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Sample records for combined bisulfite restriction

  1. Treatment of PCR products with exonuclease I and heat-labile alkaline phosphatase improves the visibility of combined bisulfite restriction analysis

    SciTech Connect

    Watanabe, Kousuke; Emoto, Noriko; Sunohara, Mitsuhiro; Kawakami, Masanori; Kage, Hidenori; Nagase, Takahide; Ohishi, Nobuya; Takai, Daiya

    2010-08-27

    Research highlights: {yields} Incubating PCR products at a high temperature causes smears in gel electrophoresis. {yields} Smears interfere with the interpretation of methylation analysis using COBRA. {yields} Treatment with exonuclease I and heat-labile alkaline phosphatase eliminates smears. {yields} The elimination of smears improves the visibility of COBRA. -- Abstract: DNA methylation plays a vital role in the regulation of gene expression. Abnormal promoter hypermethylation is an important mechanism of inactivating tumor suppressor genes in human cancers. Combined bisulfite restriction analysis (COBRA) is a widely used method for identifying the DNA methylation of specific CpG sites. Here, we report that exonuclease I and heat-labile alkaline phosphatase can be used for PCR purification for COBRA, improving the visibility of gel electrophoresis after restriction digestion. This improvement is observed when restriction digestion is performed at a high temperature, such as 60 {sup o}C or 65 {sup o}C, with BstUI and TaqI, respectively. This simple method can be applied instead of DNA purification using spin columns or phenol/chloroform extraction. It can also be applied to other situations when PCR products are digested by thermophile-derived restriction enzymes, such as PCR restriction fragment length polymorphism (RFLP) analysis.

  2. 21 CFR 582.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 6 2013-04-01 2013-04-01 false Potassium bisulfite. 582.3616 Section 582.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions,...

  3. 21 CFR 182.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Potassium bisulfite. 182.3616 Section 182.3616...) SUBSTANCES GENERALLY RECOGNIZED AS SAFE Chemical Preservatives § 182.3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions, or explanation. This substance is...

  4. 21 CFR 582.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 6 2011-04-01 2011-04-01 false Potassium bisulfite. 582.3616 Section 582.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions,...

  5. 21 CFR 182.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Potassium bisulfite. 182.3616 Section 182.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD....3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions,...

  6. 21 CFR 182.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Potassium bisulfite. 182.3616 Section 182.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD....3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions,...

  7. 21 CFR 582.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 6 2012-04-01 2012-04-01 false Potassium bisulfite. 582.3616 Section 582.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions,...

  8. 21 CFR 182.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Potassium bisulfite. 182.3616 Section 182.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD....3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions,...

  9. 21 CFR 582.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Potassium bisulfite. 582.3616 Section 582.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions,...

  10. 21 CFR 182.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Potassium bisulfite. 182.3616 Section 182.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR... Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions, or...

  11. 21 CFR 582.3616 - Potassium bisulfite.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 6 2014-04-01 2014-04-01 false Potassium bisulfite. 582.3616 Section 582.3616 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3616 Potassium bisulfite. (a) Product. Potassium bisulfite. (b) (c) Limitations, restrictions,...

  12. 21 CFR 182.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Sodium bisulfite. 182.3739 Section 182.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR... Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or explanation....

  13. 21 CFR 582.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 6 2011-04-01 2011-04-01 false Sodium bisulfite. 582.3739 Section 582.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3739 Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or...

  14. 21 CFR 182.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Sodium bisulfite. 182.3739 Section 182.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR... Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or explanation....

  15. 21 CFR 582.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 6 2013-04-01 2013-04-01 false Sodium bisulfite. 582.3739 Section 582.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3739 Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or...

  16. 21 CFR 582.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 6 2014-04-01 2014-04-01 false Sodium bisulfite. 582.3739 Section 582.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3739 Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or...

  17. 21 CFR 182.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Sodium bisulfite. 182.3739 Section 182.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR... Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or explanation....

  18. 21 CFR 582.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Sodium bisulfite. 582.3739 Section 582.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3739 Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or...

  19. 21 CFR 182.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Sodium bisulfite. 182.3739 Section 182.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR... Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or explanation....

  20. 21 CFR 582.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 6 2012-04-01 2012-04-01 false Sodium bisulfite. 582.3739 Section 582.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL....3739 Sodium bisulfite. (a) Product. Sodium bisulfite. (b) (c) Limitations, restrictions, or...

  1. Analyzing the cancer methylome through targeted bisulfite sequencing.

    PubMed

    Lee, Eun-Joon; Luo, Junfeng; Wilson, James M; Shi, Huidong

    2013-11-01

    Bisulfite conversion of genomic DNA combined with next-generation sequencing (NGS) has become a very effective approach for mapping the whole-genome and sub-genome wide DNA methylation landscapes. However, whole methylome shotgun bisulfite sequencing is still expensive and not suitable for analyzing large numbers of human cancer specimens. Recent advances in the development of targeted bisulfite sequencing approaches offer several attractive alternatives. The characteristics and applications of these methods are discussed in this review article. In addition, the bioinformatic tools that can be used for sequence capture probe design as well as downstream sequence analyses are also addressed. PMID:23200671

  2. GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data

    PubMed Central

    Benoukraf, Touati; Wongphayak, Sarawut; Hadi, Luqman Hakim Abdul; Wu, Mengchu; Soong, Richie

    2013-01-01

    High-throughput sequencing is increasingly being used in combination with bisulfite (BS) assays to study DNA methylation at nucleotide resolution. Although several programmes provide genome-wide alignment of BS-treated reads, the resulting information is not readily interpretable and often requires further bioinformatic steps for meaningful analysis. Current post-alignment BS-sequencing programmes are generally focused on the gene-specific level, a restrictive feature when analysis in the non-coding regions, such as enhancers and intergenic microRNAs, is required. Here, we present Genome Bisulfite Sequencing Analyser (GBSA—http://ctrad-csi.nus.edu.sg/gbsa), a free open-source software capable of analysing whole-genome bisulfite sequencing data with either a gene-centric or gene-independent focus. Through analysis of the largest published data sets to date, we demonstrate GBSA’s features in providing sequencing quality assessment, methylation scoring, functional data management and visualization of genomic methylation at nucleotide resolution. Additionally, we show that GBSA’s output can be easily integrated with other high-throughput sequencing data, such as RNA-Seq or ChIP-seq, to elucidate the role of methylated intergenic regions in gene regulation. In essence, GBSA allows an investigator to explore not only known loci but also all the genomic regions, for which methylation studies could lead to the discovery of new regulatory mechanisms. PMID:23268441

  3. A polymerase engineered for bisulfite sequencing

    PubMed Central

    Millar, Doug; Christova, Yonka; Holliger, Philipp

    2015-01-01

    Bisulfite sequencing is a key methodology in epigenetics. However, the standard workflow of bisulfite sequencing involves heat and strongly basic conditions to convert the intermediary product 5,6-dihydrouridine-6-sulfonate (dhU6S) (generated by reaction of bisulfite with deoxycytidine (dC)) to uracil (dU). These harsh conditions generally lead to sample loss and DNA damage while milder conditions may result in incomplete conversion of intermediates to uracil. Both can lead to poor recovery of bisulfite-treated DNA by the polymerase chain reaction (PCR) as either damaged DNA and/or intermediates of bisulfite treatment are poor substrate for standard DNA polymerases. Here we describe an engineered DNA polymerase (5D4) with an enhanced ability to replicate and PCR amplify bisulfite-treated DNA due to an ability to bypass both DNA lesions and bisulfite intermediates, allowing significantly milder conversion conditions and increased sensitivity in the PCR amplification of bisulfite-treated DNA. Incorporation of the 5D4 DNA polymerase into the bisulfite sequencing workflow thus promises significant sensitivity and efficiency gains. PMID:26271989

  4. A polymerase engineered for bisulfite sequencing.

    PubMed

    Millar, Doug; Christova, Yonka; Holliger, Philipp

    2015-12-15

    Bisulfite sequencing is a key methodology in epigenetics. However, the standard workflow of bisulfite sequencing involves heat and strongly basic conditions to convert the intermediary product 5,6-dihydrouridine-6-sulfonate (dhU6S) (generated by reaction of bisulfite with deoxycytidine (dC)) to uracil (dU). These harsh conditions generally lead to sample loss and DNA damage while milder conditions may result in incomplete conversion of intermediates to uracil. Both can lead to poor recovery of bisulfite-treated DNA by the polymerase chain reaction (PCR) as either damaged DNA and/or intermediates of bisulfite treatment are poor substrate for standard DNA polymerases. Here we describe an engineered DNA polymerase (5D4) with an enhanced ability to replicate and PCR amplify bisulfite-treated DNA due to an ability to bypass both DNA lesions and bisulfite intermediates, allowing significantly milder conversion conditions and increased sensitivity in the PCR amplification of bisulfite-treated DNA. Incorporation of the 5D4 DNA polymerase into the bisulfite sequencing workflow thus promises significant sensitivity and efficiency gains. PMID:26271989

  5. Effects of oxygen and weak magnetic field on Fe(0)/bisulfite system: performance and mechanisms.

    PubMed

    Xiong, Xinmei; Gan, Jinhong; Zhan, Wei; Sun, Bo

    2016-08-01

    The performance and mechanisms of 4-nitrophenol (4-NP) degradation by the Fe(0)/bisulfite system were systematically investigated for the first time. The evidences presented in this study verified that O2 was a crucial factor that affected the mechanism of Fe(0)/bisulfite-driven 4-NP degradation. In the Fe(0)/bisulfite/O2 system, Fe(0) acted as a supplier of Fe(2+) to catalyze bisulfite oxidation that induced a chain reaction to produce reactive radicals for 4-NP degradation. While under N2 purging condition, bisulfite worked as a specified reductant that facilitated the transformation of Fe(3+) to nascent Fe(2+) ions, which principally accounted for the reductive removal of 4-NP. The application of a weak magnetic field (WMF) efficiently improved the removal rate of 4-NP and did not alter the mechanisms in both Fe(0)/bisulfite/O2 and Fe(0)/bisulfite/N2 processes. The secondary radicals, HO(·), SO4 (·-), and SO5 (·-), were considered as the most possible active oxidants contributing to the oxidative removal of 4-NP and even partial mineralization under an oxic condition. Compared with anoxic conditions, the performance removal of 4-NP by the WMF-Fe(0)/bisulfite/O2 system showed less pHini dependence. To facilitate the application of WMF-Fe(0)/bisulfite/O2 technology in real practice, premagnetization of Fe(0) was employed to combine with bisulfite/O2 and proved to be an effective and applicable method for 4-NP removal. PMID:27184150

  6. 21 CFR 182.3739 - Sodium bisulfite.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Sodium bisulfite. 182.3739 Section 182.3739 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) SUBSTANCES GENERALLY RECOGNIZED AS SAFE Chemical Preservatives § 182.3739 Sodium bisulfite. (a) Product....

  7. Alcohol and Sleep Restriction Combined Reduces Vigilant Attention, Whereas Sleep Restriction Alone Enhances Distractibility

    PubMed Central

    Lee, James; Manousakis, Jessica; Fielding, Joanne; Anderson, Clare

    2015-01-01

    Study Objectives: Alcohol and sleep loss are leading causes of motor vehicle crashes, whereby attention failure is a core causal factor. Despite a plethora of data describing the effect of alcohol and sleep loss on vigilant attention, little is known about their effect on voluntary and involuntary visual attention processes. Design: Repeated-measures, counterbalanced design. Setting: Controlled laboratory setting. Participants: Sixteen young (18–27 y; M = 21.90 ± 0.60 y) healthy males. Interventions: Participants completed an attention test battery during the afternoon (13:00–14:00) under four counterbalanced conditions: (1) baseline; (2) alcohol (0.05% breath alcohol concentration); (3) sleep restriction (02:00–07:00); and (4) alcohol/sleep restriction combined. This test battery included a Psychomotor Vigilance Task (PVT) as a measure of vigilant attention, and two ocular motor tasks—visually guided and antisaccade—to measure the involuntary and voluntary allocation of visual attention. Measurements and Results: Only the combined condition led to reductions in vigilant attention characterized by slower mean reaction time, fastest 10% responses, and increased number of lapses (P < 0.05) on the PVT. In addition, the combined condition led to a slowing in the voluntary allocation of attention as reflected by increased antisaccade latencies (P < 0.05). Sleep restriction alone however increased both antisaccade inhibitory errors [45.8% errors versus < 28.4% all others; P < 0.001] and the involuntary allocation of attention, as reflected by faster visually guided latencies (177.7 msec versus > 185.0 msec all others) to a peripheral target (P < 0.05). Conclusions: Our data reveal specific signatures for sleep related attention failure: the voluntary allocation of attention is impaired, whereas the involuntary allocation of attention is enhanced. This provides key evidence for the role of distraction in attention failure during sleep loss. Citation: Lee J

  8. Soil cations influence bryophyte susceptibility to bisulfite.

    PubMed

    Bharali, Bhagawan; Bates, Jeffrey W

    2002-09-01

    The hypothesis that metal ions absorbed by bryophytes from the underlying soil may ameliorate adverse effects of SO2 was investigated in the terricolous moss species Pleurozium schreberi (Brid.) Mitt. and Rhytidiadelphus triquetrus (Hedw.) Warnst. Dilute sodium bisulfite solutions (equivalent to dissolved SO2) were applied to shoots isolated from soil or in contact with artificial substrata. Marked inhibition of net photosynthesis was observed within 2 h of treatment with 0.3 mM bisulfite in both mosses. Progressive recovery of net photosynthesis occurred 2-8 h after bisulfite treatment, although the extent of this depended on the concentration and pH of the solution. When R. triquetrus and P. schreberi were grown on artificial substrata (calcareous, acid-mineral or acid-organic) with weekly bisulfite applications, the only significant effect was poorer growth of P. schreberi receiving bisulfite on the calcareous and acid-organic substrata. In both species, growth on the calcareous substratum led to increased concentrations of exchangeable Ca2+, whereas exchangeable Fe3+ concentrations increased following growth on the acid-mineral soil. In another experiment the two mosses were pre-treated with either Ca2+ or Fe3+ before incubation with bisulfite. In P. schreberi, the depression of net photosynthetic rate caused by bisulfite was ameliorated from 33 to 64% of the control by pre-treatment with Fe3+, but it was unaffected by Ca2+ pre-treatment. In R. triquetrus, the amelioration caused by Fe3+ pre-treatment was from 16 to 60% of the control, but pre-treatment with Ca2+ gave a greater amelioration, to 75% of the control value. The responses are discussed in terms of soil preferences of the mosses and possible underlying bisulfite amelioration mechanisms. PMID:12234145

  9. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.

    PubMed

    Kunde-Ramamoorthy, Govindarajan; Coarfa, Cristian; Laritsky, Eleonora; Kessler, Noah J; Harris, R Alan; Xu, Mingchu; Chen, Rui; Shen, Lanlan; Milosavljevic, Aleksandar; Waterland, Robert A

    2014-04-01

    Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered >70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation (r(2) ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8-12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage. PMID:24391148

  10. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing

    PubMed Central

    Kunde-Ramamoorthy, Govindarajan; Coarfa, Cristian; Laritsky, Eleonora; Kessler, Noah J.; Harris, R. Alan; Xu, Mingchu; Chen, Rui; Shen, Lanlan; Milosavljevic, Aleksandar; Waterland, Robert A.

    2014-01-01

    Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered >70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation (r2 ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8–12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage. PMID:24391148

  11. Fluorescence polarization-based method with bisulfite conversion-specific one-label extension for quantification of single CpG dinucleotide methylation.

    PubMed

    Li, Shufen; Wang, Zhongju; Zhou, Lin; Luo, Fu; Zhao, Cunyou

    2015-07-01

    To quantify the methylation at individual CpG dinucleotide sites in large biological or clinical samples, we developed a bisulfite conversion-specific one-label extension (BS-OLE) method using visualization by fluorescence polarization (FP) measurement of methylation at single CpG sites in small amounts of genomic DNA. Genomic DNA was treated with sodium bisulfite to convert unmethylated cytosine to uracil leaving 5-methylcytosine unaltered, and BS-PCR was used to generate DNA template containing target CpG sites. BS-OLE uses a BS-primer hybridized immediately upstream of the target CpG site being examined and then fluorescent dCTP or dUTP is incorporated into the methylated (CpG) or unmethylated (TpG) form of the target site through single-nucleotide chain extension, yielding an FP ratio between the fluorescent dCTP- and dUTP-incorporated products as a measure of methylation. This provides stable estimates of the methylation level of human genomic DNA and of a 250-bp plasmid DNA segment containing a single TCGA TaqI cleavage site, in accordance with the results of a combined bisulfite restriction analysis method. We used BS-OLE to measure dose-dependent DNA hypomethylation in human embryonic kidney 293T cells treated with the DNA methyltransferase inhibitor 5-aza-dC. BS-OLE is well suited to high-throughput multi-sample applications in biological and medical studies. PMID:26334496

  12. Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data

    PubMed Central

    2015-01-01

    Background DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technology to sequence bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation statuses of Cs. However, despite intense effort, a much smaller proportion of the reads derived from bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (> 90%), and it is unclear what factors lead to this low mapping efficiency. Results To address this issue, we used the hairpin bisulfite sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-bisulfite-converted sequences. We used Bismark for bisulfite read mapping and Bowtie2 for recovered read mapping. We found that recovering the reads improved unique mapping efficiency by 9-10% compared to the bisulfite reads. Such improvement in mapping efficiency is related to sequence entropy. Conclusions The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency. PMID:26576456

  13. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

    PubMed Central

    Stevens, Michael; Cheng, Jeffrey B.; Li, Daofeng; Xie, Mingchao; Hong, Chibo; Maire, Cécile L.; Ligon, Keith L.; Hirst, Martin; Marra, Marco A.; Costello, Joseph F.; Wang, Ting

    2013-01-01

    Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to map complete DNA methylomes. These include whole-genome bisulfite sequencing (WGBS, MethylC-seq, or BS-seq), reduced-representation bisulfite sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. These methods yield largely comparable results but differ significantly in extent of genomic CpG coverage, resolution, quantitative accuracy, and cost, at least while using current algorithms to interrogate the data. None of these existing methods provides single-CpG resolution, comprehensive genome-wide coverage, and cost feasibility for a typical laboratory. We introduce methylCRF, a novel conditional random fields–based algorithm that integrates methylated DNA immunoprecipitation (MeDIP-seq) and methylation-sensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single-CpG resolution. Our method is a combined computational and experimental strategy to produce DNA methylomes of all 28 million CpGs in the human genome for a fraction (<10%) of the cost of whole-genome bisulfite sequencing methods. methylCRF was benchmarked for accuracy against Infinium arrays, RRBS, WGBS sequencing, and locus-specific bisulfite sequencing performed on the same human embryonic stem cell line. methylCRF transformation of MeDIP-seq/MRE-seq was equivalent to a biological replicate of WGBS in quantification, coverage, and resolution. We used conventional bisulfite conversion, PCR, cloning, and sequencing to validate loci where our predictions do not agree with whole-genome bisulfite data, and in 11 out of 12 cases, methylCRF predictions of methylation level agree better with validated results than does whole-genome bisulfite sequencing. Therefore, methylCRF transformation of MeDIP-seq/MRE-seq data provides an accurate, inexpensive, and widely accessible strategy to create full DNA methylomes. PMID:23804401

  14. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.

    PubMed

    Stevens, Michael; Cheng, Jeffrey B; Li, Daofeng; Xie, Mingchao; Hong, Chibo; Maire, Cécile L; Ligon, Keith L; Hirst, Martin; Marra, Marco A; Costello, Joseph F; Wang, Ting

    2013-09-01

    Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to map complete DNA methylomes. These include whole-genome bisulfite sequencing (WGBS, MethylC-seq, or BS-seq), reduced-representation bisulfite sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. These methods yield largely comparable results but differ significantly in extent of genomic CpG coverage, resolution, quantitative accuracy, and cost, at least while using current algorithms to interrogate the data. None of these existing methods provides single-CpG resolution, comprehensive genome-wide coverage, and cost feasibility for a typical laboratory. We introduce methylCRF, a novel conditional random fields-based algorithm that integrates methylated DNA immunoprecipitation (MeDIP-seq) and methylation-sensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single-CpG resolution. Our method is a combined computational and experimental strategy to produce DNA methylomes of all 28 million CpGs in the human genome for a fraction (<10%) of the cost of whole-genome bisulfite sequencing methods. methylCRF was benchmarked for accuracy against Infinium arrays, RRBS, WGBS sequencing, and locus-specific bisulfite sequencing performed on the same human embryonic stem cell line. methylCRF transformation of MeDIP-seq/MRE-seq was equivalent to a biological replicate of WGBS in quantification, coverage, and resolution. We used conventional bisulfite conversion, PCR, cloning, and sequencing to validate loci where our predictions do not agree with whole-genome bisulfite data, and in 11 out of 12 cases, methylCRF predictions of methylation level agree better with validated results than does whole-genome bisulfite sequencing. Therefore, methylCRF transformation of MeDIP-seq/MRE-seq data provides an accurate, inexpensive, and widely accessible strategy to create full DNA methylomes. PMID:23804401

  15. 21 CFR 573.625 - Menadione nicotinamide bisulfite.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing § 573.625 Menadione nicotinamide bisulfite. The food additive may be safely... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Menadione nicotinamide bisulfite. 573.625...

  16. 21 CFR 573.625 - Menadione nicotinamide bisulfite.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing § 573.625 Menadione nicotinamide bisulfite. The food additive may be safely... 21 Food and Drugs 6 2011-04-01 2011-04-01 false Menadione nicotinamide bisulfite. 573.625...

  17. 21 CFR 573.620 - Menadione dimethylpyrimidinol bisulfite.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing § 573.620 Menadione dimethylpyrimidinol bisulfite. The food additive... 21 Food and Drugs 6 2011-04-01 2011-04-01 false Menadione dimethylpyrimidinol bisulfite....

  18. 21 CFR 573.620 - Menadione dimethylpyrimidinol bisulfite.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing § 573.620 Menadione dimethylpyrimidinol bisulfite. The food additive... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Menadione dimethylpyrimidinol bisulfite....

  19. 21 CFR 573.620 - Menadione dimethylpyrimidinol bisulfite.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing § 573.620 Menadione dimethylpyrimidinol bisulfite. The food additive... 21 Food and Drugs 6 2012-04-01 2012-04-01 false Menadione dimethylpyrimidinol bisulfite....

  20. Bisulfite Conversion of DNA: Performance Comparison of Different Kits and Methylation Quantitation of Epigenetic Biomarkers that Have the Potential to Be Used in Non-Invasive Prenatal Testing

    PubMed Central

    Leontiou, Chrysanthia A.; Hadjidaniel, Michael D.; Mina, Petros; Antoniou, Pavlos; Ioannides, Marios; Patsalis, Philippos C.

    2015-01-01

    Introduction Epigenetic alterations, including DNA methylation, play an important role in the regulation of gene expression. Several methods exist for evaluating DNA methylation, but bisulfite sequencing remains the gold standard by which base-pair resolution of CpG methylation is achieved. The challenge of the method is that the desired outcome (conversion of unmethylated cytosines) positively correlates with the undesired side effects (DNA degradation and inappropriate conversion), thus several commercial kits try to adjust a balance between the two. The aim of this study was to compare the performance of four bisulfite conversion kits [Premium Bisulfite kit (Diagenode), EpiTect Bisulfite kit (Qiagen), MethylEdge Bisulfite Conversion System (Promega) and BisulFlash DNA Modification kit (Epigentek)] regarding conversion efficiency, DNA degradation and conversion specificity. Methods Performance was tested by combining fully methylated and fully unmethylated λ-DNA controls in a series of spikes by means of Sanger sequencing (0%, 25%, 50% and 100% methylated spikes) and Next-Generation Sequencing (0%, 3%, 5%, 7%, 10%, 25%, 50% and 100% methylated spikes). We also studied the methylation status of two of our previously published differentially methylated regions (DMRs) at base resolution by using spikes of chorionic villus sample in whole blood. Results The kits studied showed different but comparable results regarding DNA degradation, conversion efficiency and conversion specificity. However, the best performance was observed with the MethylEdge Bisulfite Conversion System (Promega) followed by the Premium Bisulfite kit (Diagenode). The DMRs, EP6 and EP10, were confirmed to be hypermethylated in the CVS and hypomethylated in whole blood. Conclusion Our findings indicate that the MethylEdge Bisulfite Conversion System (Promega) was shown to have the best performance among the kits. In addition, the methylation level of two of our DMRs, EP6 and EP10, was confirmed

  1. Fractionation of oil palm empty fruit bunch by bisulfite pretreatment for the production of bioethanol and high value products.

    PubMed

    Tan, Liping; Wang, Meimei; Li, Xuezhi; Li, Hongxing; Zhao, Jian; Qu, Yinbo; Choo, Yuen May; Loh, Soh Kheang

    2016-01-01

    In this work, fractionation of empty fruit bunch (EFB) by bisulfite pretreatment was studied for the production of bioethanol and high value products to achieve biorefinery of EFB. EFB was fractionated to solid and liquor components by bisulfite process. The solid components were used for bioethanol production by quasi-simultaneous saccharification and fermentation. The liquor components were then converted to furfural by hydrolysis with sulfuric acid. Preliminary results showed that the concentration of furfural was highest at 18.8g/L with 0.75% sulfuric acid and reaction time of 25min. The conversion of xylose to furfural was 82.5%. Furthermore, we attempted to fractionate the liquor into hemicellulose sugars and lignin by different methods for producing potential chemicals, such as xylose, xylooligosaccharide, and lignosulfonate. Our research showed that the combination of bisulfite pretreatment and resin separation could effectively fractionate EFB components to produce bioethanol and other high value chemicals. PMID:26539970

  2. An integrative approach for efficient analysis of whole genome bisulfite sequencing data

    PubMed Central

    2015-01-01

    Background Whole genome bisulfite sequencing (WGBS) is a high-throughput technique for profiling genome-wide DNA methylation at single nucleotide resolution. However, the applications of WGBS are limited by low accuracy resulting from bisulfite-induced damage on DNA fragments. Although many computer programs have been developed for accurate detecting, most of the programs have barely succeeded in improving either quantity or quality of the methylation results. To improve both, we attempted to develop a novel integration of most widely used bisulfite-read mappers: Bismark, BSMAP, and BS-seeker2. Results A comprehensive analysis of the three mappers revealed that the mapping results of the mappers were mutually complementary under diverse read conditions. Therefore, we sought to integrate the characteristics of the mappers by scoring them to gain robustness against artifacts. As a result, the integration significantly increased detection accuracy compared with the individual mappers. In addition, the amount of detected cytosine was higher than that by Bismark. Furthermore, the integration successfully reduced the fluctuation of detection accuracy induced by read conditions. We applied the integration to real WGBS samples and succeeded in classifying the samples according to the originated tissues by both CpG and CpH methylation patterns. Conclusions In this study, we improved both quality and quantity of methylation results from WGBS data by integrating the mapping results of three bisulfite-read mappers. Also, we succeeded in combining and comparing WGBS samples by reducing the effects of read heterogeneity on methylation detection. This study contributes to DNA methylation researches by improving efficiency of methylation detection from WGBS data and facilitating the comprehensive analysis of public WGBS data. PMID:26680746

  3. Detoxification of Dissolved SO2 (Bisulfite) by Terricolous Mosses

    PubMed Central

    BHARALI, BHAGAWAN; BATES, JEFFREY W.

    2006-01-01

    • Background and Aims The widespread calcifuge moss Pleurozium schreberi is moderately tolerant of SO2, whereas Rhytidiadelphus triquetrus is limited to calcareous soils in regions of the UK that were strongly affected by SO2 pollution in the 20th century. The proposition that tolerance of SO2 by these terricolous mosses depends on metabolic detoxification of dissolved bisulfite was investigated. • Methods The capacities of the two mosses to accelerate loss of bisulfite from aqueous solutions of NaHSO3 were studied using DTNB [5, 5-dithio-(2-nitrobenzoic acid)] to assay bisulfite, and HPLC to assay sulfate in the incubation solutions. Incubations were performed for different durations, in the presence and absence of light, at a range of solution pH values, in the presence of metabolic inhibitors and with altered moss apoplastic Ca2+ and Fe3+ levels. • Key Results Bisulfite disappearance was markedly stimulated in the light and twice as great for R. triquetrus as for P. schreberi. DCMU, an inhibitor of photosynthetic electron chain transport, significantly reduced bisufite loss. • Conclusions Bisulfite (SO2) tolerance in these terricolous mosses involves extracellular oxidation using metabolic (photo-oxidative) energy, passive oxidation by adsorbed Fe3+ (only available to the calcifuge) and probably also internal metabolic detoxification. PMID:16319108

  4. Comparison and quantitative verification of mapping algorithms for whole genome bisulfite sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitat...

  5. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters

    PubMed Central

    Grunau, C.; Clark, S. J.; Rosenthal, A.

    2001-01-01

    Bisulfite genomic sequencing is the method of choice for the generation of methylation maps with single-base resolution. The method is based on the selective deamination of cytosine to uracil by treatment with bisulfite and the sequencing of subsequently generated PCR products. In contrast to cytosine, 5-methylcytosine does not react with bisulfite and can therefore be distinguished. In order to investigate the potential for optimization of the method and to determine the critical experimental parameters, we determined the influence of incubation time and incubation temperature on the deamination efficiency and measured the degree of DNA degradation during the bisulfite treatment. We found that maximum conversion rates of cytosine occurred at 55°C (4–18 h) and 95°C (1 h). Under these conditions at least 84–96% of the DNA is degraded. To study the impact of primer selection, homologous DNA templates were constructed possessing cytosine-containing and cytosine-free primer binding sites, respectively. The recognition rates for cytosine (≥97%) and 5-methylcytosine (≥94%) were found to be identical for both templates. PMID:11433041

  6. Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools

    PubMed Central

    Zhang, Liqing

    2014-01-01

    Background. Large-scale bisulfite treatment and short reads sequencing technology allow comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate characterization of DNA methylation is essential for understanding genotype phenotype association, gene and environment interaction, diseases, and cancer. Aligning bisulfite short reads to a reference genome has been a challenging task. We compared five bisulfite short read mapping tools, BSMAP, Bismark, BS-Seeker, BiSS, and BRAT-BW, representing two classes of mapping algorithms (hash table and suffix/prefix tries). We examined their mapping efficiency (i.e., the percentage of reads that can be mapped to the genomes), usability, running time, and effects of changing default parameter settings using both real and simulated reads. We also investigated how preprocessing data might affect mapping efficiency. Conclusion. Among the five programs compared, in terms of mapping efficiency, Bismark performs the best on the real data, followed by BiSS, BSMAP, and finally BRAT-BW and BS-Seeker with very similar performance. If CPU time is not a constraint, Bismark is a good choice of program for mapping bisulfite treated short reads. Data quality impacts a great deal mapping efficiency. Although increasing the number of mismatches allowed can increase mapping efficiency, it not only significantly slows down the program, but also runs the risk of having increased false positives. Therefore, users should carefully set the related parameters depending on the quality of their sequencing data. PMID:24839440

  7. Objective and comprehensive evaluation of bisulfite short read mapping tools.

    PubMed

    Tran, Hong; Porter, Jacob; Sun, Ming-An; Xie, Hehuang; Zhang, Liqing

    2014-01-01

    Background. Large-scale bisulfite treatment and short reads sequencing technology allow comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate characterization of DNA methylation is essential for understanding genotype phenotype association, gene and environment interaction, diseases, and cancer. Aligning bisulfite short reads to a reference genome has been a challenging task. We compared five bisulfite short read mapping tools, BSMAP, Bismark, BS-Seeker, BiSS, and BRAT-BW, representing two classes of mapping algorithms (hash table and suffix/prefix tries). We examined their mapping efficiency (i.e., the percentage of reads that can be mapped to the genomes), usability, running time, and effects of changing default parameter settings using both real and simulated reads. We also investigated how preprocessing data might affect mapping efficiency. Conclusion. Among the five programs compared, in terms of mapping efficiency, Bismark performs the best on the real data, followed by BiSS, BSMAP, and finally BRAT-BW and BS-Seeker with very similar performance. If CPU time is not a constraint, Bismark is a good choice of program for mapping bisulfite treated short reads. Data quality impacts a great deal mapping efficiency. Although increasing the number of mismatches allowed can increase mapping efficiency, it not only significantly slows down the program, but also runs the risk of having increased false positives. Therefore, users should carefully set the related parameters depending on the quality of their sequencing data. PMID:24839440

  8. Base-resolution detection of N 4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing

    DOE PAGESBeta

    Yu, Miao; Ji, Lexiang; Neumann, Drexel A.; Chung, Dae -Hwan; Groom, Joseph; Westpheling, Janet; He, Chuan; Schmitz, Robert J.

    2015-07-15

    Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification of DNA methylation in R-M systems, including N6-methyladenine (6mA), 5-methylcytosine (5mC) and N4-methylcytosine (4mC), will enable strategies to make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable of detecting 4mC directly for any bacterial species regardless of whether an assembled genome exists or not, it is not as scalable to profiling hundreds to thousands of samples compared with the commonly used next-generation sequencing technologies. Here, we present 4mC-Tet-assisted bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that rapidly andmore » cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. In 4mC-TAB-seq, both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out as cytosines, revealing their specific positions throughout the genome. We applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc genus, Caldicellulosiruptor, in which 4mC-related restriction is a major barrier to DNA transformation from other species. Lastly, in combination with MethylC-seq, both 4mC- and 5mC-containing motifs are identified which can assist in rapid and efficient genetic engineering of these bacteria in the future.« less

  9. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing

    PubMed Central

    Yu, Miao; Ji, Lexiang; Neumann, Drexel A.; Chung, Dae-hwan; Groom, Joseph; Westpheling, Janet; He, Chuan; Schmitz, Robert J.

    2015-01-01

    Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification of DNA methylation in R-M systems, including N6-methyladenine (6mA), 5-methylcytosine (5mC) and N4-methylcytosine (4mC), will enable strategies to make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable of detecting 4mC directly for any bacterial species regardless of whether an assembled genome exists or not, it is not as scalable to profiling hundreds to thousands of samples compared with the commonly used next-generation sequencing technologies. Here, we present 4mC-Tet-assisted bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that rapidly and cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. In 4mC-TAB-seq, both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out as cytosines, revealing their specific positions throughout the genome. We applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc genus, Caldicellulosiruptor, in which 4mC-related restriction is a major barrier to DNA transformation from other species. In combination with MethylC-seq, both 4mC- and 5mC-containing motifs are identified which can assist in rapid and efficient genetic engineering of these bacteria in the future. PMID:26184871

  10. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing

    DOE PAGESBeta

    Yu, Miao; Ji, Lexiang; Neumann, Drexel A.; Chung, Dae -Hwan; Groom, Joseph; Westpheling, Janet; He, Chuan; Schmitz, Robert J.

    2015-07-15

    Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification of DNA methylation in R-M systems, including N6-methyladenine (6mA), 5-methylcytosine (5mC) and N4-methylcytosine (4mC), will enable strategies to make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable of detecting 4mC directly for any bacterial species regardless of whether an assembled genome exists or not, it is not as scalable to profiling hundreds to thousands of samples compared with the commonly used next-generation sequencing technologies. Here, we present 4mC-Tet-assisted bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that rapidly andmore » cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. In 4mC-TAB-seq, both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out as cytosines, revealing their specific positions throughout the genome. We applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc genus, Caldicellulosiruptor, in which 4mC-related restriction is a major barrier to DNA transformation from other species. Lastly, in combination with MethylC-seq, both 4mC- and 5mC-containing motifs are identified which can assist in rapid and efficient genetic engineering of these bacteria in the future.« less

  11. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

    PubMed Central

    Hodges, Emily; Smith, Andrew D.; Kendall, Jude; Xuan, Zhenyu; Ravi, Kandasamy; Rooks, Michelle; Zhang, Michael Q.; Ye, Kenny; Bhattacharjee, Arindam; Brizuela, Leonardo; McCombie, W. Richard; Wigler, Michael; Hannon, Gregory J.; Hicks, James B.

    2009-01-01

    DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. This single molecule strategy enables methylation variable positions to be quantitatively examined with high sampling precision. Using bisulfite capture, we assessed methylation patterns across 324 randomly selected CpG islands (CGI) representing more than 25,000 CpG sites. A single lane of Illumina sequencing permitted methylation states to be definitively called for >90% of target sties. The accuracy of the hybrid-selection approach was verified using conventional bisulfite capillary sequencing of cloned PCR products amplified from a subset of the selected regions. This confirmed that even partially methylated states could be successfully called. A comparison of human primary and cancer cells revealed multiple differentially methylated regions. More than 25% of islands showed complex methylation patterns either with partial methylation states defining the entire CGI or with contrasting methylation states appearing in specific regional blocks within the island. We observed that transitions in methylation state often correlate with genomic landmarks, including transcriptional start sites and intron-exon junctions. Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs. PMID:19581485

  12. Restricted heterogeneity of T lymphocytes in combined immunodeficiency with hypereosinophilia (Omenn's syndrome).

    PubMed Central

    de Saint-Basile, G; Le Deist, F; de Villartay, J P; Cerf-Bensussan, N; Journet, O; Brousse, N; Griscelli, C; Fischer, A

    1991-01-01

    We report the immunological characteristics of five patients with Omenn's syndrome, a rare inherited immunodeficiency also known as combined immunodeficiency with hypereosinophilia. The syndrome is characterized by T cell infiltration of skin, gut, liver, and spleen leading to diffuse erythroderma, protracted diarrhea, failure to thrive, and hepatosplenomegaly. Blood T cells as well as those infiltrating the skin and gut were found to express activation markers and were partially activated by mitogens but not by antigens. Although the lesions resembled those in graft-versus-host disease, the blood T cells were shown by DNA haplotype analysis using probes revealing variable number of tandem repeats to belong to the patients as well as the T cells infiltrating the gut and skin in one patient. A given T cell subset (TCR alpha beta+, CD4+/CD8+, or TCR gamma delta+) was predominant in each patient, with a specific distribution in the skin lesions. Moreover, the study of T cell receptor beta, gamma, and delta gene rearrangements in four patients revealed oligoclonality involving C beta 1, C beta 2, or different V gamma J gamma or V delta J delta genes. This indicates that restricted heterogeneity of the T cell repertoire, previously reported in one case, is a major feature of this syndrome. The occurrence of alymphocytosis-type severe combined immunodeficiency in the brother of one of the patients suggests that the restricted heterogeneity of T cell receptor gene usage in Omenn's syndrome may arise from leakiness, within the context of a genetically determined faulty T cell differentiation. Images PMID:2010548

  13. A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads

    PubMed Central

    Tran, Hong; Wu, Xiaowei; Tithi, Saima; Sun, Ming-an; Xie, Hehuang; Zhang, Liqing

    2016-01-01

    DNA methylation is an epigenetic modification critical for normal development and diseases. The determination of genome-wide DNA methylation at single-nucleotide resolution is made possible by sequencing bisulfite treated DNA with next generation high-throughput sequencing. However, aligning bisulfite short reads to a reference genome remains challenging as only a limited proportion of them (around 50–70%) can be aligned uniquely; a significant proportion, known as multireads, are mapped to multiple locations and thus discarded from downstream analyses, causing financial waste and biased methylation inference. To address this issue, we develop a Bayesian model that assigns multireads to their most likely locations based on the posterior probability derived from information hidden in uniquely aligned reads. Analyses of both simulated data and real hairpin bisulfite sequencing data show that our method can effectively assign approximately 70% of the multireads to their best locations with up to 90% accuracy, leading to a significant increase in the overall mapping efficiency. Moreover, the assignment model shows robust performance with low coverage depth, making it particularly attractive considering the prohibitive cost of bisulfite sequencing. Additionally, results show that longer reads help improve the performance of the assignment model. The assignment model is also robust to varying degrees of methylation and varying sequencing error rates. Finally, incorporating prior knowledge on mutation rate and context specific methylation level into the assignment model increases inference accuracy. The assignment model is implemented in the BAM-ABS package and freely available at https://github.com/zhanglabvt/BAM_ABS. PMID:27011215

  14. Inhibition of phospholipase A/sub 2/ from human plasma by sodium bisulfite

    SciTech Connect

    Wiggins, C.W.; Franson, R.C.

