Sample records for ion torrent pgm
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Hwang, Sang Mee; Lee, Ki Chan; Lee, Min Seob; Park, Kyoung Un
2018-01-01
Transition to next generation sequencing (NGS) for BRCA1 / BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1 /2. The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1 / BRCA2 . Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite. Fifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both false-positive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant. Ion PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.
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Wilkinson, Samuel L.; John, Shibu; Walsh, Roddy; Novotny, Tomas; Valaskova, Iveta; Gupta, Manu; Game, Laurence; Barton, Paul J R.; Cook, Stuart A.; Ware, James S.
2013-01-01
Background Molecular genetic testing is recommended for diagnosis of inherited cardiac disease, to guide prognosis and treatment, but access is often limited by cost and availability. Recently introduced high-throughput bench-top DNA sequencing platforms have the potential to overcome these limitations. Methodology/Principal Findings We evaluated two next-generation sequencing (NGS) platforms for molecular diagnostics. The protein-coding regions of six genes associated with inherited arrhythmia syndromes were amplified from 15 human samples using parallelised multiplex PCR (Access Array, Fluidigm), and sequenced on the MiSeq (Illumina) and Ion Torrent PGM (Life Technologies). Overall, 97.9% of the target was sequenced adequately for variant calling on the MiSeq, and 96.8% on the Ion Torrent PGM. Regions missed tended to be of high GC-content, and most were problematic for both platforms. Variant calling was assessed using 107 variants detected using Sanger sequencing: within adequately sequenced regions, variant calling on both platforms was highly accurate (Sensitivity: MiSeq 100%, PGM 99.1%. Positive predictive value: MiSeq 95.9%, PGM 95.5%). At the time of the study the Ion Torrent PGM had a lower capital cost and individual runs were cheaper and faster. The MiSeq had a higher capacity (requiring fewer runs), with reduced hands-on time and simpler laboratory workflows. Both provide significant cost and time savings over conventional methods, even allowing for adjunct Sanger sequencing to validate findings and sequence exons missed by NGS. Conclusions/Significance MiSeq and Ion Torrent PGM both provide accurate variant detection as part of a PCR-based molecular diagnostic workflow, and provide alternative platforms for molecular diagnosis of inherited cardiac conditions. Though there were performance differences at this throughput, platforms differed primarily in terms of cost, scalability, protocol stability and ease of use. Compared with current molecular genetic diagnostic tests for inherited cardiac arrhythmias, these NGS approaches are faster, less expensive, and yet more comprehensive. PMID:23861798
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Muñoz-Colmenero, Marta; Martínez, Jose Luis; Roca, Agustín; Garcia-Vazquez, Eva
2017-01-01
The Next Generation Sequencing methodologies are considered the next step within DNA-based methods and their applicability in different fields is being evaluated. Here, we tested the usefulness of the Ion Torrent Personal Genome Machine (PGM) in food traceability analyzing candies as a model of high processed foods, and compared the results with those obtained by PCR-cloning-sequencing (PCR-CS). The majority of samples exhibited consistency between methodologies, yielding more information and species per product from the PGM platform than PCR-CS. Significantly higher AT-content in sequences of the same species was also obtained from PGM. This together with some taxonomical discrepancies between methodologies suggest that the PGM platform is still pre-mature for its use in food traceability of complex highly processed products. It could be a good option for analysis of less complex food, saving time and cost per sample. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Quail, Michael A; Smith, Miriam; Coupland, Paul; Otto, Thomas D; Harris, Simon R; Connor, Thomas R; Bertoni, Anna; Swerdlow, Harold P; Gu, Yong
2012-07-24
Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent's PGM, Pacific Biosciences' RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform. All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.
