estimates of fine-scale ancestry within Europe, the method performs well with coverage of 0.1×. On an even finer scale, the method improves discrimination between exome-sequenced study participants originating from different provinces within Finland. Finally, we show that our method can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure.

  13. FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

    PubMed

    Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

    2014-06-14

    Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

  14. A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

    PubMed Central

    Eddy, Sean R.

    2008-01-01

    Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (λ) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty (“Forward” scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores (“Viterbi” scores) are Gumbel-distributed with constant λ = log 2, and the high scoring tail of Forward scores is exponential with the same constant λ. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments. PMID:18516236

  15. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

    PubMed

    Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

    2015-02-01

    The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  16. 40 CFR 410.51 - Specialized definitions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Knit Fabric Finishing Subcategory § 410.51 Specialized... the knit fabric finishing subcategory for facilities that are engaged primarily in dyeing or finishing...

  17. 40 CFR 410.51 - Specialized definitions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... STANDARDS TEXTILE MILLS POINT SOURCE CATEGORY Knit Fabric Finishing Subcategory § 410.51 Specialized... the knit fabric finishing subcategory for facilities that are engaged primarily in dyeing or finishing...

  18. Construction of a Dip Tank for Finishing Wood Siding or Decking

    Treesearch

    Mark Knaebe

    2013-01-01

    Dipping new siding or decking pieces before installation is faster than finishing after installation, and it gets finish on the backside and ends of the pieces, thereby extending their service life. This method is appropriate for any penetrating finish, such as waterrepellent preservatives or semitransparent stains. It may also be used to pre-treat siding with water-...

  19. 40 CFR 425.30 - Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 31 2012-07-01 2012-07-01 false Applicability; description of the hair... TANNING AND FINISHING POINT SOURCE CATEGORY Hair Save or Pulp, Non-Chrome Tan, Retan-Wet Finish Subcategory § 425.30 Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish...

  20. 40 CFR 425.30 - Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 30 2014-07-01 2014-07-01 false Applicability; description of the hair... TANNING AND FINISHING POINT SOURCE CATEGORY Hair Save or Pulp, Non-Chrome Tan, Retan-Wet Finish Subcategory § 425.30 Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish...

  1. 40 CFR 425.30 - Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 30 2011-07-01 2011-07-01 false Applicability; description of the hair... FINISHING POINT SOURCE CATEGORY Hair Save or Pulp, Non-Chrome Tan, Retan-Wet Finish Subcategory § 425.30 Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory. The...

  2. 40 CFR 425.30 - Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish subcategory.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 31 2013-07-01 2013-07-01 false Applicability; description of the hair... TANNING AND FINISHING POINT SOURCE CATEGORY Hair Save or Pulp, Non-Chrome Tan, Retan-Wet Finish Subcategory § 425.30 Applicability; description of the hair save or pulp, non-chrome tan, retan-wet finish...

  3. Clear exterior finishes : finding the balance between aesthetics and durability

    Treesearch

    Tom Daniel; Marc S. Hirsch; Ken McClelland; Alan S. Ross; R. Sam Williams

    2004-01-01

    Consumers can easily be confused by the abundance of choices to make when selecting a clear wood finish. There are many types of clear finishes with different characteristics and product claims. This article is designed to help consumers sort out the different finishes and effectively choose which product would be best for their purpose. First, we cover the causes and...

  4. Chronicle of 65 years of wood finishing research at the Forest Products Laboratory

    Treesearch

    Thomas M. Gorman; William C. Feist

    1989-01-01

    For 65 years, the Forest Products Laboratory (FPL) in Madison, Wisconsin, has had a continuous and extensive program of research on finishing wood for outdoor use. The research has stressed the fundamental aspects of wood weathering and the interactions of pretreatments and finishes on wood surfaces. This report outlines the history of the FPL wood finishing research...

  5. Performance evaluation of a dental handpiece in simulation of clinical finishing using a novel 2DOF in vitro apparatus.

    PubMed

    Yin, L; Song, X F; Qu, S F; Huang, T; Mei, J P; Yang, Z Y; Li, J

    2006-11-01

    This paper reports on the performance evaluation of a dental handpiece in simulation of clinical finishing using a novel two-degrees-of-freedom (2DOF) in vitro apparatus. The instrumented apparatus consisted of a two-dimensional computer-controlled coordinate worktable carrying a dental handpiece, a piezoelectric force dynamometer, and a high-speed data acquisition and signal conditioning system for simulating the clinical operations and monitoring the dental finishing processes. The performance of the dental handpiece was experimentally evaluated with respect to rotational speed, torque, and specific finishing energy under the applied clinical finishing conditions. The results show that the rotational speeds of the dental handpiece decreased by increasing either the depth of cut or the feed rate at a constant clinically applied air pressure and water flowrate. They also decreased when increasing both the tangential and normal finishing forces. The specific finishing energy decreased with an increase in either depth of cut or feed rate, while the finishing torque increased as either the depth of cut or the feed rate was increased. Implications of these results were to provide guidance for proper applications of dental handpieces in clinical practice.

  6. Effect of Plasma Surface Finish on Wettability and Mechanical Properties of SAC305 Solder Joints

    NASA Astrophysics Data System (ADS)

    Kim, Kyoung-Ho; Koike, Junichi; Yoon, Jeong-Won; Yoo, Sehoon

    2016-12-01

    The wetting behavior, interfacial reactions, and mechanical reliability of Sn-Ag-Cu solder on a plasma-coated printed circuit board (PCB) substrate were evaluated under multiple heat-treatments. Conventional organic solderability preservative (OSP) finished PCBs were used as a reference. The plasma process created a dense and highly cross-linked polymer coating on the Cu substrates. The plasma finished samples had higher wetting forces and shorter zero-cross times than those with OSP surface finish. The OSP sample was degraded after sequential multiple heat treatments and reflow processes, whereas the solderability of the plasma finished sample was retained after multiple heat treatments. After the soldering process, similar microstructures were observed at the interfaces of the two solder joints, where the development of intermetallic compounds was observed. From ball shear tests, it was found that the shear force for the plasma substrate was consistently higher than that for the OSP substrate. Deterioration of the OSP surface finish was observed after multiple heat treatments. Overall, the plasma surface finish was superior to the conventional OSP finish with respect to wettability and joint reliability, indicating that it is a suitable material for the fabrication of complex electronic devices.

  7. Effects of Wet and Dry Finishing and Polishing on Surface Roughness and Microhardness of Composite Resins

    PubMed Central

    Nasoohi, Negin; Hoorizad, Maryam

    2017-01-01

    Objectives: This study aimed to assess the effect of wet and dry finishing and polishing on microhardness and roughness of microhybrid and nanohybrid composites. Materials and Methods: Thirty samples were fabricated of each of the Polofil Supra and Aelite Aesthetic All-Purpose Body microhybrid and Grandio and Aelite Aesthetic Enamel nanohybrid composite resins. Each group (n=30) was divided into three subgroups of D, W and C (n=10). Finishing and polishing were performed dry in group D and under water coolant in group W. Group C served as the control group and did not receive finishing and polishing. Surface roughness of samples was measured by a profilometer and their hardness was measured by a Vickers hardness tester. Data were analyzed using two-way ANOVA (P<0.05). Results: The smoothest surfaces with the lowest microhardness were obtained under Mylar strip without finishing/polishing for all composites (P<0.0001). The highest surface roughness was recorded for dry finishing/polishing for all composites (P<0.0001). Dry finishing/polishing increased the microhardness of all composites (P<0.0001). Conclusions: Dry finishing and polishing increases the microhardness and surface roughness of microhybrid and nanohybrid composite resins. PMID:29104597

  8. JSC Metal Finishing Waste Minimization Methods

    NASA Technical Reports Server (NTRS)

    Sullivan, Erica

    2003-01-01

    THe paper discusses the following: Johnson Space Center (JSC) has achieved VPP Star status and is ISO 9001 compliant. The Structural Engineering Division in the Engineering Directorate is responsible for operating the metal finishing facility at JSC. The Engineering Directorate is responsible for $71.4 million of space flight hardware design, fabrication and testing. The JSC Metal Finishing Facility processes flight hardware to support the programs in particular schedule and mission critical flight hardware. The JSC Metal Finishing Facility is operated by Rothe Joint Venture. The Facility provides following processes: anodizing, alodining, passivation, and pickling. JSC Metal Finishing Facility completely rebuilt in 1998. Total cost of $366,000. All new tanks, electrical, plumbing, and ventilation installed. Designed to meet modern safety, environmental, and quality requirements. Designed to minimize contamination and provide the highest quality finishes.

  9. Polymerase Spiral Reaction (PSR): A novel isothermal nucleic acid amplification method.

    PubMed

    Liu, Wei; Dong, Derong; Yang, Zhan; Zou, Dayang; Chen, Zeliang; Yuan, Jing; Huang, Liuyu

    2015-07-29

    In this study, we report a novel isothermal nucleic acid amplification method only requires one pair of primers and one enzyme, termed Polymerase Spiral Reaction (PSR) with high specificity, efficiency, and rapidity under isothermal condition. The recombinant plasmid of blaNDM-1 was imported to Escherichia coli BL21, and selected as the microbial target. PSR method employs a Bst DNA polymerase and a pair of primers designed targeting the blaNDM-1 gene sequence. The forward and reverse Tab primer sequences are reverse to each other at their 5' end (Nr and N), whereas their 3' end sequences are complementary to their respective target nucleic acid sequences. The PSR method was performed at a constant temperature 61 °C-65 °C, yielding a complicated spiral structure. PSR assay was monitored continuously in a real-time turbidimeter instrument or visually detected with the aid of a fluorescent dye (SYBR Greenı), and could be finished within 1 h with a high accumulation of 10(9) copies of the target and a fine sensitivity of 6 CFU per reaction. Clinical evaluation was also conducted using PSR, showing high specificity of this method. The PSR technique provides a convenient and cost-effective alternative for clinical screening, on-site diagnosis and primary quarantine purposes.

  10. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701 T) and emended description of the genus Thermanaerovibrio

    DOE PAGES

    Palaniappan, Krishna; Meier-Kolthoff, Jan P.; Teshima, Hazuki; ...