    1987-05-01

    The anti-oxidant sodium bisulfite has been shown to inhibit acid active(lysosomal), non-Ca/sup + +/-dependent phospholipase A/sub 2/ (PLA/sub 2/), and to interact reversibly with unsaturated fatty acids, altering their chromatographic mobility. The authors examined the effect of bisulfite on neutral active, Ca/sup + +/-dependent PLA/sub 2/ from human plasma. Using (1-/sup 14/C)oleate-labelled autoclaved E. coli as substrate, PLA/sub 2/ activity was inhibited in a dose-dependent manner by bisulfite. Maximal inhibition occurred at 100..mu..M bisulfite. Preincubation of plasma for 0-30 minutes with bisulfite resulted in a time-dependent increase in PLA/sub 2/ inhibition. Preincubation of substrate with bisulfite had no such effect. When the plasma PLA/sub 2/ was purified 25-fold by SP-Sephadex chromatography it was no longer inhibited by bisulfite. The SP-Sephadex wash through fraction, which contained greater than 95% of the applied protein but not PLA/sub 2/ activity, did not inhibit the purified enzyme. When incubated with bisulfite however, the SP-wash through fraction produced dose-dependent inhibition of the purified enzyme. These results indicate that sodium bisulfite inhibits human plasma PLA/sub 2/, in vitro, indirectly by interaction with a factor(s) present in plasma and suggests that anti-oxidants may similarly influence expression of extracellular PLA/sub 2/ in vivo.

  15. A comparative study of the corrosion of tin-free steel and iron in sodium bisulfite

    SciTech Connect

    Seshadri, G.; Bower, K.A.; Brooks, R.W.; Kelber, J.A.

    1995-03-01

    The authors have examined the electrochemical behavior of tin-free steel chromium type (TFS-CT) and polycrystalline iron electrodes in sodium bisulfite containing Perchlorate and nitrate solutions. Their experiments indicate that TFS-CT corrodes on exposure to sodium bisulfite. The extent to which passivation is prevented depends on the supporting electrolyte. A very interesting feature that the authors have observed is that TFS-CT exhibits a ``memory`` of exposure to sodium bisulfite, in that it does not repassivate when subsequently cycled in a bisulfite-free supporting electrolyte. This ``memory effect`` and the extent of corrosion depend on the supporting electrolyte used. Polycrystalline iron electrodes on the other hand, corrode on exposure to sodium bisulfite, but repassivate when returned to a supporting electrolyte that is free of bisulfite. The results indicate that bisulfite attacks the protective chrome oxide coating partially or completely, inhibiting subsequent passivation even in bisulfite-free electrolytes. The results also indicate that reactions of the bisulfite exposed surface with Perchlorate or nitrate anions significantly affect corrosion behavior.

  16. Ultrasound Evaluation of the Combined Effects of Thoracolumbar Fascia Injury and Movement Restriction in a Porcine Model

    PubMed Central

    Bishop, James H.; Fox, James R.; Maple, Rhonda; Loretan, Caitlin; Badger, Gary J.; Henry, Sharon M.; Vizzard, Margaret A.; Langevin, Helene M.

    2016-01-01

    The persistence of back pain following acute back “sprains” is a serious public health problem with poorly understood pathophysiology. The recent finding that human subjects with chronic low back pain (LBP) have increased thickness and decreased mobility of the thoracolumbar fascia measured with ultrasound suggest that the fasciae of the back may be involved in LBP pathophysiology. This study used a porcine model to test the hypothesis that similar ultrasound findings can be produced experimentally in a porcine model by combining a local injury of fascia with movement restriction using a “hobble” device linking one foot to a chest harness for 8 weeks. Ultrasound measurements of thoracolumbar fascia thickness and shear plane mobility (shear strain) during passive hip flexion were made at the 8 week time point on the non-intervention side (injury and/or hobble). Injury alone caused both an increase in fascia thickness (p = .007) and a decrease in fascia shear strain on the non-injured side (p = .027). Movement restriction alone did not change fascia thickness but did decrease shear strain on the non-hobble side (p = .024). The combination of injury plus movement restriction had additive effects on reducing fascia mobility with a 52% reduction in shear strain compared with controls and a 28% reduction compared to movement restriction alone. These results suggest that a back injury involving fascia, even when healed, can affect the relative mobility of fascia layers away from the injured area, especially when movement is also restricted. PMID:26820883

  17. Kinetics, mechanism and thermodynamics of bisulfite-aldehyde adduct formation

    SciTech Connect

    Olson, T.M.; Boyce, S.D.; Hoffmann, M.R.

    1986-04-01

    The kinetics and mechanism of bisulfite addition to benzaldehyde were studied at low pH in order to assess the importance of this reaction in stabilizing S(IV) in fog-, cloud-, and rainwater. Previously, the authors established that appreciable concentrations of the formaldehyde-bisulfite adduct (HMSA) are often present in fogwater. Measured HMSA concentrations in fogwater often do not fully account for observed excess S(IV) concentrations, however, so that other S(IV)-aldehyde adducts may be present. Reaction rates were determined by monitoring the disappearance of benzaldehyde by U.V. spectrophotometry under pseudo-first order conditions, (S(IV))/sub T/ >>(phi-CHO)/sub T/, in the pH range 0 - 4.4 at 25/sup 0/C. The equilibrium constant was determined by dissolving the sodium salt of the addition compound in a solution adjusted to pH 3.9, and measuring the absorbance of the equilibrated solution at 250 nm. A literature value of the extinction coefficient for benzaldehyde was used to calculate the concentration of free benzaldehyde. All solutions were prepared under an N/sub 2/ atmosphere using deoxygenated, deionized water and ionic strength was maintained at 1.0 M with sodium chloride.

  18. MethylCoder: software pipeline for bisulfite-treated sequences

    PubMed Central

    Pedersen, Brent; Hsieh, Tzung-Fu; Ibarra, Christian; Fischer, Robert L.

    2011-01-01

    Motivation: MethylCoder is a software program that generates per-base methylation data given a set of bisulfite-treated reads. It provides the option to use either of two existing short-read aligners, each with different strengths. It accounts for soft-masked alignments and overlapping paired-end reads. MethylCoder outputs data in text and binary formats in addition to the final alignment in SAM format, so that common high-throughput sequencing tools can be used on the resulting output. It is more flexible than existing software and competitive in terms of speed and memory use. Availability: MethylCoder requires only a python interpreter and a C compiler to run. Extensive documentation and the full source code are available under the MIT license at: https://github.com/brentp/methylcode. Contact: bpederse@gmail.com PMID:21724594

  19. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes

    PubMed Central

    Fu, Yong-Bi; Peterson, Gregory W.; Dong, Yibo

    2016-01-01

    Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7–6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0–16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications. PMID:26818077

  20. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing

    SciTech Connect

    Yu, Miao; Ji, Lexiang; Neumann, Drexel A.; Chung, Dae -Hwan; Groom, Joseph; Westpheling, Janet; He, Chuan; Schmitz, Robert J.

    2015-07-15

    Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification of DNA methylation in R-M systems, including N6-methyladenine (6mA), 5-methylcytosine (5mC) and N4-methylcytosine (4mC), will enable strategies to make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable of detecting 4mC directly for any bacterial species regardless of whether an assembled genome exists or not, it is not as scalable to profiling hundreds to thousands of samples compared with the commonly used next-generation sequencing technologies. Here, we present 4mC-Tet-assisted bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that rapidly and cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. In 4mC-TAB-seq, both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out as cytosines, revealing their specific positions throughout the genome. We applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc genus, Caldicellulosiruptor, in which 4mC-related restriction is a major barrier to DNA transformation from other species. Lastly, in combination with MethylC-seq, both 4mC- and 5mC-containing motifs are identified which can assist in rapid and efficient genetic engineering of these bacteria in the future.

  1. Novel restricted access materials combined to molecularly imprinted polymers for selective solid-phase extraction of organophosphorus pesticides from honey.

    PubMed

    He, Juan; Song, Lixin; Chen, Si; Li, Yuanyuan; Wei, Hongliang; Zhao, Dongxin; Gu, Keren; Zhang, Shusheng

    2015-11-15

    A novel restricted access materials (RAM) combined to molecularly imprinted polymers (MIPs), using malathion as template molecule and glycidilmethacrylate (GMA) as pro-hydrophilic co-monomer, were prepared for the first time. RAM-MIPs with hydrophilic external layer were characterized by scanning electron microscopy and recognition and selectivity properties were compared with the restricted access materials-non-molecularly imprinted polymers (RAM-NIPs) and unmodified MIPs. RAM-MIPs were used as the adsorbent enclosed in solid phase extraction column and several important extraction parameters were comprehensively optimized to evaluate the extraction performance. Under the optimum extraction conditions, RAM-MIPs exhibited comparable or even higher selectivity with greater extraction capacity toward six kinds of organophosphorus pesticides (including malathion, ethoprophos, phorate, terbufos, dimethoate, and fenamiphos) compared with the MIPs and commercial solid phase extraction columns. The RAM-MIPs solid phase extraction coupled with gas chromatography was successfully applied to simultaneously determine six kinds of organophosphorus pesticides from honey sample. The new established method showed good linearity in the range of 0.01-1.0 μg mL(-1), low limits of detection (0.0005-0.0019 μg mL(-1)), acceptable reproducibility (RSD, 2.26-4.81%, n = 6), and satisfactory relative recoveries (90.9-97.6%). It was demonstrated that RAM-MIPs solid phase extraction with excellent selectivity and restricted access function was a simple, rapid, selective, and effective sample pretreatment method. PMID:25977034

  2. Information recovery from low coverage whole-genome bisulfite sequencing

    PubMed Central

    Libertini, Emanuele; Heath, Simon C.; Hamoudi, Rifat A.; Gut, Marta; Ziller, Michael J.; Czyz, Agata; Ruotti, Victor; Stunnenberg, Hendrik G.; Frontini, Mattia; Ouwehand, Willem H.; Meissner, Alexander; Gut, Ivo G.; Beck, Stephan

    2016-01-01

    The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs). Using this tool, we demonstrate recovery of ∼30% of the lost DMP information content as DMCs even at very low (5X) coverage. This constitutes twice the amount that can be recovered using an existing method based on differentially methylated regions (DMRs). In addition, we explored the relationship between COMETs and haplotypes in lymphoblastoid cell lines of African and European origin. Using best fit analysis, we show COMETs to be correlated in a population-specific manner, suggesting that this type of dynamic segmentation may be useful for integrated (epi)genome-wide association studies in the future. PMID:27346250

  3. Information recovery from low coverage whole-genome bisulfite sequencing.

    PubMed

    Libertini, Emanuele; Heath, Simon C; Hamoudi, Rifat A; Gut, Marta; Ziller, Michael J; Czyz, Agata; Ruotti, Victor; Stunnenberg, Hendrik G; Frontini, Mattia; Ouwehand, Willem H; Meissner, Alexander; Gut, Ivo G; Beck, Stephan

    2016-01-01

    The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs). Using this tool, we demonstrate recovery of ∼30% of the lost DMP information content as DMCs even at very low (5X) coverage. This constitutes twice the amount that can be recovered using an existing method based on differentially methylated regions (DMRs). In addition, we explored the relationship between COMETs and haplotypes in lymphoblastoid cell lines of African and European origin. Using best fit analysis, we show COMETs to be correlated in a population-specific manner, suggesting that this type of dynamic segmentation may be useful for integrated (epi)genome-wide association studies in the future. PMID:27346250

  4. Lung Injury Combined with Loss of Regulatory T Cells Leads to De Novo Lung-Restricted Autoimmunity.

    PubMed

    Chiu, Stephen; Fernandez, Ramiro; Subramanian, Vijay; Sun, Haiying; DeCamp, Malcolm M; Kreisel, Daniel; Perlman, Harris; Budinger, G R Scott; Mohanakumar, Thalachallour; Bharat, Ankit

    2016-07-01

    More than one third of patients with chronic lung disease undergoing lung transplantation have pre-existing Abs against lung-restricted self-Ags, collagen type V (ColV), and k-α1 tubulin (KAT). These Abs can also develop de novo after lung transplantation and mediate allograft rejection. However, the mechanisms leading to lung-restricted autoimmunity remain unknown. Because these self-Ags are normally sequestered, tissue injury is required to expose them to the immune system. We previously showed that respiratory viruses can induce apoptosis in CD4(+)CD25(+)Foxp3(+) regulatory T cells (Tregs), the key mediators of self-tolerance. Therefore, we hypothesized that lung-tissue injury can lead to lung-restricted immunity if it occurs in a setting when Tregs are impaired. We found that human lung recipients who suffer respiratory viral infections experienced a decrease in peripheral Tregs. Pre-existing lung allograft injury from donor-directed Abs or gastroesophageal reflux led to new ColV and KAT Abs post respiratory viral infection. Similarly, murine parainfluenza (Sendai) respiratory viral infection caused a decrease in Tregs. Intratracheal instillation of anti-MHC class I Abs, but not isotype control, followed by murine Sendai virus infection led to development of Abs against ColV and KAT, but not collagen type II (ColII), a cartilaginous protein. This was associated with expansion of IFN-γ-producing CD4(+) T cells specific to ColV and KAT, but not ColII. Intratracheal anti-MHC class I Abs or hydrochloric acid in Foxp3-DTR mice induced ColV and KAT, but not ColII, immunity, only if Tregs were depleted using diphtheria toxin. We conclude that tissue injury combined with loss of Tregs can lead to lung-tissue-restricted immunity. PMID:27194786

  5. Effects of low concentrations of bisulfite-sulfite and nitrite on microorganisms.

    PubMed Central

    Wodzinski, R S; Labeda, D P; Alexander, M

    1978-01-01

    A wide range of microorganisms was tested to determine their sensitivity to low concentrations of bisulfite-sulfite and nitrite, solubility products of SO2 and NO2, respectively. Photosynthesis by blue-green algae (cyanobacteria) was more strongly inhibited by 0.1 mM bisulfite-sulfite and 1 mM nitrite at pH 6.0 than photosynthesis by eucaryotic algae and respiration of bacteria, fungi, and protozoa. At pH 7.7, blue-green algae were still more sensitive to bisulfite-sulfite and nitrite than eucaryotic algae, but the toxicity of bisulfite-sulfite and nitrite decreased as the pH increased. Photosynthesis by Anabaena flos-aquae at pH 6.0 was inhibited 25% by a bisulfite-sulfite concentration of 10 micrometer and 15% by a nitrite concentration of 50 micrometer. Photosynthesis by the blue-green alga, Lyngbya sp., was not exceptionally sensitive to chlorate and thiosulfate. Acetylene-reducing activity of Beijerinckia indica was completely inhibited by 0.1 mM bisulfite-sulfite at pH 4.0, the suppression being decreased with increasing pH. PMID:646357

  6. Is Patent “Evergreening” Restricting Access to Medicine/Device Combination Products?

    PubMed Central

    Beall, Reed F.; Nickerson, Jason W.; Kaplan, Warren A.; Attaran, Amir

    2016-01-01

    Background Not all new drug products are truly new. Some are the result of marginal innovation and incremental patenting of existing products, but in such a way that confers no major therapeutic improvement. This phenomenon, pejoratively known as “evergreening”, can allow manufacturers to preserve market exclusivity, but without significantly bettering the standard of care. Other studies speculate that evergreening is especially problematic for medicine/device combination products, because patents on the device component may outlast expired patents on the medicine component, and thereby keep competing, possibly less-expensive generic products off the market. Materials and Methods We focused on four common conditions that are often treated by medicine/device product combinations: asthma and chronic obstructive pulmonary disease (COPD), diabetes, and severe allergic reactions. The patent data for a sample of such products (n = 49) for treating these conditions was extracted from the United States Food and Drug Administration’s Orange Book. Additional patent-related data (abstracts, claims, etc) were retrieved using LexisNexis TotalPatent. Comparisons were then made between each product’s device patents and medicine patents. Results Unexpired device patents exist for 90 percent of the 49 medicine/device product combinations studied, and were the only sort of unexpired patent for 14 products. Overall, 55 percent of the 235 patents found by our study were device patents. Comparing the last-to-expire device patent to that of the last-to-expire active ingredient patent, the median additional years of patent protection afforded by device patents was 4.7 years (range: 1.3–15.2 years). Conclusion Incremental, patentable innovation in devices to extend the overall patent protection of medicine/device product combinations is very common. Whether this constitutes “evergreening” depends on whether these incremental innovations and the years of extra patent

  7. Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning

    PubMed Central

    Su, Chang; Wang, Chao; He, Lin; Yang, Chuanping; Wang, Yucheng

    2014-01-01

    DNA methylation plays a critical role in the regulation of gene expression. Most studies of DNA methylation have been performed in herbaceous plants, and little is known about the methylation patterns in tree genomes. In the present study, we generated a map of methylated cytosines at single base pair resolution for Betula platyphylla (white birch) by bisulfite sequencing combined with transcriptomics to analyze DNA methylation and its effects on gene expression. We obtained a detailed view of the function of DNA methylation sequence composition and distribution in the genome of B. platyphylla. There are 34,460 genes in the whole genome of birch, and 31,297 genes are methylated. Conservatively, we estimated that 14.29% of genomic cytosines are methylcytosines in birch. Among the methylation sites, the CHH context accounts for 48.86%, and is the largest proportion. Combined transcriptome and methylation analysis showed that the genes with moderate methylation levels had higher expression levels than genes with high and low methylation. In addition, methylated genes are highly enriched for the GO subcategories of binding activities, catalytic activities, cellular processes, response to stimulus and cell death, suggesting that methylation mediates these pathways in birch trees. PMID:25514241

  8. Effects of 12 weeks of combined training without caloric restriction on inflammatory markers in overweight girls.

    PubMed

    Lopes, Wendell Arthur; Leite, Neiva; da Silva, Larissa Rosa; Brunelli, Diego Trevisan; Gáspari, Arthur Fernandes; Radominski, Rosana Bento; Chacon-Mikahil, Mara Patrícia Traina; Cavaglieri, Cláudia Regina

    2016-10-01

    The objective of the present study was to investigate the effects of combined training without caloric restriction on inflammatory markers in overweight girls. Thirty-three girls (13-17 years) were assigned into overweight training (n = 17) or overweight control (n = 16) groups. Additionally, a normal-weight group (n = 15) was used as control for the baseline values. The combined training programme consisted of six resistance exercises (three sets of 6-10 repetitions at 60-70% 1 RM) followed by 30 min of aerobic exercise (walking/running) at 50-80% VO2peak, performed in the same 60 min session, 3 days/weeks, for 12 weeks. Body composition, dietary intake, aerobic fitness (VO2peak), muscular strength (1 RM), glycaemia, insulinemia, lipid profile and inflammatory markers (C-reactive protein, interleukin-6, tumour necrosis factor-alpha, interleukin-10, leptin, resistin and adiponectin) were measured before and after intervention. There was a significant decrease in body fat (P < 0.01) and increase in fat-free mass (P < 0.01), VO2peak (P < 0.01), 1 RM for leg press (P < 0.01) and bench press (P < 0.01) in the overweight training group. Concomitantly, this group presented significant decreases in serum concentrations of C-reactive protein (P < 0.05) and leptin (P < 0.05), as well as in insulin resistance (P < 0.05) after the experimental period. In conclusion, 12 weeks of combined training without caloric restriction reduced inflammatory markers associated with obesity in overweight girls. PMID:26852885

  9. Ultrasensitive electrochemical biosensing for DNA using quantum dots combined with restriction endonuclease.

    PubMed

    Zhang, Can; Lou, Jing; Tu, Wenwen; Bao, Jianchun; Dai, Zhihui

    2015-01-21

    A universal and sensitive electrochemical biosensing platform for the detection and identification of DNA using CdSe quantum dots (CdSe QDs) as signal markers was designed. The detection mechanism was based on the specific recognition of MspI endonuclease combined with the signal amplification of gold nanoparticles (AuNPs). MspI endonuclease could recognize its specific sequence in the double-strand DNA (dsDNA) and cleave the dsDNA fragments linked with CdSe QDs from the electrode. The remaining attached CdSe QDs can be easily read out by square-wave voltammetry using an electrodeposited bismuth (Bi) film-modified glass carbon electrode. The concentrations of target DNA could be simultaneously detected by the signal of metal markers. Using mycobacterium tuberculosis (Mtb) DNA as a model, under the optimal conditions, the proposed biosensor could detect Mtb DNA down to 8.7 × 10(-15) M with a linear range of 5 orders of magnitude (from 1.0 × 10(-14) to 1.0 × 10(-9) M) and discriminate mismatched DNA with high selectivity. This strategy presented a universal and convenient biosensing platform for DNA assay, and its satisfactory performances make it a potential candidate for the early diagnosis of gene-related diseases. PMID:25408952

  10. Development of a restriction length polymorphism combined with direct PCR technique to differentiate goose and Muscovy duck parvoviruses.

    PubMed

    Wan, Chun-He; Chen, Hong-Mei; Fu, Qiu-Ling; Shi, Shao-Hua; Fu, Guang-Hua; Cheng, Long-Fei; Chen, Cui-Teng; Huang, Yu; Hu, Kai-Hui

    2016-06-01

    A restriction fragment length polymorphism combined with direct PCR technique to differentiate goose and Muscovy duck parvoviruses (GPV and MDPV) was developed based on comparison of the NS gene of GPV and MDPV. Both GPV and MDPV genomic DNA can be amplified with 641 bp using the specific PCR primers. The PCR fragments can be cut into 463 bp and 178 bp only in the case of MDPV-derived PCR products, whereas the GPV-derived PCR products cannot. The method established in this study can be used to differentiate GPV and MDPV with high specificity and precision, by using a direct PCR kit and QuickCut enzyme, as quickly as conventional PCR. PMID:26854108

  11. Development of a restriction length polymorphism combined with direct PCR technique to differentiate goose and Muscovy duck parvoviruses

    PubMed Central

    WAN, Chun-He; CHEN, Hong-Mei; FU, Qiu-Ling; SHI, Shao-Hua; FU, Guang-Hua; CHENG, Long-Fei; CHEN, Cui-Teng; HUANG, Yu; HU, Kai-Hui

    2016-01-01

    A restriction fragment length polymorphism combined with direct PCR technique to differentiate goose and Muscovy duck parvoviruses (GPV and MDPV) was developed based on comparison of the NS gene of GPV and MDPV. Both GPV and MDPV genomic DNA can be amplified with 641 bp using the specific PCR primers. The PCR fragments can be cut into 463 bp and 178 bp only in the case of MDPV-derived PCR products, whereas the GPV-derived PCR products cannot. The method established in this study can be used to differentiate GPV and MDPV with high specificity and precision, by using a direct PCR kit and QuickCut enzyme, as quickly as conventional PCR. PMID:26854108

  12. Intermittent fasting combined with calorie restriction is effective for weight loss and cardio-protection in obese women

    PubMed Central

    2012-01-01

    Background Intermittent fasting (IF; severe restriction 1 d/week) facilitates weight loss and improves coronary heart disease (CHD) risk indicators. The degree to which weight loss can be enhanced if IF is combined with calorie restriction (CR) and liquid meals, remains unknown. Objective This study examined the effects of IF plus CR (with or without a liquid diet) on body weight, body composition, and CHD risk. Methods Obese women (n = 54) were randomized to either the IFCR-liquid (IFCR-L) or IFCR-food based (IFCR-F) diet. The trial had two phases: 1) 2-week weight maintenance period, and 2) 8-week weight loss period. Results Body weight decreased more (P = 0.04) in the IFCR-L group (3.9 ± 1.4 kg) versus the IFCR-F group (2.5 ± 0.6 kg). Fat mass decreased similarly (P < 0.0001) in the IFCR-L and IFCR-F groups (2.8 ± 1.2 kg and 1.9 ± 0.7 kg, respectively). Visceral fat was reduced (P < 0.001) by IFCR-L (0.7 ± 0.5 kg) and IFCR-F (0.3 ± 0.5 kg) diets. Reductions in total and LDL cholesterol levels were greater (P = 0.04) in the IFCR-L (19 ± 10%; 20 ± 9%, respectively) versus the IFCR-F group (8 ± 3%; 7 ± 4%, respectively). LDL peak particle size increased (P < 0.01), while heart rate, glucose, insulin, and homocysteine decreased (P < 0.05), in the IFCR-L group only. Conclusion These findings suggest that IF combined with CR and liquid meals is an effective strategy to help obese women lose weight and lower CHD risk. PMID:23171320

  13. Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment.

    PubMed

    Doherty, Rachael; Couldrey, Christine

    2014-01-01

    Recent advances made in "omics" technologies are contributing to a revolution in livestock selection and breeding practices. Epigenetic mechanisms, including DNA methylation are important determinants for the control of gene expression in mammals. DNA methylation research will help our understanding of how environmental factors contribute to phenotypic variation of complex production and health traits. High-throughput sequencing is a vital tool for the comprehensive analysis of DNA methylation, and bisulfite-based strategies coupled with DNA sequencing allows for quantitative, site-specific methylation analysis at the genome level or genome wide. Reduced representation bisulfite sequencing (RRBS) and more recently whole genome bisulfite sequencing (WGBS) have proven to be effective techniques for studying DNA methylation in both humans and mice. Here we report the development of RRBS and WGBS for use in sheep, the first application of this technology in livestock species. Important technical issues associated with these methodologies including fragment size selection and sequence depth are examined and discussed. PMID:24860595

  14. An effective colorimetric and ratiometric fluorescent probe based FRET with a large Stokes shift for bisulfite

    PubMed Central

    Wu, Wen-Li; Wang, Zhao-Yang; Dai, Xi; Miao, Jun-Ying; Zhao, Bao-Xiang

    2016-01-01

    Bisulfite plays crucial roles in diverse physiological processes. Therefore, the efficient detection of bisulfite is very important. In this study, we report a colorimetric and ratiometric fluorescent probe (CPT) with a large Stokes shift (162 nm) for bisulfite (HSO3−) based FRET mechanism. The probe can quantitatively detect HSO3− with low detection limit (45 nM) and high specificity over other common anions and biothiols. A nucleophilic addition reaction was proposed for the sensing mechanism, which was confirmed by HRMS spectra. The test strips of the probe were made and used easily. Moreover, probe CPT was used to ratiometric fluorescent imaging of exogenous and endogenous HSO3− in living cells. PMID:27137791

  15. An effective colorimetric and ratiometric fluorescent probe for bisulfite in aqueous solution.

    PubMed

    Dai, Xi; Zhang, Tao; Du, Zhi-Fang; Cao, Xiang-Jian; Chen, Ming-Yu; Hu, Sheng-Wen; Miao, Jun-Ying; Zhao, Bao-Xiang

    2015-08-12

    We have developed the first two-photon colorimetric and ratiometric fluorescent probe, BICO, for the detection of bisulfite (HSO3(-)) in aqueous solution. The probe contains coumarin and benzimidazole moieties and can detect HSO3(-) based on the Michael addition reaction with a limit of detection 5.3 × 10(-8) M in phosphate-buffered saline solution. The probe was used to detect bisulfite in tap water, sugar and dry white wine. Moreover, test strips were made and used easily. We successfully applied the probe to image living cells, using one-photon fluorescence imaging. BICO overcomes the limitations in sensitivity of previously reported probes and the solvation effect of bisulfite, which demonstrates its excellent value in practical application. PMID:26320969

  16. An effective colorimetric and ratiometric fluorescent probe based FRET with a large Stokes shift for bisulfite.

    PubMed

    Wu, Wen-Li; Wang, Zhao-Yang; Dai, Xi; Miao, Jun-Ying; Zhao, Bao-Xiang

    2016-01-01

    Bisulfite plays crucial roles in diverse physiological processes. Therefore, the efficient detection of bisulfite is very important. In this study, we report a colorimetric and ratiometric fluorescent probe (CPT) with a large Stokes shift (162 nm) for bisulfite (HSO3(-)) based FRET mechanism. The probe can quantitatively detect HSO3(-) with low detection limit (45 nM) and high specificity over other common anions and biothiols. A nucleophilic addition reaction was proposed for the sensing mechanism, which was confirmed by HRMS spectra. The test strips of the probe were made and used easily. Moreover, probe CPT was used to ratiometric fluorescent imaging of exogenous and endogenous HSO3(-) in living cells. PMID:27137791

  17. THE EFFECTS OF THE DASH DIET ALONE AND IN COMBINATION WITH EXERCISE AND CALORIC RESTRICTION ON INSULIN SENSITIVITY AND LIPIDS

    PubMed Central

    Blumenthal, James A.; Babyak, Michael A.; Sherwood, Andrew; Craighead, Linda; Lin, Pao-Hwa; Johnson, Julie; Watkins, Lana L.; Wang, Jenny T.; Kuhn, Cynthia; Feinglos, Mark; Hinderliter, Alan

    2010-01-01

    This study examined the effects of the Dietary Approaches to Stop Hypertension (DASH) diet on insulin sensitivity and lipids. In a randomized control trial, 144 overweight (body mass index 25–40) men (N= 47) and women (N= 97) with high blood pressure (130–159/85–99 mm Hg) were randomly assigned to either: (1) DASH diet alone (DASH-A); (2) DASH diet with aerobic exercise and caloric restriction (DASH-WM); or usual diet controls (UC). Body composition, fitness, insulin sensitivity, and fasting lipids were measured before and following 4 months of treatment. Insulin sensitivity was estimated based on glucose and insulin levels in the fasting state and after an oral glucose load. Participants in the DASH-WM condition lost weight (−8.7 [95% CI = −2.0, −9.7] kg,), and exhibited a significant increase in aerobic capacity, while the DASH-A and UC participants maintained their weight (−0.3 [95% CI = −1.2, 0.5] kg and +0.9 [95% CI = 0.0, 1.7] kg, respectively) and had no improvement in exercise capacity. DASH-WM demonstrated lower glucose levels following the oral glucose load, improved insulin sensitivity, and lower total cholesterol and triglycerides compared to both DASH-A and UC, and lower fasting glucose and low-density lipoprotein cholesterol compared to UC; DASH-A participants generally did not differ from UC in these measures. Combining the DASH diet with exercise and weight loss resulted in significant improvements in insulin sensitivity and lipids. Despite clinically significant reductions in blood pressure, the DASH diet alone, without caloric restriction or exercise, resulted in minimal improvements in insulin sensitivity or lipids. PMID:20212264

  18. A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data.

    PubMed

    Lea, Amanda J; Tung, Jenny; Zhou, Xiang

    2015-11-01

    Identifying sources of variation in DNA methylation levels is important for understanding gene regulation. Recently, bisulfite sequencing has become a popular tool for investigating DNA methylation levels. However, modeling bisulfite sequencing data is complicated by dramatic variation in coverage across sites and individual samples, and because of the computational challenges of controlling for genetic covariance in count data. To address these challenges, we present a binomial mixed model and an efficient, sampling-based algorithm (MACAU: Mixed model association for count data via data augmentation) for approximate parameter estimation and p-value computation. This framework allows us to simultaneously account for both the over-dispersed, count-based nature of bisulfite sequencing data, as well as genetic relatedness among individuals. Using simulations and two real data sets (whole genome bisulfite sequencing (WGBS) data from Arabidopsis thaliana and reduced representation bisulfite sequencing (RRBS) data from baboons), we show that our method provides well-calibrated test statistics in the presence of population structure. Further, it improves power to detect differentially methylated sites: in the RRBS data set, MACAU detected 1.6-fold more age-associated CpG sites than a beta-binomial model (the next best approach). Changes in these sites are consistent with known age-related shifts in DNA methylation levels, and are enriched near genes that are differentially expressed with age in the same population. Taken together, our results indicate that MACAU is an efficient, effective tool for analyzing bisulfite sequencing data, with particular salience to analyses of structured populations. MACAU is freely available at www.xzlab.org/software.html. PMID:26599596

  19. A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data

    PubMed Central

    Lea, Amanda J.

    2015-01-01

    Identifying sources of variation in DNA methylation levels is important for understanding gene regulation. Recently, bisulfite sequencing has become a popular tool for investigating DNA methylation levels. However, modeling bisulfite sequencing data is complicated by dramatic variation in coverage across sites and individual samples, and because of the computational challenges of controlling for genetic covariance in count data. To address these challenges, we present a binomial mixed model and an efficient, sampling-based algorithm (MACAU: Mixed model association for count data via data augmentation) for approximate parameter estimation and p-value computation. This framework allows us to simultaneously account for both the over-dispersed, count-based nature of bisulfite sequencing data, as well as genetic relatedness among individuals. Using simulations and two real data sets (whole genome bisulfite sequencing (WGBS) data from Arabidopsis thaliana and reduced representation bisulfite sequencing (RRBS) data from baboons), we show that our method provides well-calibrated test statistics in the presence of population structure. Further, it improves power to detect differentially methylated sites: in the RRBS data set, MACAU detected 1.6-fold more age-associated CpG sites than a beta-binomial model (the next best approach). Changes in these sites are consistent with known age-related shifts in DNA methylation levels, and are enriched near genes that are differentially expressed with age in the same population. Taken together, our results indicate that MACAU is an efficient, effective tool for analyzing bisulfite sequencing data, with particular salience to analyses of structured populations. MACAU is freely available at www.xzlab.org/software.html. PMID:26599596

  20. Identification of Mycobacterium avium Genotypes with Distinctive Traits by Combination of IS1245-Based Restriction Fragment Length Polymorphism and Restriction Analysis of hsp65

    PubMed Central

    Oliveira, R. S.; Sircili, M. P.; Oliveira, E. M. D.; Balian, S. C.; Ferreira-Neto, J. S.; Leão, S. C.

    2003-01-01

    One-hundred eight Mycobacterium avium isolates from pigs, humans, birds, and bovines were typed by the IS1245-based restriction fragment length polymorphism (RFLP) method and PCR-restriction enzyme analysis (PRA) of hsp65. Nine clusters of isolates showing more than 80% similarity in their RFLP profiles were detected. The largest cluster (cluster B) included 32 of 79 pig isolates (40.5%), 3 of 25 human isolates (12%), and 1 of 2 bovine isolates, comprising 33% of all isolates. The second largest cluster (cluster A) included 18 pig isolates (22.8%) and 6 human isolates (24%). Six smaller clusters included six pig isolates (clusters C and D), four and two human isolates (clusters E and F, respectively), two pig isolates (cluster I), and two pig isolates plus one bovine isolate and the avian purified protein derivative strain (cluster H). Cluster G represented the “bird-type” profile and included the bird isolate in this series, one pig isolate, plus reference strain R13. PRA revealed four allelic variants. Seventy-seven isolates were identified as M. avium PRA variant I, 24 were identified as M. avium PRA variant II, 6 were identified as M. avium PRA variant III, and 1 was identified as M. avium PRA variant IV. Except for three isolates from cluster B, each of the RFLP clusters was associated with a single PRA pattern. Isolates with unique (nonclustered) RFLP profiles were distributed between PRA variants I and II, and there was one unique isolate of PRA variant IV. These observations are consistent with divergent evolution within M. avium, resulting in the emergence of distinct lineages with particular competence to infect animals and humans. PMID:12517823

  1. Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing

    PubMed Central

    Smith, Rick W. A.; Monroe, Cara; Bolnick, Deborah A.

    2015-01-01

    While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches. PMID:26016479

  2. Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing.

    PubMed

    Smith, Rick W A; Monroe, Cara; Bolnick, Deborah A

    2015-01-01

    While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches. PMID:26016479

  3. Hydrophilic Indolium Cycloruthenated Complex System for Visual Detection of Bisulfite with a Large Red Shift in Absorption.

    PubMed

    Su, Xianlong; Hu, Rongrong; Li, Xianghong; Zhu, Jun; Luo, Facheng; Niu, Xuehu; Li, Mei; Zhao, Qiang

    2016-01-19

    Bisulfite, as an important additive in foodstuffs, is one of the most widely distributed environmental pollutants. The excessive intake of bisulfite may cause asthmatic attacks and allergic reactions. Therefore, the determination and visual detection of bisulfite are very important. Herein, a newly designed hydrophilic indolium cycloruthenated complex, [Ru(mepbi)(bpy)2](+) [1; bpy = 2,2'-bipyridine and Hmepbi = 3,3-dimethyl-1-ethyl-2-[4-(pyridin-2-yl)styryl]benzo[e]indolium iodide (3)], was successfully synthesized and used as a bisulfite probe. The bisulfite underwent a 1,4-addition reaction with complex 1 in PBS buffer (10 mM, pH 7.40), resulting in a dramatic change in absorption spectra with a red shift of over 100 nm and a remarkable change in solution color from yellow to pink. It is worth noting that this obvious bathochromic shift is rarely observed in the detection of bisulfite through an addition reaction. The detection limit was calculated to be as low as 0.12 μM by UV-vis absorption spectroscopy. Moreover, complex 1 was also used to detect bisulfite in sugar samples (granulated and crystal sugar) with good recovery. PMID:26700219

  4. Bisulfite pretreatment changes the structure and properties of oil palm empty fruit bunch to improve enzymatic hydrolysis and bioethanol production.

    PubMed

    Tan, Liping; Sun, Wan; Li, Xuezhi; Zhao, Jian; Qu, Yinbo; Choo, Yuen May; Loh, Soh Kheang

    2015-06-01

    Bisulfite pretreatment is a proven effective method for improving the enzymatic hydrolysis of empty fruit bunch (EFB) from oil palm for bioethanol production. In this study, we set out to determine the changes that occur in the structure and properties of EFB materials and fractions of hemicellulose and lignin during the bisulfite pretreatment process. The results showed that the crystallinity of cellulose in EFB increased after bisulfite pretreatment, whereas the EFB surface was damaged to various degrees. The orderly structure of EFB, which was maintained by hydrogen bonds, was destroyed by bisulfite pretreatment. Bisulfite pretreatment also hydrolyzed the glycosidic bonds of the xylan backbone of hemicellulose, thereby decreasing the molecular weight and shortening the xylan chains. The lignin fractions obtained from EFB and pretreated EFB were typically G-S lignin, and with low content of H units. Meanwhile, de-etherification occurred at the β-O-4 linkage, which was accompanied by polymerization and demethoxylation as a result of bisulfite pretreatment. The adsorption ability of cellulase differed for the various lignin fractions, and the water-soluble lignin fractions had higher adsorption capacity on cellulase than the milled wood lignin. In general, the changes in the structure and properties of EFB provided insight into the benefits of bisulfite pretreatment. PMID:25866127

  5. Isolation of a Bisulfite Reductase Activity from Desulfotomaculum nigrificans and Its Identification as the Carbon Monoxide-Binding Pigment P582

    PubMed Central

    Akagi, J. M.; Adams, Verna

    1973-01-01

    Crude preparations of Desulfotomaculum nigrificans were found to reduce bisulfite to trithionate, thiosulfate, and sulfide. The bisulfite reductase of this organism was partially purified and observed to reduce bisulfite to trithionate as the major product and with thiosulfate and sulfide as minor products. The enzyme exhibited spectral properties identical to the carbon monoxide-reacting pigment (P582) isolated from this organism. It is concluded that the bisulfite reductase of D. nigrificans is P582 and that this organism utilizes a pathway which involves trithionate during the reduction of bisulfite to sulfide. PMID:4745421

  6. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers

    PubMed Central

    Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M.; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

    2016-01-01

    Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely

  7. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    PubMed

    Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

    2016-01-01

    Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely

  8. Chemiluminescence analysis of menadione sodium bisulfite and analgin in pharmaceutical preparations and biological fluids.