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Yeo, Zhen Xuan; Wong, Joshua Chee Leong; Rozen, Steven G; Lee, Ann Siew Gek
2014-06-24
The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM's reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting insertions and deletions (indels), which may hinder its utility for clinical genetic testing. Recently, the proprietary analytical workflow for the Ion Torrent sequencer, Torrent Suite (TS), underwent a series of upgrades. We evaluated three major upgrades of TS by calling indels in the BRCA1 and BRCA2 genes. Our analysis revealed that false negative indels could be generated by TS under both default calling parameters and parameters adjusted for maximum sensitivity. However, indel calling with the same data using the open source variant callers, GATK and SAMtools showed that false negatives could be minimised with the use of appropriate bioinformatics analysis. Furthermore, we identified two variant calling measures, Quality-by-Depth (QD) and VARiation of the Width of gaps and inserts (VARW), which substantially reduced false positive indels, including non-homopolymer associated errors without compromising sensitivity. In our best case scenario that involved the TMAP aligner and SAMtools, we achieved 100% sensitivity, 99.99% specificity and 29% False Discovery Rate (FDR) in indel calling from all 23 samples, which is a good performance for mutation screening using PGM. New versions of TS, BWA and GATK have shown improvements in indel calling sensitivity and specificity over their older counterpart. However, the variant caller of TS exhibits a lower sensitivity than GATK and SAMtools. Our findings demonstrate that although indel calling from PGM sequences may appear to be noisy at first glance, proper computational indel calling analysis is able to maximize both the sensitivity and specificity at the single base level, paving the way for the usage of this technology for future clinical genetic testing.
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Comparison of Next-Generation Sequencing Systems
Liu, Lin; Li, Yinhu; Li, Siliang; Hu, Ni; He, Yimin; Pong, Ray; Lin, Danni; Lu, Lihua; Law, Maggie
2012-01-01
With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized. PMID:22829749
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Lu, Chaoxia; Wu, Wei; Xiao, Jifang; Meng, Yan; Zhang, Shuyang; Zhang, Xue
2013-06-01
To detect pathogenic mutations in Marfan syndrome (MFS) using an Ion Torrent Personal Genome Machine (PGM) and to validate the result of targeted next-generation semiconductor sequencing for the diagnosis of genetic disorders. Peripheral blood samples were collected from three MFS patients and a normal control with informed consent. Genomic DNA was isolated by standard method and then subjected to targeted sequencing using an Ion Ampliseq(TM) Inherited Disease Panel. Three multiplex PCR reactions were carried out to amplify the coding exons of 328 genes including FBN1, TGFBR1 and TGFBR2. DNA fragments from different samples were ligated with barcoded sequencing adaptors. Template preparation and emulsion PCR, and Ion Sphere Particles enrichment were carried out using an Ion One Touch system. The ion sphere particles were sequenced on a 318 chip using the PGM platform. Data from the PGM runs were processed using an Ion Torrent Suite 3.2 software to generate sequence reads. After sequence alignment and extraction of SNPs and indels, all the variants were filtered against dbSNP137. DNA sequences were visualized with an Integrated Genomics Viewer. The most likely disease-causing variants were analyzed by Sanger sequencing. The PGM sequencing has yielded an output of 855.80 Mb, with a > 100 × median sequencing depth and a coverage of > 98% for the targeted regions in all the four samples. After data analysis and database filtering, one known missense mutation (p.E1811K) and two novel premature termination mutations (p.E2264X and p.L871FfsX23) in the FBN1 gene were identified in the three MFS patients. All mutations were verified by conventional Sanger sequencing. Pathogenic FBN1 mutations have been identified in all patients with MFS, indicating that the targeted next-generation sequencing on the PGM sequencers can be applied for accurate and high-throughput testing of genetic disorders.
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Brown, Shawn P; Callaham, Mac A; Oliver, Alena K; Jumpponen, Ari
2013-12-01
Prescribed burning is a common management tool to control fuel loads, ground vegetation, and facilitate desirable game species. We evaluated soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia and utilized deep Internal Transcribed Spacer Region 1 (ITS1) amplicon sequencing afforded by the recent Ion Torrent Personal Genome Machine (PGM). These deep sequence data (19,000 + reads per sample after subsampling) indicate that frequent fires (3-year fire interval) shift soil fungus communities, whereas infrequent fires (6-year fire interval) permit system resetting to a state similar to that without prescribed fire. Furthermore, in nonmetric multidimensional scaling analyses, primarily ectomycorrhizal taxa were correlated with axes associated with long fire intervals, whereas soil saprobes tended to be correlated with the frequent fire recurrence. We conclude that (1) multiplexed Ion Torrent PGM analyses allow deep cost effective sequencing of fungal communities but may suffer from short read lengths and inconsistent sequence quality adjacent to the sequencing adaptor; (2) frequent prescribed fires elicit a shift in soil fungal communities; and (3) such shifts do not occur when fire intervals are longer. Our results emphasize the general responsiveness of these forests to management, and the importance of fire return intervals in meeting management objectives. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.