    2013-10-16

    Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of itsmore » morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883 T, the type strain of T. acidaminovorans, stain Z-9701 T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

  11. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701 T) and emended description of the genus Thermanaerovibrio

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Palaniappan, Krishna; Meier-Kolthoff, Jan P.; Teshima, Hazuki

    Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of itsmore » morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883 T, the type strain of T. acidaminovorans, stain Z-9701 T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

  12. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio

    PubMed Central

    Palaniappan, Krishna; Meier-Kolthoff, Jan P.; Teshima, Hazuki; Nolan, Matt; Lapidus, Alla; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Rohde, Manfred; Mayilraj, Shanmugam; Spring, Stefan; Detter, John C.; Göker, Markus; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Woyke, Tanja

    2013-01-01

    Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883T, the type strain of T. acidaminovorans, stain Z-9701T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:24501645

  13. Towards a flat 45%-efficient concentrator module

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mohedano, Rubén, E-mail: rmohedano@lpi-europe.com; Hernandez, Maikel; Vilaplana, Juan

    2015-09-28

    The so-called CCS{sup 4}FK is an ultra-flat photovoltaic system of high concentration and high efficiency, with potential to convert, ideally, the equivalent of a 45% of direct solar radiation into electricity by optimizing the usage of sun spectrum and by collecting part of the diffuse radiation, as a flat plate does. LPI has recently finished a design based on this concept and is now developing a prototype based on this technology, thanks to the support of FUNDACION REPSOL-Fondo de Emprendedores, which promotes entrepreneur projects in different areas linked to energy. This works shows some details of the actual design andmore » preliminary potential performance expected, according to accurate spectral simulations.« less

  14. Towards a flat 45%-efficient concentrator module

    NASA Astrophysics Data System (ADS)

    Mohedano, Rubén; Hernandez, Maikel; Vilaplana, Juan; Chaves, Julio; Miñano, Juan C.; Benitez, Pablo; Sorgato, S.; Falicoff, Waqidi

    2015-09-01

    The so-called CCS4FK is an ultra-flat photovoltaic system of high concentration and high efficiency, with potential to convert, ideally, the equivalent of a 45% of direct solar radiation into electricity by optimizing the usage of sun spectrum and by collecting part of the diffuse radiation, as a flat plate does. LPI has recently finished a design based on this concept and is now developing a prototype based on this technology, thanks to the support of FUNDACION REPSOL-Fondo de Emprendedores, which promotes entrepreneur projects in different areas linked to energy. This works shows some details of the actual design and preliminary potential performance expected, according to accurate spectral simulations.

  15. Genome Sequencing and Analysis of Yersina pestis KIM D27, an Avirulent Strain Exempt from Select Agent Regulation

    PubMed Central

    Losada, Liliana; Varga, John J.; Hostetler, Jessica; Radune, Diana; Kim, Maria; Durkin, Scott; Schneewind, Olaf; Nierman, William C.

    2011-01-01

    Yersinia pestis is the causative agent of the plague. Y. pestis KIM 10+ strain was passaged and selected for loss of the 102 kb pgm locus, resulting in an attenuated strain, KIM D27. In this study, whole genome sequencing was performed on KIM D27 in order to identify any additional differences. Initial assemblies of 454 data were highly fragmented, and various bioinformatic tools detected between 15 and 465 SNPs and INDELs when comparing both strains, the vast majority associated with A or T homopolymer sequences. Consequently, Illumina sequencing was performed to improve the quality of the assembly. Hybrid sequence assemblies were performed and a total of 56 validated SNP/INDELs and 5 repeat differences were identified in the D27 strain relative to published KIM 10+ sequence. However, further analysis showed that 55 of these SNP/INDELs and 3 repeats were errors in the KIM 10+ reference sequence. We conclude that both 454 and Illumina sequencing were required to obtain the most accurate and rapid sequence results for Y. pestis KIMD27. SNP and INDELS calls were most accurate when both Newbler and CLC Genomics Workbench were employed. For purposes of obtaining high quality genome sequence differences between strains, any identified differences should be verified in both the new and reference genomes. PMID:21559501

  16. Genome sequencing and analysis of Yersina pestis KIM D27, an avirulent strain exempt from select agent regulation.

    PubMed

    Losada, Liliana; Varga, John J; Hostetler, Jessica; Radune, Diana; Kim, Maria; Durkin, Scott; Schneewind, Olaf; Nierman, William C

    2011-04-29

    Yersinia pestis is the causative agent of the plague. Y. pestis KIM 10+ strain was passaged and selected for loss of the 102 kb pgm locus, resulting in an attenuated strain, KIM D27. In this study, whole genome sequencing was performed on KIM D27 in order to identify any additional differences. Initial assemblies of 454 data were highly fragmented, and various bioinformatic tools detected between 15 and 465 SNPs and INDELs when comparing both strains, the vast majority associated with A or T homopolymer sequences. Consequently, Illumina sequencing was performed to improve the quality of the assembly. Hybrid sequence assemblies were performed and a total of 56 validated SNP/INDELs and 5 repeat differences were identified in the D27 strain relative to published KIM 10+ sequence. However, further analysis showed that 55 of these SNP/INDELs and 3 repeats were errors in the KIM 10+ reference sequence. We conclude that both 454 and Illumina sequencing were required to obtain the most accurate and rapid sequence results for Y. pestis KIMD27. SNP and INDELS calls were most accurate when both Newbler and CLC Genomics Workbench were employed. For purposes of obtaining high quality genome sequence differences between strains, any identified differences should be verified in both the new and reference genomes.

  17. Application Of Numerical Modelling To Ribbed Wire Rod Dimensions Precision Increase

    NASA Astrophysics Data System (ADS)

    Szota, Piotr; Mróz, Sebastian; Stefanik, Andrzej

    2007-05-01

    The paper presents the results of theoretical and experimental investigations of the process of rolling square ribbed wire rod designed for concrete reinforcement. Numerical modelling of the process of rolling in the finishing and pre-finishing grooves was carried out using the Forge2005® software. In the investigation, particular consideration was given to the analysis of the effect of pre-finished band shape on the formation of ribs on the finished wire rod in the finishing groove. The results of theoretical studies were verified in experimental tests, which were carried out in a wire rolling mill.

  18. Performance, profitability and greenhouse gas emissions of alternative finishing strategies for Holstein-Friesian bulls and steers.

    PubMed

    Murphy, B; Crosson, P; Kelly, A K; Prendiville, R

    2018-02-06

    Modifying finishing strategies within established production systems has the potential to increase beef output and farm profit while reducing greenhouse gas (GHG) emissions. Thus, the objectives of this study were to investigate the effects of finishing duration on animal performance of Holstein-Friesian (HF) bulls and steers and evaluate the profitability and GHG emissions of these finishing strategies. A total of 90 HF calves were assigned to a complete randomised block design; three bull and three steer finishing strategies. Calves were rotationally grazed in a paddock system for the first season at pasture, housed and offered grass silage ad libitum plus 1.5 kg DM of concentrate per head daily for the first winter and returned to pasture for a second season. Bulls were slaughtered at 19 months of age and either finished indoors on concentrates ad libitum for 100 days (19AL), finished at pasture supplemented with 5 kg DM of concentrate per head daily for 100 (19SP) or 150 days (19LP). Steers were slaughtered at 21 months of age and finished at pasture, supplemented with 5 kg DM of concentrate per head daily for 60 (21SP) and 110 days (21LP) or slaughtered at 24 months of age and finished indoors over the second winter on grass silage ad libitum plus 5 kg DM of concentrate per head daily (24MO). The Grange Dairy Beef Systems Model and the Beef Systems Greenhouse Gas Emissions Model were used to evaluate profitability and GHG emissions, respectively. Average daily gain during the finishing period (P<0.001), live weight at slaughter (P<0.01), carcass weight (P<0.05) and fat score (P<0.001) were greater for 19AL than 19SP and 19LP, respectively. Similarly, concentrate dry matter intake was greater for 19AL than 19SP; 19LP was intermediate (P<0.001). Live weight at slaughter (P<0.001), carcass weight (P<0.001), conformation score (P<0.05) and fat score (P<0.001) were greater for 24MO than 21SP and 21LP, respectively. During the finishing period concentrate dry matter intake was greater for 21LP than 21SP with 24MO intermediate; 542, 283 and 436 kg DM, respectively. Although pasture-based finishing strategies had lower gross output values, concentrate feed costs were also reduced thus net margin was greater than indoor finishing strategies. Reducing concentrate input increased GHG emissions for bulls and steers slaughtered at the same age, respectively. Although prolonging the finishing duration reduced GHG emissions for bull and steer production systems, finishing bulls and steers over a longer period at pasture did not enhance animal performance and profit.

  19. Centrifuge: rapid and sensitive classification of metagenomic sequences

    PubMed Central

    Song, Li; Breitwieser, Florian P.

    2016-01-01

    Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space. PMID:27852649

  20. snpAD: An ancient DNA genotype caller.

    PubMed

    Prüfer, Kay

    2018-06-21

    The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling. I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals. The C ++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/. Supplementary data are available at Bioinformatics online.

  1. The effects of finishing diet and postmortem ageing on the eating quality of the M. longissimus thoracis of electrically stimulated Brahman steer carcasses.

    PubMed

    Bruce, H L; Stark, J L; Beilken, S L

    2004-06-01

    Beef from cattle finished on grass will be of similar quality to that from cattle finished on grain when their carcasses are processed using best practice protocols. To test this hypothesis, carcasses of twenty Brahman steers, finished to 400 kg live weight on either Buffel grass pasture (n=10) or grain (n=10), were electrically stimulated with 400 V for 50 s 45 min postmortem, and their beef quality assessed 1 and 14 days postmortem. Hot weight, rump subcutaneous fat thickness and animal rate of growth in the 205 days preceding slaughter were recorded for each carcass as potential influences on beef quality. Quality of the M. longissimus thoracis (LT) at 1 and 14 days postmortem was evaluated using peak Warner-Bratzler shear force, compression, pH, cooking loss and taste panel acceptability, as well as by moisture and crude fat contents measured at 1 day postmortem. Results showed that steers finished on pasture grew the slowest and had the least subcutaneous fat at the same carcass weight. LT from carcasses of steers finished on pasture also had the shortest mean sarcomere lengths, suggesting these muscles may have been cold-affected, but there was no effect of diet on peak shear force. LT from carcasses of steers finished on pasture had the highest mean compression value, possibly because of increased collagen cross-linking associated with slow growth or increased exercise. Ageing significantly decreased LT peak shear force and compression values and increased cooking loss, L (∗), a (∗) and b (∗) values. Taste panellists rated the aged, grass-finished beef the most tender and the best quality; however, the taste panel in this study may have favoured LT from grass-finished steers because it was significantly juicier than LT from the grain-finished steer carcasses. These results indicated that carcass composition and processing conditions interact to exert a greater effect on LT toughness and sensory acceptability than finishing diet. Ageing LT from steers finished on grass improved its colour, and thus may enhance its consumer acceptability.