    PubMed

    Huang, Y; Zhang, C; Zhang, X; Zhang, Z

    1999-12-01

    A novel chemiluminescence (CL) flow system for two sulfite-containing drugs, namely, menadione sodium bisulfite (MSB) and analgin is described. It is based on the weak chemiluminescence induced by the oxidation of sulfite group in drugs with dissolved oxygen in the presence of acidic Rh6G. Tween 80 surfactant micelles showed a strong enhancement effect on this weak chemiluminescence. For MSB analysis, online conversion of MSB in alkaline medium into sodium bisulfite was necessary, whereas analgin could be determined directly. The proposed method allowed the measurement of 0.05-50 microg/ml(-1) MSB and 0.05-10 microg/ml(-1) analgin. The limits of detection (3sigma) were 0.01 microg/ml(-1) MSB and 0.003 microg/ml(-1) analgin. The method was applied satisfactorily to pharmaceutical preparations as well as biological fluids. PMID:10701947

  9. Genotypic characterization of Indian isolates of infectious bursal disease virus strains by reverse transcription-polymerase chain reaction combined with restriction fragment length polymorphism analysis.

    PubMed

    Priyadharsini, C V; Senthilkumar, T M A; Raja, P; Kumanan, K

    2016-03-01

    The reverse transcription PCR (RT-PCR) combined with restriction fragment length polymorphism (RFLP) is used for the differentiation of classical virulent (cv), virulent (v) and very virulent (vv) strains of infectious bursal disease virus (IBDV) isolates from chicken bursal tissues in southern states of India. In the present study, six different isolates (MB11, HY12, PY12, BGE14, VCN14 and NKL14) of IBDV strains were subjected for genotyping along with vaccine virus (Georgia, intermediate strain) using RT-PCR for amplification of a 743 bp sequence in the hypervariable region of VP2 gene followed by restriction enzyme digestion with 5 different restriction enzymes (BspMI, SacI, HhaI, StuI and SspI). The RT-PCR products obtained from vvIBDV strains were digested by SspI enzyme except PY12, BGE14 and MB11 isolates. The SacI digested the isolate MB11, PY12 and the vaccine strain, but it did not cleave the very virulent isolates of IBDV. HhaI cleaved all the isolates with different restriction profile patterns. StuI digested all the vvIBDV isolates and BspMI was not able to differentiate field isolates from vaccine strain. Though RT-PCR combined with RFLP is a genotypic method, further confirmation of serotypes to distinguish the vvIBDV from cvIBDV has to be carried out using pathogenicity studies. PMID:26982465

  10. Combining metformin therapy with caloric restriction for the management of type 2 diabetes and nonalcoholic fatty liver disease in obese rats

    PubMed Central

    Linden, Melissa A.; Lopez, Kristi T.; Fletcher, Justin A.; Morris, E. Matthew; Meers, Grace M.; Siddique, Sameer; Laughlin, M. Harold; Sowers, James R.; Thyfault, John P.; Ibdah, Jamal A.; Rector, R. Scott

    2016-01-01

    Weight loss is recommended for patients with nonalcoholic fatty liver disease (NAFLD), while metformin may lower liver enzymes in type 2 diabetics. Yet, the efficacy of the combination of weight loss and metformin in the treatment of NAFLD is unclear. We assessed the effects of metformin, caloric restriction, and their combination on NAFLD in diabetic Otsuka Long-Evans Tokushima Fatty (OLETF) rats. Male OLETF rats (age 20 weeks; n = 6–8 per group) were fed ad libitum (AL), given metformin (300 mg·kg−1·day−1; Met), calorically restricted (70% of AL; CR), or calorically restricted and given metformin (CR+Met) for 12 weeks. Met lowered adiposity compared with AL but not to the same magnitude as CR or CR+Met (p < 0.05). Although only CR improved fasting insulin and glucose, the combination of CR+Met was needed to improve post-challenge glucose tolerance. All treatments lowered hepatic triglycerides, but further improvements were observed in the CR groups (p < 0.05, Met vs. CR or CR+Met) and a further reduction in serum alanine aminotransferases was observed in CR+Met rats. CR lowered markers of hepatic de novo lipogenesis (fatty acid synthase, acetyl-CoA carboxylase (ACC), and stearoyl-CoA desaturase-1 (SCD-1)) and increased hepatic mitochondrial activity (palmitate oxidation and β-hydroxyacyl CoA dehydrogenase (β-HAD) activity). Changes were enhanced in the CR+Met group for ACC, SCD-1, β-HAD, and the mitophagy marker BNIP3. Met decreased total hepatic mTOR content and inhibited mTOR complex 1, which may have contributed to Met-induced reductions in de novo lipogenesis. These findings in the OLETF rat suggest that the combination of caloric restriction and metformin may provide a more optimal approach than either treatment alone in the management of type 2 diabetes and NAFLD. PMID:26394261

  11. Ultra-Deep Bisulfite Sequencing to Detect Specific DNA Methylation Patterns of Minor Cell Types in Heterogeneous Cell Populations: An Example of the Pituitary Tissue

    PubMed Central

    Atozi, Takanori; Matsumoto, Shoma; Hanazono, Yutaka; Nagashima, Hiroshi; Ohgane, Jun

    2016-01-01

    DNA methylation is an epigenetic modification important for cell fate determination and cell type-specific gene expression. Transcriptional regulatory regions of the mammalian genome contain a large number of tissue/cell type-dependent differentially methylated regions (T-DMRs) with DNA methylation patterns crucial for transcription of the corresponding genes. In general, tissues consist of multiple cell types in various proportions, making it difficult to detect T-DMRs of minor cell types in tissues. The present study attempts to detect T-DMRs of minor cell types in tissues by ultra-deep bisulfite sequencing of cell type-restricted genes and to assume proportions of minor cell types based on DNA methylation patterns of sequenced reads. For this purpose, we focused on transcriptionally active hypomethylated alleles (Hypo-alleles), which can be recognized by the high ratio of unmethylated CpGs in each sequenced read (allele). The pituitary gland contains multiple cell types including five hormone-expressing cell types and stem/progenitor cells, each of which is a minor cell type in the pituitary tissue. By ultra-deep sequencing of more than 100 reads for detection of Hypo-alleles in pituitary cell type-specific genes, we identified T-DMRs specific to hormone-expressing cells and stem/progenitor cells and used them to estimate the proportions of each cell type based on the Hypo-allele ratio in pituitary tissue. Therefore, introduction of the novel Hypo-allele concept enabled us to detect T-DMRs of minor cell types with estimation of their proportions in the tissue by ultra-deep bisulfite sequencing. PMID:26752725

  12. Isolation and structures of oligomeric wine pigments by bisulfite-mediated ion-exchange chromatography.

    PubMed

    Asenstorfer, R E; Hayasaka, Y; Jones, G P

    2001-12-01

    Methods have been developed that are based on cation exchange chromatography in the absence and presence of excess bisulfite for the isolation of wine pigments from Australian red wine and grape marc extract. The pigments were identified using HPLC and electrospray ionization mass spectrometry. The mass spectral data indicate that these pigments are C4-substituted anthocyanins with a tetracyclic structure. The pigments form a series of closely related oligomeric pigments which include those previously described in the literature, such as pigment A and vitisin A, as well as some newly identified pigments. PMID:11743792

  13. Combined effects of caloric restriction and branched-chain amino acid supplementation on body composition and exercise performance in elite wrestlers.

    PubMed

    Mourier, A; Bigard, A X; de Kerviler, E; Roger, B; Legrand, H; Guezennec, C Y

    1997-01-01

    Twenty-five competitive wrestlers restricted their caloric intake (28 kcal.kg-1.day-1) for 19 days, using a hypocaloric control (hC, n = 6), hypocaloric high-protein (hHP, n = 7), hypocaloric high-branched-chain amino acid (hBCAA, n = 6), hypocaloric low-protein (hLP, n = 6) diet to determine the effects of caloric restriction on body composition and performances versus control diet (C, n = 6). Anthropometric parameters (weight, percent body fat) and adipose tissue (AT) distribution measured by magnetic resonance imaging (MRI) obtained before and after diet, were compared. A significant highest body weight loss (-4 kg, p < 0.05) and decrease in the percent of body fat (-17.3%, p < 0.05) were observed for subjects of the hBCAA group. Subjects of the hBCAA group exhibited a significant reduction (-34.4%, p < 0.05) in abdominal visceral adipose tissue (VAT). There was no change in aerobic (VO2max) (p > 0.75) and anaerobic capacities (Wingate test) (p > 0.81), and in muscular strength (p > 0.82). We conclude that under our experimental conditions, the combination of moderate energy restriction and BCAA supplementation induced significant and preferential losses of VAT, and allowed maintainance of a high level of performance. PMID:9059905

  14. Identification of spermatozoa by tissue-specific differential DNA methylation using bisulfite modification and pyrosequencing.

    PubMed

    Balamurugan, Kuppareddi; Bombardi, Robin; Duncan, George; McCord, Bruce

    2014-11-01

    The focus of this study is to evaluate the application of epigenetic markers as a forensic tool for the determination of semen present in sexual assault cases. A series of genetic loci were screened in order to identify certain epigenetic markers displaying differential methylation that can allow semen to be differentiated from blood, buccal cells, skin epidermis, and vaginal epithelial cells. Of the different loci tested, a panel of six markers, DACT1, USP49, DDX4, Hs_INSL6_03, Hs_ZC3H12D_05, and B_SPTB_03 were identified to contain tissue-specific differential methylation. Samples ranging from 9-21 for each tissue type were collected and subjected to bisulfite modification. The bisulfite modified DNA was amplified by PCR, and analyzed by pyrosequencing to quantitate the level of methylation at each marker. All six markers successfully differentiated semen samples from the other four tissue types analyzed. Sperm DNA was hypomethylated in all but one marker, B_SPTB_03, where this marker showed hypermethylation. Mean methylation percentages for semen samples were statistically significant from mean methylation percentages of the other four tissues studied (p < 0.01). The results of this study demonstrate the applicability of epigenetic markers as a novel tool for determination of spermatozoa and to identify the tissue source of origin of a DNA sample. PMID:24913642

  15. Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation.

    PubMed

    Masser, Dustin R; Stanford, David R; Hadad, Niran; Giles, Cory B; Wren, Jonathan D; Sonntag, William E; Richardson, Arlan; Freeman, Willard M

    2016-06-01

    Epigenetic regulation through DNA methylation (5mC) plays an important role in development, aging, and a variety of diseases. Genome-wide studies of base- and strand-specific 5mC are limited by the extensive sequencing required. Targeting bisulfite sequencing to specific genomic regions through sequence capture with complimentary oligonucleotide probes retains the advantages of bisulfite sequencing while focusing sequencing reads on regions of interest, enables analysis of more samples by decreasing the amount of sequence required per sample, and provides base- and strand-specific absolute quantitation of CG and non-CG methylation levels. As an example, an oligonucleotide capture set to interrogate 5mC levels in all rat RefSeq gene promoter regions (18,814) and CG islands, shores, and shelves (18,411) was generated. Validation using whole-genome methylation standards and biological samples demonstrates enrichment of the targeted regions and accurate base-specific quantitation of CG and non-CG methylation for both forward and reverse genomic strands. A total of 170 Mb of the rat genome is covered including 6.6 million CGs and over 67 million non-CG sites, while reducing the amount of sequencing required by ~85 % as compared to existing whole-genome sequencing methods. This oligonucleotide capture targeting approach and quantitative validation workflow can also be applied to any genome of interest. PMID:27091453

  16. N-Sulfomethylation of guanine, adenine and cytosine with formaldehyde-bisulfite. A selective modification of guanine in DNA.

    PubMed

    Hayatsu, H; Yamashita, Y; Yui, S; Yamagata, Y; Tomita, K; Negishi, K

    1982-10-25

    When guanine-, adenine- and cytosine-nucleosides and nucleotides were treated with formaldehyde and then with bisulfite, stable N-sulfomethyl compounds were formed. N2-Sulfomethylguanine, N6-sulfomethyladenine, N4-sulfomthylcytosine and N6-sulfomethyl-9-beta-D-arabinofuranosyladenine were isolated as crystals and characterized. A guanine-specific sulfomethylation was brought about by treatment and denatured single-stranded DNA with formaldehyde and then with bisulfite at pH 7 and 4 degrees C. Since native double-stranded DNA was not modified by this treatment, this new method of modification is expected to be useful as a conformational probe for polynucleotides. PMID:7177848

  17. N-Sulfomethylation of guanine, adenine and cytosine with formaldehyde-bisulfite. A selective modification of guanine in DNA.

    PubMed Central

    Hayatsu, H; Yamashita, Y; Yui, S; Yamagata, Y; Tomita, K; Negishi, K

    1982-01-01

    When guanine-, adenine- and cytosine-nucleosides and nucleotides were treated with formaldehyde and then with bisulfite, stable N-sulfomethyl compounds were formed. N2-Sulfomethylguanine, N6-sulfomethyladenine, N4-sulfomthylcytosine and N6-sulfomethyl-9-beta-D-arabinofuranosyladenine were isolated as crystals and characterized. A guanine-specific sulfomethylation was brought about by treatment and denatured single-stranded DNA with formaldehyde and then with bisulfite at pH 7 and 4 degrees C. Since native double-stranded DNA was not modified by this treatment, this new method of modification is expected to be useful as a conformational probe for polynucleotides. PMID:7177848

  18. Engrafted maternal T cells in a severe combined immunodeficiency patient express T-cell receptor variable beta segments characterized by a restricted V-D-J junctional diversity.

    PubMed

    Sottini, A; Quiròs-Roldan, E; Notarangelo, L D; Malagoli, A; Primi, D; Imberti, L

    1995-04-15

    To better understand the peculiar functional behavior of engrafted maternal T cells in a severe combined immunodeficiency (SCID) patient, we characterized, at the molecular level, the T-cell repertoire of a SCID child with a high number of engrafted, mature, activated lymphocytes. We found that, although these transplacentally acquired T cells express a random set of T-cell receptor variable beta (TCRBV) segments, the TCRBV transcripts are characterized by an extremely restricted V-D-J junctional diversity. Only a few cDNA clones were dominant among the TCRBV4+, TCRBV6+, and TCRBV20+ populations in engrafted cells, whereas the same TCRBV chains expressed by the mother's lymphocytes had the expected junctional hetero-geneity. Highly diverse and polyclonal junctions were also expressed by maternal cells activated in mixed lymphocyte reaction by Epstein-Barr virus (EBV)-transformed B lymphocytes from the patient, indicating that the strong clonal selection that characterizes the engrafted cells repertoire is probably not due to allorecognition. Furthermore, we report that the repertoire of the transplacentally acquired lymphocytes is dynamic over time and is characterized by waves of expression and contraction of selected clones, expressing different TCRBV segments. These results help to explain some of the abnormal functional behaviors of engrafted maternal cells and raise new questions regarding the mechanisms responsible for the restricted clonal diversity. PMID:7718881

  19. Metabolic Effects of a 24-Week Energy-Restricted Intervention Combined with Low or High Dairy Intake in Overweight Women: An NMR-Based Metabolomics Investigation

    PubMed Central

    Zheng, Hong; Lorenzen, Janne K.; Astrup, Arne; Larsen, Lesli H.; Yde, Christian C.; Clausen, Morten R.; Bertram, Hanne Christine

    2016-01-01

    We investigated the effect of a 24-week energy-restricted intervention with low or high dairy intake (LD or HD) on the metabolic profiles of urine, blood and feces in overweight/obese women by NMR spectroscopy combined with ANOVA-simultaneous component analysis (ASCA). A significant effect of dairy intake was found on the urine metabolome. HD intake increased urinary citrate, creatinine and urea excretion, and decreased urinary excretion of trimethylamine-N-oxide (TMAO) and hippurate relative to the LD intake, suggesting that HD intake was associated with alterations in protein catabolism, energy metabolism and gut microbial activity. In addition, a significant time effect on the blood metabolome was attributed to a decrease in blood lipid and lipoprotein levels due to the energy restriction. For the fecal metabolome, a trend for a diet effect was found and a series of metabolites, such as acetate, butyrate, propionate, malonate, cholesterol and glycerol tended to be affected. Overall, even though these effects were not accompanied by a higher weight loss, the present metabolomics data reveal that a high dairy intake is associated with endogenous metabolic effects and effects on gut microbial activity that potentially impact body weight regulation and health. Moreover, ASCA has a great potential for exploring the effect of intervention factors and identifying altered metabolites in a multi-factorial metabolomic study. PMID:26907339

  20. Kinetics of oxygen exchange between bisulfite ion and water as studied by oxygen-17 nuclear magnetic resonance spectroscopy

    SciTech Connect

    Horner, D.A.

    1984-08-01

    The nuclear magnetic relaxation times of oxygen-17 have been measured in aqueous sodium bisulfite solutions in the pH range from 2.5 to 5 as a function of temperature, pH, and S(IV) concentration, at an ionic strength of 1.0 m. The rate law for oxygen exchange between bisulfite ion and water was obtained from an analysis of the data, and is consistent with oxygen exchange occurring via the reaction SO/sub 2/ + H/sub 2/O right reversible H/sup +/ + SHO/sub 3//sup -/. The value of k/sub -1/ is in agreement with relaxation measurements. Direct spectroscopic evidence was found for the existence of two isomers of bisulfite ion: one with the proton bonded to the sulfur (HSO/sub 3//sup -/) and the other with the proton bonded to an oxygen (SO/sub 3/H/sup -/). (The symbol SHO/sub 3//sup -/ in the above chemical equation refers to both isomeric forms of bisulfite ion.) The relative amounts of the two isomers were determined as a function of temperature, and the rate and mechanism of oxygen exchange between the two was investigated. One of the two isomers, presumably SO/sub 3/H/sup -/, exchanges oxygens with water much more rapidly than does the other. A two-pulse sequence was developed which greatly diminished the solvent peak in the NMR spectrum.

  1. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

    PubMed Central

    Urich, Mark A; Nery, Joseph R; Lister, Ryan; Schmitz, Robert J; Ecker, Joseph R

    2015-01-01

    Current high-throughput DNA sequencing technologies enable acquisition of billions of data points through which myriad biological processes can be interrogated, including genetic variation, chromatin structure, gene expression patterns, small RNAs and protein–DNA interactions. Here we describe the MethylC-sequencing (MethylC-seq) library preparation method, a 2-d protocol that enables the genome-wide identification of cytosine DNA methylation states at single-base resolution. The technique involves fragmentation of genomic DNA followed by adapter ligation, bisulfite conversion and limited amplification using adapter-specific PCR primers in preparation for sequencing. To date, this protocol has been successfully applied to genomic DNA isolated from primary cell culture, sorted cells and fresh tissue from over a thousand plant and animal samples. PMID:25692984

  2. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale.

    PubMed

    Xia, Bo; Han, Dali; Lu, Xingyu; Sun, Zhaozhu; Zhou, Ankun; Yin, Qiangzong; Zeng, Hu; Liu, Menghao; Jiang, Xiang; Xie, Wei; He, Chuan; Yi, Chengqi

    2015-11-01

    Active DNA demethylation in mammals involves oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). However, genome-wide detection of 5fC at single-base resolution remains challenging. Here we present fC-CET, a bisulfite-free method for whole-genome analysis of 5fC based on selective chemical labeling of 5fC and subsequent C-to-T transition during PCR. Base-resolution 5fC maps showed limited overlap with 5hmC, with 5fC-marked regions more active than 5hmC-marked ones. PMID:26344045

  3. Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite

    PubMed Central

    An, Dongshan; Dong, Xiaoli; An, Annie; Park, Hyung S.; Strous, Marc; Voordouw, Gerrit

    2016-01-01

    Sodium bisulfite (SBS) is used as an oxygen scavenger to decrease corrosion in pipelines transporting brackish subsurface water used in the production of bitumen by steam-assisted gravity drainage. Sequencing 16S rRNA gene amplicons has indicated that SBS addition increased the fraction of the sulfate-reducing bacteria (SRB) Desulfomicrobium, as well as of Desulfocapsa, which can also grow by disproportionating sulfite into sulfide, sulfur, and sulfate. SRB use cathodic H2, formed by reduction of aqueous protons at the iron surface, or use low potential electrons from iron and aqueous protons directly for sulfate reduction. In order to reveal the effects of SBS treatment in more detail, metagenomic analysis was performed with pipe-associated solids (PAS) scraped from a pipe section upstream (PAS-616P) and downstream (PAS-821TP) of the SBS injection point. A major SBS-induced change in microbial community composition and in affiliated hynL genes for the large subunit of [NiFe] hydrogenase was the appearance of sulfur-metabolizing Epsilonproteobacteria of the genera Sulfuricurvum and Sulfurovum. These are chemolithotrophs, which oxidize sulfide or sulfur with O2 or reduce sulfur with H2. Because O2 was absent, this class likely catalyzed reduction of sulfur (S0) originating from the metabolism of bisulfite with cathodic H2 (or low potential electrons and aqueous protons) originating from the corrosion of steel (Fe0). Overall this accelerates reaction of of S0 and Fe0 to form FeS, making this class a potentially powerful contributor to microbial corrosion. The PAS-821TP metagenome also had increased fractions of Deltaproteobacteria including the SRB Desulfomicrobium and Desulfocapsa. Altogether, SBS increased the fraction of hydrogen-utilizing Delta- and Epsilonproteobacteria in brackish-water-transporting pipelines, potentially stimulating anaerobic pipeline corrosion if dosed in excess of the intended oxygen scavenger function. PMID:26858705

  4. Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite.

    PubMed

    An, Dongshan; Dong, Xiaoli; An, Annie; Park, Hyung S; Strous, Marc; Voordouw, Gerrit

    2016-01-01

    Sodium bisulfite (SBS) is used as an oxygen scavenger to decrease corrosion in pipelines transporting brackish subsurface water used in the production of bitumen by steam-assisted gravity drainage. Sequencing 16S rRNA gene amplicons has indicated that SBS addition increased the fraction of the sulfate-reducing bacteria (SRB) Desulfomicrobium, as well as of Desulfocapsa, which can also grow by disproportionating sulfite into sulfide, sulfur, and sulfate. SRB use cathodic H2, formed by reduction of aqueous protons at the iron surface, or use low potential electrons from iron and aqueous protons directly for sulfate reduction. In order to reveal the effects of SBS treatment in more detail, metagenomic analysis was performed with pipe-associated solids (PAS) scraped from a pipe section upstream (PAS-616P) and downstream (PAS-821TP) of the SBS injection point. A major SBS-induced change in microbial community composition and in affiliated hynL genes for the large subunit of [NiFe] hydrogenase was the appearance of sulfur-metabolizing Epsilonproteobacteria of the genera Sulfuricurvum and Sulfurovum. These are chemolithotrophs, which oxidize sulfide or sulfur with O2 or reduce sulfur with H2. Because O2 was absent, this class likely catalyzed reduction of sulfur (S(0)) originating from the metabolism of bisulfite with cathodic H2 (or low potential electrons and aqueous protons) originating from the corrosion of steel (Fe(0)). Overall this accelerates reaction of of S(0) and Fe(0) to form FeS, making this class a potentially powerful contributor to microbial corrosion. The PAS-821TP metagenome also had increased fractions of Deltaproteobacteria including the SRB Desulfomicrobium and Desulfocapsa. Altogether, SBS increased the fraction of hydrogen-utilizing Delta- and Epsilonproteobacteria in brackish-water-transporting pipelines, potentially stimulating anaerobic pipeline corrosion if dosed in excess of the intended oxygen scavenger function. PMID:26858705

  5. Applying Data Mining to Classify Age by Intestinal Microbiota in 92 Healthy Men Using a Combination of Several Restriction Enzymes for T-RFLP Experiments

    PubMed Central

    KOBAYASHI, Toshio; OSAKI, Takako; OIKAWA, Shinya

    2014-01-01

    The composition of the intestinal microbiota was measured following consumption of identical meals for 3 days in 92 Japanese men, and terminal restriction fragment length polymorphism (T-RFLP) was used to analyze their feces. The obtained operational taxonomic units (OTUs) and the subjects’ ages were classified by using Data mining (DM) software that compared these data with continuous data and for 5 partitions for age divided at 5 years intervals between the ages of 30 and 50. The DM provided Decision trees in which the selected OTUs were closely related to the ages of the subjects. DM was also used to compare the OTUs from the T-RFLP data with seven restriction enzymes (two enzymes of 516f-BslI and 516f-HaeIII, two enzymes of 27f-MspI and 27f-AluI, three enzymes of 35f-HhaI, 35f-MspI and 35f-AluI) and their various combinations. The OTUs delivered from the five enzyme-digested partitions were analyzed to classify their age clusters. For use in future DM processing, we discussed the enzymes that were effective for accurate classification. We selected two OTUs (HA624 and HA995) that were useful for classifying the subject’s ages. Depending on the 16S rRNA sequences of the OTUs, Ruminicoccus obeum clones 1-4 were present in 18 of 36 bacterial candidates in the older age group-related OTU (HA624). On the other hand, Ruminicoccus obeum clones 1-33 were present in 65 of 269 candidates in the younger age group-related OUT (HA995). PMID:25003020

  6. Combined low-thrust propulsion and invariant manifold trajectories to capture NEOs in the Sun-Earth circular restricted three-body problem

    NASA Astrophysics Data System (ADS)

    Mingotti, G.; Sánchez, J. P.; McInnes, C. R.

    2014-12-01

    In this paper, a method to capture near-Earth objects (NEOs) incorporating low-thrust propulsion into the invariant manifolds technique is investigated. Assuming that a tugboat-spacecraft is in a rendez-vous condition with the candidate asteroid, the aim is to take the joint spacecraft-asteroid system to a selected periodic orbit of the Sun-Earth restricted three-body system: the orbit can be either a libration point periodic orbit (LPO) or a distant prograde periodic orbit (DPO) around the Earth. In detail, low-thrust propulsion is used to bring the joint spacecraft-asteroid system from the initial condition to a point belonging to the stable manifold associated to the final periodic orbit: from here onward, thanks to the intrinsic dynamics of the physical model adopted, the flight is purely ballistic. Dedicated guided and capture sets are introduced to exploit the combined use of low-thrust propulsion with stable manifolds trajectories, aiming at defining feasible first guess solutions. Then, an optimal control problem is formulated to refine and improve them. This approach enables a new class of missions, whose solutions are not obtainable neither through the patched-conics method nor through the classic invariant manifolds technique.

  7. Combining nested PCR and restriction digest of the internal transcribed spacer region to characterize arbuscular mycorrhizal fungi on roots from the field.

    PubMed

    Renker, Carsten; Heinrichs, Jochen; Kaldorf, Michael; Buscot, François

    2003-08-01

    Identification of arbuscular mycorrhizal fungi (AMF) on roots is almost impossible with morphological methods and, due to the presence of contaminating fungi, it is also difficult with molecular biological techniques. To allow broad investigation of the population structure of AMF in the field, we have established a new method to selectively amplify the internal transcribed spacer (ITS) region of most AMF with a unique primer set. Based on available sequences of the rDNA, one primer pair specific for AMF and a few other fungal groups was designed and combined in a nested PCR with the already established primer pair ITS5/ITS4. Amplification from contaminating organisms was reduced by an AluI restriction after the first reaction of the nested PCR. The method was assessed at five different field sites representing different types of habitats. Members of all major groups within the Glomeromycota (except Archaeosporaceae) were detected at the different sites. Gigasporaceae also proved detectable with the method based on cultivated strains. PMID:12938031

  8. A novel restricted access material combined to molecularly imprinted polymers for selective solid-phase extraction and high performance liquid chromatography determination of 2-methoxyestradiol in plasma samples.

    PubMed

    Du, Bin; Qu, Tiantian; Chen, Zheng; Cao, Xiaohui; Han, Shuping; Shen, Guopeng; Wang, Lei

    2014-11-01

    A feasibility study was performed in order to ensure the possibilities in using a restricted access material combined to molecularly imprinted polymers (RAM-MIP) as sorbent material in solid phase extraction (SPE) for clean-up of 2-methoxyestradiol (2-ME) from plasma samples. The MIP with hydrophilic external layer was designed by precipitation polymerization. The polymer was characterized by thermogravimetric analysis (TGA) and scanning electron microscope (SEM). The use of analogs of 2-ME as templates, in combination with a chromatographic separation of the analytes in the sample, overcame the problem of the template bleeding. To demonstrate the property of the RAM-MIP obtained, a comparison of commercially available C18 SPE was performed. The results showed that the RAM-MISPE recoveries were significantly higher than that of C18 SPE for 2-ME in trace concentration. During the extraction process, 2-ME was sufficiently cleaned for further chromatographic analysis with no interferences from template leakage and matrix. Good linearity was obtained from 0.06 to 20 μg mL(-1) with the correlation coefficient r>0.9991. The coefficient of variation of the inter-assay precision was less than 11.9%. The recoveries of 2-ME in rat plasma at three spiked levels were in the range of 99.10-101.00%. Based on the analytical validation results, the proposed method (RAM-MIP off-line SPE/HPLC) can be a useful tool to determine 2-ME in rat plasma samples. PMID:25127620

  9. (Bi)sulfite Oxidation by Copper,Zinc-Superoxide Dismutase: Sulfite-Derived, Radical-Initiated Protein Radical Formation

    PubMed Central

    Ranguelova, Kalina; Bonini, Marcelo G.; Mason, Ronald P.

    2010-01-01

    Background Sulfur dioxide, formed during the combustion of fossil fuels, is a major air pollutant near large cities. Its two ionized forms in aqueous solution, sulfite and (bi)sulfite, are widely used as preservatives and antioxidants to prevent food and beverage spoilage. (Bi)sulfite can be oxidized by peroxidases to form the very reactive sulfur trioxide anion radical (•SO3−). This free radical further reacts with oxygen to form the peroxymonosulfate anion radical (−O3SOO•) and sulfate anion radical (SO4• −). Objective To explore the critical role of these radical intermediates in further oxidizing biomolecules, we examined the ability of copper,zinc-superoxide dismutase (Cu,Zn-SOD) to initiate this radical chain reaction, using human serum albumin (HSA) as a model target. Methods We used electron paramagnetic resonance, optical spectroscopy, oxygen uptake, and immuno-spin trapping to study the protein oxidations driven by sulfite-derived radicals. Results We found that when Cu,Zn-SOD reacted with (bi)sulfite, •SO3− was produced, with the concomitant reduction of SOD-Cu(II) to SOD-Cu(I). Further, we demonstrated that sulfite oxidation mediated by Cu,Zn-SOD induced the formation of radical-derived 5,5-dimethyl-1-pyrroline N-oxide (DMPO) spin-trapped HSA radicals. Conclusions The present study suggests that protein oxidative damage resulting from (bi)sulfite oxidation promoted by Cu,Zn-SOD could be involved in oxidative damage and tissue injury in (bi)sulfite-exacerbated allergic reactions. PMID:20348042

  10. Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing

    PubMed Central

    Yuan, Xiao-Long; Gao, Ning; Xing, Yan; Zhang, Hai-Bin; Zhang, Ai-Ling; Liu, Jing; He, Jin-Long; Xu, Yuan; Lin, Wen-Mian; Chen, Zan-Mou; Zhang, Hao; Zhang, Zhe; Li, Jia-Qi

    2016-01-01

    Substantial evidence has shown that DNA methylation regulates the initiation of ovarian and sexual maturation. Here, we investigated the genome-wide profile of DNA methylation in porcine ovaries at single-base resolution using reduced representation bisulfite sequencing. The biological variation was minimal among the three ovarian replicates. We found hypermethylation frequently occurred in regions with low gene abundance, while hypomethylation in regions with high gene abundance. The DNA methylation around transcriptional start sites was negatively correlated with their own CpG content. Additionally, the methylation level in the bodies of genes was higher than that in their 5′ and 3′ flanking regions. The DNA methylation pattern of the low CpG content promoter genes differed obviously from that of the high CpG content promoter genes. The DNA methylation level of the porcine ovary was higher than that of the porcine intestine. Analyses of the genome-wide DNA methylation in porcine ovaries would advance the knowledge and understanding of the porcine ovarian methylome. PMID:26912189

  11. Metabolic changes in the urine of andrographolide sodium bisulfite-treated rats.

    PubMed

    Xu, J D; Xing, W M; Yuan, T J; Chen, J; Lu, H

    2016-02-01

    In recent years, andrographolide sodium bisulfite (ASB) has been reported to cause acute renal failure frequently in clinical practice. We hypothesized that changes in metabolic profile could have occurred after administration of ASB. To investigate the metabolic changes caused by ASB-induced nephrotoxicity, metabonomics method was utilized to depict the urine metabolic characteristics and find the specific urine biomarkers associated with ASB-induced nephrotoxicity. Sprague-Dawley rats were randomly assigned into three experimental groups. They received a single daily injection of vehicle (0.9% sodium chloride solution) or ASB at a dose of 100 or 600 mg kg(-1) day(-1) for 7 days. Twelve-hour urine was collected after the last administration. The routine urinalysis was measured by a urine automatic analyzer while urinary metabolites were evaluated using gas chromatography/mass spectrometry. The acquired data were processed by multivariate principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal PLS-DA. After 7-day administration of ASB, the positive urine samples in protein, occult blood, and ketones were increased, presenting dose dependence. The PCA and PLS-DA models were capable of distinguishing the difference between ASB-treated group and control. Biomarkers such as 1,5-anhydroglucitol, d-erythro-sphingosine, and 2-ketoadipate were identified as the most influential factors in ASB-induced nephrotoxicity. PMID:25852136

  12. Comparing five statistical methods of differential methylation identification using bisulfite sequencing data.

    PubMed

    Yu, Xiaoqing; Sun, Shuying

    2016-04-01

    We are presenting a comprehensive comparative analysis of five differential methylation (DM) identification methods: methylKit, BSmooth, BiSeq, HMM-DM, and HMM-Fisher, which are developed for bisulfite sequencing (BS) data. We summarize the features of these methods from several analytical aspects and compare their performances using both simulated and real BS datasets. Our comparison results are summarized below. First, parameter settings may largely affect the accuracy of DM identification. Different from default settings, modified parameter settings yield higher sensitivity and/or lower false positive rates. Second, all five methods show more accurate results when identifying simulated DM regions that are long and have small within-group variation, but they have low concordance, probably due to the different approaches they have used for DM identification. Third, HMM-DM and HMM-Fisher yield relatively higher sensitivity and lower false positive rates than others, especially in DM regions with large variation. Finally, we have found that among the three methods that involve methylation estimation (methylKit, BSmooth, and BiSeq), BiSeq can best present raw methylation signals. Therefore, based on these results, we suggest that users select DM identification methods based on the characteristics of their data and the advantages of each method. PMID:26910753

  13. Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing.

    PubMed

    Yuan, Xiao-Long; Gao, Ning; Xing, Yan; Zhang, Hai-Bin; Zhang, Ai-Ling; Liu, Jing; He, Jin-Long; Xu, Yuan; Lin, Wen-Mian; Chen, Zan-Mou; Zhang, Hao; Zhang, Zhe; Li, Jia-Qi

    2016-01-01

    Substantial evidence has shown that DNA methylation regulates the initiation of ovarian and sexual maturation. Here, we investigated the genome-wide profile of DNA methylation in porcine ovaries at single-base resolution using reduced representation bisulfite sequencing. The biological variation was minimal among the three ovarian replicates. We found hypermethylation frequently occurred in regions with low gene abundance, while hypomethylation in regions with high gene abundance. The DNA methylation around transcriptional start sites was negatively correlated with their own CpG content. Additionally, the methylation level in the bodies of genes was higher than that in their 5' and 3' flanking regions. The DNA methylation pattern of the low CpG content promoter genes differed obviously from that of the high CpG content promoter genes. The DNA methylation level of the porcine ovary was higher than that of the porcine intestine. Analyses of the genome-wide DNA methylation in porcine ovaries would advance the knowledge and understanding of the porcine ovarian methylome. PMID:26912189

  14. Restrictive cardiomyopathy

    MedlinePlus

    ... blood returns from the body (diastole). When the disease progresses, the heart may not pump blood strongly. The abnormal heart function can affect the lungs, liver, and other body systems. Restrictive cardiomyopathy may affect either or both of the ...

  15. Restrictive cardiomyopathy

    MedlinePlus

    ... blood returns from the body (diastole). When the disease progresses, the heart may not pump blood strongly. The abnormal heart function can affect the lungs, liver, and other body systems. Restrictive cardiomyopathy may affect ...

  16. Protection against H1N1 influenza challenge by a DNA vaccine expressing H3/H1 subtype hemagglutinin combined with MHC class II-restricted epitopes

    PubMed Central

    2010-01-01

    Background Multiple subtypes of avian influenza viruses have crossed the species barrier to infect humans and have the potential to cause a pandemic. Therefore, new influenza vaccines to prevent the co-existence of multiple subtypes within a host and cross-species transmission of influenza are urgently needed. Methods Here we report a multi-epitope DNA vaccine targeted towards multiple subtypes of the influenza virus. The protective hemagglutinin (HA) antigens from H5/H7/H9 subtypes were screened for MHC II class-restricted epitopes overlapping with predicted B cell epitopes. We then constructed a DNA plasmid vaccine, pV-H3-EHA-H1, based on HA antigens from human influenza H3/H1 subtypes combined with the H5/H7/H9 subtype Th/B epitope box. Results Epitope-specific IFN-γ ELISpot responses were significantly higher in the multi-epitope DNA group than in other vaccine and control groups (P < 0.05). The multi-epitope group significantly enhanced Th2 cell responses as determined by cytokine assays. The survival rate of mice given the multi-epitope vaccine was the highest among the vaccine groups, but it was not significantly different compared to those given single antigen expressing pV-H1HA1 vaccine and dual antigen expressing pV-H3-H1 vaccine (P > 0.05). No measurable virus titers were detected in the lungs of the multi-epitope immunized group. The unique multi-epitope DNA vaccine enhanced virus-specific antibody and cellular immunity as well as conferred complete protection against lethal challenge with A/New Caledonia/20/99 (H1N1) influenza strain in mice. Conclusions This approach may be a promising strategy for developing a universal influenza vaccine to prevent multiple subtypes of influenza virus and to induce long-term protective immune against cross-species transmission. PMID:21134292

  17. Gastroprotective effect of andrographolide sodium bisulfite against indomethacin-induced gastric ulceration in rats.

    PubMed

    Liu, Yu-Hong; Zhang, Zhen-Biao; Zheng, Yi-Feng; Chen, Hai-Ming; Yu, Xiu-Ting; Chen, Xiao-Ying; Zhang, Xie; Xie, Jian-Hui; Su, Zu-Qing; Feng, Xue-Xuan; Zeng, Hui-Fang; Su, Zi-Ren

    2015-06-01

    Andrographolide sodium bisulfite (ASB), a water-soluble sulfonate of andrographolide has been shown to possess anti-inflammatory, antipyretic and analgesic activities. However, there is no report on the gastroprotective effect of ASB against indomethacin-induced gastric ulcer. Here we investigated the possible anti-ulcerogenic potential of ASB and the underlying mechanism against indomethacin-induced gastric ulcer in rats. The ulcer area, histopathological assessment, contents of gastric mucosal glutathione (GSH), catalase (CAT), superoxide dismutase (SOD), malonaldehyde (MDA) and prostaglandin E2 (PGE2) were examined. In addition, cyclooxygenase-1 (COX-1), cyclooxygenase-2 (COX-2) mRNA expression and immunohistochemical evaluation of HSP70, Bcl-2 and Bax proteins were also investigated. Results indicated that ASB pre-treatment significantly reduced the ulcer areas induced by indomethacin compared with the vehicle group. The gastric levels of GSH, CAT and SOD were markedly increased by ASB while the level of MDA was decreased. In addition, ASB pretreatment significantly promoted the gastric PGE2 levels and up-regulated the COX-1 and COX-2 mRNA expression in comparison with the vehicle group. Immunohistochemistry analysis showed obvious up-regulation of HSP70 and Bcl-2 protein expression while suppression of Bax protein in the gastric tissue of ASB-pretreated group. Taken together, these findings indicated that the gastroprotective effect of ASB might be associated with the improvement of antioxidative status, activation of COX-mediated PGE2 synthesis, down-regulation of Bax proteins and up-regulation of Bcl-2 and HSP70 proteins. ASB might have the potential for further development as a promising alternative for antiulcer treatment. PMID:25916678

  18. Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

    PubMed Central

    Müller, Albert Leopold; Kjeldsen, Kasper Urup; Rattei, Thomas; Pester, Michael; Loy, Alexander

    2015-01-01

    The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods. PMID:25343514

  19. Effect of sodium bisulfite injection on the microbial community composition in a brackish-water-transporting pipeline.