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Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng
2018-05-09
Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.
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King, Timothy L.; Eackles, Michael S.; Reshetnikov, Andrey N.
2015-01-01
Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated from two three-hour runs on the Ion Torrent PGM can generate a sufficient number of nuclear and mitochondrial markers to improve understanding of the evolutionary and ecological dynamics of non-model and in particular, invasive species.
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Comparison of the performance of Ion Torrent chips in noninvasive prenatal trisomy detection.
Wang, Yanlin; Wen, Zujia; Shen, Jiawei; Cheng, Weiwei; Li, Jun; Qin, Xiaolan; Ma, Duan; Shi, Yongyong
2014-07-01
Semiconductor high-throughput sequencing, represented by Ion Torrent PGM/Proton, proves to be feasible in the noninvasive prenatal diagnosis of fetal aneuploidies. It is commendable that, with less data and relevant cost also, an accurate result can be achieved owing to the high sensitivity and specificity of such kind of technology. We conducted a comparative analysis of the performance of four different Ion chips in detecting fetal chromosomal aneuploidies. Eight maternal plasma DNA samples, including four pregnancies with normal fetuses and four with trisomy 21 fetuses, were sequenced on Ion Torrent 314/316/318/PI chips, respectively. Results such as read mapped ratio, correlation coefficient and phred quality score were calculated and parallelly compared. All samples were correctly classified even with low-throughput chip, and, among the four chips, the 316 chip had the highest read mapped ratio, correlation coefficient, mean read length and phred quality score. All chips were well consistent with each other. Our results showed that all Ion chips are applicable in noninvasive prenatal fetal aneuploidy diagnosis. We recommend researchers or clinicians to use the appropriate chip with barcoding technology on the basis of the sample number.
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Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome.
Galindo-González, Leonardo; Pinzón-Latorre, David; Bergen, Erik A; Jensen, Dustin C; Deyholos, Michael K
2015-01-01
Detection of induced mutations is valuable for inferring gene function and for developing novel germplasm for crop improvement. Many reverse genetics approaches have been developed to identify mutations in genes of interest within a mutagenized population, including some approaches that rely on next-generation sequencing (e.g. exome capture, whole genome resequencing). As an alternative to these genome or exome-scale methods, we sought to develop a scalable and efficient method for detection of induced mutations that could be applied to a small number of target genes, using Ion Torrent technology. We developed this method in flax (Linum usitatissimum), to demonstrate its utility in a crop species. We used an amplicon-based approach in which DNA samples from an ethyl methanesulfonate (EMS)-mutagenized population were pooled and used as template in PCR reactions to amplify a region of each gene of interest. Barcodes were incorporated during PCR, and the pooled amplicons were sequenced using an Ion Torrent PGM. A pilot experiment with known SNPs showed that they could be detected at a frequency > 0.3% within the pools. We then selected eight genes for which we wanted to discover novel mutations, and applied our approach to screen 768 individuals from the EMS population, using either the Ion 314 or Ion 316 chips. Out of 29 potential mutations identified after processing the NGS reads, 16 mutations were confirmed using Sanger sequencing. The methodology presented here demonstrates the utility of Ion Torrent technology in detecting mutation variants in specific genome regions for large populations of a species such as flax. The methodology could be scaled-up to test >100 genes using the higher capacity chips now available from Ion Torrent.
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Lim, Yan Wei; Cuevas, Daniel A.; Silva, Genivaldo Gueiros Z.; Aguinaldo, Kristen; Dinsdale, Elizabeth A.; Haas, Andreas F.; Hatay, Mark; Sanchez, Savannah E.; Wegley-Kelly, Linda; Dutilh, Bas E.; Harkins, Timothy T.; Lee, Clarence C.; Tom, Warren; Sandin, Stuart A.; Smith, Jennifer E.; Zgliczynski, Brian; Vermeij, Mark J.A.; Rohwer, Forest
2014-01-01
Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines. PMID:25177534
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Lim, Yan Wei; Cuevas, Daniel A; Silva, Genivaldo Gueiros Z; Aguinaldo, Kristen; Dinsdale, Elizabeth A; Haas, Andreas F; Hatay, Mark; Sanchez, Savannah E; Wegley-Kelly, Linda; Dutilh, Bas E; Harkins, Timothy T; Lee, Clarence C; Tom, Warren; Sandin, Stuart A; Smith, Jennifer E; Zgliczynski, Brian; Vermeij, Mark J A; Rohwer, Forest; Edwards, Robert A
2014-01-01
Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.