  2. The topographic development and areal parametric characterization of a stratified surface polished by mass finishing

    NASA Astrophysics Data System (ADS)

    Walton, Karl; Blunt, Liam; Fleming, Leigh

    2015-09-01

    Mass finishing is amongst the most widely used finishing processes in modern manufacturing, in applications from deburring to edge radiusing and polishing. Processing objectives are varied, ranging from the cosmetic to the functionally critical. One such critical application is the hydraulically smooth polishing of aero engine component gas-washed surfaces. In this, and many other applications the drive to improve process control and finish tolerance is ever present. Considering its widespread use mass finishing has seen limited research activity, particularly with respect to surface characterization. The objectives of the current paper are to; characterise the mass finished stratified surface and its development process using areal surface parameters, provide guidance on the optimal parameters and sampling method to characterise this surface type for a given application, and detail the spatial variation in surface topography due to coupon edge shadowing. Blasted and peened square plate coupons in titanium alloy are wet (vibro) mass finished iteratively with increasing duration. Measurement fields are precisely relocated between iterations by fixturing and an image superimposition alignment technique. Surface topography development is detailed with ‘log of process duration’ plots of the ‘areal parameters for scale-limited stratified functional surfaces’, (the Sk family). Characteristic features of the Smr2 plot are seen to map out the processing of peak, core and dale regions in turn. These surface process regions also become apparent in the ‘log of process duration’ plot for Sq, where lower core and dale regions are well modelled by logarithmic functions. Surface finish (Ra or Sa) with mass finishing duration is currently predicted with an exponential model. This model is shown to be limited for the current surface type at a critical range of surface finishes. Statistical analysis provides a group of areal parameters including; Vvc, Sq, and Sdq, showing optimal discrimination for a specific range of surface finish outcomes. As a consequence of edge shadowing surface segregation is suggested for characterization purposes.

  3. 40 CFR 463.30 - Applicability; description of the finishing water subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS PLASTICS MOLDING AND FORMING POINT SOURCE CATEGORY Finishing... the finishing water subcategory are processes where water comes in contact with the plastic product...

  4. 40 CFR 463.30 - Applicability; description of the finishing water subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS PLASTICS MOLDING AND FORMING POINT SOURCE CATEGORY Finishing... the finishing water subcategory are processes where water comes in contact with the plastic product...

  5. SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

    PubMed

    Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

    2008-05-01

    Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods.

  6. SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

    PubMed Central

    Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

    2008-01-01

    Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods. PMID:18452616

  7. 40 CFR 425.90 - Applicability; description of the retan-wet finish-splits subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT SOURCE... resulting from any tannery which processes previously unhaired and tanned splits into finished leather by...

  8. Pattern Recognition-Assisted Infrared Library Searching of the Paint Data Query Database to Enhance Lead Information from Automotive Paint Trace Evidence.

    PubMed

    Lavine, Barry K; White, Collin G; Allen, Matthew D; Weakley, Andrew

    2017-03-01

    Multilayered automotive paint fragments, which are one of the most complex materials encountered in the forensic science laboratory, provide crucial links in criminal investigations and prosecutions. To determine the origin of these paint fragments, forensic automotive paint examiners have turned to the paint data query (PDQ) database, which allows the forensic examiner to compare the layer sequence and color, texture, and composition of the sample to paint systems of the original equipment manufacturer (OEM). However, modern automotive paints have a thin color coat and this layer on a microscopic fragment is often too thin to obtain accurate chemical and topcoat color information. A search engine has been developed for the infrared (IR) spectral libraries of the PDQ database in an effort to improve discrimination capability and permit quantification of discrimination power for OEM automotive paint comparisons. The similarity of IR spectra of the corresponding layers of various records for original finishes in the PDQ database often results in poor discrimination using commercial library search algorithms. A pattern recognition approach employing pre-filters and a cross-correlation library search algorithm that performs both a forward and backward search has been used to significantly improve the discrimination of IR spectra in the PDQ database and thus improve the accuracy of the search. This improvement permits inter-comparison of OEM automotive paint layer systems using the IR spectra alone. Such information can serve to quantify the discrimination power of the original automotive paint encountered in casework and further efforts to succinctly communicate trace evidence to the courts.

  9. BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences

    PubMed Central

    Gao, Jianzhao; Faraggi, Eshel; Zhou, Yaoqi; Ruan, Jishou; Kurgan, Lukasz

    2012-01-01

    Accurate identification of immunogenic regions in a given antigen chain is a difficult and actively pursued problem. Although accurate predictors for T-cell epitopes are already in place, the prediction of the B-cell epitopes requires further research. We overview the available approaches for the prediction of B-cell epitopes and propose a novel and accurate sequence-based solution. Our BEST (B-cell Epitope prediction using Support vector machine Tool) method predicts epitopes from antigen sequences, in contrast to some method that predict only from short sequence fragments, using a new architecture based on averaging selected scores generated from sliding 20-mers by a Support Vector Machine (SVM). The SVM predictor utilizes a comprehensive and custom designed set of inputs generated by combining information derived from the chain, sequence conservation, similarity to known (training) epitopes, and predicted secondary structure and relative solvent accessibility. Empirical evaluation on benchmark datasets demonstrates that BEST outperforms several modern sequence-based B-cell epitope predictors including ABCPred, method by Chen et al. (2007), BCPred, COBEpro, BayesB, and CBTOPE, when considering the predictions from antigen chains and from the chain fragments. Our method obtains a cross-validated area under the receiver operating characteristic curve (AUC) for the fragment-based prediction at 0.81 and 0.85, depending on the dataset. The AUCs of BEST on the benchmark sets of full antigen chains equal 0.57 and 0.6, which is significantly and slightly better than the next best method we tested. We also present case studies to contrast the propensity profiles generated by BEST and several other methods. PMID:22761950

  10. DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

    PubMed Central

    Little, Damon P.

    2011-01-01

    For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple–sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple–sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are unable to accurately differentiate between highly similar sequences and are not designed to cope with hierarchic phylogenetic relationships or within taxon variability. Here, I present a novel alignment–free sequence identification algorithm–BRONX–that accounts for observed within taxon variability and hierarchic relationships among taxa. BRONX identifies short variable segments and corresponding invariant flanking regions in reference sequences. These flanking regions are used to score variable regions in the query sequence without the production of a global multiple–sequence alignment. By incorporating observed within taxon variability into the scoring procedure, misidentifications arising from shared alleles/haplotypes are minimized. An explicit treatment of more inclusive terminals allows for separate identifications to be made for each taxonomic level and/or for user–defined terminals. BRONX performs better than all other methods when there is imperfect overlap between query and reference sequences (e.g. mini–barcode queries against a full–length barcode database). BRONX consistently produced better identifications at the genus–level for all query types. PMID:21857897

  11. Effect of Blade-surface Finish on Performance of a Single-stage Axial-flow Compressor

    NASA Technical Reports Server (NTRS)

    Moses, Jason J; Serovy, George, K

    1951-01-01

    A set of modified NACA 5509-34 rotor and stator blades was investigated with rough-machine, hand-filed, and highly polished surface finishes over a range of weight flows at six equivalent tip speeds from 672 to 1092 feet per second to determine the effect of blade-surface finish on the performance of a single-stage axial-flow compressor. Surface-finish effects decreased with increasing compressor speed and with decreasing flow at a given speed. In general, finishing blade surfaces below the roughness that may be considered aerodynamically smooth on the basis of an admissible-roughness formula will have no effect on compressor performance.

  12. The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

    PubMed Central

    Kann, Maricel G.; Sheetlin, Sergey L.; Park, Yonil; Bryant, Stephen H.; Spouge, John L.

    2007-01-01

    The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a ‘semi-global alignment’. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristic acceleration and accurate E-values. Our new tool, GLOBAL, overcomes some limitations of previous semi-global HMMs: it has accurate E-values and the possibility of the heuristic acceleration required for high-throughput applications. Moreover, according to a standard of truth based on protein structure, two semi-global HMM alignment tools (GLOBAL and HMMer) had comparable performance in identifying complete domains, but distinctly outperformed two tools based on local alignment. When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance. PMID:17596268

  13. CANVAS FINISH TO REMOVE FLOAT MARKS. View is to the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    CANVAS FINISH TO REMOVE FLOAT MARKS. View is to the northwest of deck finishing operations - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

  14. 40 CFR 425.40 - Applicability; description of the retan-wet finish-sides subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT SOURCE... resulting from any tannery which processes previously tanned hides and skins (grain side only) into finished...

  15. FINISHED CASTINGS ARE ONLY GROUND BEFORE THEY ARE SHIPPED TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FINISHED CASTINGS ARE ONLY GROUND BEFORE THEY ARE SHIPPED TO CUSTOMERS WHO COMPLETE THE FINISHING IN THEIR OWN MACHINE SHOPS. - Southern Ductile Casting Company, Grinding & Shipping, 2217 Carolina Avenue, Bessemer, Jefferson County, AL

  16. Heterosis for meat quality and fatty acid profiles in crosses among Bos indicus and Bos taurus finished on pasture or grain.

    PubMed

    Gama, L T; Bressan, M C; Rodrigues, E C; Rossato, L V; Moreira, O C; Alves, S P; Bessa, R J B

    2013-01-01

    Physicochemical properties and fatty acid profiles of meat from Bos indicus, Bos taurus and crossbred B. taurus×B. indicus bullocks (n=216), finished on pasture or grain, were used to estimate the effects of heterosis. Meat quality and fatty acid profiles generally benefited with crossbreeding, but the advantages from heterosis differed among finishing systems. The Warner-Bratzler shear-force in fresh and aged meat was reduced due to heterosis in pasture-finishing, but the effect was minor under grain-finishing. With pasture-finishing, heterosis caused an increase of 5% in CLA concentration, but few other changes in fatty acid profiles. In grain-finishing, heterosis caused a reduction in intramuscular fat and cholesterol, increased amounts of PUFA, n-6 fatty acids and PUFA/SFA ratio, and a decline in atherogenic index. The Δ(9) desaturase estimated activity in crossbreds showed a behavior close to B. indicus, suggesting the existence of few loci and a dominance genetic effect on enzymes involved in fatty acid synthesis and metabolism. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

    PubMed Central

    Burger, Lukas; van Nimwegen, Erik

    2008-01-01

    Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

  18. CpG PatternFinder: a Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA.

    PubMed

    Xu, Yi-Hua; Manoharan, Herbert T; Pitot, Henry C

    2007-09-01

    The bisulfite genomic sequencing technique is one of the most widely used techniques to study sequence-specific DNA methylation because of its unambiguous ability to reveal DNA methylation status to the order of a single nucleotide. One characteristic feature of the bisulfite genomic sequencing technique is that a number of sample sequence files will be produced from a single DNA sample. The PCR products of bisulfite-treated DNA samples cannot be sequenced directly because they are heterogeneous in nature; therefore they should be cloned into suitable plasmids and then sequenced. This procedure generates an enormous number of sample DNA sequence files as well as adding extra bases belonging to the plasmids to the sequence, which will cause problems in the final sequence comparison. Finding the methylation status for each CpG in each sample sequence is not an easy job. As a result CpG PatternFinder was developed for this purpose. The main functions of the CpG PatternFinder are: (i) to analyze the reference sequence to obtain CpG and non-CpG-C residue position information. (ii) To tailor sample sequence files (delete insertions and mark deletions from the sample sequence files) based on a configuration of ClustalW multiple alignment. (iii) To align sample sequence files with a reference file to obtain bisulfite conversion efficiency and CpG methylation status. And, (iv) to produce graphics, highlighted aligned sequence text and a summary report which can be easily exported to Microsoft Office suite. CpG PatternFinder is designed to operate cooperatively with BioEdit, a freeware on the internet. It can handle up to 100 files of sample DNA sequences simultaneously, and the total CpG pattern analysis process can be finished in minutes. CpG PatternFinder is an ideal software tool for DNA methylation studies to determine the differential methylation pattern in a large number of individuals in a population. Previously we developed the CpG Analyzer program; CpG PatternFinder is our further effort to create software tools for DNA methylation studies.