    PubMed

    Park, Hyung Soo; Chatterjee, Indranil; Dong, Xiaoli; Wang, Sheng-Hung; Sensen, Christoph W; Caffrey, Sean M; Jack, Thomas R; Boivin, Joe; Voordouw, Gerrit

    2011-10-01

    Pipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) of Pseudomonas not found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereas Deltaproteobacteria of the genera Desulfomicrobium and Desulfocapsa were not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) of Methanobacteriaceae archaea but increased fractions of sulfate-reducing Desulfomicrobium (18% and 48%) and of bisulfite-disproportionating Desulfocapsa (35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters. PMID:21856836

  20. Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline▿†

    PubMed Central

    Park, Hyung Soo; Chatterjee, Indranil; Dong, Xiaoli; Wang, Sheng-Hung; Sensen, Christoph W.; Caffrey, Sean M.; Jack, Thomas R.; Boivin, Joe; Voordouw, Gerrit

    2011-01-01

    Pipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) of Pseudomonas not found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereas Deltaproteobacteria of the genera Desulfomicrobium and Desulfocapsa were not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) of Methanobacteriaceae archaea but increased fractions of sulfate-reducing Desulfomicrobium (18% and 48%) and of bisulfite-disproportionating Desulfocapsa (35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters. PMID:21856836

  1. Single-cell, locus-specific bisulfite sequencing (SLBS) for direct detection of epimutations in DNA methylation patterns

    PubMed Central

    Gravina, Silvia; Ganapathi, Shireen; Vijg, Jan

    2015-01-01

    Stochastic epigenetic changes drive biological processes, such as development, aging and disease. Yet, epigenetic information is typically collected from millions of cells, thereby precluding a more precise understanding of cell-to-cell variability and the pathogenic history of epimutations. Here we present a novel procedure for directly detecting epimutations in DNA methylation patterns using single-cell, locus-specific bisulfite sequencing (SLBS). We show that within gene promoter regions of mouse hepatocytes the epimutation rate is two orders of magnitude higher than the mutation rate. PMID:25897117

  2. Caloric restriction.

    PubMed

    Speakman, John R; Mitchell, Sharon E

    2011-06-01

    Restricting the intake of calories has been practiced as a method for increasing both the length and quality of life for over 500 years. Experimental work confirming the success of this approach in animals has accumulated over the last 100 years. Lifelong caloric restriction (CR) may extend life by up to 50% in rodents, with progressively less impact the later in life it is started. This effect is matched by profound impacts on age related diseases including reduced risk of cancer, neurodegenerative disorders, autoimmune disease, cardiovascular disease and type II diabetes mellitus. The disposable soma theory of ageing suggests that CR evolved as a somatic protection response to enable animals to survive periods of food shortage. The shutdown of reproductive function during CR is consistent with this suggestion, but other features of the phenomenon are less consistent with this theory, and some have suggested that in rodents it may be mostly an artifact of domestication. CR induces profound effects on animals at all levels from the transcriptome to whole animal physiology and behavior. Animals under CR lose weight which is disproportionately contributed to by white adipose tissue. Generally animals on CR change their activity patterns so that they are more active prior to food delivery each day but total activity may be unchanged or reduced. Considerable debate has occurred over the effects of CR on resting metabolic rate (RMR). Total RMR declines, but as body mass and body composition also change it is unclear whether metabolism at the tissue level also declines, is unchanged or even increases. Body temperature universally decreases. Hunger is increased and does not seem to abate even with very long term restriction. Circulating adipokines are reduced reflecting the reduction in white adipose tissue (WAT) mass under restriction and there is a large reduction in circulating insulin and glucose levels. There are profound tissue level changes in metabolism with a

  3. A new fluorescent enhanced probe based on (E)-9-(2-nitrovinyl)-anthracene for the detection of bisulfite anions and its practical application

    NASA Astrophysics Data System (ADS)

    Chao, Jianbin; Liu, Yuhong; Zhang, Yan; Zhang, Yongbin; Huo, Fangjun; Yin, Caixia; Wang, Yu; Qin, Liping

    2015-07-01

    A new fluorescent enhanced probe based on (E)-9-(2-nitrovinyl)-anthracene is developed, which shows high selectivity and sensitivity for the detection of bisulfite anions at Na2HPO4 citric acid buffer solutions (pH 5.0). When addition of HSO3-, the fluorescence intensity is significantly enhanced and the probe displays apparent fluorescence color changes from non-fluorescence to blue under a UV lamp illumination, the solution color also changes from yellow to colorless. The detection limit is determined to be as low as 6.30 μM. This offers another specific colorimetric and fluorescent probe for bisulfite anions detection, furthermore it is applied in detecting the level of bisulfite in sugar samples.

  4. A Combination of Activation and Repression by a Colinear Hox Code Controls Forelimb-Restricted Expression of Tbx5 and Reveals Hox Protein Specificity

    PubMed Central

    Nishimoto, Satoko; Minguillon, Carolina; Wood, Sophie; Logan, Malcolm P. O.

    2014-01-01

    Tight control over gene expression is essential for precision in embryonic development and acquisition of the regulatory elements responsible is the predominant driver for evolution of new structures. Tbx5 and Tbx4, two genes expressed in forelimb and hindlimb-forming regions respectively, play crucial roles in the initiation of limb outgrowth. Evolution of regulatory elements that activate Tbx5 in rostral LPM was essential for the acquisition of forelimbs in vertebrates. We identified such a regulatory element for Tbx5 and demonstrated Hox genes are essential, direct regulators. While the importance of Hox genes in regulating embryonic development is clear, Hox targets and the ways in which each protein executes its specific function are not known. We reveal how nested Hox expression along the rostro-caudal axis restricts Tbx5 expression to forelimb. We demonstrate that Hoxc9, which is expressed in caudal LPM where Tbx5 is not expressed, can form a repressive complex on the Tbx5 forelimb regulatory element. This repressive capacity is limited to Hox proteins expressed in caudal LPM and carried out by two separate protein domains in Hoxc9. Forelimb-restricted expression of Tbx5 and ultimately forelimb formation is therefore achieved through co-option of two characteristics of Hox genes; their colinear expression along the body axis and the functional specificity of different paralogs. Active complexes can be formed by Hox PG proteins present throughout the rostral-caudal LPM while restriction of Tbx5 expression is achieved by superimposing a dominant repressive (Hoxc9) complex that determines the caudal boundary of Tbx5 expression. Our results reveal the regulatory mechanism that ensures emergence of the forelimbs at the correct position along the body. Acquisition of this regulatory element would have been critical for the evolution of limbs in vertebrates and modulation of the factors we have identified can be molecular drivers of the diversity in limb morphology

  5. Combination of SAHA and bortezomib up-regulates CDKN2A and CDKN1A and induces apoptosis of Epstein-Barr virus-positive Wp-restricted Burkitt lymphoma and lymphoblastoid cell lines.

    PubMed

    Hui, Kwai Fung; Leung, Yvonne Y; Yeung, Po L; Middeldorp, Jaap M; Chiang, Alan K S

    2014-12-01

    Epstein-Barr virus (EBV) latent proteins exert anti-apoptotic effects on EBV-transformed lymphoid cells by down-regulating BCL2L11 (BIM), CDKN2A (p16(INK4A) ) and CDKN1A (p21(WAF1) ). However, the potential therapeutic effects of targeting these anti-apoptotic mechanisms remain unexplored. Here, we tested both in vitro and in vivo effects of the combination of histone deacetylase (HDAC) and proteasome inhibitors on the apoptosis of six endemic Burkitt lymphoma (BL) lines of different latency patterns (types I and III and Wp-restricted) and three lymphoblastoid cell lines (LCLs). We found that the combination of HDAC and proteasome inhibitors (e.g. SAHA/bortezomib) synergistically induced the killing of Wp-restricted and latency III BL and LCLs but not latency I BL cells. The synergistic killing was due to apoptosis, as evidenced by the high percentage of annexin V positivity and strong cleavage of PARP1 (PARP) and CASP3 (caspase-3). Concomitantly, SAHA/bortezomib up-regulated the expression of CDKN2A and CDKN1A but did not affect the level of BCL2L11 or BHRF1 (viral homologue of BCL2). The apoptotic effects were dependent on reactive oxygen species generation. Furthermore, SAHA/bortezomib suppressed the growth of Wp-restricted BL xenografts in nude mice. This study provides the rationale to test the novel application of SAHA/bortezomib on the treatment of EBV-associated Wp-restricted BL and post-transplant lymphoproliferative disorder. PMID:25155625

  6. Validation of a Stability-Indicating Hydrophilic Interaction Liquid Chromatographic Method for the Quantitative Determination of Vitamin K3 (Menadione Sodium Bisulfite) in Injectable Solution Formulation

    PubMed Central

    Ghanem, Mashhour M.; Abu-Lafi, Saleh A.; Hallak, Hussein O.

    2013-01-01

    A simple, specific, accurate, and stability-indicating method was developed and validated for the quantitative determination of menadione sodium bisulfite in the injectable solution formulation. The method is based on zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) coupled with a photodiode array detector. The desired separation was achieved on the ZIC-HILIC column (250 mm × 4.6 mm, 5 μm) at 25°C temperature. The optimized mobile phase consisted of an isocratic solvent mixture of 200mM ammonium acetate (NH4AC) solution and acetonitrile (ACN) (20:80; v/v) pH-adjusted to 5.7 by glacial acetic acid. The mobile phase was fixed at 0.5 ml/min and the analytes were monitored at 261 nm using a photodiode array detector. The effects of the chromatographic conditions on the peak retention, peak USP tailing factor, and column efficiency were systematically optimized. Forced degradation experiments were carried out by exposing menadione sodium bisulfite standard and the injectable solution formulation to thermal, photolytic, oxidative, and acid-base hydrolytic stress conditions. The degradation products were well-resolved from the main peak and the excipients, thus proving that the method is a reliable, stability-indicating tool. The method was validated as per ICH and USP guidelines (USP34/NF29) and found to be adequate for the routine quantitative estimation of menadione sodium bisulfite in commercially available menadione sodium bisulfite injectable solution dosage forms. PMID:24106670

  7. Effects of sodium meta bisulfite on diffusion fermentation of fodder beets for fuel ethanol production. [Saccharomyces cerevisiae

    SciTech Connect

    Gibbons, W.R.; Westby, C.A.

    1987-01-01

    The authors designed and tested a new process for converting fodder beets to ethanol: continuous diffusion-fermentation. This process utilizes the simultaneous diffusion-fermentation concept of the EX-FERM design; however, it overcomes the material handling problems inherent in that system by utilizing a counterflow tubular auger system. This process also eliminates the need for roller mills or presses and dryers which are required for alcohol recovery from solid phase fermentation. The latter is the only other currently feasible procedure for producing distillably worthwhile amounts of ethanol from fodder beets, sweet sorghum, and other similar feedstocks. Results on the use of sodium meta bisulfite (SMB) for contamination control with fermenting fodder beet cubes are reported.

  8. Clustering of Cancer Cell Lines Using A Promoter- Targeted Liquid Hybridization Capture-Based Bisulfite Sequencing Approach.

    PubMed

    Gao, Fei; Wang, Junwen; Ji, Guanyu; Liu, Siyang; Yao, Yu; Wang, Tong; Wu, Honglong; Xia, Yudong; Gong, Desheng; Jiang, Hui; Yang, Huanming; Zhang, Xiuqing

    2015-08-01

    DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect to tissue-origins or clinically and etiologically distinct subtypes. In this study, we optimized our liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach on the gene promoter regions of 11 cell lines. Our results indicated that promoter methylomes could not only cluster cancer cell lines with respect to tissue origins but also differentiate cancer subtypes based on CpG island methylator phenotype (CIMP). Promoter-targeted LHC-BS as means for comprehensive screening and classifying cancer cells with promoter methylomes provided a powerful strategy for further complex clinical studies. PMID:26269607

  9. A combined DFT and restricted open-shell configuration interaction method including spin-orbit coupling: application to transition metal L-edge X-ray absorption spectroscopy.

    PubMed

    Roemelt, Michael; Maganas, Dimitrios; DeBeer, Serena; Neese, Frank

    2013-05-28

    A novel restricted-open-shell configuration interaction with singles (ROCIS) approach for the calculation of transition metal L-edge X-ray absorption spectra is introduced. In this method, one first calculates the ground state and a number of excited states of the non-relativistic Hamiltonian. By construction, the total spin is a good quantum number in each of these states. For a ground state with total spin S excited states with spin S' = S, S - 1, and S + 1 are constructed. Using Wigner-Eckart algebra, all magnetic sublevels with MS = S,..., -S for each multiplet of spin S are obtained. The spin-orbit operator is represented by a mean-field approximation to the full Breit-Pauli spin-orbit operator and is diagonalized over this N-particle basis. This is equivalent to a quasi-degenerate treatment of the spin-orbit interaction to all orders. Importantly, the excitation space spans all of the molecular multiplets that arise from the atomic Russell-Saunders terms. Hence, the method represents a rigorous first-principles approach to the complicated low-symmetry molecular multiplet problem met in L-edge X-ray absorption spectroscopy. In order to gain computational efficiency, as well as additional accuracy, the excitation space is restricted to single excitations and the configuration interaction matrix is slightly parameterized in order to account for dynamic correlation effects in an average way. To this end, it is advantageous to employ Kohn-Sham rather than Hartree-Fock orbitals thus defining the density functional theory∕ROCIS method. However, the method can also be used in an entirely non-empirical fashion. Only three global empirical parameters are introduced and have been determined here for future application of the method to any system containing any transition metal. The three parameters were carefully calibrated using the L-edge X-ray absorption spectroscopy spectra of a test set of coordination complexes containing first row transition metals. These

  10. A combined DFT and restricted open-shell configuration interaction method including spin-orbit coupling: Application to transition metal L-edge X-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Roemelt, Michael; Maganas, Dimitrios; DeBeer, Serena; Neese, Frank

    2013-05-01

    A novel restricted-open-shell configuration interaction with singles (ROCIS) approach for the calculation of transition metal L-edge X-ray absorption spectra is introduced. In this method, one first calculates the ground state and a number of excited states of the non-relativistic Hamiltonian. By construction, the total spin is a good quantum number in each of these states. For a ground state with total spin S excited states with spin S' = S, S - 1, and S + 1 are constructed. Using Wigner-Eckart algebra, all magnetic sublevels with MS = S, …, -S for each multiplet of spin S are obtained. The spin-orbit operator is represented by a mean-field approximation to the full Breit-Pauli spin-orbit operator and is diagonalized over this N-particle basis. This is equivalent to a quasi-degenerate treatment of the spin-orbit interaction to all orders. Importantly, the excitation space spans all of the molecular multiplets that arise from the atomic Russell-Saunders terms. Hence, the method represents a rigorous first-principles approach to the complicated low-symmetry molecular multiplet problem met in L-edge X-ray absorption spectroscopy. In order to gain computational efficiency, as well as additional accuracy, the excitation space is restricted to single excitations and the configuration interaction matrix is slightly parameterized in order to account for dynamic correlation effects in an average way. To this end, it is advantageous to employ Kohn-Sham rather than Hartree-Fock orbitals thus defining the density functional theory/ROCIS method. However, the method can also be used in an entirely non-empirical fashion. Only three global empirical parameters are introduced and have been determined here for future application of the method to any system containing any transition metal. The three parameters were carefully calibrated using the L-edge X-ray absorption spectroscopy spectra of a test set of coordination complexes containing first row transition metals. These

  11. Restricted access property supramolecular solvents for combined microextraction of endocrine disruptors in sediment and sample cleanup prior to their quantification by liquid chromatography-tandem mass spectrometry.

    PubMed

    López-Jiménez, F J; Rosales-Marcano, M; Rubio, S

    2013-08-16

    A supramolecular solvent (SUPRAS) made up of inverted hexagonal aggregates of decanol was here proposed for the simultaneous microextraction of representative estrogenic disruptors (EDs) [viz. estrone (E1), 17β-estradiol (E2), estriol (E3), 17α-ethinylestradiol (EE2) and bisphenol A (BPA)] in sediments and sample cleanup. The SUPRAS contains aqueous cavities, the size of which can be tailored by controlling the environment for decanol self-assembly. The method involved the stirring of the sample (0.3g of sediment) with 0.4mL of SUPRAS for 10min, subsequent centrifugation for extract separation from solid matrix components and direct analysis of the extract by liquid chromatography/triple quadrupole mass spectrometry (LC/QQQMS-MS). Driving forces for the microextraction of EDs in the SUPRAS involved both dispersion and hydrogen bond interactions. This mixed-mode mechanism resulted in high extraction efficiencies for EDs (viz. recoveries between 93 and 104%) and that allowed to reach low method detection limits (viz. 0.03, 0.3, 0.28, 0.4 and 0.08ngg(-1) for E1, E2, E3, EE2 and BPA, respectively) without the need for extract evaporation. The size of the aqueous cavities of the SUPRAS selected was no large enough to allow humic acids to efficiently diffuse through them. So the SUPRAS behaved as a restricted access material for these macromolecules thus facilitating sample cleanup. The method was applied to the determination of the targeted EDs in sediments from three rivers in the Southern Spain. The concentrations found ranged between below the MDL and 6.4ngg(-1). The sample treatment here proposed greatly simplifies the procedures currently used for the determination of EDs in sediments using LC/MS-MS. PMID:23849783

  12. Selective molecularly imprinted polymer combined with restricted access material for in-tube SPME/UHPLC-MS/MS of parabens in breast milk samples.

    PubMed

    Souza, Israel D; Melo, Lidervan P; Jardim, Isabel C S F; Monteiro, Juliana C S; Nakano, Ana Marcia S; Queiroz, Maria Eugênia C

    2016-08-17

    A new molecularly imprinted polymer modified with restricted access material (a hydrophilic external layer), (MIP-RAM) was synthesized via polymerization in situ in an open fused silica capillary. This stationary phase was used as sorbent for in-tube solid phase microextraction (in-tube SPME) to determine parabens in breast milk samples by ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Scanning electron micrographs (SEM) illustrate MIP surface modification after glycerol dimethacrylate (hydrophilic monomer) incorporation. The interaction between parabens and MIP-RAM was investigated by Fourier-transform infrared (FTIR) spectroscopy. The Scatchard plot for MIP-RAM presented two linear parts with different slopes, illustrating binding sites with high- and low-affinity. Endogenous compounds exclusion from the MIP-RAM capillary was demonstrated by in-tube SPME/LC-UV assays carried out with blank milk samples. The in-tube SPME/UHPLC-MS/MS method presented linear range from 10 ng mL(-1) (LLOQ) to 400 ng mL(-1) with coefficients of determination higher than 0.99, inter-assay precision with coefficient of variation (CV) values ranging from 2 to 15%, and inter-assay accuracy with relative standard deviation (RSD) values ranging from -1% to 19%. Analytical validation parameters attested that in-tube SPME/UHPLC-MS/MS is an appropriate method to determine parabens in human milk samples to assess human exposure to these compounds. Analysis of breast milk samples from lactating women demonstrated that the proposed method is effective. PMID:27286769

  13. Effects of Low-Load, Elastic Band Resistance Training Combined With Blood Flow Restriction on Muscle Size and Arterial Stiffness in Older Adults.

    PubMed

    Yasuda, Tomohiro; Fukumura, Kazuya; Uchida, Yusuke; Koshi, Hitomi; Iida, Haruko; Masamune, Ken; Yamasoba, Tatsuya; Sato, Yoshiaki; Nakajima, Toshiaki

    2015-08-01

    We examined the effect of low-load, elastic band resistance training with blood flow restriction (BFR) on muscle size and arterial stiffness in older adults. Healthy older adults (aged 61-85 years) were divided into BFR training (BFR-T, n = 9) or non-BFR training (CON-T, n = 8) groups. Both groups performed low-load arm curl and triceps down exercises (four sets, total 75 repetitions for each) using an elastic band, 2 d/wk for 12 weeks. The BFR-T group wore inflated pneumatic elastic cuffs (120-270 mm Hg) on both arms during training. Magnetic resonance imaging-measured muscle cross-sectional area of the upper arm, maximum voluntary isometric contraction of the elbow flexors and extensors, cardio-ankle vascular index testing, and ankle-brachial pressure index were measured before and 3-5 days after the final training session. Muscle cross-sectional area of the elbow flexors (17.6%) and extensors (17.4%) increased, as did elbow flexion and elbow extension maximum voluntary isometric contraction (7.8% and 16.1%, respectively) improved (p < .05) in the BFR-T group, but not in the CON-T group. In cardio-ankle vascular index and ankle-brachial pressure index testing, there were no changes between pre- and post-results in either group. In conclusion, elastic band BFR-T improves muscle cross-sectional area as well as maximal muscle strength but does not negatively affect arterial stiffness in older adults. PMID:24917178

  14. Combination of exercise training and diet restriction normalizes limited exercise capacity and impaired skeletal muscle function in diet-induced diabetic mice.

    PubMed

    Suga, Tadashi; Kinugawa, Shintaro; Takada, Shingo; Kadoguchi, Tomoyasu; Fukushima, Arata; Homma, Tsuneaki; Masaki, Yoshihiro; Furihata, Takaaki; Takahashi, Masashige; Sobirin, Mochamad A; Ono, Taisuke; Hirabayashi, Kagami; Yokota, Takashi; Tanaka, Shinya; Okita, Koichi; Tsutsui, Hiroyuki

    2014-01-01

    Exercise training (EX) and diet restriction (DR) are essential for effective management of obesity and insulin resistance in diabetes mellitus. However, whether these interventions ameliorate the limited exercise capacity and impaired skeletal muscle function in diabetes patients remains unexplored. Therefore, we investigated the effects of EX and/or DR on exercise capacity and skeletal muscle function in diet-induced diabetic mice. Male C57BL/6J mice that were fed a high-fat diet (HFD) for 8 weeks were randomly assigned for an additional 4 weeks to 4 groups: control, EX, DR, and EX+DR. A lean group fed with a normal diet was also studied. Obesity and insulin resistance induced by a HFD were significantly but partially improved by EX or DR and completely reversed by EX+DR. Although exercise capacity decreased significantly with HFD compared with normal diet, it partially improved with EX and DR and completely reversed with EX+DR. In parallel, the impaired mitochondrial function and enhanced oxidative stress in the skeletal muscle caused by the HFD were normalized only by EX+DR. Although obesity and insulin resistance were completely reversed by DR with an insulin-sensitizing drug or a long-term intervention, the exercise capacity and skeletal muscle function could not be normalized. Therefore, improvement in impaired skeletal muscle function, rather than obesity and insulin resistance, may be an important therapeutic target for normalization of the limited exercise capacity in diabetes. In conclusion, a comprehensive lifestyle therapy of exercise and diet normalizes the limited exercise capacity and impaired muscle function in diabetes mellitus. PMID:24189138

  15. Genome-wide DNA methylation profiles changes associated with constant heat stress in pigs as measured by bisulfite sequencing

    PubMed Central

    Hao, Yue; Cui, Yanjun; Gu, Xianhong

    2016-01-01

    Heat stress affects muscle development and meat quality in food animals; however, little is known regarding its regulatory mechanisms at the epigenetic level, such as via DNA methylation. In this study, we aimed to compare the DNA methylation profiles between control and heat-stressed pigs to identify candidate genes for skeletal muscle development and meat quality. Whole-genome bisulfite sequencing was used to investigate the genome-wide DNA methylation patterns in the longissimus dorsi muscles of the pigs. Both groups showed similar proportions of methylation at CpG sites but exhibited different proportions at non-CpG sites. A total of 57,147 differentially methylated regions were identified between the two groups, which corresponded to 1,422 differentially methylated genes. Gene ontogeny and KEGG pathway analyses indicated that these were mainly involved in energy and lipid metabolism, cellular defense and stress responses, and calcium signaling pathways. This study revealed the global DNA methylation pattern of pig muscle between normal and heat stress conditions. The result of this study might contribute to a better understanding of epigenetic regulation in pig muscle development and meat quality. PMID:27264107

  16. Genome-wide DNA methylation profiles changes associated with constant heat stress in pigs as measured by bisulfite sequencing.

    PubMed

    Hao, Yue; Cui, Yanjun; Gu, Xianhong

    2016-01-01

    Heat stress affects muscle development and meat quality in food animals; however, little is known regarding its regulatory mechanisms at the epigenetic level, such as via DNA methylation. In this study, we aimed to compare the DNA methylation profiles between control and heat-stressed pigs to identify candidate genes for skeletal muscle development and meat quality. Whole-genome bisulfite sequencing was used to investigate the genome-wide DNA methylation patterns in the longissimus dorsi muscles of the pigs. Both groups showed similar proportions of methylation at CpG sites but exhibited different proportions at non-CpG sites. A total of 57,147 differentially methylated regions were identified between the two groups, which corresponded to 1,422 differentially methylated genes. Gene ontogeny and KEGG pathway analyses indicated that these were mainly involved in energy and lipid metabolism, cellular defense and stress responses, and calcium signaling pathways. This study revealed the global DNA methylation pattern of pig muscle between normal and heat stress conditions. The result of this study might contribute to a better understanding of epigenetic regulation in pig muscle development and meat quality. PMID:27264107

  17. Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation

    PubMed Central

    Peat, Julian R.; Dean, Wendy; Clark, Stephen J.; Krueger, Felix; Smallwood, Sébastien A.; Ficz, Gabriella; Kim, Jong Kyoung; Marioni, John C.; Hore, Timothy A.; Reik, Wolf

    2014-01-01

    Summary Fertilization triggers global erasure of paternal 5-methylcytosine as part of epigenetic reprogramming during the transition from gametic specialization to totipotency. This involves oxidation by TET3, but our understanding of its targets and the wider context of demethylation is limited to a small fraction of the genome. We employed an optimized bisulfite strategy to generate genome-wide methylation profiles of control and TET3-deficient zygotes, using SNPs to access paternal alleles. This revealed that in addition to pervasive removal from intergenic sequences and most retrotransposons, gene bodies constitute a major target of zygotic demethylation. Methylation loss is associated with zygotic genome activation and at gene bodies is also linked to increased transcriptional noise in early development. Our data map the primary contribution of oxidative demethylation to a subset of gene bodies and intergenic sequences and implicate redundant pathways at many loci. Unexpectedly, we demonstrate that TET3 activity also protects certain CpG islands against methylation buildup. PMID:25497087

  18. swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing

    PubMed Central

    Shao, Qianzhi; Liu, Qi; Chen, BingYu; Huang, Dongsheng

    2015-01-01

    DNA methylation is a widespread epigenetic modification that plays an essential role in gene expression through transcriptional regulation and chromatin remodeling. The emergence of whole genome bisulfite sequencing (WGBS) represents an important milestone in the detection of DNA methylation. Characterization of differential methylated regions (DMRs) is fundamental as well for further functional analysis. In this study, we present swDMR (http://sourceforge.net/projects/swdmr/) for the comprehensive analysis of DMRs from whole genome methylation profiles by a sliding window approach. It is an integrated tool designed for WGBS data, which not only implements accessible statistical methods to perform hypothesis test adapted to two or more samples without replicates, but false discovery rate was also controlled by multiple test correction. Downstream analysis tools were also provided, including cluster, annotation and visualization modules. In summary, based on WGBS data, swDMR can produce abundant information of differential methylated regions. As a convenient and flexible tool, we believe swDMR will bring us closer to unveil the potential functional regions involved in epigenetic regulation. PMID:26176536

  19. Construction of effective inverted repeat silencing constructs using sodium bisulfite treatment coupled with strand-specific PCR.

    PubMed

    Taylor, Sarah H; Harmse, Johan; Arbuthnot, Patrick; Van Den Berg, Fiona; Weinberg, Marco S; Rey, Marie E C

    2012-04-01

    RNA silencing has been exploited to produce transgenic plants with resistance to viral pathogens via posttranscriptional gene silencing (PTGS). In some cases, this technology is difficult to apply due to the instability of inverted repeat (IR) constructs during cloning and plant transformation. Although such constructs have been shown to be stabilized with introns and efficiently induce RNA silencing, we found that the Pdk intron did not stabilize South African cassava mosaic virus (SACMV) silencing constructs. Therefore, we developed a method for producing long SACMV IR constructs through bisulfite-induced base pair mismatches on the sense arm prior to IR assembly. Expression of SACMV BC1 mismatched IR constructs in the model test plant Nicotiana benthamiana resulted in a reduction in viral BC1 transcript levels, hence viral replication, upon SACMV infection. Mismatched SACMV AC1 IR constructs induced PTGS more efficiently in a N. benthamiana callus system than nonmismatched IR constructs. Our novel method for IR construct generation should be applicable to many sequences where the generation of these constructs has proven difficult in the past. PMID:22482441

  20. metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.

    PubMed

    Jühling, Frank; Kretzmer, Helene; Bernhart, Stephan H; Otto, Christian; Stadler, Peter F; Hoffmann, Steve

    2016-02-01

    The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs within whole-genome and targeted data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows the detection of DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardware. metilene outperforms other state-of-the-art tools for low coverage data and can estimate missing data. Hence, metilene is a versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology on a global, genome-wide level. Whether in the framework of international consortia with dozens of samples per group, or even without biological replicates, it produces highly significant and reliable results. PMID:26631489

  1. 49 CFR 383.95 - Restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... person is restricted from operating a CMV equipped with any type of air brakes. (2) For the purposes of... transmission as defined in § 383.5. (d) Tractor-trailer. If an applicant performs the skills test in a... restricted from operating a tractor-trailer combination connected by a fifth wheel that requires a Group...

  2. 49 CFR 383.95 - Restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... person is restricted from operating a CMV equipped with any type of air brakes. (2) For the purposes of... transmission as defined in § 383.5. (d) Tractor-trailer. If an applicant performs the skills test in a... restricted from operating a tractor-trailer combination connected by a fifth wheel that requires a Group...

  3. 49 CFR 383.95 - Restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... person is restricted from operating a CMV equipped with any type of air brakes. (2) For the purposes of... transmission as defined in § 383.5. (d) Tractor-trailer. If an applicant performs the skills test in a... restricted from operating a tractor-trailer combination connected by a fifth wheel that requires a Group...

  4. Online restricted-access material combined with high-performance liquid chromatography and tandem mass spectrometry for the simultaneous determination of vanillin and its vanillic acid metabolite in human plasma.

    PubMed

    Li, De-Qiang; Zhang, Zhi-Qing; Yang, Xiu-Ling; Zhou, Chun-Hua; Qi, Jin-Long

    2016-09-01

    An automated online solid-phase extraction with restricted-access material combined with high-performance liquid chromatography and tandem mass spectrometry was developed and validated for the simultaneous quantification of vanillin and its vanillic acid metabolite in human plasma. After protein precipitation by methanol, which contained the internal standards, the supernatant of plasma samples was injected to the system, the endogenous large molecules were flushed out, and target analytes were trapped and enriched on the adsorbent, resulting in a minimization of sample complexity and ion suppression effects. Calibration curves were linear over the concentrations of 5-1000 ng/mL for vanillin and 10-5000 ng/mL for vanillic acid with a coefficient of determination >0.999 for the determined compounds. The lower limits of quantification of vanillin and vanillic acid were 5.0 and 10.0 ng/mL, respectively. The intra- and inter-run precisions expressed as the relative standard deviation were 2.6-8.6 and 3.2-10.2%, respectively, and the accuracies expressed as the relative error were in the range of -6.1 to 7.3%. Extraction recoveries of analytes were between 89.5 and 97.4%. There was no notable matrix effect for any analyte concentration. The developed method was proved to be sensitive, repeatable, and accurate for the quantification of vanillin and its vanillic acid metabolite in human plasma. PMID:27384745

  5. Effects of acute feed restriction combined with targeted use of increasing luteinizing hormone content of follicle-stimulating hormone preparations on ovarian superstimulation, fertilization, and embryo quality in lactating dairy cows.

    PubMed

    Bender, R W; Hackbart, K S; Dresch, A R; Carvalho, P D; Vieira, L M; Crump, P M; Guenther, J N; Fricke, P M; Shaver, R D; Combs, D K; Wiltbank, M C

    2014-02-01

    Multiple metabolic and hormonal factors can affect the success of protocols for ovarian superstimulation. In this study, the effect of acute feed restriction and increased LH content in the superstimulatory FSH preparation on numbers of ovulations, fertilization, and embryo quality in lactating dairy cows was evaluated. Two experiments were performed using a Latin square design with treatments arranged as a 2 × 2 factorial: feed restriction (FR; 25% reduction in dry matter intake) compared with ad libitum (AL) feeding, combined with high (H) versus low (L) LH in the last 4 injections of the superstimulatory protocol. As expected, FR decreased circulating insulin concentrations (26.7 vs. 46.0 μU/mL). Two analyses were performed: one that evaluated the complete Latin square in experiment 2 and a second that evaluated only the first periods of experiments 1 and 2. For both analyses, follicle numbers, ovulation rates, and corpora lutea on d 7 were not different. In the first period analysis of experiments 1 and 2, we observed an interaction between feed allowance and amount of LH on fertilization rates, percentage of embryos or oocytes that were quality 1 and 2 embryos, and number of embryos or oocytes that were degenerate. Fertilization rates were greater for the AL-L (89.4%) and FR-H (80.1%) treatments compared with the AL-H (47.9%) and FR-L (59.9%) treatments. Similarly, the proportion of total embryos or oocytes designated as quality 1 and 2 embryos was greater for AL-L (76.7%) and FR-H (73.4%) treatments compared with AL-H (35.6%) and FR-L (47.3%) treatments. In addition, the number of degenerate embryos was decreased for AL-L (1.3) and FR-H (0.4) treatments compared with the AL-H (2.6) and FR-L (2.3) treatments. Thus, cows with either too low (FR-L) or too high (AL-H) insulin and LH stimulation had lesser embryo production after superstimulation because of reduced fertilization rate and increased percentage of degenerate embryos. Therefore, interaction of the

  6. COLD-PCR amplification of bisulfite-converted DNA allows the enrichment and sequencing of rare un-methylated genomic regions.

    PubMed

    Castellanos-Rizaldos, Elena; Milbury, Coren A; Karatza, Elli; Chen, Clark C; Makrigiorgos, G Mike; Merewood, Anne

    2014-01-01

    Aberrant hypo-methylation of DNA is evident in a range of human diseases including cancer and diabetes. Development of sensitive assays capable of detecting traces of un-methylated DNA within methylated samples can be useful in several situations. Here we describe a new approach, fast-COLD-MS-PCR, which amplifies preferentially un-methylated DNA sequences. By employing an appropriate denaturation temperature during PCR of bi-sulfite converted DNA, fast-COLD-MS-PCR enriches un-methylated DNA and enables differential melting analysis or bisulfite sequencing. Using methylation on the MGMT gene promoter as a model, it is shown that serial dilutions of controlled methylation samples lead to the reliable sequencing of un-methylated sequences down to 0.05% un-methylated-to-methylated DNA. Screening of clinical glioma tumor and infant blood samples demonstrated that the degree of enrichment of un-methylated over methylated DNA can be modulated by the choice of denaturation temperature, providing a convenient method for analysis of partially methylated DNA or for revealing and sequencing traces of un-methylated DNA. Fast-COLD-MS-PCR can be useful for the detection of loss of methylation/imprinting in cancer, diabetes or diet-related methylation changes. PMID:24728321

  7. Identification of S-3-(hexanal)-glutathione and its bisulfite adduct in grape juice from Vitis vinifera L. cv. Sauvignon blanc as new potential precursors of 3SH.

    PubMed

    Thibon, Cécile; Böcker, Caroline; Shinkaruk, Svitlana; Moine, Virginie; Darriet, Philippe; Dubourdieu, Denis

    2016-05-15

    Two main precursors (S-3-(hexan-1-ol)-l-cysteine and S-3-(hexan-1-ol)-l-glutathione) of 3-sulfanylhexanol (3SH, formerly named 3-mercaptohexanol) have been identified so far in grape juice but a correlation between precursor concentrations in grape juices and 3SH concentrations in wines is not always observed. This suggests that there may be other compounds associated with the aromatic potential. In this work, S-3-(hexanal)-glutathione (Glut-3SH-Al) and its bisulfite (Glut-3SH-SO3) adduct were identified in Sauvignon blanc grape juice by liquid chromatography coupled to Fourier transform mass spectrometry experiments. A partial purification of the compounds was carried out by Medium Pressure Liquid Chromatography (MPLC) on the reverse phase using 5L of grape juice. The addition of synthetized Glut-3SH-Al and Glut-3SH-SO3 in the synthetic medium induced a significant release of 3SH after fermentation. Moreover, we demonstrate that Glut-3SH-Al and its bisulfite adduct are present in grape juice and could be considered as new direct 3SH precursors with molar conversion yields close to 0.4%. PMID:26776028

  8. Telomere Restriction Fragment (TRF) Analysis

    PubMed Central

    Mender, Ilgen; Shay, Jerry W.

    2016-01-01

    restriction enzyme recognition sites within TTAGGG tandem telomeric repeats, therefore digestion of genomic DNA, not telomeric DNA, with a combination of 6 base restriction endonucleases reduces genomic DNA size to less than 800 bp. PMID:27500189

  9. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation.

    PubMed

    Li, Daofeng; Zhang, Bo; Xing, Xiaoyun; Wang, Ting

    2015-01-15

    DNA CpG methylation is a widespread epigenetic mark in high eukaryotes including mammals. DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and control of gene expression. Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to measure DNA methylation in a genome-wide fashion, making it possible to comprehensively investigate the role of DNA methylation. Several methods have been developed, such as Whole Genome Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS), and enrichment-based methods including Methylation Dependent ImmunoPrecipitation followed by sequencing (MeDIP-seq), methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq), methyltransferase-directed Transfer of Activated Groups followed by sequencing (mTAG), and Methylation-sensitive Restriction Enzyme digestion followed by sequencing (MRE-seq). These methods differ by their genomic CpG coverage, resolution, quantitative accuracy, cost, and software for analyzing the data. Among these, WGBS is considered the gold standard. However, it is still a cost-prohibitive technology for a typical laboratory due to the required sequencing depth. We found that by integrating two enrichment-based methods that are complementary in nature (i.e., MeDIP-seq and MRE-seq), we can significantly increase the efficiency of whole DNA methylome profiling. By using two recently developed computational algorithms (i.e., M&M and methylCRF), the combination of MeDIP-seq and MRE-seq produces genome-wide CpG methylation measurement at high coverage and high resolution, and robust predictions of differentially methylated regions. Thus, the combination of the two enrichment-based methods provides a cost-effective alternative to WGBS. In this article we describe both the experimental protocols for performing MeDIP-seq and MRE

  10. Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing

    PubMed Central

    Bakshi, Arundhati; Ekram, Muhammad B.; Kim, Joomyeong

    2014-01-01

    DNA methylation is a major epigenetic mark associated with multiple aspects of retrotransposons within the mammalian genome. In order to study DNA methylation of a large number of retrotransposons on an individual-locus basis, we have developed a new protocol termed High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS) (Ekram and Kim, 2014 [1]). We have used this technique to characterize the locus-specific patterns of DNA methylation of 4799 members of the mouse IAP LTR (Intracisternal A Particle Long Terminal Repeat) retrotransposon family in embryonic stem, somatic and Neuro2A cells (Bakshi and Kim, 2014 [2]). Here we describe in detail the sample preparation and bioinformatics analyses used for these studies. The somatic cell data may be accessed under GEO accession number GSE49222. The ES and Neuro2A data are deposited under GEO accession number GSE60007. PMID:25554740

  11. Near BPS skyrmions and restricted harmonic maps

    NASA Astrophysics Data System (ADS)

    Speight, J. M.