  19. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.

    PubMed

    Moghaddam, Samira Mafi; Song, Qijian; Mamidi, Sujan; Schmutz, Jeremy; Lee, Rian; Cregan, Perry; Osorno, Juan M; McClean, Phillip E

    2014-01-01

    Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6× to 5.1× coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate.

  20. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

    PubMed

    Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

  1. MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

    PubMed Central

    Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

  2. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.

    PubMed Central

    Moghaddam, Samira Mafi; Song, Qijian; Mamidi, Sujan; Schmutz, Jeremy; Lee, Rian; Cregan, Perry; Osorno, Juan M.; McClean, Phillip E.

    2013-01-01

    Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6× to 5.1× coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate. PMID:24860578

  3. Impacts of visuomotor sequence learning methods on speed and accuracy: Starting over from the beginning or from the point of error.

    PubMed

    Tanaka, Kanji; Watanabe, Katsumi

    2016-02-01

    The present study examined whether sequence learning led to more accurate and shorter performance time if people who are learning a sequence start over from the beginning when they make an error (i.e., practice the whole sequence) or only from the point of error (i.e., practice a part of the sequence). We used a visuomotor sequence learning paradigm with a trial-and-error procedure. In Experiment 1, we found fewer errors, and shorter performance time for those who restarted their performance from the beginning of the sequence as compared to those who restarted from the point at which an error occurred, indicating better learning of spatial and motor representations of the sequence. This might be because the learned elements were repeated when the next performance started over from the beginning. In subsequent experiments, we increased the occasions for the repetitions of learned elements by modulating the number of fresh start points in the sequence after errors. The results showed that fewer fresh start points were likely to lead to fewer errors and shorter performance time, indicating that the repetitions of learned elements enabled participants to develop stronger spatial and motor representations of the sequence. Thus, a single or two fresh start points in the sequence (i.e., starting over only from the beginning or from the beginning or midpoint of the sequence after errors) is likely to lead to more accurate and faster performance. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. CAPSULE REPORT - MANAGING CYANIDE IN METAL FINISHING

    EPA Science Inventory

    The purpose of this document is to provide guidance to surface finishing manufacturers, metal finishing decision maker and regulators on management practices and control technologies for managing cyanide in the workplace. This information can benefit key industry stakeholder gro...

  5. 40 CFR 425.50 - Applicability; description of the no beamhouse subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS LEATHER TANNING AND FINISHING POINT SOURCE CATEGORY No... cattle hides, sheepskins, or splits (hair previously removed and pickled) into finished leather by chrome or non-chrome tanning, and retan-wet finishing. ...

  6. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

    PubMed Central

    Lai, Zhongwu; Markovets, Aleksandra; Ahdesmaki, Miika; Chapman, Brad; Hofmann, Oliver; McEwen, Robert; Johnson, Justin; Dougherty, Brian; Barrett, J. Carl; Dry, Jonathan R.

    2016-01-01

    Abstract Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood. In addition, VarDict performs amplicon aware variant calling for polymerase chain reaction (PCR)-based targeted sequencing often used in diagnostic settings, and is able to detect PCR artifacts. Finally, VarDict also detects differences in somatic and loss of heterozygosity variants between paired samples. VarDict reprocessing of The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma dataset called known driver mutations in KRAS, EGFR, BRAF, PIK3CA and MET in 16% more patients than previously published variant calls. We believe VarDict will greatly facilitate application of NGS in clinical cancer research. PMID:27060149

  7. Video Image Stabilization and Registration

    NASA Technical Reports Server (NTRS)

    Hathaway, David H. (Inventor); Meyer, Paul J. (Inventor)

    2002-01-01

    A method of stabilizing and registering a video image in multiple video fields of a video sequence provides accurate determination of the image change in magnification, rotation and translation between video fields, so that the video fields may be accurately corrected for these changes in the image in the video sequence. In a described embodiment, a key area of a key video field is selected which contains an image which it is desired to stabilize in a video sequence. The key area is subdivided into nested pixel blocks and the translation of each of the pixel blocks from the key video field to a new video field is determined as a precursor to determining change in magnification, rotation and translation of the image from the key video field to the new video field.

  8. Video Image Stabilization and Registration

    NASA Technical Reports Server (NTRS)

    Hathaway, David H. (Inventor); Meyer, Paul J. (Inventor)

    2003-01-01

    A method of stabilizing and registering a video image in multiple video fields of a video sequence provides accurate determination of the image change in magnification, rotation and translation between video fields, so that the video fields may be accurately corrected for these changes in the image in the video sequence. In a described embodiment, a key area of a key video field is selected which contains an image which it is desired to stabilize in a video sequence. The key area is subdivided into nested pixel blocks and the translation of each of the pixel blocks from the key video field to a new video field is determined as a precursor to determining change in magnification, rotation and translation of the image from the key video field to the new video field.

  9. Protein Structure Determination using Metagenome sequence data

    PubMed Central

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

    2017-01-01

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families, and that metagenome sequence data more than triples the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact based structure matching and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the PDB. This approach provides the representative models for large protein families originally envisioned as the goal of the protein structure initiative at a fraction of the cost. PMID:28104891

  10. [Experimental analysis of finishing lines in ceramometal restorations].

    PubMed

    Gascón, F; Gil, J A; Fons, A; Badal, R

    1990-11-01

    The preparation is the first step of any tooth reconstruction. The biological integration of the protesis is depending on the marginal adaptation (finish line of the preparation), occlusal adaptation (occlusal reduction), longevity of the restoration (retention and luting) and esthetics. The effect the two finish line of the preparation is studied using experimental design. In porcelain-fused-to-metal the finish line of the preparation in chanfer is superior at the beveled shoulder, because proportioning better marginal adaptation.

  11. Comparative evaluation of different thermally modified wood samples finishing with UV-curable and waterborne coatings

    NASA Astrophysics Data System (ADS)

    Herrera, René; Muszyńska, Monika; Krystofiak, Tomasz; Labidi, Jalel

    2015-12-01

    Thermally modified wood has been developed as an industrial method to improve durability and dimensional stability of wood and thus extends the range of uses and service life of wood-based products. Despite the improvements gained by treatment, surface finishing using coatings prevents esthetical changes such as color degradation or occasional growth of mold adding protection in outdoor use and extending the service life of products. The wood finishing process was carried out with commercially available waterborne and UV-curable coatings on industrially modified at 192, 200, 212 °C and unmodified European ash (Fraxinus excelsior L.) wood, using an industrial rollers system and a laboratory brushing system. Changes caused by thermal treatment which could affect the surface finish were measured and compared with control samples, such as water uptake, wettability and acidity. Following the wood finishing, surface properties and esthetic changes were evaluated; as well as the coatings performance. Thermally modified wood presented improved adherence compared with unmodified wood with a significant improvement in samples modified at 212 °C, which also present the highest hardness when UV-cured. Finishes with UV-curing maintain the hydrophobic effect of thermally modified wood, whereas waterborne finishes increase the surface wettability. Thermal modification did not negatively influence on the elastic properties of the coated substrate and thus allows this material to be finished with different coating systems in the same conditions as unmodified wood.

  12. Comparison of gene expression and fatty acid profiles in concentrate and forage finished beef.

    PubMed

    Buchanan, J W; Garmyn, A J; Hilton, G G; VanOverbeke, D L; Duan, Q; Beitz, D C; Mateescu, R G

    2013-01-01

    Fatty acid profiles and intramuscular expression of genes involved in fatty acid metabolism were characterized in concentrate- (CO) and forage- (FO) based finishing systems. Intramuscular samples from the adductor were taken at slaughter from 99 heifers finished on a CO diet and 58 heifers finished on a FO diet. Strip loins were obtained at fabrication to evaluate fatty acid profiles of LM muscle for all 157 heifers by using gas chromatography fatty acid methyl ester analysis. Composition was analyzed for differences by using the General Linear Model (GLM) procedure in SAS. Differences in fatty acid profile included a greater atherogenic index, greater percentage total MUFA, decreased omega-3 to omega-6 ratio, decreased percentage total PUFA, and decreased percentage omega-3 fatty acids in CO- compared with FO-finished heifers (P<0.05). Fatty acid profiles from intramuscular samples were ranked by the atherogenic index, and 20 heifers with either a high (HAI; n=10) or low (LAI; n=10) atherogenic index were selected for gene expression analysis using real-time PCR (RT-PCR). Gene expression data for the 20 individuals were analyzed as a 2 by 2 factorial arrangement of treatments using the GLM procedure in SAS. There was no significant diet × atherogenic index interaction identified for any gene (P>0.05). Upregulation was observed for PPARγ, fatty acid synthase (FASN), and fatty acid binding protein 4 (FABP4) in FO-finished compared with CO-finished heifers in both atherogenic index categories (P<0.05). Upregulation of diglyceride acyl transferase 2 (DGAT2) was observed in FO-finished heifers with a HAI (P<0.05). Expression of steroyl Co-A desaturase (SCD) was upregulated in CO-finished heifers with a LAI, and downregulated in FO-finished heifers with a HAI (P<0.05). Expression of adiponectin (ADIPOQ) was significantly downregulated in CO-finished heifers with a HAI compared with all other categories (P<0.05). The genes identified in this study which exhibit differential regulation in response to diet or in animals with extreme fatty acid profiles may provide genetic markers for selecting desirable fatty acid profiles in future selection programs.

  13. Evolutionary distances in the twilight zone--a rational kernel approach.

    PubMed

    Schwarz, Roland F; Fletcher, William; Förster, Frank; Merget, Benjamin; Wolf, Matthias; Schultz, Jörg; Markowetz, Florian

    2010-12-31

    Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.

  14. Screening, Isolation and Identification of Probiotic Producing Lactobacillus acidophilus Strains EMBS081 & EMBS082 by 16S rRNA Gene Sequencing.

    PubMed

    Chandok, Harshpreet; Shah, Pratik; Akare, Uday Raj; Hindala, Maliram; Bhadoriya, Sneha Singh; Ravi, G V; Sharma, Varsha; Bandaru, Srinivas; Rathore, Pragya; Nayarisseri, Anuraj

    2015-09-01

    16S rDNA sequencing which has gained wide popularity amongst microbiologists for the molecular characterization and identification of newly discovered isolates provides accurate identification of isolates down to the level of sub-species (strain). Its most important advantage over the traditional biochemical characterization methods is that it can provide an accurate identification of strains with atypical phenotypic characters as well. The following work is an application of 16S rRNA gene sequencing approach to identify a novel species of Probiotic Lactobacillus acidophilus. The sample was collected from pond water samples of rural and urban areas of Krishna district, Vijayawada, Andhra Pradesh, India. Subsequently, the sample was serially diluted and the aliquots were incubated for a suitable time period following which the suspected colony was subjected to 16S rDNA sequencing. The sequence aligned against other species was concluded to be a novel, Probiotic L. acidophilus bacteria, further which were named L. acidophilus strain EMBS081 & EMBS082. After the sequence characterization, the isolate was deposited in GenBank Database, maintained by the National Centre for Biotechnology Information NCBI. The sequence can also be retrieve from EMBL and DDBJ repositories with accession numbers JX255677 and KC150145.

  15. DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.

    PubMed

    Castle, John C; Biery, Matthew; Bouzek, Heather; Xie, Tao; Chen, Ronghua; Misura, Kira; Jackson, Stuart; Armour, Christopher D; Johnson, Jason M; Rohl, Carol A; Raymond, Christopher K

    2010-04-16

    DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.

  16. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

    PubMed Central

    Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.; Chain, Patrick S. G.

    2015-01-01

    A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools. PMID:25765641

  17. Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism

    PubMed Central

    Jeanne, Nicolas; Saliou, Adrien; Carcenac, Romain; Lefebvre, Caroline; Dubois, Martine; Cazabat, Michelle; Nicot, Florence; Loiseau, Claire; Raymond, Stéphanie; Izopet, Jacques; Delobel, Pierre

    2015-01-01

    HIV-1 coreceptor usage must be accurately determined before starting CCR5 antagonist-based treatment as the presence of undetected minor CXCR4-using variants can cause subsequent virological failure. Ultra-deep pyrosequencing of HIV-1 V3 env allows to detect low levels of CXCR4-using variants that current genotypic approaches miss. However, the computation of the mass of sequence data and the need to identify true minor variants while excluding artifactual sequences generated during amplification and ultra-deep pyrosequencing is rate-limiting. Arbitrary fixed cut-offs below which minor variants are discarded are currently used but the errors generated during ultra-deep pyrosequencing are sequence-dependant rather than random. We have developed an automated processing of HIV-1 V3 env ultra-deep pyrosequencing data that uses biological filters to discard artifactual or non-functional V3 sequences followed by statistical filters to determine position-specific sensitivity thresholds, rather than arbitrary fixed cut-offs. It allows to retain authentic sequences with point mutations at V3 positions of interest and discard artifactual ones with accurate sensitivity thresholds. PMID:26585833

  18. Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism.

    PubMed

    Jeanne, Nicolas; Saliou, Adrien; Carcenac, Romain; Lefebvre, Caroline; Dubois, Martine; Cazabat, Michelle; Nicot, Florence; Loiseau, Claire; Raymond, Stéphanie; Izopet, Jacques; Delobel, Pierre

    2015-11-20

    HIV-1 coreceptor usage must be accurately determined before starting CCR5 antagonist-based treatment as the presence of undetected minor CXCR4-using variants can cause subsequent virological failure. Ultra-deep pyrosequencing of HIV-1 V3 env allows to detect low levels of CXCR4-using variants that current genotypic approaches miss. However, the computation of the mass of sequence data and the need to identify true minor variants while excluding artifactual sequences generated during amplification and ultra-deep pyrosequencing is rate-limiting. Arbitrary fixed cut-offs below which minor variants are discarded are currently used but the errors generated during ultra-deep pyrosequencing are sequence-dependant rather than random. We have developed an automated processing of HIV-1 V3 env ultra-deep pyrosequencing data that uses biological filters to discard artifactual or non-functional V3 sequences followed by statistical filters to determine position-specific sensitivity thresholds, rather than arbitrary fixed cut-offs. It allows to retain authentic sequences with point mutations at V3 positions of interest and discard artifactual ones with accurate sensitivity thresholds.

  19. DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing

    PubMed Central

    2010-01-01

    Background DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. Results We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. Conclusion The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads. PMID:20398377

  20. METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFPPT)

    EPA Science Inventory

    The Metal Finishing Facility Pollution Tool (MFFPPT) is being developed to allow the metal finishing industry an easy method to evaluate potential pollution prevention options. In order to reduce the quantity of pollutants generated by a process, the sources of pollutants within ...

  1. Pharmaceuticals, hormones and bisphenol A in untreated source and finished drinking water in Ontario, Canada--occurrence and treatment efficiency.

    PubMed

    Kleywegt, Sonya; Pileggi, Vince; Yang, Paul; Hao, Chunyan; Zhao, Xiaoming; Rocks, Carline; Thach, Serei; Cheung, Patrick; Whitehead, Brian

    2011-03-15

    The Ontario Ministry of the Environment (MOE) conducted a survey in 2006 on emerging organic contaminants (EOCs) which included pharmaceuticals, hormones and bisphenol A (BPA). The survey collected 258 samples over a 16 month period from selected source waters and 17 drinking water systems (DWSs), and analyzed them for 48 EOCs using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and isotope dilution mass spectrometry (IDMS) for the highest precision and accuracy of analytical data possible. 27 of the 48 target EOCs were detected in source water, finished drinking water, or both. DWSs using river and lake source water accounted for>90% detections. Of the 27 EOCs found, we also reported the first detection of two antibiotics roxithromycin and enrofloxacin in environmental samples. The most frequently detected compounds (≥ 10%) in finished drinking water were carbamazepine (CBZ), gemfibrozil (GFB), ibuprofen (IBU), and BPA; with their concentrations accurately determined by using IDMS and calculated to be 4 to 10 times lower than those measured in the source water. Comparison of plant specific data allowed us to determine removal efficiency (RE) of these four most frequently detected compounds in Ontario DWSs. The RE of CBZ was determined to be from 71 to 93% for DWSs using granulated activated carbon (GAC); and was 75% for DWSs using GAC followed by ultraviolet irradiation (UV). The observed RE of GFB was between 44 and 55% in DWSs using GAC and increased to 82% when GAC was followed by UV. The use of GAC or GAC followed by UV provided an RE improvement of BPA from 80 to 99%. These detected concentration levels are well below the predicted no effect concentration or total allowable concentration reported in the literature. Additional targeted, site specific comparative research is required to fully assess the effectiveness of Ontario DWSs to remove particular compounds of concern. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. Deterministic magnetorheological finishing of optical aspheric mirrors

    NASA Astrophysics Data System (ADS)

    Song, Ci; Dai, Yifan; Peng, Xiaoqiang; Li, Shengyi; Shi, Feng

    2009-05-01

    A new method magnetorheological finishing (MRF) used for deterministical finishing of optical aspheric mirrors is applied to overcome some disadvantages including low finishing efficiency, long iterative time and unstable convergence in the process of conventional polishing. Based on the introduction of the basic principle of MRF, the key techniques to implement deterministical MRF are also discussed. To demonstrate it, a 200 mm diameter K9 class concave asphere with a vertex radius of 640mm was figured on MRF polish tool developed by ourselves. Through one process about two hours, the surface accuracy peak-to-valley (PV) is improved from initial 0.216λ to final 0.179λ and root-mean-square (RMS) is improved from 0.027λ to 0.017λ (λ = 0.6328um ). High-precision and high-efficiency convergence of optical aspheric surface error shows that MRF is an advanced optical manufacturing method that owns high convergence ratio of surface figure, high precision of optical surfacing, stabile and controllable finishing process. Therefore, utilizing MRF to finish optical aspheric mirrors determinately is credible and stabile; its advantages can be also used for finishing optical elements on varieties of types such as plane mirrors and spherical mirrors.

  3. Nanofinishing of freeform/sculptured surfaces: state-of-the-art

    NASA Astrophysics Data System (ADS)

    Nagdeve, Leeladhar; Jain, V. K.; Ramkumar, J.

    2018-06-01

    Freeform surfaces are being used in a multiplicity of applications in different kinds of industries related to Bio-medical (Bio-implants), micro channels in micro fluidics, automotives, turbine blades, impellers of artificial heart pumps, automobiles etc. Different parts in these industries need nano-level surface finish as their functional inevitability. It is very difficult and challenging to achieve high level of surface finish, especially on the components having freeform (or sculptured) surfaces, complex shapes, and 3-D features. Surface finish is a significant factor, which affects life and functionality of a product. Many traditional and advanced finishing processes have been developed for finishing of freeform/sculptured surfaces but still it has not been possible to achieve uniform nano level surface finish specially in case of freeform surfaces. To overcome the limitations of the existing nanofinishing processes, researchers are developing new processes for uniform nanofinishing of freeform surfaces. In this article, an attempt has been made to review different nanofinishing processes employed for freeform surfaces useful in different types of applications. In addition, experimental work, theoretical analysis and existing challenges of the finishing processes have been identified to fill the research gap.

  4. Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach

    PubMed Central

    Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

    2015-01-01

    Abstract Objective Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Methods Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR–RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. Results PCR–RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR–RED. Conclusion NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR–RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic? Non-invasive prenatal diagnosis (NIPD) using PCR-based methods has been reported for the detection or exclusion of individual paternally inherited or de novo alleles in maternal plasma. What does this study add? NIPD using next generation sequencing provides an accurate, more sensitive approach which can be used to detect multiple mutations in a single assay and so is ideal when screening a gene with multiple potential pathogenic mutations. Next generation sequencing thus provides a flexible approach to non-invasive prenatal diagnosis ideal for use in a busy service laboratory. PMID:25728633

  5. A New Single-Step PCR Assay for the Detection of the Zoonotic Malaria Parasite Plasmodium knowlesi

    PubMed Central

    Lucchi, Naomi W.; Poorak, Mitra; Oberstaller, Jenna; DeBarry, Jeremy; Srinivasamoorthy, Ganesh; Goldman, Ira; Xayavong, Maniphet; da Silva, Alexandre J.; Peterson, David S.; Barnwell, John W.; Kissinger, Jessica; Udhayakumar, Venkatachalam