    2015-06-01

    Motivated by a class of near BPS Skyrme models introduced by Adam, Sánchez-Guillén and Wereszczyński, the following variant of the harmonic map problem is introduced: a map φ :(M, g) →(N, h) between Riemannian manifolds is restricted harmonic if it locally extremizes E2 on its SDiff(M) orbit, where SDiff(M) denotes the group of volume preserving diffeomorphisms of (M, g), and E2 denotes the Dirichlet energy. It is conjectured that near BPS skyrmions tend to restricted harmonic maps in the BPS limit. It is shown that φ is restricted harmonic if and only if φ∗ h has exact divergence, and a linear stability theory of restricted harmonic maps is developed, from which it follows that all weakly conformal maps are stable restricted harmonic. Examples of restricted harmonic maps in every degree class R3 → SU(2) and R2 →S2 are constructed. It is shown that the axially symmetric BPS skyrmions on which all previous analytic studies of near BPS Skyrme models have been based, are not restricted harmonic, casting doubt on the phenomenological predictions of such studies. The problem of minimizing E2 for φ :Rk → N over all linear volume preserving diffeomorphisms is solved explicitly, and a deformed axially symmetric family of Skyrme fields constructed which are candidates for approximate near BPS skyrmions at low baryon number. The notion of restricted harmonicity is generalized to restricted F-criticality where F is any functional on maps (M, g) →(N, h) which is, in a precise sense, geometrically natural. The case where F is a linear combination of E2 and E4, the usual Skyrme term, is studied in detail, and it is shown that inverse stereographic projection R3 →S3 ≡ SU(2) is stable restricted F-critical for every such F.

  12. Neuroaesthetics: range and restrictions.

    PubMed

    Chatterjee, Anjan

    2013-04-01

    Bullot & Reber (B&R) should be commended for highlighting tensions between scientific aesthetics and art history. The question of how each tradition can learn from the other is timely. While I am sympathetic to their views, their diagnosis of the problem appears exaggerated and their solution partial. They underestimate the reach of scientific aesthetics while failing to identify its inherent restrictions. PMID:23507092

  13. License restrictions at Barnwell

    SciTech Connect

    Autry, V.R.

    1991-12-31

    The State of South Carolina was delegated the authority by the US Nuclear Regulatory Commission to regulate the receipt, possession, use and disposal of radioactive material as an Agreement State. Since 1970, the state has been the principal regulatory authority for the Barnwell Low-Level Waste Disposal Facility operated by Chem-Nuclear Systems, Inc. The radioactive material license issued authorizing the receipt and disposal of low-level waste contains numerous restrictions to ensure environmental protection and compliance with shallow land disposal performance criteria. Low-level waste has evolved from minimally contaminated items to complex waste streams containing high concentrations of radionuclides and processing chemicals which necessitated these restrictions. Additionally, some waste with their specific radionuclides and concentration levels, many classified as low-level radioactive waste, are not appropriate for shallow land disposal unless additional precautions are taken. This paper will represent a number of these restrictions, the rationale for them, and how they are being dealt with at the Barnwell disposal facility.

  14. Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation

    PubMed Central

    Mendizabal, Isabel; Yi, Soojin V.

    2016-01-01

    CpG islands (CGIs) are one of the most widely studied regulatory features of the human genome, with critical roles in development and disease. Despite such significance and the original epigenetic definition, currently used CGI sets are typically predicted from DNA sequence characteristics. Although CGIs are deeply implicated in practical analyses of DNA methylation, recent studies have shown that such computational annotations suffer from inaccuracies. Here we used whole-genome bisulfite sequencing from 10 diverse human tissues to identify a comprehensive, experimentally obtained, single-base resolution CGI catalog. In addition to the unparalleled annotation precision, our method is free from potential bias due to arbitrary sequence features or probe affinity differences. In addition to clarifying substantial false positives in the widely used University of California Santa Cruz (UCSC) annotations, our study identifies numerous novel epigenetic loci. In particular, we reveal significant impact of transposable elements on the epigenetic regulatory landscape of the human genome and demonstrate ubiquitous presence of transcription initiation at CGIs, including alternative promoters in gene bodies and non-coding RNAs in intergenic regions. Moreover, coordinated DNA methylation and chromatin modifications mark tissue-specific enhancers at novel CGIs. Enrichment of specific transcription factor binding from ChIP-seq supports mechanistic roles of CGIs on the regulation of tissue-specific transcription. The new CGI catalog provides a comprehensive and integrated list of genomic hotspots of epigenetic regulation. PMID:26512062

  15. Analyses of Methylomes Derived from Meso-American Common Bean (Phaseolus vulgaris L.) Using MeDIP-Seq and Whole Genome Sodium Bisulfite-Sequencing

    PubMed Central

    Crampton, Mollee; Sripathi, Venkateswara R.; Hossain, Khwaja; Kalavacharla, Venu

    2016-01-01

    Common bean (Phaseolus vulgaris L.) is economically important for its high protein, fiber, and micronutrient contents, with a relatively small genome size of ∼587 Mb. Common bean is genetically diverse with two major gene pools, Meso-American and Andean. The phenotypic variability within common bean is partly attributed to the genetic diversity and epigenetic changes that are largely influenced by environmental factors. It is well established that an important epigenetic regulator of gene expression is DNA methylation. Here, we present results generated from two high-throughput sequencing technologies, methylated DNA immunoprecipitation-sequencing (MeDIP-seq) and whole genome bisulfite-sequencing (BS-Seq). Our analyses revealed that this Meso-American common bean displays similar methylation patterns as other previously published plant methylomes, with CG ∼50%, CHG ∼30%, and CHH ∼2.7% methylation, however, these differ from the common bean reference methylome of Andean origin. We identified higher CG methylation levels in both promoter and genic regions than CHG and CHH contexts. Moreover, we found relatively higher CG methylation levels in genes than in promoters. Conversely, the CHG and CHH methylation levels were highest in promoters than in genes. This is the first genome-wide DNA methylation profiling study in a Meso-American common bean cultivar (“Sierra”) using NGS approaches. Our long-term goal is to generate genome-wide epigenomic maps in common bean focusing on chromatin accessibility, histone modifications, and DNA methylation. PMID:27199997

  16. Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution.

    PubMed

    Chen, Xun; Ge, Xianhong; Wang, Jing; Tan, Chen; King, Graham J; Liu, Kede

    2015-01-01

    Brassica rapa includes some of the most important vegetables worldwide as well as oilseed crops. The complete annotated genome sequence confirmed its paleohexaploid origins and provides opportunities for exploring the detailed process of polyploid genome evolution. We generated a genome-wide DNA methylation profile for B. rapa using a modified reduced representation bisulfite sequencing (RRBS) method. This sampling represented 2.24% of all CG loci (2.5 × 10(5)), 2.16% CHG (2.7 × 10(5)), and 1.68% CHH loci (1.05 × 10(5)) (where H = A, T, or C). Our sampling of DNA methylation in B. rapa indicated that 52.4% of CG sites were present as (5m)CG, with 31.8% of CHG and 8.3% of CHH. It was found that genic regions of single copy genes had significantly higher methylation compared to those of two or three copy genes. Differences in degree of genic DNA methylation were observed in a hierarchical relationship corresponding to the relative age of the three ancestral subgenomes, primarily accounted by single-copy genes. RNA-seq analysis revealed that overall the level of transcription was negatively correlated with mean gene methylation content and depended on copy number or was associated with the different subgenomes. These results provide new insights into the role epigenetic variation plays in polyploid genome evolution, and suggest an alternative mechanism for duplicate gene loss. PMID:26500672

  17. Laser capture microdissection–reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

    PubMed Central

    Schillebeeckx, Maximiliaan; Schrade, Anja; Löbs, Ann-Kathrin; Pihlajoki, Marjut; Wilson, David B.; Mitra, Robi D.

    2013-01-01

    DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging owing to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of cytosine–guanine dinucleotide islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared with adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development. PMID:23589626

  18. Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation.

    PubMed

    Mendizabal, Isabel; Yi, Soojin V

    2016-01-01

    CpG islands (CGIs) are one of the most widely studied regulatory features of the human genome, with critical roles in development and disease. Despite such significance and the original epigenetic definition, currently used CGI sets are typically predicted from DNA sequence characteristics. Although CGIs are deeply implicated in practical analyses of DNA methylation, recent studies have shown that such computational annotations suffer from inaccuracies. Here we used whole-genome bisulfite sequencing from 10 diverse human tissues to identify a comprehensive, experimentally obtained, single-base resolution CGI catalog. In addition to the unparalleled annotation precision, our method is free from potential bias due to arbitrary sequence features or probe affinity differences. In addition to clarifying substantial false positives in the widely used University of California Santa Cruz (UCSC) annotations, our study identifies numerous novel epigenetic loci. In particular, we reveal significant impact of transposable elements on the epigenetic regulatory landscape of the human genome and demonstrate ubiquitous presence of transcription initiation at CGIs, including alternative promoters in gene bodies and non-coding RNAs in intergenic regions. Moreover, coordinated DNA methylation and chromatin modifications mark tissue-specific enhancers at novel CGIs. Enrichment of specific transcription factor binding from ChIP-seq supports mechanistic roles of CGIs on the regulation of tissue-specific transcription. The new CGI catalog provides a comprehensive and integrated list of genomic hotspots of epigenetic regulation. PMID:26512062

  19. Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution

    PubMed Central

    Chen, Xun; Ge, Xianhong; Wang, Jing; Tan, Chen; King, Graham J.; Liu, Kede

    2015-01-01

    Brassica rapa includes some of the most important vegetables worldwide as well as oilseed crops. The complete annotated genome sequence confirmed its paleohexaploid origins and provides opportunities for exploring the detailed process of polyploid genome evolution. We generated a genome-wide DNA methylation profile for B. rapa using a modified reduced representation bisulfite sequencing (RRBS) method. This sampling represented 2.24% of all CG loci (2.5 × 105), 2.16% CHG (2.7 × 105), and 1.68% CHH loci (1.05 × 105) (where H = A, T, or C). Our sampling of DNA methylation in B. rapa indicated that 52.4% of CG sites were present as 5mCG, with 31.8% of CHG and 8.3% of CHH. It was found that genic regions of single copy genes had significantly higher methylation compared to those of two or three copy genes. Differences in degree of genic DNA methylation were observed in a hierarchical relationship corresponding to the relative age of the three ancestral subgenomes, primarily accounted by single-copy genes. RNA-seq analysis revealed that overall the level of transcription was negatively correlated with mean gene methylation content and depended on copy number or was associated with the different subgenomes. These results provide new insights into the role epigenetic variation plays in polyploid genome evolution, and suggest an alternative mechanism for duplicate gene loss. PMID:26500672

  20. Analyses of Methylomes Derived from Meso-American Common Bean (Phaseolus vulgaris L.) Using MeDIP-Seq and Whole Genome Sodium Bisulfite-Sequencing.

    PubMed

    Crampton, Mollee; Sripathi, Venkateswara R; Hossain, Khwaja; Kalavacharla, Venu

    2016-01-01

    Common bean (Phaseolus vulgaris L.) is economically important for its high protein, fiber, and micronutrient contents, with a relatively small genome size of ∼587 Mb. Common bean is genetically diverse with two major gene pools, Meso-American and Andean. The phenotypic variability within common bean is partly attributed to the genetic diversity and epigenetic changes that are largely influenced by environmental factors. It is well established that an important epigenetic regulator of gene expression is DNA methylation. Here, we present results generated from two high-throughput sequencing technologies, methylated DNA immunoprecipitation-sequencing (MeDIP-seq) and whole genome bisulfite-sequencing (BS-Seq). Our analyses revealed that this Meso-American common bean displays similar methylation patterns as other previously published plant methylomes, with CG ∼50%, CHG ∼30%, and CHH ∼2.7% methylation, however, these differ from the common bean reference methylome of Andean origin. We identified higher CG methylation levels in both promoter and genic regions than CHG and CHH contexts. Moreover, we found relatively higher CG methylation levels in genes than in promoters. Conversely, the CHG and CHH methylation levels were highest in promoters than in genes. This is the first genome-wide DNA methylation profiling study in a Meso-American common bean cultivar ("Sierra") using NGS approaches. Our long-term goal is to generate genome-wide epigenomic maps in common bean focusing on chromatin accessibility, histone modifications, and DNA methylation. PMID:27199997

  1. Identification of DNA methylation changes at cis-regulatory elements during early steps of HSC differentiation using tagmentation-based whole genome bisulfite sequencing

    PubMed Central

    Lipka, Daniel B; Wang, Qi; Cabezas-Wallscheid, Nina; Klimmeck, Daniel; Weichenhan, Dieter; Herrmann, Carl; Lier, Amelie; Brocks, David; von Paleske, Lisa; Renders, Simon; Wünsche, Peer; Zeisberger, Petra; Gu, Lei; Haas, Simon; Essers, Marieke Ag; Brors, Benedikt; Eils, Roland; Trumpp, Andreas; Milsom, Michael D; Plass, Christoph

    2014-01-01

    Epigenetic alterations during cellular differentiation are a key molecular mechanism which both instructs and reinforces the process of lineage commitment. Within the haematopoietic system, progressive changes in the DNA methylome of haematopoietic stem cells (HSCs) are essential for the effective production of mature blood cells. Inhibition or loss of function of the cellular DNA methylation machinery has been shown to lead to a severe perturbation in blood production and is also an important driver of malignant transformation. HSCs constitute a very rare cell population in the bone marrow, capable of life-long self-renewal and multi-lineage differentiation. The low abundance of HSCs has been a major technological barrier to the global analysis of the CpG methylation status within both HSCs and their immediate progeny, the multipotent progenitors (MPPs). Within this Extra View article, we review the current understanding of how the DNA methylome regulates normal and malignant hematopoiesis. We also discuss the current methodologies that are available for interrogating the DNA methylation status of HSCs and MPPs and describe a new data set that was generated using tagmentation-based whole genome bisulfite sequencing (TWGBS) in order to comprehensively map methylated cytosines using the limited amount of genomic DNA that can be harvested from rare cell populations. Extended analysis of this data set clearly demonstrates the added value of genome-wide sequencing of methylated cytosines and identifies novel important cis-acting regulatory regions that are dynamically remodeled during the first steps of haematopoietic differentiation. PMID:25483069

  2. Restricted immunoglobulin VH usage and VDJ combinations in the human response to Haemophilus influenzae type b capsular polysaccharide. Nucleotide sequences of monospecific anti-Haemophilus antibodies and polyspecific antibodies cross-reacting with self antigens.

    PubMed Central

    Adderson, E E; Shackelford, P G; Quinn, A; Wilson, P M; Cunningham, M W; Insel, R A; Carroll, W L

    1993-01-01

    To examine the human antibody repertoire generated against a biologically significant antigen we have obtained sequences of heavy chain variable region genes (IgVH) from 15 monoclonal antibodies specific for the capsular polysaccharide of Haemophilus influenzae type b (Hib PS). All VH segments are members of the VH3 family and 9 of 15 are members of the smaller VH3b subfamily. Restriction is evident by the shared use of certain VDJ joints in independent hybridomas from different subjects. Two hybridomas generated from the same subject demonstrate identical heavy chain variable region gene sequences but differ in isotype and rearrange alternative light chain variable region genes (IgVL), suggesting that in a normal immune response, a single pre-B cell clone may use different light chain rearrangements and give rise to progeny capable of reacting with antigen. Using a polymerase chain reaction assay optimized to detect base pair differences among VH genes we demonstrate that at least a portion of expressed anti-Hib PS VH genes have undergone somatic mutation. Anti-Hib PS heavy chain genes are homologous to VH segments encoding autoantibodies and two hybridomas secrete anti-Hib PS antibody that cross-reacts with self antigens (double-stranded DNA and single-stranded DNA). Comparison of VH regions of self-reactive and monospecific anti-Hib PS Ab demonstrates no consistent structural feature correlating with fine antigen specificity. These data demonstrate significant restriction in VH usage and VDJ recombination in the anti-Hib PS response and confirm that autoantibodies may be elicited during normal immune responses. Images PMID:8514881

  3. 12 CFR 563.36 - Tying restriction exception.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...-OPERATIONS Operation and Structure § 563.36 Tying restriction exception. (a) Safe harbor for combined-balance... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Tying restriction exception. 563.36 Section 563.... (b) Limitations on exception. This exception shall terminate upon a finding by the OTS that...

  4. APOBECs and Virus Restriction

    PubMed Central

    Harris, Reuben S.; Dudley, Jaquelin P.

    2015-01-01

    The APOBEC family of single-stranded DNA cytosine deaminases comprises a formidable arm of the vertebrate innate immune system. Pre-vertebrates express a single APOBEC, whereas some mammals produce as many as eleven enzymes. The APOBEC3 subfamily displays both copy number variation and polymorphisms, consistent with ongoing pathogenic pressures. These enzymes restrict the replication of many DNA-based parasites, such as exogenous viruses and endogenous transposable elements. APOBEC1 and activation-induced cytosine deaminase (AID) have specialized functions in RNA editing and antibody gene diversification, respectively, whereas APOBEC2 and APOBEC4 appear to have different functions. Nevertheless, the APOBEC family protects against both periodic viral zoonoses as well as exogenous and endogenous parasite replication. This review highlights viral pathogens that are restricted by APOBEC enzymes, but manage to escape through unique mechanisms. The sensitivity of viruses that lack counterdefense measures highlights the need to develop APOBEC-enabling small molecules as a new class of anti-viral drugs. PMID:25818029

  5. Range Restriction and Attenuation Corrections.

    ERIC Educational Resources Information Center

    Mumford, Michael D.; Mendoza, Jorge L.

    The present paper reviews the techniques commonly used to correct an observed correlation coefficient for the simultaneous influence of attenuation and range restriction effects. It is noted that the procedure which is currently in use may be somewhat biased because it treats range restriction and attenuation as independent restrictive influences.…

  6. A combination of probiotics and whey proteins enhances anti-obesity effects of calcium and dairy products during nutritional energy restriction in aP2-agouti transgenic mice.

    PubMed

    Yoda, Kazutoyo; Sun, Xiaocum; Kawase, Manabu; Kubota, Akira; Miyazawa, Kenji; Harata, Gaku; Hosoda, Masataka; Hiramatsu, Masaru; He, Fang; Zemel, Michael B

    2015-06-14

    Lactobacillus rhamnosus GG, Lactobacillus paracasei TMC0409, Streptococcus thermophilus TMC1543 and whey proteins were used to prepare fermented milk. For the experiment aP2- agouti transgenic mice were pre-treated with a high-sucrose/high-fat diet for 6 weeks to induce obesity. The obese mice were fed a diet containing 1·2% Ca and either non-fat dried milk (NFDM) or probiotic-fermented milk (PFM) with nutritional energy restriction for 6 weeks. The animals were examined after the treatment for changes in body weight, fat pad weight, fatty acid synthase (FAS) activity, lypolysis, the expression levels of genes related to lipid metabolism, insulin sensitivity in adipocytes and skeletal muscle and the presence of biomarkers for oxidative and inflammatory stress in plasma. It was found that the PFM diet significantly reduced body weight, fat accumulation, and adipocyte FAS activity, and increased adipocyte lipolysis as compared with the effects of the NFDM diet (P<0·05). The adipose tissue gene expression of 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1) was significantly suppressed in mice that were fed PFM as compared with those that were fed NFDM (P<0·05). PFM caused a greater up-regulation of skeletal muscle PPARα, PPARδ, uncoupling protein 3 (UCP3) and GLUT4 expression and a significant decrease in the plasma concentration of insulin, malondialdehyde, TNF-α, monocyte chemotactic protein-1 and C-reactive protein as compared with the effects of NFDM (P<0·05). Fermentation of milk with selected probiotics and supplementation of milk with whey proteins may thus enhance anti-obesity effects of Ca and dairy products by the suppression of adipose tissue lipogenesis, activation of fat oxidation in skeletal muscle and reduction of oxidative and inflammatory stress. PMID:25871498

  7. Protein deficiency and energy restriction in young cebus monkeys.

    PubMed Central

    Samonds, K W; Hegsted, D M

    1978-01-01

    Infant cebus monkeys (Cebus albifrons) were fed liquid formulas that were limited in protein, energy, or a combination of the two restrictions. Weight gain, food intake, hematological development, and plasma protein and cholesterol levels were monitored over a 20-week period. The animals restricted in protein developed the classical signs of protein deficiency--reductions in plasma albumin, a mild anemia, accumulation of fat in the liver, and, in a few cases, facial edema. These animals maintained a relatively high energy intake, and apparently wasted energy when compared to similarly non-growing energy-restricted animals. Energy-restricted animals did not exhibit these symptoms, even when their daily protein intake was reduced to match that of protein-restricted monkeys. It is concluded that an energy restriction superimposed upon a limited protein intake did not increase protein requirements or precipitate protein deficiency. Images PMID:418417

  8. Dietary restriction with and without caloric restriction for healthy aging

    PubMed Central

    Lee, Changhan; Longo, Valter

    2016-01-01

    Caloric restriction is the most effective and reproducible dietary intervention known to regulate aging and increase the healthy lifespan in various model organisms, ranging from the unicellular yeast to worms, flies, rodents, and primates. However, caloric restriction, which in most cases entails a 20–40% reduction of food consumption relative to normal intake, is a severe intervention that results in both beneficial and detrimental effects. Specific types of chronic, intermittent, or periodic dietary restrictions without chronic caloric restriction have instead the potential to provide a significant healthspan increase while minimizing adverse effects. Improved periodic or targeted dietary restriction regimens that uncouple the challenge of food deprivation from the beneficial effects will allow a safe intervention feasible for a major portion of the population. Here we focus on healthspan interventions that are not chronic or do not require calorie restriction. PMID:26918181

  9. Restrictive vs. non-restrictive composition: a magnetoencephalography study

    PubMed Central

    Leffel, Timothy; Lauter, Miriam; Westerlund, Masha; Pylkkänen, Liina

    2014-01-01

    Recent research on the brain mechanisms underlying language processing has implicated the left anterior temporal lobe (LATL) as a central region for the composition of simple phrases. Because these studies typically present their critical stimuli without contextual information, the sensitivity of LATL responses to contextual factors is unknown. In this magnetoencephalography (MEG) study, we employed a simple question-answer paradigm to manipulate whether a prenominal adjective or determiner is interpreted restrictively, i.e., as limiting the set of entities under discussion. Our results show that the LATL is sensitive to restriction, with restrictive composition eliciting higher responses than non-restrictive composition. However, this effect was only observed when the restricting element was a determiner, adjectival stimuli showing the opposite pattern, which we hypothesise to be driven by the special pragmatic properties of non-restrictive adjectives. Overall, our results demonstrate a robust sensitivity of the LATL to high level contextual and potentially also pragmatic factors. PMID:25379512

  10. Fatigue, sleep restriction and driving performance.

    PubMed

    Philip, Pierre; Sagaspe, Patricia; Moore, Nicholas; Taillard, Jacques; Charles, André; Guilleminault, Christian; Bioulac, Bernard

    2005-05-01

    We ran a randomized cross-over design study under sleep-deprived and non-sleep-deprived driving conditions to test the effects of sleep restriction on real driving performance. The study was performed in a sleep laboratory and on an open French highway. Twenty-two healthy male subjects (age = 21.5 +/- 2 years; distance driven per year = 12,225 +/- 4739 km (7641 +/- 2962 miles) [mean +/- S.D.]) drove 1000 km (625 miles) over 10 h during five 105 min sessions on an open highway. Self-rated fatigue and sleepiness before each session, number of inappropriate line crossings from video recordings and simple reaction time (RT) were measured. Total crossings increased after sleep restriction (535 crossings in the sleep-restricted condition versus 66 after non-restricted sleep (incidence rate ratio (IRR): 8.1; 95% confidence interval (95% CI): 3.2-20.5; p < 0.001)), from the first driving session. The interaction between the two factors (conditionxtime of day) was also significant (F(5, 105) = 3.229; p < 0.05). Increasing sleepiness score was associated with increasing crossings during the next driving session in the sleep-restricted (IRR: 1.9; 95% CI: 1.4-2.4) but not in the non-restricted condition (IRR: 1.0; 95% CI: 0.8-1.3). Increasing self-perceived fatigue was not associated with increasing crossings in either condition (IRR: 0.95; 95% CI: 0.93-0.98 and IRR: 1.0; 95% CI: 0.98-1.02). Rested subjects drove 1000 km with four shorts breaks with only a minor performance decrease. Sleep restriction induced important performance degradation even though time awake (8h) and session driving times (105 min) were relatively short. Major inter-individual differences were observed under sleep restriction. Performance degradation was associated with sleepiness and not fatigue. Sleepiness combined with fatigue significantly affected RT. Road safety campaigns should encourage drivers to avoid driving after sleep restriction, even on relatively short trips especially if they feel

  11. Restricting retrotransposons: a review.

    PubMed

    Goodier, John L

    2016-01-01

    Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research. PMID:27525044

  12. Dietary restrictions and cancer.

    PubMed Central

    Hart, R W; Turturro, A

    1997-01-01

    Dietary restriction (DR) alters a significant environmental factor in carcinogenesis, dietary intake, thus inhibiting both spontaneous and induced tumorigenesis. Potential mechanisms for the inhibition of spontaneous cancer may include the effects of DR to do the following: decrease body weight, which decreases cellular proliferation and increases apoptosis in a number of organs that increase and decrease with body size; decrease body temperature, thereby lowering the amount of endogenous DNA damage temperature generates; decrease oxidative damage, by increasing antioxidant damage defense systems; decrease, generally, cellular proliferation; and protect the fidelity of the genome by decreasing DNA damage, increasing DNA repair, and preventing aberrant gene expression. Potential mechanisms for reducing induced tumor incidence include lowering agent activation, changing agent disposition, decreasing the adducts most associated with agent toxicity, and inhibiting tumor progression through mechanisms similar to those that can effect spontaneous tumorigenesis. As a method to control a major source of environmental cancer, and as the major modulator of the agent induction of this disease, understanding how DR works may significantly contribute to the efforts to explain how diet impacts on development of cancer in the United States, and may suggest methods to reduce the adverse impacts of other environmental agents on the disease. PMID:9255593

  13. Combinations Therapies.

    PubMed

    Reinmuth, Niels; Reck, Martin

    2015-01-01

    Immunotherapy of cancer encompasses different strategies that elicit or enhance the immune response against tumors. The first results from clinical studies have provided promising data for the treatment of lung cancer patients with immunomodulating monotherapies. To improve the potential benefit of cancer immunotherapy, synergistic combinations of the various immunotherapy approaches or of different elements within each of the immunotherapy approaches are being explored. The rationale typically involves different but complementary mechanisms of action, eventually impinging on more than one immune system mechanism. As a prominent example, the simultaneous blockade of PD-1 and CTLA-4 is giving rise to therapeutic synergy, while still offering room for efficacy improvement. Moreover, combinations of immunomodulating agents with chemotherapy or targeted molecules are being tested. Animal models suggest that immunotherapies in combination with these various options offer evidence for synergistic effects and are likely to radically change cancer treatment paradigms. However, data obtained so far indicate that toxic side effects are also potentiated, which may even restrict the selection of patients that are suitable for these combinational approaches. Advancing the field of combinatorial immunotherapy will require changes in the way investigational agents are clinically developed as well as novel experimental end-points for efficacy evaluation. However, this combined therapeutic manipulation of both tumor and stromal cells may lead to a dramatic change in the therapeutic options of lung cancer patients in any disease stage that can only grossly be appreciated by the current studies. PMID:26384009

  14. Predictive factors for intrauterine growth restriction

    PubMed Central

    Albu, AR; Anca, AF; Horhoianu, VV; Horhoianu, IA

    2014-01-01

    Abstract Reduced fetal growth is seen in about 10% of the pregnancies but only a minority has a pathological background and is known as intrauterine growth restriction or fetal growth restriction (IUGR / FGR). Increased fetal and neonatal mortality and morbidity as well as adult pathologic conditions are often associated to IUGR. Risk factors for IUGR are easy to assess but have poor predictive value. For the diagnostic purpose, biochemical serum markers, ultrasound and Doppler study of uterine and spiral arteries, placental volume and vascularization, first trimester growth pattern are object of assessment today. Modern evaluations propose combined algorithms using these strategies, all with the goal of a better prediction of risk pregnancies. Abbreviations: SGA = small for gestational age; IUGR = intrauterine growth restriction; FGR = fetal growth restriction; IUFD = intrauterine fetal demise; HIV = human immunodeficiency virus; PAPP-A = pregnancy associated plasmatic protein A; β-hCG = beta human chorionic gonadotropin; MoM = multiple of median; ADAM-12 = A-disintegrin and metalloprotease 12; PP-13 = placental protein 13; VEGF = vascular endothelial growth factor; PlGF = placental growth factor; sFlt-1 = soluble fms-like tyrosine kinase-1; UAD = uterine arteries Doppler ultrasound; RI = resistence index; PI = pulsatility index; VOCAL = Virtual Organ Computer–Aided Analysis software; VI = vascularization index; FI = flow index; VFI = vascularization flow index; PQ = placental quotient PMID:25408721

  15. Methionine restriction and lifespan control

    PubMed Central

    Lee, Byung Cheon; Kaya, Alaattin; Gladyshev, Vadim N.

    2016-01-01

    Dietary restriction (DR) without malnutrition is associated with longevity in various organisms. However, it has also been shown that reduced calorie intake is often ineffective in extending lifespan. Selecting optimal dietary regimens for DR studies is complicated, as the same regimen may lead to different outcomes depending on genotype and environmental factors. Recent studies suggested that interventions such as moderate protein restriction with/without adequate nutrition (e.g. particular amino acids or carbohydrates) may have additional beneficial effects mediated by certain metabolic and hormonal factors implicated in the biology of aging, regardless of total calorie intake. In particular, it was shown that restriction of a single amino acid, methionine, can mimic the effects of DR and extend lifespan in various model organisms. We discuss beneficial effects of methionine-restricted (MR) diet, the molecular pathways involved, and the use of this regimen in longevity interventions. PMID:26663138

  16. Using Pinochle to Motivate the Restricted Combinations with Repetitions Problem

    ERIC Educational Resources Information Center

    Gorman, Patrick S.; Kunkel, Jeffrey D.; Vasko, Francis J.

    2011-01-01

    A standard example used in introductory combinatoric courses is to count the number of five-card poker hands possible from a straight deck of 52 distinct cards. A more interesting problem is to count the number of distinct hands possible from a Pinochle deck in which there are multiple, but obviously limited, copies of each type of card (two…

  17. Combining treatments to improve the fermentation of sugarcane bagasse hydrolysates by ethanologenic Escherichia coli LY180.

    PubMed

    Geddes, Ryan; Shanmugam, Keelnatham T; Ingram, Lonnie O

    2015-01-01

    Inhibitory side products from dilute acid pretreatment is a major challenge for conversion of lignocellulose into ethanol. Six strategies to detoxify sugarcane hydrolysates were investigated alone, and in combinations (vacuum evaporation of volatiles, high pH treatment with ammonia, laccase, bisulfite, microaeration, and inoculum size). High pH was the most beneficial single treatment, increasing the minimum inhibitory concentration (measured by ethanol production) from 15% (control) to 70% hydrolysate. Combining treatments provided incremental improvements, consistent with different modes of action and multiple inhibitory compounds. Screening toxicity using tube cultures proved to be an excellent predictor of relative performance in pH-controlled fermenters. A combination of treatments (vacuum evaporation, laccase, high pH, bisulfite, microaeration) completely eliminated all inhibitory activity present in hydrolysate. With this combination, fermentation of hemicellulose sugars (90% hydrolysate) to ethanol was complete within 48 h, identical to the fermentation of laboratory xylose (50 g/L) in AM1 mineral salts medium (without hydrolysate). PMID:25864026

  18. 48 CFR 225.7003-2 - Restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7003-2 Restrictions. The following restrictions...) Missile or space systems. (3) Ships. (4) Tank or automotive items. (5) Weapon systems. (6) Ammunition....

  19. 48 CFR 225.7003-2 - Restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7003-2 Restrictions. The following restrictions...) Missile or space systems. (3) Ships. (4) Tank or automotive items. (5) Weapon systems. (6) Ammunition....

  20. 48 CFR 225.7003-2 - Restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7003-2 Restrictions. The following restrictions...) Missile or space systems. (3) Ships. (4) Tank or automotive items. (5) Weapon systems. (6) Ammunition....

  1. 48 CFR 225.7003-2 - Restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7003-2 Restrictions. The following restrictions...) Missile or space systems. (3) Ships. (4) Tank or automotive items. (5) Weapon systems. (6) Ammunition....

  2. 48 CFR 225.7003-2 - Restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7003-2 Restrictions. The following restrictions...) Missile or space systems. (3) Ships. (4) Tank or automotive items. (5) Weapon systems. (6) Ammunition....

  3. Alphavirus Restriction by IFITM Proteins.

    PubMed

    Weston, Stuart; Czieso, Stephanie; White, Ian J; Smith, Sarah E; Wash, Rachael S; Diaz-Soria, Carmen; Kellam, Paul; Marsh, Mark

    2016-09-01

    Interferon inducible transmembrane proteins (IFITMs) are broad-spectrum antiviral factors. In cell culture the entry of many enveloped viruses, including orthomyxo-, flavi-, and filoviruses, is inhibited by IFITMs, though the mechanism(s) involved remain unclear and may vary between viruses. We demonstrate that Sindbis and Semliki Forest virus (SFV), which both use endocytosis and acid-induced membrane fusion in early endosomes to infect cells, are restricted by the early endosomal IFITM3. The late endosomal IFITM2 is less restrictive and the plasma membrane IFITM1 does not inhibit normal infection by either virus. IFITM3 inhibits release of the SFV capsid into the cytosol, without inhibiting binding, internalization, trafficking to endosomes or low pH-induced conformational changes in the envelope glycoprotein. Infection by SFV fusion at the cell surface was inhibited by IFITM1, but was equally inhibited by IFITM3. Furthermore, an IFITM3 mutant (Y20A) that is localized to the plasma membrane inhibited infection by cell surface fusion more potently than IFITM1. Together, these results indicate that IFITMs, in particular IFITM3, can restrict alphavirus infection by inhibiting viral fusion with cellular membranes. That IFITM3 can restrict SFV infection by fusion at the cell surface equivalently to IFITM1 suggests that IFITM3 has greater antiviral potency against SFV. PMID:27219333

  4. Generalized Pump-restriction Theorem

    SciTech Connect

    Sinitsyn, Nikolai A; Chernyak, Vladimir Y

    2008-01-01

    We formulate conditions under which periodic modulations of parameters on a finite graph with stochastic transitions among its nodes do not lead to overall pump currents through any given link. Our theorem unifies previously known results with the new ones and provides a universal approach to explore futher restrictions on stochastic pump effect in non-adiabatically driven systems with detailed balance.

  5. Restricted Diffusion in Biophysical Systems

    PubMed Central

    Cooper, Robert L.; Chang, David B.; Young, Allan C.; Martin, Carroll J.; Ancker-Johnson, Betsy

    1974-01-01

    The pulsed-gradient spin echo nuclear magnetic resonance (PGSENMR) technique was used to measure restricted diffusion of water in three types of animal tissue: human blood plasma and red cells; rat and rabbit heart; rat and rabbit liver. Characteristic lengths (L) for restriction of diffusion are estimated from dependence on the measuring time. Limitations on the range of observable restrictive lengths (1.5-15 μm) are discussed. The decrease in diffusivity due to 1 μm alumina powder (volume fraction = 0.18) in glycerin/water mixtures agrees with the Wang theory assuming spherical particles and no hydration. The characteristic length (L ≃ 4 μm) is larger than the particle size (1 μm) or separation (1.8 μm). Comparison of the diffusivities in tissues at short diffusion times with the Wang theory indicates some bound or trapped water. For packed red blood cells, a restriction (L ≃ 2.3 μm) was attributed tothe red cell membrane. A permeability p ≃ 0.014 cm/s may be estimated from the decrease in diffusivity. Average values of diffusivity ratio in heart were: 0.36 ± 0.02 for rat; and 0.26 ± 0.03 for rabbit; and in liver: 0.25 ± 0.01 for rat; 0.25 ± .04 for 10-day old rabbit; and 0.195 ± 0.03 for 2-yr old rabbit. A restriction (L ≃ 2.7 μm) in rat liver probably results from the mitochondria. PMID:4823458

  6. 49 CFR 215.203 - Restricted cars.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 4 2014-10-01 2014-10-01 false Restricted cars. 215.203 Section 215.203..., DEPARTMENT OF TRANSPORTATION RAILROAD FREIGHT CAR SAFETY STANDARDS Restricted Equipment § 215.203 Restricted cars. (a) This section restricts the operation of any railroad freight car that is— (1) More than...

  7. 49 CFR 215.203 - Restricted cars.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 4 2013-10-01 2013-10-01 false Restricted cars. 215.203 Section 215.203..., DEPARTMENT OF TRANSPORTATION RAILROAD FREIGHT CAR SAFETY STANDARDS Restricted Equipment § 215.203 Restricted cars. (a) This section restricts the operation of any railroad freight car that is— (1) More than...

  8. 49 CFR 215.203 - Restricted cars.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 4 2012-10-01 2012-10-01 false Restricted cars. 215.203 Section 215.203..., DEPARTMENT OF TRANSPORTATION RAILROAD FREIGHT CAR SAFETY STANDARDS Restricted Equipment § 215.203 Restricted cars. (a) This section restricts the operation of any railroad freight car that is— (1) More than...

  9. 14 CFR 1203.305 - Restricted data.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Restricted data. 1203.305 Section 1203.305... Classification Principles and Considerations § 1203.305 Restricted data. Restricted Data or Formerly Restricted Data is so classified when originated, as required by the Atomic Energy Act of 1954, as...

  10. 14 CFR 1203.305 - Restricted data.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 5 2013-01-01 2013-01-01 false Restricted data. 1203.305 Section 1203.305... Classification Principles and Considerations § 1203.305 Restricted data. Restricted Data or Formerly Restricted Data is so classified when originated, as required by the Atomic Energy Act of 1954, as...

  11. 14 CFR 1203.305 - Restricted data.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 5 2012-01-01 2012-01-01 false Restricted data. 1203.305 Section 1203.305... Classification Principles and Considerations § 1203.305 Restricted data. Restricted Data or Formerly Restricted Data is so classified when originated, as required by the Atomic Energy Act of 1954, as...

  12. 14 CFR 1203.305 - Restricted data.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Restricted data. 1203.305 Section 1203.305... Classification Principles and Considerations § 1203.305 Restricted data. Restricted Data or Formerly Restricted Data is so classified when originated, as required by the Atomic Energy Act of 1954, as...

  13. 49 CFR 215.203 - Restricted cars.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Restricted cars. 215.203 Section 215.203 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RAILROAD FREIGHT CAR SAFETY STANDARDS Restricted Equipment § 215.203 Restricted cars. (a) This section restricts...

  14. 49 CFR 215.203 - Restricted cars.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 4 2011-10-01 2011-10-01 false Restricted cars. 215.203 Section 215.203..., DEPARTMENT OF TRANSPORTATION RAILROAD FREIGHT CAR SAFETY STANDARDS Restricted Equipment § 215.203 Restricted cars. (a) This section restricts the operation of any railroad freight car that is— (1) More than...

  15. Overcoming Communication Restrictions in Collectives

    NASA Technical Reports Server (NTRS)

    Tumer, Kagan; Agogino, Adrian K.

    2004-01-01

    Many large distributed system are characterized by having a large number of components (eg., agents, neurons) whose actions and interactions determine a %orld utility which rates the performance of the overall system. Such collectives are often subject to communication restrictions, making it difficult for components which try to optimize their own private utilities, to take actions that also help optimize the world utility. In this article we address that coordination problem and derive four utility functions which present different compromises between how aligned a component s private utility is with the world utility and how readily that component can determine the actions that optimize its utility. The results show that the utility functions specifically derived to operate under communication restrictions outperform both traditional methods and previous collective-based methods by up to 75%.

  16. Temperature based Restricted Boltzmann Machines

    NASA Astrophysics Data System (ADS)

    Li, Guoqi; Deng, Lei; Xu, Yi; Wen, Changyun; Wang, Wei; Pei, Jing; Shi, Luping

    2016-01-01

    Restricted Boltzmann machines (RBMs), which apply graphical models to learning probability distribution over a set of inputs, have attracted much attention recently since being proposed as building blocks of multi-layer learning systems called deep belief networks (DBNs). Note that temperature is a key factor of the Boltzmann distribution that RBMs originate from. However, none of existing schemes have considered the impact of temperature in the graphical model of DBNs. In this work, we propose temperature based restricted Boltzmann machines (TRBMs) which reveals that temperature is an essential parameter controlling the selectivity of the firing neurons in the hidden layers. We theoretically prove that the effect of temperature can be adjusted by setting the parameter of the sharpness of the logistic function in the proposed TRBMs. The performance of RBMs can be improved by adjusting the temperature parameter of TRBMs. This work provides a comprehensive insights into the deep belief networks and deep learning architectures from a physical point of view.

  17. Restricted Transport in Small Pores

    PubMed Central

    Anderson, John L.; Quinn, John A.

    1974-01-01

    The basic hydrodynamic equations governing transport in submicron pores are reexamined. Conditions necessary for a simplified, one-dimensional treatment of the diffusion/convection process are established. Steric restrictions and Brownian motion are incorporated directly into the resulting model. Currently available fluid mechanical results are used to evaluate an upper limit on hindered diffusion; this limit is valid for small particle-to-pore ratios. Extensions of the analysis are shown to depend on numerical solutions of the related hydrodynamic problem, that of asymmetrical particle motion in a bounded fluid. PMID:4813157

  18. 9 CFR 78.20 - General restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions on Interstate Movement of Bison Because of Brucellosis § 78.20 General restrictions. Bison may not be...

  19. 9 CFR 78.5 - General restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions on Interstate Movement of Cattle Because of Brucellosis § 78.5 General restrictions. Cattle may not be...

  20. 9 CFR 78.20 - General restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions on Interstate Movement of Bison Because of Brucellosis § 78.20 General restrictions. Bison may not be...

  1. 9 CFR 78.5 - General restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions on Interstate Movement of Cattle Because of Brucellosis § 78.5 General restrictions. Cattle may not be...

  2. Avoidant/Restrictive Food Intake Disorder

    MedlinePlus

    ... Professional Version Eating Disorders Definition of Eating Disorders Anorexia Nervosa Avoidant/Restrictive Food Intake Disorder Binge Eating ... they eat. Eating Disorders Definition of Eating Disorders Anorexia Nervosa Avoidant/Restrictive Food Intake Disorder Binge Eating ...

  3. Genetics Home Reference: familial restrictive cardiomyopathy

    MedlinePlus

    ... CARDIOMYOPATHY, FAMILIAL RESTRICTIVE, 3 Sources for This Page Elliott P, Andersson B, Arbustini E, Bilinska Z, Cecchi ... Sebire N, Ashworth M, Deanfield JE, McKenna WJ, Elliott PM. Idiopathic restrictive cardiomyopathy in children is caused ...

  4. Temperature based Restricted Boltzmann Machines

    PubMed Central

    Li, Guoqi; Deng, Lei; Xu, Yi; Wen, Changyun; Wang, Wei; Pei, Jing; Shi, Luping

    2016-01-01

    Restricted Boltzmann machines (RBMs), which apply graphical models to learning probability distribution over a set of inputs, have attracted much attention recently since being proposed as building blocks of multi-layer learning systems called deep belief networks (DBNs). Note that temperature is a key factor of the Boltzmann distribution that RBMs originate from. However, none of existing schemes have considered the impact of temperature in the graphical model of DBNs. In this work, we propose temperature based restricted Boltzmann machines (TRBMs) which reveals that temperature is an essential parameter controlling the selectivity of the firing neurons in the hidden layers. We theoretically prove that the effect of temperature can be adjusted by setting the parameter of the sharpness of the logistic function in the proposed TRBMs. The performance of RBMs can be improved by adjusting the temperature parameter of TRBMs. This work provides a comprehensive insights into the deep belief networks and deep learning architectures from a physical point of view. PMID:26758235

  5. 28 CFR 68.51 - Restricted access.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Restricted access. 68.51 Section 68.51... ALIENS, UNFAIR IMMIGRATION-RELATED EMPLOYMENT PRACTICES, AND DOCUMENT FRAUD § 68.51 Restricted access. On... be a restricted access portion of the record to contain any material in the record to which...

  6. 29 CFR 18.56 - Restricted access.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Restricted access. 18.56 Section 18.56 Labor Office of the... ADMINISTRATIVE LAW JUDGES General § 18.56 Restricted access. On his or her own motion, or on the motion of any party, the administrative law judge may direct that there be a restricted access portion of the...

  7. 29 CFR 18.56 - Restricted access.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 1 2011-07-01 2011-07-01 false Restricted access. 18.56 Section 18.56 Labor Office of the... ADMINISTRATIVE LAW JUDGES General § 18.56 Restricted access. On his or her own motion, or on the motion of any party, the administrative law judge may direct that there be a restricted access portion of the...

  8. 28 CFR 68.51 - Restricted access.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Restricted access. 68.51 Section 68.51... ALIENS, UNFAIR IMMIGRATION-RELATED EMPLOYMENT PRACTICES, AND DOCUMENT FRAUD § 68.51 Restricted access. On... be a restricted access portion of the record to contain any material in the record to which...

  9. Problem-Solving Test: Restriction Endonuclease Mapping

    ERIC Educational Resources Information Center

    Szeberenyi, Jozsef

    2011-01-01

    The term "restriction endonuclease mapping" covers a number of related techniques used to identify specific restriction enzyme recognition sites on small DNA molecules. A method for restriction endonuclease mapping of a 1,000-basepair (bp)-long DNA molecule is described in the fictitious experiment of this test. The most important fact needed to…

  10. Restriction Enzyme Mapping: A Simple Student Practical.

    ERIC Educational Resources Information Center

    Higgins, Stephen J.; And Others

    1990-01-01

    An experiment that uses the recombinant plasmid pX1108 to illustrate restriction mapping is described. The experiment involves three restriction enzymes and employs single and double restriction enzyme digestions. A list of needed materials, procedures, safety precautions, results, and discussion are included. (KR)

  11. Restricted Schur polynomials and finite N counting

    SciTech Connect

    Collins, Storm

    2009-01-15

    Restricted Schur polynomials have been posited as orthonormal operators for the change of basis from N=4 SYM to type IIB string theory. In this paper we briefly expound the relationship between the restricted Schur polynomials and the operators forwarded by Brown, Heslop, and Ramgoolam. We then briefly examine the finite N counting of the restricted Schur polynomials.

  12. 5 CFR 330.205 - Employment restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Employment restrictions. 330.205 Section 330.205 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS RECRUITMENT, SELECTION, AND PLACEMENT (GENERAL) Reemployment Priority List (RPL) § 330.205 Employment restrictions. (a) The restrictions in paragraph (b)...

  13. 47 CFR 1.1208 - Restricted proceedings.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Restricted proceedings. 1.1208 Section 1.1208 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Grants by Random Selection Ex Parte Communications Restricted Proceedings § 1.1208 Restricted proceedings. Unless otherwise provided by the Commission or its...

  14. Microbial Populations Associated with Restricted Shell Eggs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Restricted shell eggs are found in all shell egg processing facilities. The manner with which companies handle them can vary greatly. In most cases, restricted eggs are diverted to further processing. Some facilities do not rewash eggs, choosing instead to include dirts in restricted eggs. Eggs ...

  15. 36 CFR 13.1176 - Speed restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Speed restrictions. 13.1176... Operating Restrictions § 13.1176 Speed restrictions. (a) From May 15 through September 30, in designated whale waters the following are prohibited: (1) Operating a motor vessel at more than 20 knots...

  16. 36 CFR 13.1176 - Speed restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false Speed restrictions. 13.1176... Operating Restrictions § 13.1176 Speed restrictions. (a) From May 15 through September 30, in designated whale waters the following are prohibited: (1) Operating a motor vessel at more than 20 knots...

  17. 7 CFR 982.14 - Restricted hazelnuts.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 8 2014-01-01 2014-01-01 false Restricted hazelnuts. 982.14 Section 982.14... AGREEMENTS AND ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE HAZELNUTS GROWN IN OREGON AND WASHINGTON Order Regulating Handling Definitions § 982.14 Restricted hazelnuts. Restricted hazelnuts...

  18. 7 CFR 982.14 - Restricted hazelnuts.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 8 2011-01-01 2011-01-01 false Restricted hazelnuts. 982.14 Section 982.14... Agreements and Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE HAZELNUTS GROWN IN OREGON AND WASHINGTON Order Regulating Handling Definitions § 982.14 Restricted hazelnuts. Restricted hazelnuts...

  19. 7 CFR 982.14 - Restricted hazelnuts.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 8 2013-01-01 2013-01-01 false Restricted hazelnuts. 982.14 Section 982.14... AGREEMENTS AND ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE HAZELNUTS GROWN IN OREGON AND WASHINGTON Order Regulating Handling Definitions § 982.14 Restricted hazelnuts. Restricted hazelnuts...

  20. 7 CFR 982.14 - Restricted hazelnuts.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Restricted hazelnuts. 982.14 Section 982.14... Agreements and Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE HAZELNUTS GROWN IN OREGON AND WASHINGTON Order Regulating Handling Definitions § 982.14 Restricted hazelnuts. Restricted hazelnuts...

  1. 7 CFR 982.14 - Restricted hazelnuts.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 8 2012-01-01 2012-01-01 false Restricted hazelnuts. 982.14 Section 982.14... Agreements and Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE HAZELNUTS GROWN IN OREGON AND WASHINGTON Order Regulating Handling Definitions § 982.14 Restricted hazelnuts. Restricted hazelnuts...

  2. Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes

    PubMed Central

    Liu, Hongbo; Liu, Xiaojuan; Zhang, Shumei; Lv, Jie; Li, Song; Shang, Shipeng; Jia, Shanshan; Wei, Yanjun; Wang, Fang; Su, Jianzhong; Wu, Qiong; Zhang, Yan

    2016-01-01

    DNA methylation is a key epigenetic mark that is critical for gene regulation in multicellular eukaryotes. Although various human cell types may have the same genome, these cells have different methylomes. The systematic identification and characterization of methylation marks across cell types are crucial to understand the complex regulatory network for cell fate determination. In this study, we proposed an entropy-based framework termed SMART to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and identified 757 887 genome segments. Nearly 75% of the segments showed uniform methylation across all cell types. From the remaining 25% of the segments, we identified cell type-specific hypo/hypermethylation marks that were specifically hypo/hypermethylated in a minority of cell types using a statistical approach and presented an atlas of the human methylation marks. Further analysis revealed that the cell type-specific hypomethylation marks were enriched through H3K27ac and transcription factor binding sites in cell type-specific manner. In particular, we observed that the cell type-specific hypomethylation marks are associated with the cell type-specific super-enhancers that drive the expression of cell identity genes. This framework provides a complementary, functional annotation of the human genome and helps to elucidate the critical features and functions of cell type-specific hypomethylation. PMID:26635396

  3. Non-random distribution of methyl-CpG sites and non-CpG methylation in the human rDNA promoter identified by next generation bisulfite sequencing.

    PubMed

    Pietrzak, Maciej; Rempala, Grzegorz A; Nelson, Peter T; Hetman, Michal

    2016-07-01

    A next generation bisulfite sequencing (NGBS) was used to study rDNA promoter methylation in human brain using postmortem samples of the parietal cortex. Qualitative analysis of patterns of CpG methylation was performed at the individual rDNA unit level. CpG site-specific differences in methylation frequency were observed with the core promoter harboring three out of four most methylated CpGs. Moreover, there was an overall trend towards co-methylation for all possible pairs of 26 CpG sites. The hypermethylated CpGs from the core promoter were also most likely to be co-methylated. Finally, although rare, non-CpG (CpH) methylation was detected at several sites with one of them confirmed using the PspGI-qPCR assay. Similar trends were observed in samples from control individuals as well as patients suffering of Alzheimer's disease (AD), mild cognitive impairment (MCI) or ataxia telangiectasia (AT). Taken together, while some methyl-CpG sites including those in the core promoter may have relatively greater inhibitory effect on rRNA transcription, co-methylation at multiple sites may be required for full and/or long lasting silencing of human rDNA. PMID:27008990

  4. Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.

    PubMed

    Liu, Hongbo; Liu, Xiaojuan; Zhang, Shumei; Lv, Jie; Li, Song; Shang, Shipeng; Jia, Shanshan; Wei, Yanjun; Wang, Fang; Su, Jianzhong; Wu, Qiong; Zhang, Yan

    2016-01-01

    DNA methylation is a key epigenetic mark that is critical for gene regulation in multicellular eukaryotes. Although various human cell types may have the same genome, these cells have different methylomes. The systematic identification and characterization of methylation marks across cell types are crucial to understand the complex regulatory network for cell fate determination. In this study, we proposed an entropy-based framework termed SMART to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and identified 757 887 genome segments. Nearly 75% of the segments showed uniform methylation across all cell types. From the remaining 25% of the segments, we identified cell type-specific hypo/hypermethylation marks that were specifically hypo/hypermethylated in a minority of cell types using a statistical approach and presented an atlas of the human methylation marks. Further analysis revealed that the cell type-specific hypomethylation marks were enriched through H3K27ac and transcription factor binding sites in cell type-specific manner. In particular, we observed that the cell type-specific hypomethylation marks are associated with the cell type-specific super-enhancers that drive the expression of cell identity genes. This framework provides a complementary, functional annotation of the human genome and helps to elucidate the critical features and functions of cell type-specific hypomethylation. PMID:26635396

  5. Restrictive lung disease in pregnancy.

    PubMed

    King, T E

    1992-12-01

    Restrictive ventilatory defects characterized by a reduction in lung volumes and an increase in the ratio of forced expiratory volume in 1 second to forced vital capacity occur when lung expansion is limited because of alterations in the lung parenchyma or because of abnormalities in the pleura, chest wall, or neuromuscular apparatus. Few studies have examined pregnant women with carefully defined restrictive lung disorders. The majority of pulmonary diseases have their onset after the childbearing years. When present, most do not alter fertility. Further, these disorders are only a relative contraindication to pregnancy because both the fetus and mother are able to survive without a high risk of increased morbidity or mortality. The clinical course of sarcoidosis is generally not altered by pregnancy. Factors indicative of a poor prognosis in sarcoidosis and pregnancy include parenchymal lesions on chest radiography, advanced roentgenologic staging, advanced maternal age, low inflammatory activity, requirement for drugs other than corticosteroids, and the presence of extrapulmonary sarcoidosis. Pregnancy seldom has a significant effect on the course of the connective tissue diseases. In PSS with significant renal involvement, pregnancy has the potential for poor fetal prognosis and the risk of maternal death due to a lethal progression of renal failure. Worsening of SLE is uncommon in pregnancy, and prophylactic therapy is generally not necessary. Most women with LAM are advised to avoid pregnancy or the use of estrogens because of the concern that it will lead to worsening of their disease. The incidence of kyphoscoliosis in pregnancy is relatively high. Premature birth rates are higher than that in the normal population. The risk of progression of the abnormal curve in a scoliotic patient appears low. However, women with unstable scolioses at the time of pregnancy can demonstrate progression of the curve with the pregnancy. Respiratory complications during

  6. 10 CFR 1016.21 - Protection of Restricted Data in storage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 1016.21 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) SAFEGUARDING OF RESTRICTED DATA Physical... alarm protection. (b) Changes of combination: Each permittee shall change the combination on locks of... combination no longer requires access to the repository as a result of change in duties or position in...

  7. An Infinite Restricted Boltzmann Machine.

    PubMed

    Côté, Marc-Alexandre; Larochelle, Hugo

    2016-07-01

    We present a mathematical construction for the restricted Boltzmann machine (RBM) that does not require specifying the number of hidden units. In fact, the hidden layer size is adaptive and can grow during training. This is obtained by first extending the RBM to be sensitive to the ordering of its hidden units. Then, with a carefully chosen definition of the energy function, we show that the limit of infinitely many hidden units is well defined. As with RBM, approximate maximum likelihood training can be performed, resulting in an algorithm that naturally and adaptively adds trained hidden units during learning. We empirically study the behavior of this infinite RBM, showing that its performance is competitive to that of the RBM, while not requiring the tuning of a hidden layer size. PMID:27171012

  8. 10 CFR 1045.16 - Criteria for evaluation of restricted data and formerly restricted data information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Criteria for evaluation of restricted data and formerly restricted data information. 1045.16 Section 1045.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) NUCLEAR CLASSIFICATION AND DECLASSIFICATION Identification of Restricted Data and Formerly Restricted Data Information § 1045.16 Criteria...

  9. Prenatal Depression Restricts Fetal Growth

    PubMed Central

    Diego, Miguel A.; Field, Tiffany; Hernandez-Reif, Maria; Schanberg, Saul; Kuhn, Cynthia; Gonzalez-Quintero, Victor Hugo

    2009-01-01

    Objective To identify whether prenatal depression is a risk factor for fetal growth restriction. Methods Midgestation (18-20 weeks GA) estimated fetal weight and urine cortisol and birth weight and gestational age at birth data were collected on a sample of 40 depressed and 40 non-depressed women. Estimated fetal weight and birthweight data were then used to compute fetal growth rates. Results Depressed women had a 13% greater incidence of premature delivery (Odds Ratio (OR) = 2.61) and 15% greater incidence of low birthweight (OR = 4.75) than non-depressed women. Depressed women also had elevated prenatal cortisol levels (p = .006) and fetuses who were smaller (p = .001) and who showed slower fetal growth rates (p = .011) and lower birthweights (p = .008). Mediation analyses further revealed that prenatal maternal cortisol levels were a potential mediator for the relationship between maternal symptoms of depression and both gestational age at birth and the rate of fetal growth. After controlling for maternal demographic variables, prenatal maternal cortisol levels were associated with 30% of the variance in gestational age at birth and 14% of the variance in the rate of fetal growth. Conclusion Prenatal depression was associated with adverse perinatal outcomes, including premature delivery and slower fetal growth rates. Prenatal maternal cortisol levels appear to play a role in mediating these outcomes. PMID:18723301

  10. Placental Adaptations in Growth Restriction

    PubMed Central

    Zhang, Song; Regnault, Timothy R.H.; Barker, Paige L.; Botting, Kimberley J.; McMillen, Isabella C.; McMillan, Christine M.; Roberts, Claire T.; Morrison, Janna L.

    2015-01-01

    The placenta is the primary interface between the fetus and mother and plays an important role in maintaining fetal development and growth by facilitating the transfer of substrates and participating in modulating the maternal immune response to prevent immunological rejection of the conceptus. The major substrates required for fetal growth include oxygen, glucose, amino acids and fatty acids, and their transport processes depend on morphological characteristics of the placenta, such as placental size, morphology, blood flow and vascularity. Other factors including insulin-like growth factors, apoptosis, autophagy and glucocorticoid exposure also affect placental growth and substrate transport capacity. Intrauterine growth restriction (IUGR) is often a consequence of insufficiency, and is associated with a high incidence of perinatal morbidity and mortality, as well as increased risk of cardiovascular and metabolic diseases in later life. Several different experimental methods have been used to induce placental insufficiency and IUGR in animal models and a range of factors that regulate placental growth and substrate transport capacity have been demonstrated. While no model system completely recapitulates human IUGR, these animal models allow us to carefully dissect cellular and molecular mechanisms to improve our understanding and facilitate development of therapeutic interventions. PMID:25580812

  11. 42 CFR 73.13 - Restricted experiments.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...) Restricted experiments: (1) Experiments utilizing recombinant DNA that involve the deliberate transfer of a... agriculture. (2) Experiments involving the deliberate formation of recombinant DNA containing genes for...

  12. 42 CFR 73.13 - Restricted experiments.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...) Restricted experiments: (1) Experiments utilizing recombinant DNA that involve the deliberate transfer of a... agriculture. (2) Experiments involving the deliberate formation of recombinant DNA containing genes for...

  13. 42 CFR 73.13 - Restricted experiments.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...) Restricted experiments: (1) Experiments utilizing recombinant DNA that involve the deliberate transfer of a... agriculture. (2) Experiments involving the deliberate formation of recombinant DNA containing genes for...

  14. Prolonged Activity Restriction After Concussion: Are We Worsening Outcomes?

    PubMed

    DiFazio, Marc; Silverberg, Noah D; Kirkwood, Michael W; Bernier, Raquel; Iverson, Grant L

    2016-05-01

    The current treatment of concussion or mild traumatic brain injury (mTBI) is primarily based on expert consensus. Most clinical practice guidelines advise cognitive and physical rest after injury including withdrawal from normal life activities such as school attendance, sports participation, and technology use until symptoms resolve. Some individuals who sustain an mTBI experience persistent physical, cognitive, and mental health problems. Activity restriction itself may contribute to protracted recovery and other complications. Williamson's Activity Restriction Model of Depression, formulated more than 20 years ago, is central to this hypothesis. We review research evidence for potential harms of prolonged activity restriction and report an mTBI case as an example of how an "activity restriction cascade" can unfold. According to this model, psychological consequences of removal from validating life activities, combined with physical deconditioning, contribute to the development and persistence of postconcussive symptoms after mTBI in some youth. A modification to mTBI guidelines that emphasizes prompt reengagement in life activities as tolerated is encouraged. PMID:26130391

  15. A population response analysis approach to assign class II HLA-epitope restrictions

    PubMed Central

    Arlehamn, Cecilia S. Lindestam; Huang, Huang; Davis, Mark M.; McKinney, Denise M.; Scriba, Thomas Jens; Sidney, John; Peters, Bjoern; Sette, Alessandro

    2015-01-01

    Identification of the specific HLA locus and allele presenting an epitope for recognition by specific T cell receptors (HLA restriction) is necessary to fully characterize the immune response to antigens. Experimental determination of HLA restriction is complex and technically challenging. As an alternative, the restricting HLA locus and allele can be inferred by genetic association, utilizing response data in an HLA typed population. However, simple odds ratio calculations can be problematic when dealing with large numbers of subjects and antigens and because the same epitope can be presented by multiple alleles (epitope promiscuity). Here, we develop a tool, denominated Restrictor Analysis Tool for Epitopes (RATE), to extract inferred restriction from HLA class II -typed epitope responses. This automated method infers HLA class II restriction from large datasets of T cell responses in HLA class II typed subjects by calculating Odds Ratios and relative frequencies from simple data tables. The program is validated by 1. Analyzing data of previously determined HLA restrictions. 2. Experimentally determining in selected individuals new HLA restrictions using HLA transfected cell lines 3. Predicting HLA restriction of particular peptides, and showing that corresponding HLA class II tetramers efficiently bind to epitope specific T cells. We further design a specific iterative algorithm to account for promiscuous recognition by calculation of Odds Ratio values for combinations of different HLA molecules while incorporating predicted HLA binding affinity. The RATE program streamlines the prediction of HLA class II restriction across multiple T cell epitopes and HLA types. PMID:25948811

  16. Improving computer security for authentication of users: influence of proactive password restrictions.

    PubMed

    Proctor, Robert W; Lien, Mei-Ching; Vu, Kim-Phuong L; Schultz, E Eugene; Salvendy, Gavriel

    2002-05-01

    Entering a username-password combination is a widely used procedure for identification and authentication in computer systems. However, it is a notoriously weak method, in that the passwords adopted by many users are easy to crack. In an attempt to improve security, proactive password checking may be used, in which passwords must meet several criteria to be more resistant to cracking. In two experiments, we examined the influence of proactive password restrictions on the time that it took to generate an acceptable password and to use it subsequently to long in. The required length was a minimum of five characters in Experiment 1 and eight characters in Experiment 2. In both experiments, one condition had only the length restriction, and the other had additional restrictions. The additional restrictions greatly increased the time it took to generate the password but had only a small effect on the time it took to use it subsequently to long in. For the five-character passwords, 75% were cracked when no other restrictions were imposed, and this was reduced to 33% with the additional restrictions. For the eight-character passwords, 17% were cracked with no other restrictions, and 12.5% with restrictions. The results indicate that increasing the minimum character length reduces crackability and increases security, regardless of whether additional restrictions are imposed. PMID:12109007

  17. 12 CFR 1807.904 - Lobbying restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 10 2014-01-01 2014-01-01 false Lobbying restrictions. 1807.904 Section 1807.904 Banks and Banking COMMUNITY DEVELOPMENT FINANCIAL INSTITUTIONS FUND, DEPARTMENT OF THE TREASURY CAPITAL MAGNET FUND Terms and Conditions of Assistance § 1807.904 Lobbying restrictions. No...

  18. 12 CFR 1807.904 - Lobbying restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 9 2012-01-01 2012-01-01 false Lobbying restrictions. 1807.904 Section 1807.904 Banks and Banking COMMUNITY DEVELOPMENT FINANCIAL INSTITUTIONS FUND, DEPARTMENT OF THE TREASURY CAPITAL MAGNET FUND Terms and Conditions of Assistance § 1807.904 Lobbying restrictions. No...

  19. 12 CFR 1807.904 - Lobbying restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 9 2013-01-01 2013-01-01 false Lobbying restrictions. 1807.904 Section 1807.904 Banks and Banking COMMUNITY DEVELOPMENT FINANCIAL INSTITUTIONS FUND, DEPARTMENT OF THE TREASURY CAPITAL MAGNET FUND Terms and Conditions of Assistance § 1807.904 Lobbying restrictions. No...

  20. 12 CFR 1807.904 - Lobbying restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 7 2011-01-01 2011-01-01 false Lobbying restrictions. 1807.904 Section 1807.904 Banks and Banking COMMUNITY DEVELOPMENT FINANCIAL INSTITUTIONS FUND, DEPARTMENT OF THE TREASURY CAPITAL MAGNET FUND Terms and Conditions of Assistance § 1807.904 Lobbying restrictions. No...

  1. 40 CFR 1033.740 - Credit restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... restrictions. Use of emission credits generated under this part 1033 or 40 CFR part 92 is restricted depending on the standards against which they were generated. (a) Credits from 40 CFR part 92. NOX and PM credits generated under 40 CFR part 92 may be used under this part in the same manner as NOX and...

  2. 40 CFR 1033.740 - Credit restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... restrictions. Use of emission credits generated under this part 1033 or 40 CFR part 92 is restricted depending on the standards against which they were generated. (a) Credits from 40 CFR part 92. NOX and PM credits generated under 40 CFR part 92 may be used under this part in the same manner as NOX and...

  3. 40 CFR 1033.740 - Credit restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... restrictions. Use of emission credits generated under this part 1033 or 40 CFR part 92 is restricted depending on the standards against which they were generated. (a) Credits from 40 CFR part 92. NOX and PM credits generated under 40 CFR part 92 may be used under this part in the same manner as NOX and...

  4. 40 CFR 1033.740 - Credit restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... restrictions. Use of emission credits generated under this part 1033 or 40 CFR part 92 is restricted depending on the standards against which they were generated. (a) Credits from 40 CFR part 92. NOX and PM credits generated under 40 CFR part 92 may be used under this part in the same manner as NOX and...

  5. 10 CFR 110.29 - Restricted destinations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 2 2012-01-01 2012-01-01 false Restricted destinations. 110.29 Section 110.29 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Licenses § 110.29 Restricted destinations. Afghanistan Andorra Angola Burma (Myanmar) Djibouti India Israel...

  6. 10 CFR 110.29 - Restricted destinations.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 2 2013-01-01 2013-01-01 false Restricted destinations. 110.29 Section 110.29 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Licenses § 110.29 Restricted destinations. Afghanistan Andorra Angola Burma (Myanmar) Djibouti India Israel...

  7. 10 CFR 110.29 - Restricted destinations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 2 2014-01-01 2014-01-01 false Restricted destinations. 110.29 Section 110.29 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Licenses § 110.29 Restricted destinations. Afghanistan Andorra Angola Burma (Myanmar) Djibouti India Israel...

  8. 10 CFR 110.29 - Restricted destinations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 2 2011-01-01 2011-01-01 false Restricted destinations. 110.29 Section 110.29 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Licenses § 110.29 Restricted destinations. Afghanistan Andorra Angola Burma (Myanmar) Djibouti India Israel...

  9. 10 CFR 110.29 - Restricted destinations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Restricted destinations. 110.29 Section 110.29 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Licenses § 110.29 Restricted destinations. Afghanistan Andorra Angola Burma (Myanmar) Djibouti India Israel...

  10. 9 CFR 78.30 - General restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions on Interstate Movement of Swine Because of Brucellosis § 78.30 General restrictions. (a) Brucellosis reactor swine, brucellosis exposed swine, feral swine, sows, and boars may not be moved interstate or...

  11. 9 CFR 78.30 - General restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions on Interstate Movement of Swine Because of Brucellosis § 78.30 General restrictions. (a) Brucellosis reactor swine, brucellosis exposed swine, feral swine, sows, and boars may not be moved interstate or...

  12. 18 CFR 1304.410 - Navigation restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 2 2012-04-01 2012-04-01 false Navigation restrictions... Miscellaneous § 1304.410 Navigation restrictions. (a) Except for the placement of riprap along the shoreline... established for commercial navigation. (b) Structures shall not be located in such a way as to block...

  13. 18 CFR 1304.410 - Navigation restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 2 2014-04-01 2014-04-01 false Navigation restrictions... Miscellaneous § 1304.410 Navigation restrictions. (a) Except for the placement of riprap along the shoreline... established for commercial navigation. (b) Structures shall not be located in such a way as to block...

  14. 18 CFR 1304.410 - Navigation restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false Navigation restrictions... Miscellaneous § 1304.410 Navigation restrictions. (a) Except for the placement of riprap along the shoreline... established for commercial navigation. (b) Structures shall not be located in such a way as to block...

  15. 18 CFR 1304.410 - Navigation restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 2 2013-04-01 2012-04-01 true Navigation restrictions... Miscellaneous § 1304.410 Navigation restrictions. (a) Except for the placement of riprap along the shoreline... established for commercial navigation. (b) Structures shall not be located in such a way as to block...

  16. 18 CFR 1304.410 - Navigation restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Navigation restrictions... Miscellaneous § 1304.410 Navigation restrictions. (a) Except for the placement of riprap along the shoreline... established for commercial navigation. (b) Structures shall not be located in such a way as to block...

  17. 7 CFR 400.407 - Restricted access.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 6 2011-01-01 2011-01-01 false Restricted access. 400.407 Section 400.407 Agriculture... Social Security Account Numbers and Employer Identification Numbers § 400.407 Restricted access. The Manager, other officer, or employee of FCIC or an authorized person may have access to the SSNs and...

  18. 7 CFR 400.407 - Restricted access.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 6 2010-01-01 2010-01-01 false Restricted access. 400.407 Section 400.407 Agriculture... Social Security Account Numbers and Employer Identification Numbers § 400.407 Restricted access. The Manager, other officer, or employee of FCIC or an authorized person may have access to the SSNs and...

  19. 46 CFR 119.405 - Fuel restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 4 2011-10-01 2011-10-01 false Fuel restrictions. 119.405 Section 119.405 Shipping... Machinery Requirements § 119.405 Fuel restrictions. The use of a fuel, other than diesel fuel, as an alternative fuel for an internal combustion engine, except gasoline when used as a fuel for outboard motors...

  20. 46 CFR 182.405 - Fuel restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 7 2012-10-01 2012-10-01 false Fuel restrictions. 182.405 Section 182.405 Shipping...) MACHINERY INSTALLATION Specific Machinery Requirements § 182.405 Fuel restrictions. The use of alternative fuels, other than diesel fuel or gasoline, as fuel for an internal combustion engine will be reviewed...

  1. 46 CFR 119.405 - Fuel restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 4 2014-10-01 2014-10-01 false Fuel restrictions. 119.405 Section 119.405 Shipping... Machinery Requirements § 119.405 Fuel restrictions. The use of a fuel, other than diesel fuel, as an alternative fuel for an internal combustion engine, except gasoline when used as a fuel for outboard motors...

  2. 46 CFR 182.405 - Fuel restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 7 2013-10-01 2013-10-01 false Fuel restrictions. 182.405 Section 182.405 Shipping...) MACHINERY INSTALLATION Specific Machinery Requirements § 182.405 Fuel restrictions. The use of alternative fuels, other than diesel fuel or gasoline, as fuel for an internal combustion engine will be reviewed...

  3. 46 CFR 182.405 - Fuel restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Fuel restrictions. 182.405 Section 182.405 Shipping...) MACHINERY INSTALLATION Specific Machinery Requirements § 182.405 Fuel restrictions. The use of alternative fuels, other than diesel fuel or gasoline, as fuel for an internal combustion engine will be reviewed...

  4. 46 CFR 119.405 - Fuel restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 4 2013-10-01 2013-10-01 false Fuel restrictions. 119.405 Section 119.405 Shipping... Machinery Requirements § 119.405 Fuel restrictions. The use of a fuel, other than diesel fuel, as an alternative fuel for an internal combustion engine, except gasoline when used as a fuel for outboard motors...

  5. 46 CFR 119.405 - Fuel restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 4 2012-10-01 2012-10-01 false Fuel restrictions. 119.405 Section 119.405 Shipping... Machinery Requirements § 119.405 Fuel restrictions. The use of a fuel, other than diesel fuel, as an alternative fuel for an internal combustion engine, except gasoline when used as a fuel for outboard motors...

  6. 46 CFR 182.405 - Fuel restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 7 2014-10-01 2014-10-01 false Fuel restrictions. 182.405 Section 182.405 Shipping...) MACHINERY INSTALLATION Specific Machinery Requirements § 182.405 Fuel restrictions. The use of alternative fuels, other than diesel fuel or gasoline, as fuel for an internal combustion engine will be reviewed...

  7. 46 CFR 119.405 - Fuel restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Fuel restrictions. 119.405 Section 119.405 Shipping... Machinery Requirements § 119.405 Fuel restrictions. The use of a fuel, other than diesel fuel, as an alternative fuel for an internal combustion engine, except gasoline when used as a fuel for outboard motors...

  8. 46 CFR 182.405 - Fuel restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 7 2011-10-01 2011-10-01 false Fuel restrictions. 182.405 Section 182.405 Shipping...) MACHINERY INSTALLATION Specific Machinery Requirements § 182.405 Fuel restrictions. The use of alternative fuels, other than diesel fuel or gasoline, as fuel for an internal combustion engine will be reviewed...

  9. 7 CFR 3550.118 - Grant restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Grant restrictions. 3550.118 Section 3550.118... AGRICULTURE DIRECT SINGLE FAMILY HOUSING LOANS AND GRANTS Section 504 Origination and Section 306C Water and Waste Disposal Grants § 3550.118 Grant restrictions. (a) Maximum grant. Lifetime assistance to...

  10. 7 CFR 3550.118 - Grant restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Grant restrictions. 3550.118 Section 3550.118... AGRICULTURE DIRECT SINGLE FAMILY HOUSING LOANS AND GRANTS Section 504 Origination and Section 306C Water and Waste Disposal Grants § 3550.118 Grant restrictions. (a) Maximum grant. Lifetime assistance to...

  11. 50 CFR 648.102 - Time restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Time restrictions. 648.102 Section 648.102... Flounder Fisheries § 648.102 Time restrictions. Unless otherwise specified pursuant to § 648.107, vessels... possession limit may fish for summer flounder from May 1 through September 30. This time period may...

  12. 50 CFR 648.102 - Time restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Time restrictions. 648.102 Section 648... Summer Flounder Fisheries § 648.102 Time restrictions. Link to an amendment published at 76 FR 60626... flounder from May 1 through September 30. This time period may be adjusted pursuant to the procedures...

  13. 50 CFR 648.142 - Time restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Time restrictions. 648.142 Section 648.142... Fishery § 648.142 Time restrictions. Vessels that are not eligible for a moratorium permit under § 648.4(a... bass from May 22 through October 11 and November 1 through December 31, unless this time period...

  14. 50 CFR 648.142 - Time restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Time restrictions. 648.142 Section 648... Black Sea Bass Fishery § 648.142 Time restrictions. Link to an amendment published at 76 FR 60636, Sept... October 11 and November 1 through December 31, unless this time period is adjusted pursuant to...

  15. 42 CFR 73.13 - Restricted experiments.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 1 2014-10-01 2014-10-01 false Restricted experiments. 73.13 Section 73.13 Public... SELECT AGENTS AND TOXINS § 73.13 Restricted experiments. (a) An individual or entity may not conduct, or possess products resulting from, the following experiments unless approved by and conducted in...

  16. 7 CFR 331.13 - Restricted experiments.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 5 2014-01-01 2014-01-01 false Restricted experiments. 331.13 Section 331.13... Restricted experiments. (a) An individual or entity may not conduct, or possess products resulting from, the following experiments unless approved by and conducted in accordance with the conditions prescribed by...

  17. 7 CFR 331.13 - Restricted experiments.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 5 2013-01-01 2013-01-01 false Restricted experiments. 331.13 Section 331.13... Restricted experiments. (a) An individual or entity may not conduct, or possess products resulting from, the following experiments unless approved by and conducted in accordance with the conditions prescribed by...

  18. 32 CFR 806.24 - Fee restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false Fee restrictions. 806.24 Section 806.24 National Defense Department of Defense (Continued) DEPARTMENT OF THE AIR FORCE ADMINISTRATION AIR FORCE FREEDOM OF INFORMATION ACT PROGRAM § 806.24 Fee restrictions. For FOIA purposes, Air Force activities will consider...

  19. 32 CFR 806.24 - Fee restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Fee restrictions. 806.24 Section 806.24 National Defense Department of Defense (Continued) DEPARTMENT OF THE AIR FORCE ADMINISTRATION AIR FORCE FREEDOM OF INFORMATION ACT PROGRAM § 806.24 Fee restrictions. For FOIA purposes, Air Force activities will consider...

  20. 32 CFR 806.24 - Fee restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Fee restrictions. 806.24 Section 806.24 National Defense Department of Defense (Continued) DEPARTMENT OF THE AIR FORCE ADMINISTRATION AIR FORCE FREEDOM OF INFORMATION ACT PROGRAM § 806.24 Fee restrictions. For FOIA purposes, Air Force activities will consider...

  1. 32 CFR 806.24 - Fee restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Fee restrictions. 806.24 Section 806.24 National Defense Department of Defense (Continued) DEPARTMENT OF THE AIR FORCE ADMINISTRATION AIR FORCE FREEDOM OF INFORMATION ACT PROGRAM § 806.24 Fee restrictions. For FOIA purposes, Air Force activities will consider...

  2. 32 CFR 806.24 - Fee restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Fee restrictions. 806.24 Section 806.24 National Defense Department of Defense (Continued) DEPARTMENT OF THE AIR FORCE ADMINISTRATION AIR FORCE FREEDOM OF INFORMATION ACT PROGRAM § 806.24 Fee restrictions. For FOIA purposes, Air Force activities will consider...

  3. 49 CFR 236.812 - Speed, restricted.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 4 2013-10-01 2013-10-01 false Speed, restricted. 236.812 Section 236.812 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Speed, restricted. A speed that will permit stopping within one-half the range of vision, but...

  4. 49 CFR 236.812 - Speed, restricted.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 4 2012-10-01 2012-10-01 false Speed, restricted. 236.812 Section 236.812 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Speed, restricted. A speed that will permit stopping within one-half the range of vision, but...

  5. 49 CFR 236.812 - Speed, restricted.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 4 2014-10-01 2014-10-01 false Speed, restricted. 236.812 Section 236.812 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Speed, restricted. A speed that will permit stopping within one-half the range of vision, but...