    2012-01-01

    Background Recent studies in Southeast Asia have demonstrated substantial zoonotic transmission of Plasmodium knowlesi to humans. Microscopically, P. knowlesi exhibits several stage-dependent morphological similarities to P. malariae and P. falciparum. These similarities often lead to misdiagnosis of P. knowlesi as either P. malariae or P. falciparum and PCR-based molecular diagnostic tests are required to accurately detect P. knowlesi in humans. The most commonly used PCR test has been found to give false positive results, especially with a proportion of P. vivax isolates. To address the need for more sensitive and specific diagnostic tests for the accurate diagnosis of P. knowlesi, we report development of a new single-step PCR assay that uses novel genomic targets to accurately detect this infection. Methodology and Significant Findings We have developed a bioinformatics approach to search the available malaria parasite genome database for the identification of suitable DNA sequences relevant for molecular diagnostic tests. Using this approach, we have identified multi-copy DNA sequences distributed in the P. knowlesi genome. We designed and tested several novel primers specific to new target sequences in a single-tube, non-nested PCR assay and identified one set of primers that accurately detects P. knowlesi. We show that this primer set has 100% specificity for the detection of P. knowlesi using three different strains (Nuri, H, and Hackeri), and one human case of malaria caused by P. knowlesi. This test did not show cross reactivity with any of the four human malaria parasite species including 11 different strains of P. vivax as well as 5 additional species of simian malaria parasites. Conclusions The new PCR assay based on novel P. knowlesi genomic sequence targets was able to accurately detect P. knowlesi. Additional laboratory and field-based testing of this assay will be necessary to further validate its utility for clinical diagnosis of P. knowlesi. PMID:22363751

  6. Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA+)

    PubMed Central

    Jeong, Haeyoung; Sim, Young Mi; Kim, Hyun Ju; Lee, Sang Jun

    2017-01-01

    There have been extensive genome sequencing studies for Escherichia coli strains, particularly for pathogenic isolates, because fast determination of pathogenic potential and/or drug resistance and their propagation routes is crucial. For laboratory E. coli strains, however, genome sequence information is limited except for several well-known strains. We determined the complete genome sequence of laboratory E. coli strain RR1 (HB101 RecA+), which has long been used as a general cloning host. A hybrid genome sequence of K-12 MG1655 and B BL21(DE3) was constructed based on the initial mapping of Illumina HiSeq reads to each reference, and iterative rounds of read mapping, variant detection, and consensus extraction were carried out. Finally, PCR and Sanger sequencing-based finishing were applied to resolve non-single nucleotide variant regions with aberrant read depths and breakpoints, most of them resulting from prophages and insertion sequence transpositions that are not present in the reference genome sequence. We found that 96.9% of the RR1 genome is derived from K-12, and identified exact crossover junctions between K-12 and B genomic fragments. However, because RR1 has experienced a series of genetic manipulations since branching from the common ancestor, it has a set of mutations different from those found in K-12 MG1655. As well as identifying all known genotypes of RR1 on the basis of genomic context, we found novel mutations. Our results extend current knowledge of the genotype of RR1 and its relatives, and provide insights into the pedigree, genomic background, and physiology of common laboratory strains. PMID:28421066

  7. EPA'S METAL FINISHING FACILITY POLLUTION PREVENTION TOOL - 2002

    EPA Science Inventory

    To help metal finishing facilities meet the goal of profitable pollution prevention, the USEPA is developing the Metal Finishing Facility Pollution Prevention Tool (MFFP2T), a computer program that estimates the rate of solid, liquid waste generation and air emissions. This progr...

  8. 25 CFR 301.8 - Finish.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 2 2010-04-01 2010-04-01 false Finish. 301.8 Section 301.8 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER AND TURQUOISE PRODUCTS; STANDARDS § 301.8 Finish. All silver is to be hand polished. ...

  9. 40 CFR 410.40 - Applicability; description of the woven fabric finishing subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 28 2010-07-01 2010-07-01 true Applicability; description of the woven fabric finishing subcategory. 410.40 Section 410.40 Protection of Environment ENVIRONMENTAL PROTECTION... proofing, soil repellency application and a special finish application. ...

  10. 77 FR 48992 - Tobacco Product Manufacturing Facility Visits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-15

    ... manufacturing operations--from the receipt of raw materials to the distribution of finished products, and Learn... Manufacturing facilities for materials used for further processing in finished tobacco products (including, but..., parts, accessories, and Manufacturers of materials used for further processing in finished tobacco...

  11. Fluoroalkyl Siloxanes as Liquid-Repellent Fabric Finishes. Part 2. The Homopolymers and their Copolymers with Alkyl Silanes

    DTIC Science & Technology

    1979-06-01

    LUOROALKYL SILOXANES AS LIQUID-JEPELLENT FABiRIC FINISHES YARUJF- THE 1OMOPOLYMERS AND /,THEIR CUPOLYMERS WITH !IxKL LALEK i.W o D DC BEST AVAILABLE...NATIONAL DEFENCE CANADA DEFENCE RESEARCH ESTABLISHMENT OTTAWA REPORT NO. 804 FLUOROALKYL SILOXANES AS LIQUID-REPELLENT FABRIC FINISHES PART II THE...cent) and cotton as finishes , and the oil and water repellency imparted to these fabrics ascertained by standard tests. In this manner it is possible

  12. Dielectric Properties of Polymer Matrix Composites Prepared from Conductive Polymer Treated Fabrics

    DTIC Science & Technology

    1992-02-01

    JPS 09827 finish. The doping agent used was anthraquinone-2 sulfonic acid. (3) A 5 x 5 S2-glass 24 oz. woven roving with an Owens Corning 463 finish...x- I S2-glass 27 oz. woven roving with an Owens Corning 933 finish, nominally equiv- alent to the JPS 09827 finish. The doping agent used was...were fabricated by laminating the layers of Fabric with wet polyester resin ( Owens Corning E-780) and subsequently processing the com- posites using the

  13. A novel approach to multiple sequence alignment using hadoop data grids.

    PubMed

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

    Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

  14. FRAGS: estimation of coding sequence substitution rates from fragmentary data

    PubMed Central

    Swart, Estienne C; Hide, Winston A; Seoighe, Cathal

    2004-01-01

    Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the coding sequence divergence of orthologous genes. Although complete genome sequence data are not available for all organisms, fragmentary sequence data can provide accurate estimates of substitution rates provided that an appropriate and consistent methodology is used and that differences in the estimates obtainable from different data sources are taken into account. Results We have developed FRAGS, an application framework that uses existing, freely available software components to construct in-frame alignments and estimate coding substitution rates from fragmentary sequence data. Coding sequence substitution estimates for human and chimpanzee sequences, generated by FRAGS, reveal that methodological differences can give rise to significantly different estimates of important substitution parameters. The estimated substitution rates were also used to infer upper-bounds on the amount of sequencing error in the datasets that we have analysed. Conclusion We have developed a system that performs robust estimation of substitution rates for orthologous sequences from a pair of organisms. Our system can be used when fragmentary genomic or transcript data is available from one of the organisms and the other is a completely sequenced genome within the Ensembl database. As well as estimating substitution statistics our system enables the user to manage and query alignment and substitution data. PMID:15005802

  15. Effects of finishing/polishing techniques on microleakage of resin-modified glass ilonomer cement restorations.

    PubMed

    Yap, Adrian U J; Yap, W Y; Yeo, Egwin J C; Tan, Jane W S; Ong, Debbie S B

    2003-01-01

    This study investigated the effect of finishing/polishing techniques on the microleakage of resin-modified glass ionomer restorations. Class V preparations were made on the buccal and lingual/palatal surfaces of freshly extracted teeth. The cavities on each tooth were restored with Fuji II LC (FT [GC]) and Photac-Fil Quick (PF [3M-ESPE]) according to manufacturers' instructions. Immediately after light-polymerization, gross finishing was done with eight-fluted tungsten carbide burs. The teeth were then randomly divided into four groups and finishing/polishing was done with one of the following systems: (a) Robot Carbides (RC); (b) Super-Snap system (SS); (c) OneGloss (OG) and (d) CompoSite Polishers (CS). The sample size for each material-finishing/polishing system combination was eight. After finishing/polishing, the teeth were stored in distilled water at 37 degrees C for one week. The root apices were then sealed with acrylic and two coats of varnish was applied 1 mm beyond the restoration margins. The teeth were subsequently subjected to dye penetration testing (0.5% basic fuchsin), sectioned and scored. Data was analyzed using Kruskal-Wallis and Mann-Whitney U tests at a significance level of 0.05. Results of statistical analysis were as follows: Enamel margins: PF-OG

  16. Effect of finishing/polishing techniques and time on surface roughness of esthetic restorative materials.

    PubMed

    Madhyastha, Prashanthi Sampath; Hegde, Shreya; Srikant, N; Kotian, Ravindra; Iyer, Srividhya Sriraman

    2017-01-01

    Surface roughness associated with improper finishing/polishing of restorations can result in plaque accumulation, gingival irritation, surface staining, and poor esthetic of restored teeth. The study aimed to evaluate the efficiency of various finishing and polishing systems and time using various procedures on surface roughness of some esthetic restorative materials. In this in vitro study, samples of two composite materials, compomer and glass ionomer cement (GIC) materials, were fabricated. Finishing and polishing were done immediately ( n = 40) and after 1 week ( n = 40) using four systems (diamond bur + soflex discs; diamond bur + Astropol polishing brush; tungsten carbide bur + soflex discs; tungsten carbide bur + Astropol polishing brush). Surface roughness was measured using surface profilometer. Data were statistically analyzed by t -test (for each material and time period) and one-way analysis of variance followed by Tukey's post hoc (for finishing and polishing systems) at a significant level of P < 0.05. Analysis of time period, irrespective of finishing and polishing system showed that Ra values were greater ( P < 0.05) in delayed polishing in GIC > Z100 > Filtek P90 > Dyract AP, suggesting immediate polishing is better. Among the materials, Filtek P90 had the least Ra values indicating the smoothest surface among all materials, followed by Z100, Dyract AP, and GIC. Comparison of polishing and finishing systems irrespective of materials showed that Ra values were lower ( P > 0.05) in diamond + Astropol combination whereas diamond + soflex had the greatest Ra values. It might be concluded that: (i) Filtek P90 showed least Ra values followed by < Z100 < Dyract < GIC; (ii) immediate (24 h) finishing/polishing of materials is better than delayed; and (iii) among all these polishing systems, diamond bur-Astropol and Astrobrush showed good surface finish.

  17. Design and control of a macro-micro robot for precise force applications

    NASA Technical Reports Server (NTRS)

    Wang, Yulun; Mangaser, Amante; Laby, Keith; Jordan, Steve; Wilson, Jeff

    1993-01-01

    Creating a robot which can delicately interact with its environment has been the goal of much research. Primarily two difficulties have made this goal hard to attain. The execution of control strategies which enable precise force manipulations are difficult to implement in real time because such algorithms have been too computationally complex for available controllers. Also, a robot mechanism which can quickly and precisely execute a force command is difficult to design. Actuation joints must be sufficiently stiff, frictionless, and lightweight so that desired torques can be accurately applied. This paper describes a robotic system which is capable of delicate manipulations. A modular high-performance multiprocessor control system was designed to provide sufficient compute power for executing advanced control methods. An 8 degree of freedom macro-micro mechanism was constructed to enable accurate tip forces. Control algorithms based on the impedance control method were derived, coded, and load balanced for maximum execution speed on the multiprocessor system. Delicate force tasks such as polishing, finishing, cleaning, and deburring, are the target applications of the robot.