  6. 7 CFR 3430.905 - Funding restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Funding restrictions. 3430.905 Section 3430.905 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS New Era Rural Technology Competitive Grants Program § 3430.905 Funding restrictions....

  7. 7 CFR 3430.705 - Funding restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Funding restrictions. 3430.705 Section 3430.705 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Biomass Research and Development Initiative § 3430.705 Funding restrictions....

  8. 7 CFR 3430.1005 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 3430.1005 Section 3430.1005 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Sun Grant Program § 3430.1005 Funding restrictions. (a) Facility costs. Funds...

  9. 7 CFR 3430.605 - Funding restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Funding restrictions. 3430.605 Section 3430.605 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Beginning Farmer and Rancher Development Program § 3430.605 Funding restrictions....

  10. 7 CFR 3430.605 - Funding restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Funding restrictions. 3430.605 Section 3430.605 Agriculture Regulations of the Department of Agriculture (Continued) COOPERATIVE STATE RESEARCH, EDUCATION... § 3430.605 Funding restrictions. (a) Facility costs. Funds made available under this subpart shall not...

  11. 7 CFR 3430.905 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 3430.905 Section 3430.905 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS New Era Rural Technology Competitive Grants Program § 3430.905 Funding restrictions....

  12. 7 CFR 3430.305 - Funding restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Funding restrictions. 3430.305 Section 3430.305 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Agriculture and Food Research Initiative § 3430.305 Funding restrictions....

  13. 7 CFR 3430.305 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 3430.305 Section 3430.305 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Agriculture and Food Research Initiative § 3430.305 Funding restrictions....

  14. 7 CFR 3430.505 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 3430.505 Section 3430.505 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... Funding restrictions. (a) Construction. Funds made available for grants under this subsection shall not...

  15. 7 CFR 3430.905 - Funding restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Funding restrictions. 3430.905 Section 3430.905 Agriculture Regulations of the Department of Agriculture (Continued) COOPERATIVE STATE RESEARCH, EDUCATION... Program § 3430.905 Funding restrictions. (a) Prohibition against construction. Grant funds awarded...

  16. 7 CFR 3430.205 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 3430.205 Section 3430.205 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Specialty Crop Research Initiative § 3430.205 Funding restrictions. (a)...

  17. 7 CFR 3430.1005 - Funding restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Funding restrictions. 3430.1005 Section 3430.1005 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Sun Grant Program § 3430.1005 Funding restrictions. (a) Facility costs. Funds...

  18. 7 CFR 3430.605 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 3430.605 Section 3430.605 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Beginning Farmer and Rancher Development Program § 3430.605 Funding restrictions....

  19. 7 CFR 3430.705 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 3430.705 Section 3430.705 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Biomass Research and Development Initiative § 3430.705 Funding restrictions....

  20. 7 CFR 3430.505 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 3430.505 Section 3430.505 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... Funding restrictions. (a) Construction. Funds made available for grants under this subsection shall not...

  1. 7 CFR 3430.305 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 3430.305 Section 3430.305 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Agriculture and Food Research Initiative § 3430.305 Funding restrictions....

  2. 7 CFR 3430.705 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 3430.705 Section 3430.705 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Biomass Research and Development Initiative § 3430.705 Funding restrictions....

  3. 7 CFR 3430.305 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 3430.305 Section 3430.305 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Agriculture and Food Research Initiative § 3430.305 Funding restrictions....

  4. 7 CFR 3430.1005 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 3430.1005 Section 3430.1005 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Sun Grant Program § 3430.1005 Funding restrictions. (a) Facility costs. Funds...

  5. 7 CFR 3430.1005 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 3430.1005 Section 3430.1005 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Sun Grant Program § 3430.1005 Funding restrictions. (a) Facility costs. Funds...

  6. 7 CFR 3430.505 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 3430.505 Section 3430.505 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... Funding restrictions. (a) Construction. Funds made available for grants under this subsection shall not...

  7. 7 CFR 3430.605 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 3430.605 Section 3430.605 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Beginning Farmer and Rancher Development Program § 3430.605 Funding restrictions....

  8. 7 CFR 3430.905 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 3430.905 Section 3430.905 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS New Era Rural Technology Competitive Grants Program § 3430.905 Funding restrictions....

  9. 7 CFR 3430.205 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 3430.205 Section 3430.205 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Specialty Crop Research Initiative § 3430.205 Funding restrictions. (a)...

  10. 7 CFR 3430.705 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 3430.705 Section 3430.705 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Biomass Research and Development Initiative § 3430.705 Funding restrictions....

  11. 7 CFR 3430.905 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 3430.905 Section 3430.905 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS New Era Rural Technology Competitive Grants Program § 3430.905 Funding restrictions....

  12. 7 CFR 3430.205 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 3430.205 Section 3430.205 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Specialty Crop Research Initiative § 3430.205 Funding restrictions. (a)...

  13. 7 CFR 3430.505 - Funding restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Funding restrictions. 3430.505 Section 3430.505 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... Funding restrictions. (a) Construction. Funds made available for grants under this subsection shall not...

  14. 7 CFR 3430.205 - Funding restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Funding restrictions. 3430.205 Section 3430.205 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Specialty Crop Research Initiative § 3430.205 Funding restrictions. (a)...

  15. 7 CFR 3430.605 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 3430.605 Section 3430.605 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Beginning Farmer and Rancher Development Program § 3430.605 Funding restrictions....

  16. 7 CFR 3430.205 - Funding restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Funding restrictions. 3430.205 Section 3430.205 Agriculture Regulations of the Department of Agriculture (Continued) COOPERATIVE STATE RESEARCH, EDUCATION... Funding restrictions. (a) Prohibition against construction. Funds made available under this subpart...

  17. 18 CFR 35.39 - Affiliate restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Sales of Electric Energy, Capacity and Ancillary Services at Market-Based Rates § 35.39 Affiliate... authority, the conditions provided in this section, including the restriction on affiliate sales of electric... the Seller's market-based rate tariff. (b) Restriction on affiliate sales of electric energy...

  18. 40 CFR 1033.740 - Credit restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... restrictions. Use of emission credits generated under this part 1033 or 40 CFR part 92 is restricted depending on the standards against which they were generated. (a) Credits from 40 CFR part 92. NOX and PM credits generated under 40 CFR part 92 may be used under this part in the same manner as NOX and...

  19. 9 CFR 78.30 - General restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false General restrictions. 78.30 Section 78.30 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions...

  20. 9 CFR 78.30 - General restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false General restrictions. 78.30 Section 78.30 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions...

  1. 9 CFR 78.30 - General restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false General restrictions. 78.30 Section 78.30 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS BRUCELLOSIS Restrictions on Interstate Movement of Swine Because...

  2. 50 CFR 660.506 - Gear restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... restrictions. The only fishing gear authorized for use in the reduction fishery for northern anchovy off... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Gear restrictions. 660.506 Section 660.506 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC...

  3. 50 CFR 665.664 - Gear restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Gear restrictions. 665.664 Section 665.664 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION... § 665.664 Gear restrictions. Only selective gear may be used to harvest coral from any precious...

  4. 50 CFR 665.605 - Gear restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Gear restrictions. 665.605 Section 665.605 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION... § 665.605 Gear restrictions. (a) Bottom trawls and bottom set gillnets. Fishing for PRIA bottomfish...

  5. 30 CFR 56.11008 - Restricted clearance.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Restricted clearance. 56.11008 Section 56.11008 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-SURFACE METAL AND NONMETAL MINES Travelways § 56.11008 Restricted clearance. Where...

  6. An Event Restriction Interval Theory of Tense

    ERIC Educational Resources Information Center

    Beamer, Brandon Robert

    2012-01-01

    This dissertation presents a novel theory of tense and tense-like constructions. It is named after a key theoretical component of the theory, the event restriction interval. In Event Restriction Interval (ERI) Theory, sentences are semantically evaluated relative to an index which contains two key intervals, the evaluation interval and the event…

  7. Restricting mutualistic partners to enforce trade reliance.

    PubMed

    Wyatt, Gregory A K; Kiers, E Toby; Gardner, Andy; West, Stuart A

    2016-01-01

    Mutualisms are cooperative interactions between members of different species, often involving the trade of resources. Here, we suggest that otherwise-cooperative mutualists might be able to gain a benefit from actively restricting their partners' ability to obtain resources directly, hampering the ability of the restricted partner to survive and/or reproduce without the help of the restricting mutualist. We show that (i) restriction can be favoured when it makes the resources of the restricting individual more valuable to their partner, and thus allows them to receive more favourable terms of trade; (ii) restriction maintains cooperation in conditions where cooperative behaviour would otherwise collapse; and (iii) restriction can lead to either an increase or decrease in a restricted individual's fitness. We discuss the applicability of this scenario to mutualisms such as those between plants and mycorrhizal fungi. These results identify a novel conflict in mutualisms as well as several public goods dilemmas, but also demonstrate how conflict can help maintain cooperation. PMID:26813888

  8. 18 CFR 35.39 - Affiliate restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... Sales of Electric Energy, Capacity and Ancillary Services at Market-Based Rates § 35.39 Affiliate... authority, the conditions provided in this section, including the restriction on affiliate sales of electric... the Seller's market-based rate tariff. (b) Restriction on affiliate sales of electric energy...

  9. 18 CFR 35.39 - Affiliate restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Sales of Electric Energy, Capacity and Ancillary Services at Market-Based Rates § 35.39 Affiliate... authority, the conditions provided in this section, including the restriction on affiliate sales of electric... the Seller's market-based rate tariff. (b) Restriction on affiliate sales of electric energy...

  10. 18 CFR 35.39 - Affiliate restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... Sales of Electric Energy, Capacity and Ancillary Services at Market-Based Rates § 35.39 Affiliate... authority, the conditions provided in this section, including the restriction on affiliate sales of electric... the Seller's market-based rate tariff. (b) Restriction on affiliate sales of electric energy...

  11. 18 CFR 35.39 - Affiliate restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... Sales of Electric Energy, Capacity and Ancillary Services at Market-Based Rates § 35.39 Affiliate... authority, the conditions provided in this section, including the restriction on affiliate sales of electric... the Seller's market-based rate tariff. (b) Restriction on affiliate sales of electric energy...

  12. Restricting mutualistic partners to enforce trade reliance

    PubMed Central

    Wyatt, Gregory A. K.; Kiers, E. Toby; Gardner, Andy; West, Stuart A.

    2016-01-01

    Mutualisms are cooperative interactions between members of different species, often involving the trade of resources. Here, we suggest that otherwise-cooperative mutualists might be able to gain a benefit from actively restricting their partners' ability to obtain resources directly, hampering the ability of the restricted partner to survive and/or reproduce without the help of the restricting mutualist. We show that (i) restriction can be favoured when it makes the resources of the restricting individual more valuable to their partner, and thus allows them to receive more favourable terms of trade; (ii) restriction maintains cooperation in conditions where cooperative behaviour would otherwise collapse; and (iii) restriction can lead to either an increase or decrease in a restricted individual's fitness. We discuss the applicability of this scenario to mutualisms such as those between plants and mycorrhizal fungi. These results identify a novel conflict in mutualisms as well as several public goods dilemmas, but also demonstrate how conflict can help maintain cooperation. PMID:26813888

  13. 40 CFR 258.28 - Liquids restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 1 CFR part 51. This material is incorporated as it exists on the date of approval and a notice of... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Liquids restrictions. 258.28 Section... MUNICIPAL SOLID WASTE LANDFILLS Operating Criteria § 258.28 Liquids restrictions. (a) Bulk...

  14. 40 CFR 258.28 - Liquids restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 1 CFR part 51. This material is incorporated as it exists on the date of approval and a notice of... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Liquids restrictions. 258.28 Section... MUNICIPAL SOLID WASTE LANDFILLS Operating Criteria § 258.28 Liquids restrictions. (a) Bulk...

  15. 40 CFR 258.28 - Liquids restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 1 CFR part 51. This material is incorporated as it exists on the date of approval and a notice of... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Liquids restrictions. 258.28 Section... MUNICIPAL SOLID WASTE LANDFILLS Operating Criteria § 258.28 Liquids restrictions. (a) Bulk...

  16. 40 CFR 258.28 - Liquids restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 1 CFR part 51. This material is incorporated as it exists on the date of approval and a notice of... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Liquids restrictions. 258.28 Section... MUNICIPAL SOLID WASTE LANDFILLS Operating Criteria § 258.28 Liquids restrictions. (a) Bulk...

  17. 50 CFR 216.35 - Permit restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... parts is subject to the provisions of 50 CFR part 14. (d) The permit holder shall not take from the wild... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Special Exceptions § 216.35 Permit restrictions. The following restrictions shall apply to...

  18. 50 CFR 216.35 - Permit restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... parts is subject to the provisions of 50 CFR part 14. (d) The permit holder shall not take from the wild... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Special Exceptions § 216.35 Permit restrictions. The following restrictions shall apply to...

  19. 32 CFR 763.4 - Entry restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 5 2014-07-01 2014-07-01 false Entry restrictions. 763.4 Section 763.4 National Defense Department of Defense (Continued) DEPARTMENT OF THE NAVY ISLANDS UNDER NAVY JURISDICTION RULES GOVERNING PUBLIC ACCESS Entry Regulations for Kaho'olawe Island, Hawaii § 763.4 Entry restrictions. (a) Entry by any person upon Kaho'olawe...

  20. 32 CFR 763.4 - Entry restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 5 2012-07-01 2012-07-01 false Entry restrictions. 763.4 Section 763.4 National Defense Department of Defense (Continued) DEPARTMENT OF THE NAVY ISLANDS UNDER NAVY JURISDICTION RULES GOVERNING PUBLIC ACCESS Entry Regulations for Kaho'olawe Island, Hawaii § 763.4 Entry restrictions. (a) Entry by any person upon Kaho'olawe...

  1. 32 CFR 763.4 - Entry restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 5 2010-07-01 2010-07-01 false Entry restrictions. 763.4 Section 763.4 National Defense Department of Defense (Continued) DEPARTMENT OF THE NAVY ISLANDS UNDER NAVY JURISDICTION RULES GOVERNING PUBLIC ACCESS Entry Regulations for Kaho'olawe Island, Hawaii § 763.4 Entry restrictions. (a) Entry by any person upon Kaho'olawe...

  2. 48 CFR 225.7009-2 - Restriction.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7009-2 Restriction. (a) Do not acquire ball and... each ball or roller bearing, the cost of the bearing components manufactured in the United States or Canada exceeds 50 percent of the total cost of the bearing components of that ball or roller bearing....

  3. 48 CFR 225.7009-2 - Restriction.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7009-2 Restriction. (a) Do not acquire ball and... each ball or roller bearing, the cost of the bearing components manufactured in the United States or Canada exceeds 50 percent of the total cost of the bearing components of that ball or roller bearing....

  4. 48 CFR 225.7009-2 - Restriction.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7009-2 Restriction. (a) Do not acquire ball and... each ball or roller bearing, the cost of the bearing components manufactured in the United States or Canada exceeds 50 percent of the total cost of the bearing components of that ball or roller bearing....

  5. 48 CFR 225.7009-2 - Restriction.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Other Statutory Restrictions on Foreign Acquisition 225.7009-2 Restriction. (a) Do not acquire ball and... each ball or roller bearing, the cost of the bearing components manufactured in the United States or Canada exceeds 50 percent of the total cost of the bearing components of that ball or roller bearing....

  6. 21 CFR 203.20 - Sales restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL PRESCRIPTION DRUG MARKETING Sales Restrictions § 203.20 Sales restrictions. Except as provided in § 203.22 or... drug that was: (a) Purchased by a public or private hospital or other health care entity; or...

  7. 47 CFR 64.1200 - Delivery restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 3 2013-10-01 2013-10-01 false Delivery restrictions. 64.1200 Section 64.1200 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) MISCELLANEOUS RULES RELATING TO COMMON CARRIERS Restrictions on Telemarketing, Telephone Solicitation, and Facsimile Advertising § 64.1200...

  8. Restricted Interests and Teacher Presentation of Items

    ERIC Educational Resources Information Center

    Stocco, Corey S.; Thompson, Rachel H.; Rodriguez, Nicole M.

    2011-01-01

    Restricted and repetitive behavior (RRB) is more pervasive, prevalent, frequent, and severe in individuals with autism spectrum disorders (ASDs) than in their typical peers. One subtype of RRB is restricted interests in items or activities, which is evident in the manner in which individuals engage with items (e.g., repetitious wheel spinning),…

  9. Freedom and Restrictions in Language Use.

    ERIC Educational Resources Information Center

    O'Donnell, Roy C.

    Since freedom of thought and expression is essential in a democracy, censorship of language is rightly regarded as a threat to all other freedoms. Still, it is inevitable that certain restrictions will occasionally be imposed on language in America and in other societies. Restrictions on language date back to the Ten Commandments, which condemned…

  10. 19 CFR 114.31 - Restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Restrictions. 114.31 Section 114.31 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CARNETS Miscellaneous § 114.31 Restrictions. (a) Mail importations. Carnets shall not be accepted...

  11. 19 CFR 114.31 - Restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 1 2011-04-01 2011-04-01 false Restrictions. 114.31 Section 114.31 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CARNETS Miscellaneous § 114.31 Restrictions. (a) Mail importations. Carnets shall not be accepted...

  12. 5 CFR 451.105 - Award restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Awards § 451.105 Award restrictions. (a) In accordance with 5 U.S.C. 4508, agencies shall not grant awards under this subpart during a Presidential election period to employees who are— (1) In a Senior... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Award restrictions. 451.105 Section...

  13. 5 CFR 451.105 - Award restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Awards § 451.105 Award restrictions. (a) In accordance with 5 U.S.C. 4508, agencies shall not grant awards under this subpart during a Presidential election period to employees who are— (1) In a Senior... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Award restrictions. 451.105 Section...

  14. 5 CFR 451.105 - Award restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Awards § 451.105 Award restrictions. (a) In accordance with 5 U.S.C. 4508, agencies shall not grant awards under this subpart during a Presidential election period to employees who are— (1) In a Senior... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Award restrictions. 451.105 Section...

  15. 5 CFR 451.105 - Award restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Awards § 451.105 Award restrictions. (a) In accordance with 5 U.S.C. 4508, agencies shall not grant awards under this subpart during a Presidential election period to employees who are— (1) In a Senior... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Award restrictions. 451.105 Section...

  16. 5 CFR 451.105 - Award restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Award restrictions. 451.105 Section 451.105 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS AWARDS Agency Awards § 451.105 Award restrictions. (a) In accordance with 5 U.S.C. 4508, agencies shall not grant awards under this subpart during a...

  17. 50 CFR 648.123 - Gear restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Gear restrictions. 648.123 Section 648.123 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION... § 648.123 Gear restrictions. (a) Trawl vessel gear restrictions—(1) Minimum mesh size. No owner...

  18. 5 CFR 451.303 - Restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Restrictions. 451.303 Section 451.303 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS AWARDS Presidential Rank Awards § 451.303 Restrictions. (a) Governmentwide limitations—SES. During any fiscal year— (1) The number of career SES appointees awarded...

  19. 49 CFR 236.812 - Speed, restricted.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 4 2011-10-01 2011-10-01 false Speed, restricted. 236.812 Section 236.812 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Speed, restricted. A speed that will permit stopping within one-half the range of vision, but...

  20. 49 CFR 236.812 - Speed, restricted.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Speed, restricted. 236.812 Section 236.812 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Speed, restricted. A speed that will permit stopping within one-half the range of vision, but...

  1. 25 CFR 163.12 - Harvesting restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Harvesting restrictions. 163.12 Section 163.12 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER GENERAL FORESTRY REGULATIONS Forest Management and Operations § 163.12 Harvesting restrictions. (a) Harvesting timber on commercial forest...

  2. 25 CFR 163.12 - Harvesting restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 1 2014-04-01 2014-04-01 false Harvesting restrictions. 163.12 Section 163.12 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER GENERAL FORESTRY REGULATIONS Forest Management and Operations § 163.12 Harvesting restrictions. (a) Harvesting timber on commercial forest...

  3. 25 CFR 163.12 - Harvesting restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 1 2012-04-01 2011-04-01 true Harvesting restrictions. 163.12 Section 163.12 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER GENERAL FORESTRY REGULATIONS Forest Management and Operations § 163.12 Harvesting restrictions. (a) Harvesting timber on commercial forest...

  4. 25 CFR 163.12 - Harvesting restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false Harvesting restrictions. 163.12 Section 163.12 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER GENERAL FORESTRY REGULATIONS Forest Management and Operations § 163.12 Harvesting restrictions. (a) Harvesting timber on commercial forest...

  5. 25 CFR 163.12 - Harvesting restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Harvesting restrictions. 163.12 Section 163.12 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER GENERAL FORESTRY REGULATIONS Forest Management and Operations § 163.12 Harvesting restrictions. (a) Harvesting timber on commercial forest...

  6. 45 CFR 9.5 - Restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Restrictions. 9.5 Section 9.5 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION USE OF HHS RESEARCH FACILITIES BY ACADEMIC SCIENTISTS, ENGINEERS, AND STUDENTS § 9.5 Restrictions. (a) Each individual authorized to use...

  7. 45 CFR 9.5 - Restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Restrictions. 9.5 Section 9.5 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION USE OF HHS RESEARCH FACILITIES BY ACADEMIC SCIENTISTS, ENGINEERS, AND STUDENTS § 9.5 Restrictions. (a) Each individual authorized to use...

  8. Measuring the Restrictiveness of Living Environments for Children and Youth: Reconceptualizing Restriction

    ERIC Educational Resources Information Center

    Rauktis, Mary E.; Huefner, Jonathan C.; O'Brien, Kirk; Pecora, Peter J.; Doucette, Ann; Thompson, Ronald W.

    2009-01-01

    The "Restrictiveness of Living Environment Scale" has long been the primary way to conceptualize the "restrictiveness" of a child's living situation. However, changes in systems of care and other factors have created a need to revisit how restrictiveness is conceptualized and measured. A measure was created to assess an environment's level of…

  9. Urban water restrictions: Attitudes and avoidance

    NASA Astrophysics Data System (ADS)

    Cooper, Bethany; Burton, Michael; Crase, Lin

    2011-12-01

    In most urban cities across Australia, water restrictions remain the dominant policy mechanism to restrict urban water consumption. The extensive adoption of water restrictions as a means to limit demand, over several years, means that Australian urban water prices have consistently not reflected the opportunity cost of water. Given the generally strong political support for water restrictions and the likelihood that they will persist for some time, there is value in understanding households' attitudes in this context. More specifically, identifying the welfare gains associated with avoiding urban water restrictions entirely would be a nontrivial contribution to our knowledge and offer insights into the benefits of alternative policy responses. This paper describes the results from a contingent valuation study that investigates consumers' willingness to pay to avoid urban water restrictions. Importantly, the research also investigates the influence of cognitive and exogenous dimensions on the utility gain associated with avoiding water restrictions. The results provide insights into the impact of the current policy mechanism on economic welfare.

  10. Host restriction factors for hepatitis C virus

    PubMed Central

    Zhou, Li-Ya; Zhang, Lei-Liang

    2016-01-01

    Host-hepatitis C virus (HCV) interactions have both informed fundamental concepts of viral replication and pathogenesis and provided novel insights into host cell biology. These findings are illustrated by the recent discovery of host-encoded factors that restrict HCV infection. In this review, we briefly discuss these restriction factors in different steps of HCV infection. In each case, we discuss how these restriction factors were identified, the mechanisms by which they inhibit HCV infection and their potential contribution to viral pathogenesis. PMID:26819515

  11. Investigation of restricted baby Skyrme models

    SciTech Connect

    Adam, C.; Romanczukiewicz, T.; Wereszczynski, A.; Sanchez-Guillen, J.

    2010-04-15

    A restriction of the baby Skyrme model consisting of the quartic and potential terms only is investigated in detail for a wide range of potentials. Further, its properties are compared with those of the corresponding full baby Skyrme models. We find that topological (charge) as well as geometrical (nucleus/shell shape) features of baby Skyrmions are captured already by the soliton solutions of the restricted model. Further, we find a coincidence between the compact or noncompact nature of solitons in the restricted model, on the one hand, and the existence or nonexistence of multi-Skyrmions in the full baby Skyrme model, on the other hand.

  12. 50 CFR 665.99 - Area restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Area restrictions. 665.99 Section 665.99 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION... Ocean Survey Chart Number 83484....

  13. 50 CFR 665.99 - Area restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Area restrictions. 665.99 Section 665.99 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION... Ocean Survey Chart Number 83484....

  14. 50 CFR 665.99 - Area restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Area restrictions. 665.99 Section 665.99 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION... Ocean Survey Chart Number 83484....

  15. 50 CFR 665.99 - Area restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Area restrictions. 665.99 Section 665.99 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION... Ocean Survey Chart Number 83484....

  16. 32 CFR 770.38 - Entry restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... in Puerto Rico § 770.38 Entry restrictions. Except for duly authorized military personnel and... duties, entry upon any U.S. Navy installation or property in Puerto Rico at anytime, by any person...

  17. 9 CFR 78.5 - General restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Interstate Movement of Cattle Because of Brucellosis § 78.5 General restrictions. Cattle may not be moved interstate except in compliance with this subpart and with 9 CFR part 86. Cattle moved interstate...

  18. 50 CFR 660.511 - Catch restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES Coastal Pelagics Fisheries § 660.511 Catch restrictions. (a) All CPS harvested shoreward of the outer boundary of the EEZ...

  19. 50 CFR 660.511 - Catch restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES Coastal Pelagics Fisheries § 660.511 Catch restrictions. (a) All CPS harvested shoreward of the outer boundary of the EEZ...

  20. 50 CFR 660.511 - Catch restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES Coastal Pelagics Fisheries § 660.511 Catch restrictions. (a) All CPS harvested shoreward of the outer boundary of the EEZ...

  1. 50 CFR 660.511 - Catch restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES Coastal Pelagics Fisheries § 660.511 Catch restrictions. (a) All CPS harvested shoreward of the outer boundary of the EEZ...

  2. 50 CFR 660.511 - Catch restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES Coastal Pelagics Fisheries § 660.511 Catch restrictions. (a) All CPS harvested shoreward of the outer boundary of the EEZ...

  3. 19 CFR 12.17 - Importation restricted.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... TREASURY SPECIAL CLASSES OF MERCHANDISE Viruses, Serums, and Toxins for Treatment of Domestic Animals § 12.17 Importation restricted. The importation into the United States of viruses, serums, toxins,...

  4. 19 CFR 12.17 - Importation restricted.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... TREASURY SPECIAL CLASSES OF MERCHANDISE Viruses, Serums, and Toxins for Treatment of Domestic Animals § 12.17 Importation restricted. The importation into the United States of viruses, serums, toxins,...

  5. 19 CFR 12.17 - Importation restricted.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... TREASURY SPECIAL CLASSES OF MERCHANDISE Viruses, Serums, and Toxins for Treatment of Domestic Animals § 12.17 Importation restricted. The importation into the United States of viruses, serums, toxins,...

  6. Restriction/modification polypeptides, polynucleotides, and methods

    SciTech Connect

    Westpheling, Janet; Chung, DaeHwan; Huddleston, Jennifer; Farkas, Joel A

    2015-02-24

    The present invention relates to the discovery of a novel restriction/modification system in Caldicellulosiruptor bescii. The discovered restriction enzyme is a HaeIII-like restriction enzyme that possesses a thermophilic activity profile. The restriction/modification system also includes a methyltransferase, M.CbeI, that methylates at least one cytosine residue in the CbeI recognition sequence to m.sup.4C. Thus, the invention provides, in various aspects, isolated CbeI or M.CbeI polypeptides, or biologically active fragments thereof; isolated polynucleotides that encode the CbeI or M.CbeI polypeptides or biologically active fragments thereof, including expression vectors that include such polynucleotide sequences; methods of digesting DNA using a CbeI polypeptide; methods of treating a DNA molecule using a M.CbeI polypeptide; and methods of transforming a Caldicellulosiruptor cell.

  7. Methionine restriction and life-span control.

    PubMed

    Lee, Byung Cheon; Kaya, Alaattin; Gladyshev, Vadim N

    2016-01-01

    Dietary restriction (DR) without malnutrition is associated with longevity in various organisms. However, it has also been shown that reduced calorie intake is often ineffective in extending life span. Selecting optimal dietary regimens for DR studies is complicated, as the same regimen may lead to different outcomes depending on genotype and environmental factors. Recent studies suggested that interventions such as moderate protein restriction with or without adequate nutrition (e.g., particular amino acids or carbohydrates) may have additional beneficial effects mediated by certain metabolic and hormonal factors implicated in the biology of aging, regardless of total calorie intake. In particular, it was shown that restriction of a single amino acid, methionine, can mimic the effects of DR and extend life span in various model organisms. We discuss the beneficial effects of a methionine-restricted diet, the molecular pathways involved, and the use of this regimen in longevity interventions. PMID:26663138

  8. Tighten Teens' Nighttime Driving Restrictions: CDC

    MedlinePlus

    ... past the time most teens are off the road, the CDC reported. "Restrictions that start at 12 ... just 26 states want young drivers off the road before midnight, the CDC reported. Shults believes that ...

  9. 19 CFR 12.37 - Restricted importations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... TREASURY SPECIAL CLASSES OF MERCHANDISE Liquors § 12.37 Restricted importations. (a) The basic permit... port director is satisfied that the liquor is for personal use or for experimental purposes in...

  10. Restrictions on Database Use: Are They Necessary?

    ERIC Educational Resources Information Center

    Molster, H. C.

    1979-01-01

    Discusses restrictions regarding use of bibliographic data bases, cites their rationale in terms of cooperation in input creation, economics and administrative control, and notes their effect on use. (Author/CWM)

  11. 5 CFR 359.503 - Restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Than Fully Successful Executive Performance § 359.503 Restrictions. (a) Removal from the SES under this... section, a noncareer appointee includes an SES noncareer or limited appointee, an appointee in a...

  12. The design of artificial retroviral restriction factors

    SciTech Connect

    Yap, Melvyn W.; Mortuza, Gulnahar B.; Taylor, Ian A.; Stoye, Jonathan P.

    2007-09-01

    In addition to the ability to bind the retroviral capsid protein, the retroviral restriction factors Fv1, Trim5{alpha} and Trim5-CypA share the common property of containing sequences that promote self-association. Otherwise Fv1 and Trim5{alpha} appear unrelated. Mutational analyses showed that restriction was invariably lost when changes designed to disrupt the sequences responsible for multimerization were introduced. A novel restriction protein could be obtained by substituting sequences from the self-associating domain of Fv1 for the Trim5 sequences in Trim5-CypA. Similarly, a fusion protein containing cyclophilin A joined to arfaptin2, a protein known to form extended dimers, was also shown to restrict HIV-1. Hence, multimerization of a capsid-binding domain could be the common minimum design feature for capsid-dependent retroviral restriction factors. However, not all domains that promote multimerization can substitute for the N-terminal domains of Fv1 and Trim5{alpha}. Moreover, only CypA can provide a capsid-binding site with different N-terminal domains. It is suggested that the spatial relationship between the multiple target binding sites may be important for restriction.

  13. Disability due to restrictions in childhood epilepsy.

    PubMed

    Carpay, H A; Vermeulen, J; Stroink, H; Brouwer, O F; Peters, A C; van Donselaar, C A; Aldenkamp, A P; Arts, W F

    1997-08-01

    Parents and doctors impose restrictions on children with epilepsy to avoid seizure-related injuries. We intended to quantify disability due to such restrictions by using a newly developed parent-completed 10-item scale (The Hague Restrictions in Childhood Epilepsy Scale, HARCES). Parents reported disability on at least one item of the HARCES in 83% of 122 children with epilepsy and a remission from seizures for less than 1 year. Psychometric analysis of the scale's reliability demonstrated good internal consistency and retest stability. Its validity was supported by the association between HARCES scores and the physicians' advice imposing restrictions. We found no substantial association with such variables as seizure type, short-term remission, or seizure activity. These findings suggest that in children with recurrent seizures, restrictions were probably not optimally adapted to seizure-related risks. A repeat test after 1 year showed that a seizure remission of more than 1 year substantially reduced restrictions, which is probably associated with an improvement in quality of life. PMID:9295847

  14. Model of adipose tissue cellularity dynamics during food restriction.

    PubMed

    Soula, H A; Géloën, A; Soulage, C O

    2015-01-01

    Adipose tissue and adipocytes play a central role in the pathogenesis of metabolic diseases related to obesity. Size of fat cells depends on the balance of synthesis and mobilization of lipids and can undergo important variations throughout the life of the organism. These variations usually occur when storing and releasing lipids according to energy demand. In particular when confronted to severe food restriction, adipocyte releases its lipid content via a process called lipolysis. We propose a mathematical model that combines cell diameter distribution and lipolytic response to show that lipid release is a surface (radius squared) limited mechanism. Since this size-dependent rate affects the cell׳s shrinkage speed, we are able to predict the cell size distribution evolution when lipolysis is the only factor at work: such as during an important food restriction. Performing recurrent surgical biopsies on rats, we measured the evolution of adipose cell size distribution for the same individual throughout the duration of the food restriction protocol. We show that our microscopic model of size dependent lipid release can predict macroscopic size distribution evolution. PMID:25196549

  15. Reduced placental volume and flow in severe growth restricted fetuses

    PubMed Central

    Abulé, Renata Montes Dourado; Bernardes, Lisandra Stein; Doro, Giovana Farina; Miyadahira, Seizo; Francisco, Rossana Pulcinelli Vieira

    2016-01-01

    OBJECTIVES: To evaluate placental volume and vascular indices in pregnancies with severe fetal growth restriction and determine their correlations to normal reference ranges and Doppler velocimetry results of uterine and umbilical arteries. METHODS: Twenty-seven fetuses with estimated weights below the 3rd percentile for gestational age were evaluated. Placental volume and vascular indices, including vascularization, flow, and vascularization flow indices, were measured by three-dimensional ultrasound using a rotational technique and compared to a previously described nomogram. The observed-to-expected placental volume ratio for gestational age and observed-to-expected placental volume ratio for fetal weight were calculated. Placental parameters correlated with the Doppler velocimetry results of uterine and umbilical arteries. RESULTS: The mean uterine artery pulsatility index was negatively correlated with the observed-to-expected placental volume ratio for gestational age, vascularization index and vascularization flow index. The observed-to-expected placental volume ratio for gestational age and observed-to-expected placental volume ratio for fetal weight and vascularization index were significantly lower in the group with a bilateral protodiastolic notch. No placental parameter correlated with the umbilical artery pulsatility index. CONCLUSIONS: Pregnancies complicated by severe fetal growth restriction are associated with reduced placental volume and vascularization. These findings are related to changes in uterine artery Doppler velocimetry. Future studies on managing severe fetal growth restriction should focus on combined results of placental three-dimensional ultrasound and Doppler studies of uterine arteries. PMID:27438567

  16. Fasting and Caloric Restriction in Cancer Prevention and Treatment.

    PubMed

    Brandhorst, Sebastian; Longo, Valter D

    2016-01-01

    Cancer is the second leading cause of death in the USA and among the leading major diseases in the world. It is anticipated to continue to increase because of the growth of the aging population and prevalence of risk factors such as obesity, smoking, and/or poor dietary habits. Cancer treatment has remained relatively similar during the past 30 years with chemotherapy and/or radiotherapy in combination with surgery remaining the standard therapies although novel therapies are slowly replacing or complementing the standard ones. According to the American Cancer Society, the dietary recommendation for cancer patients receiving chemotherapy is to increase calorie and protein intake. In addition, there are no clear guidelines on the type of nutrition that could have a major impact on cancer incidence. Yet, various forms of reduced caloric intake such as calorie restriction (CR) or fasting demonstrate a wide range of beneficial effects able to help prevent malignancies and increase the efficacy of cancer therapies. Whereas chronic CR provides both beneficial and detrimental effects as well as major compliance challenges, periodic fasting (PF), fasting-mimicking diets (FMDs), and dietary restriction (DR) without a reduction in calories are emerging as interventions with the potential to be widely used to prevent and treat cancer. Here, we review preclinical and preliminary clinical studies on dietary restriction and fasting and their role in inducing cellular protection and chemotherapy resistance. PMID:27557543

  17. Early Vertebrate Evolution of the Host Restriction Factor Tetherin

    PubMed Central

    Heusinger, Elena; Kluge, Silvia F.; Kirchhoff, Frank

    2015-01-01

    release of newly formed progeny virions from infected cells. Although tetherin targets a broad range of enveloped viruses, including retro-, filo-, herpes-, and arenaviruses, the evolutionary origin of this restriction factor and its antiviral activity remained obscure. Here, we examined diverse vertebrate genomes for genes encoding cellular proteins that share with tetherin the highly unusual combination of an N-terminal transmembrane domain and a C-terminal glycosylphosphatidylinositol anchor. We show that tetherin orthologs are found in fish, reptiles, and birds and demonstrate that alligator tetherin efficiently inhibits the release of retroviral particles. Our findings identify tetherin as an evolutionarily ancient restriction factor and provide new important insights into the continuous arms race between viruses and their hosts. PMID:26401043

  18. Power combiner

    DOEpatents

    Arnold, Mobius; Ives, Robert Lawrence

    2006-09-05

    A power combiner for the combining of symmetric and asymmetric traveling wave energy comprises a feed waveguide having an input port and a launching port, a reflector for reflecting launched wave energy, and a final waveguide for the collection and transport of launched wave energy. The power combiner has a launching port for symmetrical waves which comprises a cylindrical section coaxial to the feed waveguide, and a launching port for asymmetric waves which comprises a sawtooth rotated about a central axis.