  18. [Individual indirect bonding technique (IIBT) using set-up model].

    PubMed

    Kyung, H M

    1989-01-01

    There has been much progress in Edgewise Appliance since E.H. Angle. One of the most important procedures in edgewise appliance is correct bracket position. Not only conventional edgewise appliance but also straight wire appliance & lingual appliance cannot be used more effectively unless the bracket position is accurate. Improper bracket positioning may reveal much problems during treatment, especially in finishing state. It may require either rebonding after the removal of the malpositioned bracket or the greater number of arch wire and the more complex wire bending, causing much difficulty in performing effective treatments. This made me invent Individual Indirect Bonding Technique with the use of multi-purpose set-up model in order to determine a correct and objective bracket position according to individual patients. This technique is more accurate than former indirect bonding techniques in bracket positioning, because it decides the bracket position on a set-up model which has produced to have the occlusal relationship the clinician desired. This technique is especially effective in straight wire appliance and lingual appliance in which the correct bracket positioning is indispensible.

  19. Combined fabrication technique for high-precision aspheric optical windows

    NASA Astrophysics Data System (ADS)

    Hu, Hao; Song, Ci; Xie, Xuhui

    2016-07-01

    Specifications made on optical components are becoming more and more stringent with the performance improvement of modern optical systems. These strict requirements not only involve low spatial frequency surface accuracy, mid-and-high spatial frequency surface errors, but also surface smoothness and so on. This presentation mainly focuses on the fabrication process for square aspheric window which combines accurate grinding, magnetorheological finishing (MRF) and smoothing polishing (SP). In order to remove the low spatial frequency surface errors and subsurface defects after accurate grinding, the deterministic polishing method MRF with high convergence and stable material removal rate is applied. Then the SP technology with pseudo-random path is adopted to eliminate the mid-and-high spatial frequency surface ripples and high slope errors which is the defect for MRF. Additionally, the coordinate measurement method and interferometry are combined in different phase. Acid-etched method and ion beam figuring (IBF) are also investigated on observing and reducing the subsurface defects. Actual fabrication result indicates that the combined fabrication technique can lead to high machining efficiency on manufaturing the high-precision and high-quality optical aspheric windows.

  20. Estimation Accuracy on Execution Time of Run-Time Tasks in a Heterogeneous Distributed Environment

    PubMed Central

    Liu, Qi; Cai, Weidong; Jin, Dandan; Shen, Jian; Fu, Zhangjie; Liu, Xiaodong; Linge, Nigel

    2016-01-01

    Distributed Computing has achieved tremendous development since cloud computing was proposed in 2006, and played a vital role promoting rapid growth of data collecting and analysis models, e.g., Internet of things, Cyber-Physical Systems, Big Data Analytics, etc. Hadoop has become a data convergence platform for sensor networks. As one of the core components, MapReduce facilitates allocating, processing and mining of collected large-scale data, where speculative execution strategies help solve straggler problems. However, there is still no efficient solution for accurate estimation on execution time of run-time tasks, which can affect task allocation and distribution in MapReduce. In this paper, task execution data have been collected and employed for the estimation. A two-phase regression (TPR) method is proposed to predict the finishing time of each task accurately. Detailed data of each task have drawn interests with detailed analysis report being made. According to the results, the prediction accuracy of concurrent tasks’ execution time can be improved, in particular for some regular jobs. PMID:27589753

  1. Positive dwell time algorithm with minimum equal extra material removal in deterministic optical surfacing technology.

    PubMed

    Li, Longxiang; Xue, Donglin; Deng, Weijie; Wang, Xu; Bai, Yang; Zhang, Feng; Zhang, Xuejun

    2017-11-10

    In deterministic computer-controlled optical surfacing, accurate dwell time execution by computer numeric control machines is crucial in guaranteeing a high-convergence ratio for the optical surface error. It is necessary to consider the machine dynamics limitations in the numerical dwell time algorithms. In this paper, these constraints on dwell time distribution are analyzed, and a model of the equal extra material removal is established. A positive dwell time algorithm with minimum equal extra material removal is developed. Results of simulations based on deterministic magnetorheological finishing demonstrate the necessity of considering machine dynamics performance and illustrate the validity of the proposed algorithm. Indeed, the algorithm effectively facilitates the determinacy of sub-aperture optical surfacing processes.

  2. Final Report,

    DTIC Science & Technology

    compare the effects of elevated temperature on 801-finish glass. The strength qualities at 75 F of Owens - Corning ECG-140 continuous-filament roving glass...with an 801 epoxy compatible finish and the same glass with an HTS epoxy compatible finish were tested. The strength qualities of Owens - Corning ECG

  3. Meat goat kids finished on alfalfa, red clover or orchardgrass pastures: carcass merit and meat quality.

    PubMed

    Turner, K E; Cassida, K A; Zerby, H N

    2014-12-01

    This experiment was conducted in 2005-2007 to evaluate carcass and chevon (goat meat) quality parameters when meat-goat kids (n=72) were finished on alfalfa (Medicago sativa L; ALF); red clover (Trifolium pratense L.; RCG); or orchardgrass (Dactylis glomerata L.; OGR) pastures. Carcass conformation score was greater (P=0.08) when meat-goat kids were finished on ALF compared to OGR with RCG intermediate. Chevon meat samples from goats finished on the three pasture treatments did not differ in ash, intramuscular fat, or crude protein content or in concentrations of omega6 and omega3 fatty acids, or the omega6 to omega3 ratio. Goats finished on OGR had higher (P<0.001) 18:1 trans-11 fatty acids (FA) compared to ALF or RCG. Overall, meat-goat kids finished on ALF, RCG, or ORG produced desirable carcass weights for most niche markets in the USA. Chevon is a low-fat meat option with high desirable fatty acids for human diets. Published by Elsevier Ltd.

  4. Influence of finishing systems on hydrophilic and lipophilic oxygen radical absorbance capacity (ORAC) in beef.

    PubMed

    Wu, C; Duckett, S K; Neel, J P S; Fontenot, J P; Clapham, W M

    2008-11-01

    The aim of this research was to: (1) develop a reliable extraction procedure and assay to determine antioxidant activity in meat products, and (2) assess the effect of beef finishing system (forage-finished: alfalfa, pearl millet or mixed pastures vs. concentrate-finished) on longissimus muscle antioxidant activity. The effect of extraction method (ethanol concentration and extraction time), protein removal, and sample preparation method (pulverization or freeze drying) were first evaluated to develop an antioxidant assay for meat products. Beef extracts prepared with low ethanol concentrations (20%) demonstrated higher hydrophilic ORAC. Protein removal prior to extraction reduced hydrophilic ORAC values. Sample preparation method influenced both hydrophilic and lipophilic ORAC, with pulverized samples containing higher hydrophilic and lipophilic ORAC values. Beef cattle finishing system (Forage: alfalfa, pearl millet, or natural pasture vs. concentrates) had little impact on muscle hydrophilic ORAC, but muscle from forage finished beef contained greater lipophilic ORAC. In addition, broiling of steaks reduced hydrophilic ORAC.

  5. The bench scientist's guide to RNA-Seq analysis

    USDA-ARS?s Scientific Manuscript database

    RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatic specialists. Here we outline a methods strategy desi...

  6. Fast imputation using medium or low-coverage sequence data

    USDA-ARS?s Scientific Manuscript database

    Accurate genotype imputation can greatly reduce costs and increase benefits by combining whole-genome sequence data of varying read depth and microarray genotypes of varying densities. For large populations, an efficient strategy chooses the two haplotypes most likely to form each genotype and updat...

  7. Centrifuge: rapid and sensitive classification of metagenomic sequences.

    PubMed

    Kim, Daehwan; Song, Li; Breitwieser, Florian P; Salzberg, Steven L

    2016-12-01

    Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space. © 2016 Kim et al.; Published by Cold Spring Harbor Laboratory Press.

  8. Uniform, optimal signal processing of mapped deep-sequencing data.

    PubMed

    Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul; Kraus, Petra; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam

    2013-07-01

    Despite their apparent diversity, many problems in the analysis of high-throughput sequencing data are merely special cases of two general problems, signal detection and signal estimation. Here we adapt formally optimal solutions from signal processing theory to analyze signals of DNA sequence reads mapped to a genome. We describe DFilter, a detection algorithm that identifies regulatory features in ChIP-seq, DNase-seq and FAIRE-seq data more accurately than assay-specific algorithms. We also describe EFilter, an estimation algorithm that accurately predicts mRNA levels from as few as 1-2 histone profiles (R ∼0.9). Notably, the presence of regulatory motifs in promoters correlates more with histone modifications than with mRNA levels, suggesting that histone profiles are more predictive of cis-regulatory mechanisms. We show by applying DFilter and EFilter to embryonic forebrain ChIP-seq data that regulatory protein identification and functional annotation are feasible despite tissue heterogeneity. The mathematical formalism underlying our tools facilitates integrative analysis of data from virtually any sequencing-based functional profile.

  9. Direct sequencing of hepatitis A virus and norovirus RT-PCR products from environmentally contaminated oyster using M13-tailed primers.

    PubMed

    Williams-Woods, Jacquelina; González-Escalona, Narjol; Burkhardt, William

    2011-12-01

    Human norovirus (HuNoV) and hepatitis A (HAV) are recognized as leading causes of non-bacterial foodborne associated illnesses in the United States. DNA sequencing is generally considered the standard for accurate viral genotyping in support of epidemiological investigations. Due to the genetic diversity of noroviruses (NoV), degenerate primer sets are often used in conventional reverse transcription (RT) PCR and real-time RT-quantitative PCR (RT-qPCR) for the detection of these viruses and cDNA fragments are generally cloned prior to sequencing. HAV detection methods that are sensitive and specific for real-time RT-qPCR yields small fragments sizes of 89-150bp, which can be difficult to sequence. In order to overcome these obstacles, norovirus and HAV primers were tailed with M13 forward and reverse primers. This modification increases the sequenced product size and allows for direct sequencing of the amplicons utilizing complementary M13 primers. HuNoV and HAV cDNA products from environmentally contaminated oysters were analyzed using this method. Alignments of the sequenced samples revealed ≥95% nucleotide identities. Tailing NoV and HAV primers with M13 sequence increases the cDNA product size, offers an alternative to cloning, and allows for rapid, accurate and direct sequencing of cDNA products produced by conventional or real time RT-qPCR assays. Published by Elsevier B.V.