  19. Legitimate vs. illegitimate restrictions – a motivational and physiological approach investigating reactance processes

    PubMed Central

    Sittenthaler, Sandra; Steindl, Christina; Jonas, Eva

    2015-01-01

    combined dual-process and intertwined-process model explaining people’s reactions to legitimate vs. illegitimate restrictions. PMID:26042065

  20. Cellular Restriction Factors of Feline Immunodeficiency Virus

    PubMed Central

    Zielonka, Jörg; Münk, Carsten

    2011-01-01

    Lentiviruses are known for their narrow cell- and species-tropisms, which are determined by cellular proteins whose absence or presence either support viral replication (dependency factors, cofactors) or inhibit viral replication (restriction factors). Similar to Human immunodeficiency virus type 1 (HIV-1), the cat lentivirus Feline immunodeficiency virus (FIV) is sensitive to recently discovered cellular restriction factors from non-host species that are able to stop viruses from replicating. Of particular importance are the cellular proteins APOBEC3, TRIM5α and tetherin/BST-2. In general, lentiviruses counteract or escape their species’ own variant of the restriction factor, but are targeted by the orthologous proteins of distantly related species. Most of the knowledge regarding lentiviral restriction factors has been obtained in the HIV-1 system; however, much less is known about their effects on other lentiviruses. We describe here the molecular mechanisms that explain how FIV maintains its replication in feline cells, but is largely prevented from cross-species infections by cellular restriction factors. PMID:22069525

  1. RESTRICTED INTERESTS AND TEACHER PRESENTATION OF ITEMS

    PubMed Central

    Stocco, Corey S; Thompson, Rachel H; Rodriguez, Nicole M

    2011-01-01

    Restricted and repetitive behavior (RRB) is more pervasive, prevalent, frequent, and severe in individuals with autism spectrum disorders (ASDs) than in their typical peers. One subtype of RRB is restricted interests in items or activities, which is evident in the manner in which individuals engage with items (e.g., repetitious wheel spinning), the types of items or activities they select (e.g., preoccupation with a phone book), or the range of items or activities they select (i.e., narrow range of items). We sought to describe the relation between restricted interests and teacher presentation of items. Overall, we observed 5 teachers interacting with 2 pairs of students diagnosed with an ASD. Each pair included 1 student with restricted interests. During these observations, teachers were free to present any items from an array of 4 stimuli selected by experimenters. We recorded student responses to teacher presentation of items and analyzed the data to determine the relation between teacher presentation of items and the consequences for presentation provided by the students. Teacher presentation of items corresponded with differential responses provided by students with ASD, and those with restricted preferences experienced a narrower array of items. PMID:21941381

  2. Restricted interests and teacher presentation of items.

    PubMed

    Stocco, Corey S; Thompson, Rachel H; Rodriguez, Nicole M

    2011-01-01

    Restricted and repetitive behavior (RRB) is more pervasive, prevalent, frequent, and severe in individuals with autism spectrum disorders (ASDs) than in their typical peers. One subtype of RRB is restricted interests in items or activities, which is evident in the manner in which individuals engage with items (e.g., repetitious wheel spinning), the types of items or activities they select (e.g., preoccupation with a phone book), or the range of items or activities they select (i.e., narrow range of items). We sought to describe the relation between restricted interests and teacher presentation of items. Overall, we observed 5 teachers interacting with 2 pairs of students diagnosed with an ASD. Each pair included 1 student with restricted interests. During these observations, teachers were free to present any items from an array of 4 stimuli selected by experimenters. We recorded student responses to teacher presentation of items and analyzed the data to determine the relation between teacher presentation of items and the consequences for presentation provided by the students. Teacher presentation of items corresponded with differential responses provided by students with ASD, and those with restricted preferences experienced a narrower array of items. PMID:21941381

  3. Newer antidiabetic drugs and calorie restriction mimicry.

    PubMed

    Kalra, Sanjay; Jacob, Jubbin Jagan; Gupta, Yashdeep

    2016-01-01

    De-acceleration of aging and delayed development of age-related morbidity accompanies the restriction of calories (without malnutrition) in laboratory mice, nematodes, yeast, fish, and dogs. Recent results from long-term longitudinal studies conducted on primates have suggested longevity benefits of a 30% restriction of calories in rhesus monkeys as well. Among calorie restricted rhesus monkeys one of the mechanisms for the improvement in lifespan was the reduction in the development of glucose intolerance and cardiovascular disease. Although there are no comparable human studies, it is likely that metabolic and longevity benefits will accompany a reduction in calories in humans as well. However, considering the difficulties in getting healthy adults to limit food intake science has focused on understanding the biochemical processes that accompany calorie restriction (CR) to formulate drugs that would mimic the effects of CR without the need to actually restrict calories. Drugs in this emerging therapeutic field are called CR mimetics. Some of the currently used anti-diabetic agents may have some CR mimetic like effects. This review focuses on the CR mimetic properties of the currently available anti-diabetic agents. PMID:26904485

  4. Miles In Trail (MIT) Restrictions: A Perspective

    NASA Technical Reports Server (NTRS)

    Kopardekar, Parimal; Green, Steven; Roherty, Tom; Aston, John

    2003-01-01

    Miles-in-trail restrictions are issued to meet the airport and/or airspace capacity. The purpose of this paper is to review the currently practiced miles-in-trail operations for traffic flow management at a typical en route Air Traffic Control Center. The paper describes roles and considerations of both traffic management coordinators and the controllers in planning, coordination, execution, and monitoring of miles-in-trail restrictions. The paper addresses the type of decisions that traffic management coordinators must make and the different information required to plan and monitor miles-in-trail restrictions. The implications of miles-in-trail restrictions on controller workload are also addressed. Using the Cleveland center as an example, the paper also identified some challenging traffic situations that required miles-in-trail restrictions on a regular basis. The paper is expected to benefit the research and development community as it provides the current challenges in traffic flow management and strengths and weakness of miles-in-trail operations.

  5. Newer antidiabetic drugs and calorie restriction mimicry

    PubMed Central

    Kalra, Sanjay; Jacob, Jubbin Jagan; Gupta, Yashdeep

    2016-01-01

    De-acceleration of aging and delayed development of age-related morbidity accompanies the restriction of calories (without malnutrition) in laboratory mice, nematodes, yeast, fish, and dogs. Recent results from long-term longitudinal studies conducted on primates have suggested longevity benefits of a 30% restriction of calories in rhesus monkeys as well. Among calorie restricted rhesus monkeys one of the mechanisms for the improvement in lifespan was the reduction in the development of glucose intolerance and cardiovascular disease. Although there are no comparable human studies, it is likely that metabolic and longevity benefits will accompany a reduction in calories in humans as well. However, considering the difficulties in getting healthy adults to limit food intake science has focused on understanding the biochemical processes that accompany calorie restriction (CR) to formulate drugs that would mimic the effects of CR without the need to actually restrict calories. Drugs in this emerging therapeutic field are called CR mimetics. Some of the currently used anti-diabetic agents may have some CR mimetic like effects. This review focuses on the CR mimetic properties of the currently available anti-diabetic agents. PMID:26904485

  6. Placental Nutrient Transport and Intrauterine Growth Restriction

    PubMed Central

    Gaccioli, Francesca; Lager, Susanne

    2016-01-01

    Intrauterine growth restriction refers to the inability of the fetus to reach its genetically determined potential size. Fetal growth restriction affects approximately 5–15% of all pregnancies in the United States and Europe. In developing countries the occurrence varies widely between 10 and 55%, impacting about 30 million newborns per year. Besides having high perinatal mortality rates these infants are at greater risk for severe adverse outcomes, such as hypoxic ischemic encephalopathy and cerebral palsy. Moreover, reduced fetal growth has lifelong health consequences, including higher risks of developing metabolic and cardiovascular diseases in adulthood. Numerous reports indicate placental insufficiency as one of the underlying causes leading to altered fetal growth and impaired placental capacity of delivering nutrients to the fetus has been shown to contribute to the etiology of intrauterine growth restriction. Indeed, reduced expression and/or activity of placental nutrient transporters have been demonstrated in several conditions associated with an increased risk of delivering a small or growth restricted infant. This review focuses on human pregnancies and summarizes the changes in placental amino acid, fatty acid, and glucose transport reported in conditions associated with intrauterine growth restriction, such as maternal undernutrition, pre-eclampsia, young maternal age, high altitude and infection. PMID:26909042

  7. The hepatic transcriptome of young suckling and aging intrauterine growth restricted male rats.

    PubMed

    Freije, William A; Thamotharan, Shanthie; Lee, Regina; Shin, Bo-Chul; Devaskar, Sherin U

    2015-04-01

    Intrauterine growth restriction leads to the development of adult onset obesity/metabolic syndrome, diabetes mellitus, cardiovascular disease, hypertension, stroke, dyslipidemia, and non-alcoholic fatty liver disease/steatohepatitis. Continued postnatal growth restriction has been shown to ameliorate many of these sequelae. To further our understanding of the mechanism of how intrauterine and early postnatal growth affects adult health we have employed Affymetrix microarray-based expression profiling to characterize hepatic gene expression of male offspring in a rat model of maternal nutrient restriction in early and late life. At day 21 of life (p21) combined intrauterine and postnatal calorie restriction treatment led to expression changes in circadian, metabolic, and insulin-like growth factor genes as part of a larger transcriptional response that encompasses 144 genes. Independent and controlled experiments at p21 confirm the early life circadian, metabolic, and growth factor perturbations. In contrast to the p21 transcriptional response, at day 450 of life (d450) only seven genes, largely uncharacterized, were differentially expressed. This lack of a transcriptional response identifies non-transcriptional mechanisms mediating the adult sequelae of intrauterine growth restriction. Independent experiments at d450 identify a circadian defect as well as validate expression changes to four of the genes identified by the microarray screen which have a novel association with growth restriction. Emerging from this rich dataset is a portrait of how the liver responds to growth restriction through circadian dysregulation, energy/substrate management, and growth factor modulation. PMID:25371150

  8. The compartmental restriction of cerebellar interneurons

    PubMed Central

    Consalez, G. Giacomo; Hawkes, Richard

    2013-01-01

    The Purkinje cells (PC's) of the cerebellar cortex are subdivided into multiple different molecular phenotypes that form an elaborate array of parasagittal stripes. This array serves as a scaffold around which afferent topography is organized. The ways in which cerebellar interneurons may be restricted by this scaffolding are less well-understood. This review begins with a brief survey of cerebellar topography. Next, it reviews the development of stripes in the cerebellum with a particular emphasis on the embryological origins of cerebellar interneurons. These data serve as a foundation to discuss the hypothesis that cerebellar compartment boundaries also restrict cerebellar interneurons, both excitatory [granule cells, unipolar brush cells (UBCs)] and inhibitory (e.g., Golgi cells, basket cells). Finally, it is proposed that the same PC scaffold that restricts afferent terminal fields to stripes may also act to organize cerebellar interneurons. PMID:23346049

  9. Optimizing Restriction Site Placement for Synthetic Genomes

    NASA Astrophysics Data System (ADS)

    Montes, Pablo; Memelli, Heraldo; Ward, Charles; Kim, Joondong; Mitchell, Joseph S. B.; Skiena, Steven

    Restriction enzymes are the workhorses of molecular biology. We introduce a new problem that arises in the course of our project to design virus variants to serve as potential vaccines: we wish to modify virus-length genomes to introduce large numbers of unique restriction enzyme recognition sites while preserving wild-type function by substitution of synonymous codons. We show that the resulting problem is NP-Complete, give an exponential-time algorithm, and propose effective heuristics, which we show give excellent results for five sample viral genomes. Our resulting modified genomes have several times more unique restriction sites and reduce the maximum gap between adjacent sites by three to nine-fold.

  10. IFITM Proteins Restrict Viral Membrane Hemifusion

    PubMed Central

    Golfetto, Ottavia; Bungart, Brittani; Li, Minghua; Ding, Shilei; He, Yuxian; Liang, Chen; Lee, James C.; Gratton, Enrico; Cohen, Fredric S.; Liu, Shan-Lu

    2013-01-01

    The interferon-inducible transmembrane (IFITM) protein family represents a new class of cellular restriction factors that block early stages of viral replication; the underlying mechanism is currently not known. Here we provide evidence that IFITM proteins restrict membrane fusion induced by representatives of all three classes of viral membrane fusion proteins. IFITM1 profoundly suppressed syncytia formation and cell-cell fusion induced by almost all viral fusion proteins examined; IFITM2 and IFITM3 also strongly inhibited their fusion, with efficiency somewhat dependent on cell types. Furthermore, treatment of cells with IFN also markedly inhibited viral membrane fusion and entry. By using the Jaagsiekte sheep retrovirus envelope and influenza A virus hemagglutinin as models for study, we showed that IFITM-mediated restriction on membrane fusion is not at the steps of receptor- and/or low pH-mediated triggering; instead, the creation of hemifusion was essentially blocked by IFITMs. Chlorpromazine (CPZ), a chemical known to promote the transition from hemifusion to full fusion, was unable to rescue the IFITM-mediated restriction on fusion. In contrast, oleic acid (OA), a lipid analog that generates negative spontaneous curvature and thereby promotes hemifusion, virtually overcame the restriction. To explore the possible effect of IFITM proteins on membrane molecular order and fluidity, we performed fluorescence labeling with Laurdan, in conjunction with two-photon laser scanning and fluorescence-lifetime imaging microscopy (FLIM). We observed that the generalized polarizations (GPs) and fluorescence lifetimes of cell membranes expressing IFITM proteins were greatly enhanced, indicating higher molecularly ordered and less fluidized membranes. Collectively, our data demonstrated that IFITM proteins suppress viral membrane fusion before the creation of hemifusion, and suggested that they may do so by reducing membrane fluidity and conferring a positive spontaneous

  11. Combined nitrogen oxides/sulfur dioxide control in dry scrubber systems

    SciTech Connect

    Harkness, J. B.L.; Gorski, A. J.; Huang, H. S.

    1989-02-01

    Argonne National Laboratory (ANL) is investigating alternative control concepts that involve modifying existing SO{sub 2}-removal processes and sorbents, with the objective of achieving simultaneous removal of nitrogen oxides (NO{sub x}) and sulfur dioxide (SO{sub 2}). Laboratory-scale research conducted using a fixed-bed reactor and a spray-dryer/fabric-filter system has been paralleled by field tests at ANL's commercial-scale (20-MW electric equivalent) dry scrubber. In the fixed-bed experiments, a range of chemical reagents was surveyed, and the best-performing additives were studied in detail. Sodium chloride, sodium bisulfite, sodium hydroxide, and Fe(II)*EDTA were found to increase both NO{sub x} and SO{sub 2} removals; the additives did not appear to increase NO{sub x} removal directly, but they interacted strongly with the other primary variables to improve sorbent performance. The laboratory spray-dryer system was used to study the effects on combined NO{sub x}/SO{sub 2} removal of the best-performing fixed-bed additives and certain process modifications. The tests showed that sodium chloride increased NO{sub x} removal at all temperatures; sodium bisulfite was generally less effective, and calcium chloride was effective only at 65{degree}C. Up to 80{degree}C, all three additives significantly improved SO{sub 2} removal, but improvement ceased at higher temperatures. This report discusses the experimental results in terms of the effects the additives and principal process variables had on NO{sub x} and SO{sub 2} removals and the mechanistic implications. 14 refs., 74 figs., 33 tabs.

  12. World knowledge affects prediction as quickly as selectional restrictions: Evidence from the visual world paradigm

    PubMed Central

    Milburn, Evelyn; Warren, Tessa; Dickey, Michael Walsh

    2016-01-01

    There has been considerable debate regarding the question of whether linguistic knowledge and world knowledge are separable and used differently during processing or not (Hagoort, Hald, Bastiaansen, & Petersson, 2004; Matsuki et al., 2011; Paczynski & Kuperberg, 2012; Warren & McConnell, 2007; Warren, McConnell, & Rayner, 2008). Previous investigations into this question have provided mixed evidence as to whether violations of selectional restrictions are detected earlier than violations of world knowledge. We report a visual-world eye-tracking study comparing the timing of facilitation contributed by selectional restrictions versus world knowledge. College-aged adults (n=36) viewed photographs of natural scenes while listening to sentences. Participants anticipated upcoming direct objects similarly regardless of whether facilitation was provided by only world knowledge or a combination of selectional restrictions and world knowledge. These results suggest that selectional restrictions are not available earlier in comprehension than world knowledge. PMID:27148555

  13. 10 CFR 1045.16 - Criteria for evaluation of restricted data and formerly restricted data information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ..., produce nuclear weapons materials, or make other military use of nuclear energy; (4) Whether publication... 10 Energy 4 2012-01-01 2012-01-01 false Criteria for evaluation of restricted data and formerly restricted data information. 1045.16 Section 1045.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS)...

  14. 10 CFR 1045.16 - Criteria for evaluation of restricted data and formerly restricted data information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., produce nuclear weapons materials, or make other military use of nuclear energy; (4) Whether publication... 10 Energy 4 2014-01-01 2014-01-01 false Criteria for evaluation of restricted data and formerly restricted data information. 1045.16 Section 1045.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS)...

  15. 10 CFR 1045.16 - Criteria for evaluation of restricted data and formerly restricted data information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ..., produce nuclear weapons materials, or make other military use of nuclear energy; (4) Whether publication... 10 Energy 4 2011-01-01 2011-01-01 false Criteria for evaluation of restricted data and formerly restricted data information. 1045.16 Section 1045.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS)...

  16. 7 CFR 319.75 - Restrictions on importation of restricted articles; disposal of articles refused importation.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 5 2014-01-01 2014-01-01 false Restrictions on importation of restricted articles; disposal of articles refused importation. 319.75 Section 319.75 Agriculture Regulations of the Department...; disposal of articles refused importation. (a) The Secretary has determined that in order to prevent...

  17. 7 CFR 319.75 - Restrictions on importation of restricted articles; disposal of articles refused importation.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 5 2012-01-01 2012-01-01 false Restrictions on importation of restricted articles; disposal of articles refused importation. 319.75 Section 319.75 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE FOREIGN QUARANTINE NOTICES Khapra Beetle §...

  18. Quantum Hall transitions: An exact theory based on conformal restriction

    NASA Astrophysics Data System (ADS)

    Bettelheim, E.; Gruzberg, I. A.; Ludwig, A. W. W.

    2012-10-01

    We revisit the problem of the plateau transition in the integer quantum Hall effect. Here we develop an analytical approach for this transition, and for other two-dimensional disordered systems, based on the theory of “conformal restriction.” This is a mathematical theory that was recently developed within the context of the Schramm-Loewner evolution which describes the “stochastic geometry” of fractal curves and other stochastic geometrical fractal objects in two-dimensional space. Observables elucidating the connection with the plateau transition include the so-called point-contact conductances (PCCs) between points on the boundary of the sample, described within the language of the Chalker-Coddington network model for the transition. We show that the disorder-averaged PCCs are characterized by a classical probability distribution for certain geometric objects in the plane (which we call pictures), occurring with positive statistical weights, that satisfy the crucial so-called restriction property with respect to changes in the shape of the sample with absorbing boundaries; physically, these are boundaries connected to ideal leads. At the transition point, these geometrical objects (pictures) become fractals. Upon combining this restriction property with the expected conformal invariance at the transition point, we employ the mathematical theory of “conformal restriction measures” to relate the disorder-averaged PCCs to correlation functions of (Virasoro) primary operators in a conformal field theory (of central charge c=0). We show how this can be used to calculate these functions in a number of geometries with various boundary conditions. Since our results employ only the conformal restriction property, they are equally applicable to a number of other critical disordered electronic systems in two spatial dimensions, including for example the spin quantum Hall effect, the thermal metal phase in symmetry class D, and classical diffusion in two

  19. Design implications of extremely restricted patterning

    NASA Astrophysics Data System (ADS)

    Vaidyanathan, Kaushik; Liu, Renzhi; Liebmann, Lars; Lai, Kafai; Strojwas, Andzrej J.; Pileggi, Larry

    2014-07-01

    Escalating manufacturing cost and complexity is challenging the premise of affordable scaling. With lithography accounting for a large fraction of wafer costs, researchers are actively exploring several cost-effective alternative lithographic techniques, such as directed self-assembly, self-aligned multiple patterning, etc. However, most of the alternative lithographic techniques are restrictive, and it is important to understand the impact of such pattering restrictions on system-on-chip (SoC) design. To this end, we artificially restricted all layers in a 14 nm process to be pure gratings and observed that the pure gratings approach results in an inefficient SoC design with several process integration concerns. To come up with a technology definition that is mindful of designer requirements, it is essential to undertake a holistic design technology co-optimization (DTCO) considering several SoC design elements, such as standard cell logic, static random access memory bitcells, analog blocks, and physical synthesis. Our DTCO on the IBM 14 nm process with additional 10- and 7-nm node-like pattern restrictions leads us to converge on a set of critical pattern constructs that are required for an efficient and affordable SoC design.

  20. 50 CFR 665.399 - Area restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Area restrictions. 665.399 Section 665.399 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION.... EEZ seaward of Guam west of 144°30′ E. long. except in the event of an emergency caused by...

  1. 50 CFR 665.399 - Area restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Area restrictions. 665.399 Section 665.399 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC... ocean conditions or by a vessel malfunction that can be documented....

  2. 50 CFR 665.399 - Area restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Area restrictions. 665.399 Section 665.399 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC... ocean conditions or by a vessel malfunction that can be documented....

  3. 9 CFR 82.20 - General restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false General restrictions. 82.20 Section 82.20 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS EXOTIC NEWCASTLE DIS- EASE...

  4. 9 CFR 82.20 - General restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false General restrictions. 82.20 Section 82.20 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS EXOTIC NEWCASTLE DIS- EASE...

  5. 50 CFR 16.3 - General restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false General restrictions. 16.3 Section 16.3 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR TAKING, POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS INJURIOUS WILDLIFE Introduction § 16.3...

  6. 50 CFR 16.3 - General restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false General restrictions. 16.3 Section 16.3 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR TAKING, POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS INJURIOUS WILDLIFE Introduction § 16.3...

  7. 12 CFR 1805.808 - Lobbying restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 7 2010-01-01 2010-01-01 false Lobbying restrictions. 1805.808 Section 1805.808 Banks and Banking COMMUNITY DEVELOPMENT FINANCIAL INSTITUTIONS FUND, DEPARTMENT OF THE TREASURY COMMUNITY DEVELOPMENT FINANCIAL INSTITUTIONS PROGRAM Terms and Conditions of Assistance § 1805.808...

  8. 36 CFR 327.12 - Restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 3 2013-07-01 2012-07-01 true Restrictions. 327.12 Section 327.12 Parks, Forests, and Public Property CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY RULES AND REGULATIONS GOVERNING PUBLIC USE OF WATER RESOURCE DEVELOPMENT PROJECTS ADMINISTERED BY THE CHIEF OF...

  9. 50 CFR 654.22 - Gear restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... restrictions. (a) Trap construction requirements. No person fishing for stone crab may transport on the water or fish with any trap which does not meet the following requirements: (1) Each trap must be... by 61 by 61 cm) or 8.0 ft3 (0.23 m3). (3) The throats (entrances) to all wood and plastic traps...

  10. 47 CFR 97.121 - Restricted operation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Station Operation Standards § 97.121 Restricted operation. (a) If the operation of an amateur... characteristics, are used to receive such transmissions, and this fact is made known to the amateur...

  11. 47 CFR 97.121 - Restricted operation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Station Operation Standards § 97.121 Restricted operation. (a) If the operation of an amateur... characteristics, are used to receive such transmissions, and this fact is made known to the amateur...

  12. 47 CFR 97.121 - Restricted operation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Station Operation Standards § 97.121 Restricted operation. (a) If the operation of an amateur... characteristics, are used to receive such transmissions, and this fact is made known to the amateur...

  13. 47 CFR 97.121 - Restricted operation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Station Operation Standards § 97.121 Restricted operation. (a) If the operation of an amateur... characteristics, are used to receive such transmissions, and this fact is made known to the amateur...

  14. 47 CFR 97.121 - Restricted operation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Station Operation Standards § 97.121 Restricted operation. (a) If the operation of an amateur... characteristics, are used to receive such transmissions, and this fact is made known to the amateur...

  15. 32 CFR 154.67 - Access restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... information shall be authorized only in accordance with 32 CFR parts 286 and 286a and with the following: (a.... (d) Access to personnel security clearance determination information shall be made available, other... 32 National Defense 1 2010-07-01 2010-07-01 false Access restrictions. 154.67 Section...

  16. 32 CFR 154.67 - Access restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... information shall be authorized only in accordance with 32 CFR parts 286 and 286a and with the following: (a.... (d) Access to personnel security clearance determination information shall be made available, other... 32 National Defense 1 2011-07-01 2011-07-01 false Access restrictions. 154.67 Section...

  17. 36 CFR 13.1182 - Noise restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Noise restrictions. 13.1182 Section 13.1182 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Special Regulations-Glacier Bay National Park and Preserve...

  18. 36 CFR 13.1176 - Speed restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Speed restrictions. 13.1176 Section 13.1176 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Special Regulations-Glacier Bay National Park and Preserve...

  19. 36 CFR 13.1182 - Noise restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Noise restrictions. 13.1182 Section 13.1182 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Special Regulations-Glacier Bay National Park and Preserve...

  20. 36 CFR 13.1176 - Speed restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Speed restrictions. 13.1176 Section 13.1176 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Special Regulations-Glacier Bay National Park and Preserve...

  1. 36 CFR 13.1176 - Speed restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Speed restrictions. 13.1176 Section 13.1176 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Special Regulations-Glacier Bay National Park and Preserve...

  2. 36 CFR 13.1182 - Noise restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false Noise restrictions. 13.1182 Section 13.1182 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Special Regulations-Glacier Bay National Park and Preserve...

  3. 36 CFR 13.1182 - Noise restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Noise restrictions. 13.1182 Section 13.1182 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Special Regulations-Glacier Bay National Park and Preserve...

  4. 36 CFR 13.1182 - Noise restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Noise restrictions. 13.1182 Section 13.1182 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL PARK SYSTEM UNITS IN ALASKA Special Regulations-Glacier Bay National Park and Preserve...

  5. 50 CFR 665.164 - Gear restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Gear restrictions. 665.164 Section 665.164 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC American Samoa...

  6. 50 CFR 665.264 - Gear restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Gear restrictions. 665.264 Section 665.264 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC Hawaii Fisheries §...

  7. 50 CFR 665.664 - Gear restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Gear restrictions. 665.664 Section 665.664 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC Pacific Remote Island...

  8. 50 CFR 665.164 - Gear restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Gear restrictions. 665.164 Section 665.164 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC American Samoa...

  9. 50 CFR 665.264 - Gear restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Gear restrictions. 665.264 Section 665.264 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC Hawaii Fisheries §...

  10. 50 CFR 648.163 - Gear restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Gear restrictions. 648.163 Section 648.163 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE FISHERIES OF THE NORTHEASTERN UNITED STATES Management Measures for the...

  11. 50 CFR 665.164 - Gear restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Gear restrictions. 665.164 Section 665.164 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC American Samoa...

  12. 50 CFR 665.264 - Gear restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Gear restrictions. 665.264 Section 665.264 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC Hawaii Fisheries §...

  13. 50 CFR 648.25 - Possession restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Atlantic Mackerel, Squid, and Butterfish Fisheries § 648.25 Possession restrictions. Link to an amendment... Atlantic Mackerel, squid, and butterfish framework adjustments to management measures. (a) Within season... the Atlantic Mackerel, Squid, and Butterfish FMP if it finds that action is necessary to meet or...

  14. 50 CFR 648.105 - Possession restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Summer Flounder Fisheries § 648.105 Possession restrictions. (a) Unless otherwise specified pursuant to § 648.107, no person shall possess more than two summer flounder in, or harvested from, the EEZ, unless that person is the owner or operator of a fishing vessel issued a summer flounder moratorium permit,...

  15. 45 CFR 400.44 - Restriction.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Immigration Status and Identification of Refugees Documentation of Refugee Status § 400.44 Restriction. An applicant for asylum is...

  16. 45 CFR 400.44 - Restriction.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Immigration Status and Identification of Refugees Documentation of Refugee Status § 400.44 Restriction. An applicant for asylum is...

  17. 45 CFR 3.42 - Restricted activities.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 1 2012-10-01 2012-10-01 false Restricted activities. 3.42 Section 3.42 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CONDUCT OF PERSONS AND TRAFFIC ON... contrary to security regulations or Department of Health and Human Services policies, or where...

  18. 45 CFR 3.42 - Restricted activities.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Restricted activities. 3.42 Section 3.42 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CONDUCT OF PERSONS AND TRAFFIC ON... contrary to security regulations or Department of Health and Human Services policies, or where...

  19. 45 CFR 3.42 - Restricted activities.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Restricted activities. 3.42 Section 3.42 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CONDUCT OF PERSONS AND TRAFFIC ON... contrary to security regulations or Department of Health and Human Services policies, or where...

  20. 45 CFR 3.42 - Restricted activities.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 1 2014-10-01 2014-10-01 false Restricted activities. 3.42 Section 3.42 Public Welfare Department of Health and Human Services GENERAL ADMINISTRATION CONDUCT OF PERSONS AND TRAFFIC ON... contrary to security regulations or Department of Health and Human Services policies, or where...

  1. 45 CFR 3.42 - Restricted activities.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Restricted activities. 3.42 Section 3.42 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CONDUCT OF PERSONS AND TRAFFIC ON... contrary to security regulations or Department of Health and Human Services policies, or where...

  2. 30 CFR 57.4400 - Use restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Use restrictions. 57.4400 Section 57.4400 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-UNDERGROUND METAL AND NONMETAL MINES Fire Prevention and Control Flammable and Combustible Liquids and...

  3. 9 CFR 83.2 - General restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false General restrictions. 83.2 Section 83.2 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS VIRAL HEMORRHAGIC...

  4. 9 CFR 83.2 - General restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false General restrictions. 83.2 Section 83.2 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS VIRAL HEMORRHAGIC...

  5. 36 CFR 331.18 - Restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Restrictions. 331.18 Section 331.18 Parks, Forests, and Public Property CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY REGULATIONS GOVERNING THE PROTECTION, USE AND MANAGEMENT OF THE FALLS OF THE OHIO NATIONAL WILDLIFE CONSERVATION...

  6. 36 CFR 331.18 - Restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 3 2014-07-01 2014-07-01 false Restrictions. 331.18 Section 331.18 Parks, Forests, and Public Property CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY REGULATIONS GOVERNING THE PROTECTION, USE AND MANAGEMENT OF THE FALLS OF THE OHIO NATIONAL WILDLIFE CONSERVATION...

  7. 36 CFR 331.18 - Restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Restrictions. 331.18 Section 331.18 Parks, Forests, and Public Property CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY REGULATIONS GOVERNING THE PROTECTION, USE AND MANAGEMENT OF THE FALLS OF THE OHIO NATIONAL WILDLIFE CONSERVATION...

  8. 36 CFR 331.18 - Restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 3 2012-07-01 2012-07-01 false Restrictions. 331.18 Section 331.18 Parks, Forests, and Public Property CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY REGULATIONS GOVERNING THE PROTECTION, USE AND MANAGEMENT OF THE FALLS OF THE OHIO NATIONAL WILDLIFE CONSERVATION...

  9. 36 CFR 331.18 - Restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 3 2013-07-01 2012-07-01 true Restrictions. 331.18 Section 331.18 Parks, Forests, and Public Property CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY REGULATIONS GOVERNING THE PROTECTION, USE AND MANAGEMENT OF THE FALLS OF THE OHIO NATIONAL WILDLIFE CONSERVATION...

  10. 50 CFR 665.599 - Area restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... § 665.599 Area restrictions. (a) Fishing is prohibited in all no-take MPAs. The following U.S. EEZ waters are no-take MPAs: Landward of the 50 fathom (fm) (91.5 m) curve at Jarvis, Howland, and Baker... MPAs. The following U.S. EEZ waters in the Western Pacific Region are low-use MPAs: All waters...

  11. 33 CFR 203.46 - Restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Restrictions. 203.46 Section 203.46 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE EMERGENCY EMPLOYMENT OF ARMY AND OTHER RESOURCES, NATURAL DISASTER PROCEDURES Rehabilitation Assistance...

  12. 32 CFR 701.44 - Restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 5 2013-07-01 2013-07-01 false Restrictions. 701.44 Section 701.44 National Defense Department of Defense (Continued) DEPARTMENT OF THE NAVY UNITED STATES NAVY REGULATIONS AND OFFICIAL RECORDS AVAILABILITY OF DEPARTMENT OF THE NAVY RECORDS AND PUBLICATION OF DEPARTMENT OF THE...

  13. 32 CFR 701.44 - Restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 5 2011-07-01 2011-07-01 false Restrictions. 701.44 Section 701.44 National Defense Department of Defense (Continued) DEPARTMENT OF THE NAVY UNITED STATES NAVY REGULATIONS AND OFFICIAL RECORDS AVAILABILITY OF DEPARTMENT OF THE NAVY RECORDS AND PUBLICATION OF DEPARTMENT OF THE...

  14. 32 CFR 701.44 - Restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 5 2014-07-01 2014-07-01 false Restrictions. 701.44 Section 701.44 National Defense Department of Defense (Continued) DEPARTMENT OF THE NAVY UNITED STATES NAVY REGULATIONS AND OFFICIAL RECORDS AVAILABILITY OF DEPARTMENT OF THE NAVY RECORDS AND PUBLICATION OF DEPARTMENT OF THE...

  15. 32 CFR 701.44 - Restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 5 2012-07-01 2012-07-01 false Restrictions. 701.44 Section 701.44 National Defense Department of Defense (Continued) DEPARTMENT OF THE NAVY UNITED STATES NAVY REGULATIONS AND OFFICIAL RECORDS AVAILABILITY OF DEPARTMENT OF THE NAVY RECORDS AND PUBLICATION OF DEPARTMENT OF THE...

  16. 7 CFR 2500.106 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 2500.106 Section 2500.106 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF ADVOCACY AND OUTREACH... Outreach and Assistance For Socially Disadvantaged Farmers and Ranchers Program § 2500.106...

  17. 7 CFR 3430.405 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 3430.405 Section 3430.405 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Organic Agriculture Research and Extension Initiative § 3430.405 Funding...

  18. 7 CFR 2500.106 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 2500.106 Section 2500.106 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF ADVOCACY AND OUTREACH... Outreach and Assistance For Socially Disadvantaged Farmers and Ranchers Program § 2500.106...

  19. 7 CFR 3430.405 - Funding restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Funding restrictions. 3430.405 Section 3430.405 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Organic Agriculture Research and Extension Initiative § 3430.405 Funding...

  20. 7 CFR 2500.106 - Funding restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Funding restrictions. 2500.106 Section 2500.106 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF ADVOCACY AND OUTREACH... Outreach and Assistance For Socially Disadvantaged Farmers and Ranchers Program § 2500.106...

  1. 7 CFR 3430.405 - Funding restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Funding restrictions. 3430.405 Section 3430.405 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Organic Agriculture Research and Extension Initiative § 3430.405 Funding...

  2. 7 CFR 3430.405 - Funding restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Funding restrictions. 3430.405 Section 3430.405 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND... ADMINISTRATIVE PROVISIONS Organic Agriculture Research and Extension Initiative § 3430.405 Funding...

  3. Full Inclusion: The Least Restrictive Environment

    ERIC Educational Resources Information Center

    Mullings, Shirley E.

    2011-01-01

    The purpose of the phenomenological study was to examine elementary educators' perceptions of full inclusion as the least restrictive environment for students with disabilities. Thirty-six teachers and administrators participated in interviews and responded to multiple-choice survey items. The recorded data from the interviews were…

  4. 46 CFR 121.202 - Restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... gases as cooking fuels by 46 Code of Federal Regulations (CFR) part 147 must meet the requirements of § 121.240. The use of these fuels for cooking, heating, and lighting on ferry vessels is prohibited by... SYSTEMS AND EQUIPMENT Cooking and Heating § 121.202 Restrictions. (a) The use of gasoline for...

  5. 46 CFR 184.202 - Restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... use liquefied and non-liquefied gases as cooking fuels by 46 CFR part 147 must meet the requirements... CONTROL AND MISCELLANEOUS SYSTEMS AND EQUIPMENT Cooking and Heating § 184.202 Restrictions. (a) The use of gasoline for cooking, heating, or lighting is prohibited on all vessels. (b) Fireplaces or other...

  6. 46 CFR 184.202 - Restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... use liquefied and non-liquefied gases as cooking fuels by 46 CFR part 147 must meet the requirements... CONTROL AND MISCELLANEOUS SYSTEMS AND EQUIPMENT Cooking and Heating § 184.202 Restrictions. (a) The use of gasoline for cooking, heating, or lighting is prohibited on all vessels. (b) Fireplaces or other...

  7. 46 CFR 121.202 - Restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... gases as cooking fuels by 46 Code of Federal Regulations (CFR) part 147 must meet the requirements of § 121.240. The use of these fuels for cooking, heating, and lighting on ferry vessels is prohibited by... SYSTEMS AND EQUIPMENT Cooking and Heating § 121.202 Restrictions. (a) The use of gasoline for...

  8. 46 CFR 184.202 - Restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... use liquefied and non-liquefied gases as cooking fuels by 46 CFR part 147 must meet the requirements... CONTROL AND MISCELLANEOUS SYSTEMS AND EQUIPMENT Cooking and Heating § 184.202 Restrictions. (a) The use of gasoline for cooking, heating, or lighting is prohibited on all vessels. (b) Fireplaces or other...

  9. 46 CFR 121.202 - Restrictions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... gases as cooking fuels by 46 Code of Federal Regulations (CFR) part 147 must meet the requirements of § 121.240. The use of these fuels for cooking, heating, and lighting on ferry vessels is prohibited by... SYSTEMS AND EQUIPMENT Cooking and Heating § 121.202 Restrictions. (a) The use of gasoline for...

  10. 46 CFR 121.202 - Restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... gases as cooking fuels by 46 Code of Federal Regulations (CFR) part 147 must meet the requirements of § 121.240. The use of these fuels for cooking, heating, and lighting on ferry vessels is prohibited by... SYSTEMS AND EQUIPMENT Cooking and Heating § 121.202 Restrictions. (a) The use of gasoline for...

  11. 46 CFR 184.202 - Restrictions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... use liquefied and non-liquefied gases as cooking fuels by 46 CFR part 147 must meet the requirements... CONTROL AND MISCELLANEOUS SYSTEMS AND EQUIPMENT Cooking and Heating § 184.202 Restrictions. (a) The use of gasoline for cooking, heating, or lighting is prohibited on all vessels. (b) Fireplaces or other...

  12. 46 CFR 184.202 - Restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... use liquefied and non-liquefied gases as cooking fuels by 46 CFR part 147 must meet the requirements... CONTROL AND MISCELLANEOUS SYSTEMS AND EQUIPMENT Cooking and Heating § 184.202 Restrictions. (a) The use of gasoline for cooking, heating, or lighting is prohibited on all vessels. (b) Fireplaces or other...

  13. 46 CFR 121.202 - Restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... gases as cooking fuels by 46 Code of Federal Regulations (CFR) part 147 must meet the requirements of § 121.240. The use of these fuels for cooking, heating, and lighting on ferry vessels is prohibited by... SYSTEMS AND EQUIPMENT Cooking and Heating § 121.202 Restrictions. (a) The use of gasoline for...

  14. 38 CFR 1.462 - Confidentiality restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Sickle Cell Anemia § 1.462 Confidentiality restrictions. (a) General. The patient records to which §§ 1..., infection with the HIV, or sickle cell anemia may be acknowledged only if the patient's written consent is... with the HIV, or sickle cell anemia. (2) Any answer to a request for a disclosure of patient...

  15. 9 CFR 166.2 - General restrictions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false General restrictions. 166.2 Section 166.2 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... to the treatment of garbage that is to be fed to swine or the feeding thereof which are...

  16. 9 CFR 166.2 - General restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false General restrictions. 166.2 Section 166.2 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... to the treatment of garbage that is to be fed to swine or the feeding thereof which are...

  17. Mechanisms of Salmonella Typhi Host Restriction.

    PubMed

    Spanò, Stefania

    2016-01-01

    Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, a life-threatening bacterial infection that is very common in the developing world. Recent spread of antimicrobial resistant isolates of S. Typhi makes typhoid fever, a global public health risk. Despite being a common disease, still very little is known about the molecular mechanisms underlying typhoid fever and S. Typhi pathogenesis. In contrast to other Salmonellae, S. Typhi can only infect humans. The molecular bases of this human restriction are mostly unknown. Recent studies identified a novel pathway that contributes to S. Typhi human restriction and is required for killing S. Typhi in macrophages of nonsusceptible species. The small Rab GTPase Rab32 and its guanine nucleotide exchange factor BLOC-3 are the critical components of this pathway. These proteins were already well known as important regulators of intracellular membrane transport. In particular, they are central for the transport of enzymes that synthetize melanin in pigment cells. The recent findings that Rab32 and BLOC-3 are required for S. Typhi host restriction point out to a novel mechanism restricting the growth of bacterial pathogen, dependent on the transport of still unknown molecule(s) to the S. Typhi vacuole. The identification of this novel antimicrobial pathway constitutes a critical starting point to study molecular mechanisms killing bacterial pathogens and possibly identify novel antimicrobial molecules. PMID:27193549

  18. 50 CFR 665.264 - Gear restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Gear restrictions. 665.264 Section 665.264 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC Hawaii Fisheries § 665.264...

  19. 50 CFR 665.164 - Gear restrictions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Gear restrictions. 665.164 Section 665.164 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES IN THE WESTERN PACIFIC American Samoa Fisheries § 665.164...

  20. 32 CFR 171.3 - Restrictions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... WILDFIRE SUPPRESSION AIRCRAFT TRANSFER ACT OF 1996 § 171.3 Restrictions. Aircraft and aircraft parts sold under the Act shall be used only for wildfire suppression purposes and shall not be flown or removed... agreement to assist in wildfire suppression, or for other purposes jointly approved in advance, in...