  10. Effects of Early and Late Rest Intervals on Performance and Overnight Consolidation of a Keyboard Sequence

    ERIC Educational Resources Information Center

    Cash, Carla Davis

    2009-01-01

    Thirty-six nonmusicians practiced a five-element key-press sequence on a digital piano, repeating the sequence as quickly and accurately as possible during twelve 30-s practice blocks alternating with 30-s pauses. Twelve learners rested for 5 min between Blocks 3 and 4, another 12 learners rested for 5 min between Blocks 9 and 10, and the…

  11. Determination of nitrogen to carbon abundance ratios from transition layer emission lines

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, Erika

    1992-01-01

    We have finished studying the nitrogen to carbon abundance ratios for stars with different effective temperatures T(sub eff) and luminosities using transition layer emission lines and using spectra available in the IUE archives. The N/C abundance ratio determinations using transition layer emission lines are as accurate as the photospheric abundance determinations as found by comparison of results obtained by both methods for the same stars. Our measurements confirm photospheric abundance determinations in regions of the HR diagram where they can be obtained. Our studies have extended the temperature range to higher temperatures. They have shown the exact positions in the HR diagram where the mixing due to the outer convection zones reaches deep enough to bring nuclear processed material to the surface. This occurs at effective temperatures which are higher by delta log T(sub eff) approximately 0.04 or roughly 400 K than expected theoretically. Since the depth of the convection zone increases rapidly with decreasing T(sub eff) this may indicate considerable overshoot beyond the lower boundary of the convection zone. Our N/C abundance ratio determinations from transition layer emission lines have confirmed that the actual enrichment observed for some cool giants is larger than expected theoretically, again indicating a larger degree of mixing in several stars either from below or from above. For the supergiants it probably indicates overshoot above the convective core in the progenitor main sequence stars. For the more massive giants this may also be the case, though we did not find a correlation between delta log N/C and the absolute magnitudes, but these are rather uncertain. As byproducts of these studies we also found anomalies in Si/C and N/C abundance ratios for F giants which can be understood as the relict of surface abundance changes for their main sequence progenitors due to diffusion. This anomaly disappears for G giants, for which the depths of the convection zones are apparently deep enough to wipe out these element separations (Bohm-Vitense 1992).

  12. Virtual sensors for on-line wheel wear and part roughness measurement in the grinding process.

    PubMed

    Arriandiaga, Ander; Portillo, Eva; Sánchez, Jose A; Cabanes, Itziar; Pombo, Iñigo

    2014-05-19

    Grinding is an advanced machining process for the manufacturing of valuable complex and accurate parts for high added value sectors such as aerospace, wind generation, etc. Due to the extremely severe conditions inside grinding machines, critical process variables such as part surface finish or grinding wheel wear cannot be easily and cheaply measured on-line. In this paper a virtual sensor for on-line monitoring of those variables is presented. The sensor is based on the modelling ability of Artificial Neural Networks (ANNs) for stochastic and non-linear processes such as grinding; the selected architecture is the Layer-Recurrent neural network. The sensor makes use of the relation between the variables to be measured and power consumption in the wheel spindle, which can be easily measured. A sensor calibration methodology is presented, and the levels of error that can be expected are discussed. Validation of the new sensor is carried out by comparing the sensor's results with actual measurements carried out in an industrial grinding machine. Results show excellent estimation performance for both wheel wear and surface roughness. In the case of wheel wear, the absolute error is within the range of microns (average value 32 μm). In the case of surface finish, the absolute error is well below Ra 1 μm (average value 0.32 μm). The present approach can be easily generalized to other grinding operations.

  13. Diamond Turning Of Infra-Red Components

    NASA Astrophysics Data System (ADS)

    Hodgson, B.; Lettington, A. H.; Stillwell, P. F. T. C.

    1986-05-01

    Single point diamond machining of infra-red optical components such as aluminium mirrors, germanium lenses and zinc sulphide domes is potentially the most cost effective method for their manufacture since components may be machined from the blanks to a high surface finish, requiring no subsequent polishing, in a few minutes. Machines for the production of flat surfaces are well established. Diamond turning lathes for curved surfaces however require a high capital investment which can be justified only for research purposes or high volume production. The present paper describes the development of a low cost production machine based on a Bryant Symons diamond turning lathe which is able to machine spherical components to the required form and finish. It employs two horizontal spindles one for the workpiece the other for the tool. The machined radius of curvature is set by the alignment of the axes and the radius of the tool motion, as in conventional generation. The diamond tool is always normal to the workpiece and does not need to be accurately profiled. There are two variants of this basic machine. For machining hemispherical domes the axes are at right angles while for lenses with positive or negative curvature these axes are adjustable. An aspherical machine is under development, based on the all mechanical spherical machine, but in which a ± 2 mm aspherecity may be imposed on the best fit sphere by moving the work spindle under numerical control.

  14. Effect of different surface finishing/polishing procedures on color stability of esthetic restorative materials: A spectrophotometric evaluation

    PubMed Central

    Beltrami, Riccardo; Ceci, Matteo; De Pani, Gabriele; Vialba, Lodovico; Federico, Ricaldone; Poggio, Claudio; Colombo, Marco

    2018-01-01

    Objective: To evaluate the color stability of different esthetic restorative materials after surface finishing/polishing with different procedures. Materials and Methods: All materials were polymerized into silicone rubber rings to obtain specimens identical in size. Samples were randomly assigned into four groups (10 specimens of each composite for each group), and they were finished with different procedures: Control group (Group 1), three or two polishers interspersed with diamond grit (Groups 3 and 2, respectively), and one tungsten carbide bur + one polisher interspersed with diamond grit (Group 4). After staining process in coffee, a colorimetric evaluation according to the CIE L*a*b* system was performed by a blind trained operator at 7, 14, 21, and 28 days. Shapiro–Wilk test and Kruskal–Wallis analysis of variance were applied to assess significant differences among restorative materials. Means of the different polishing/finishing groups were compared with Scheffe's multiple comparison test at the 0.05 level of significance. Results: In control group, significant lower discolorations were recorded for Essentia, Admira Fusion, and Estelite. After finishing, Filtek Supreme XTE and Ceram.X Universal showed a significantly lower degree of staining. The finishing technique used for Group 4 produced higher color changes. Conclusions: Tungsten carbide burs produced the higher color variations; after finishing, the nanofilled composites showed lower discoloration than nanohybrid ones, and the time of exposure to the staining agent and the polishing/finishing technique influenced the color change. PMID:29657525

  15. Wall finish selection in hospital design: a survey of facility managers.

    PubMed

    Lavy, Sarel; Dixit, Manish K

    2012-01-01

    This paper seeks to analyze healthcare facility managers' perceptions regarding the materials used for interior wall finishes and the criteria used to select them. It also examines differences in wall finish materials and the selection process in three major hospital spaces: emergency, surgery, and in-patient units. These findings are compared with healthcare designers' perceptions on similar issues, as currently documented in the literature. Hospital design and the materials used for hospital construction have a considerable effect on the environment and health of patients. A 2002 survey revealed which characteristics healthcare facility designers consider when selecting materials for healthcare facilities; however, no similar study has examined the views of facility managers on building finish selection. A 22-question survey questionnaire was distributed to 210 facility managers of metropolitan, for-profit hospitals in Texas; IRB approval was obtained. Respondents were asked to rank 10 interior wall finish materials and 11 selection criteria for wall finishes. Data from 48 complete questionnaires were analyzed using descriptive statistics and nonparametric statistical analysis methods. The study found no statistically significant differences in terms of wall finish materials or the characteristics for material selection in the three major spaces studied. It identified facility managers' four most-preferred wall finish materials and the five-most preferred characteristics, with a statistical confidence level of greater than 95%. The paper underscores the importance of incorporating all perspectives: facility designers and facility managers should work together toward achieving common organizational goals.

  16. TRL-6 for JWST wavefront sensing and control

    NASA Astrophysics Data System (ADS)

    Feinberg, Lee D.; Dean, Bruce H.; Aronstein, David L.; Bowers, Charles W.; Hayden, William; Lyon, Richard G.; Shiri, Ron; Smith, J. Scott; Acton, D. Scott; Carey, Larkin; Contos, Adam; Sabatke, Erin; Schwenker, John; Shields, Duncan; Towell, Tim; Shi, Fang; Meza, Luis

    2007-09-01

    NASA's Technology Readiness Level (TRL)-6 is documented for the James Webb Space Telescope (JWST) Wavefront Sensing and Control (WFSC) subsystem. The WFSC subsystem is needed to align the Optical Telescope Element (OTE) after all deployments have occurred, and achieves that requirement through a robust commissioning sequence consisting of unique commissioning algorithms, all of which are part of the WFSC algorithm suite. This paper identifies the technology need, algorithm heritage, describes the finished TRL-6 design platform, and summarizes the TRL-6 test results and compliance. Additionally, the performance requirements needed to satisfy JWST science goals as well as the criterion that relate to the TRL-6 Testbed Telescope (TBT) performance requirements are discussed.

  17. TRL-6 for JWST Wavefront Sensing and Control

    NASA Technical Reports Server (NTRS)

    Feinberg, Lee; Dean, Bruce; Smith, Scott; Aronstein, David; Shiri, Ron; Lyon, Rick; Hayden, Bill; Bowers, Chuck; Acton, D. Scott; Shields, Duncan; hide

    2007-01-01

    NASA's Technology Readiness Level (TRL)-6 is documented for the James Webb Space Telescope (JWST) Wavefront Sensing and Control (WFSC) subsystem. The WFSC subsystem is needed to align the Optical Telescope Element (OTE) after all deployments have occurred, and achieves that requirement through a robust commissioning sequence consisting of unique commissioning algorithms, all of which are part of the WFSC algorithm suite. This paper identifies the technology need, algorithm heritage, describes the finished TRL-6 design platform, and summarizes the TRL-6 test results and compliance. Additionally, the performance requirements needed to satisfy JWST science goals as well as the criterion that relate to the TRL-6 Testbed Telescope (TBT) performance requirements are discussed

  18. Low-cost directionally-solidified turbine blades, volume 2. [TFE731-3 turbofan engine

    NASA Technical Reports Server (NTRS)

    Dennis, R. E.; Hoppin, G. S., III; Hurst, L. G.

    1979-01-01

    An endothermically heated technology was used to manufacture low cost, directionally solidified, uncooled nickel-alloy blades for the TFE731-3 turbofan engine. The MAR-M 247 and MER-M 100+Hf blades were finish processed through heat treatment, machining, and coating operations prior to 150 hour engine tests consisting of the following sequences: (1) 50 hours of simulated cruise cycling (high fatigue evaluation); (2) 50 hours at the maximum continuous power rating (stress rupture endurance (low cycle fatigue). None of the blades visually showed any detrimental effects from the test. This was verified by post test metallurgical evaluation. The specific fuel consumption was reduced by 2.4% with the uncooled blades.

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

    PubMed

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

    2015-01-01

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

  20. THE USEPA'S METAL FINISHING FACILITY POLLUTION PREVENTION TOOL (MFFP2T)

    EPA Science Inventory

    The USEPA has developed a pre-release version of a process simulation tool, the Metal Finishing Facility Pollution Prevention Tool (MFFP2T), for the metal finishing industry. This presentation will provide a demonstration of the current version of this tool. The presentation will...

Some links on this page may take you to non-federal websites. Their policies may differ from this site.
Top