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Draft genome sequence of a GES-5-producing Serratia marcescens isolated in southern Brazil.
Nodari, Carolina Silva; Siebert, Marina; Matte, Ursula da Silveira; Barth, Afonso Luís
Serratia marcescens is a Gram-negative rod intrinsically resistant to polymyxins and usually associated with wound, respiratory and urinary tract infections. The whole genome of the first GES-5-producing S. marcescens isolated from a Brazilian patient was sequenced using Ion Torrent PGM System. Besides bla GES-5 , we were able to identify genes encoding for other β-lactamases, for aminoglycoside modifying enzymes and for an efflux pump to tetracyclines. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.
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Behera, Bijay Kumar; Kumari, Kavita; Baisvar, Vishwamitra Singh; Rout, Ajaya Kumar; Pakrashi, Sudip; Paria, Prasenjet; Jena, J K
2017-01-01
In the present study, the complete mitochondrial genome sequence of Labeo gonius is reported using PGM sequencer (Ion Torrent). The complete mitogenome of L. gonius is obtained by the de novo sequences assembly of genomic reads using the Torrent Mapping Alignment Program (TMAP) which is 16 614 bp in length. The mitogenome of L. gonius comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and D-loop as control region along with gene order and organization, being similar to most of other fish mitogenomes of NCBI databases. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of Labeo fimbriatus, as reported earlier. The phylogenetic analysis of Cypriniformes depicted that their mitogenomes are closely related to each other. The complete mitogenome sequence of L. gonius would be helpful in understanding the population genetics, phylogenetics, and evolution of Indian Carps.
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de la Fuente, Gabriel; Belanche, Alejandro; Girwood, Susan E.; Pinloche, Eric; Wilkinson, Toby; Newbold, C. Jamie
2014-01-01
The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population. PMID:25051490
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Zhao, Yue; Cao, Hong; Song, Yindi; Feng, Yue; Ding, Xiaoxue; Pang, Mingjie; Zhang, Yunmei; Zhang, Hong; Ding, Jiahuan; Xia, Xueshan
2016-06-01
Inherited cardiomyopathy is the major cause of sudden cardiac death (SCD) and heart failure (HF). The disease is associated with extensive genetic heterogeneity; pathogenic mutations in cardiac sarcomere protein genes, cytoskeletal protein genes and nuclear envelope protein genes have been linked to its etiology. Early diagnosis is conducive to clinical monitoring and allows for presymptomatic interventions as needed. In the present study, the entire coding sequences and flanking regions of 12 major disease (cardiomyopathy)-related genes [namely myosin, heavy chain 7, cardiac muscle, β (MYH7); myosin binding protein C, cardiac (MYBPC3); lamin A/C (LMNA); troponin I type 3 (cardiac) (TNNI3); troponin T type 2 (cardiac) (TNNT2); actin, α, cardiac muscle 1 (ACTC1); tropomyosin 1 (α) (TPM1); sodium channel, voltage gated, type V alpha subunit (SCN5A); myosin, light chain 2, regulatory, cardiac, slow (MYL2); myosin, heavy chain 6, cardiac muscle, α (MYH6); myosin, light chain 3, alkali, ventricular, skeletal, slow (MYL3); and protein kinase, AMP-activated, gamma 2 non-catalytic subunit (PRKAG2)] in 8 patients with dilated cardiomyopathy (DCM) and in 8 patients with hypertrophic cardiomyopathy (HCM) were amplified and then sequenced using the Ion Torrent Personal Genome Machine (PGM) system. As a result, a novel heterozygous mutation (MYH7, p.Asn885Thr) and a variant of uncertain significance (TNNT2, p.Arg296His) were identified in 2 patients with HCM. These 2 missense mutations, which were absent in the samples obtained from the 200 healthy control subjects, altered the amino acid that was evolutionarily conserved among a number of vertebrate species; this illustrates that these 2 non-synonymous mutations play a role in the pathogenesis of HCM. Moreover, a double heterozygous mutation (PRKAG2, p.Gly100Ser plus MYH7, p.Arg719Trp) was identified in a patient with severe familial HCM, for the first time to the best of our knowledge. This patient provided us with more information regarding the genotype-phenotype correlation between mutations of MYH7 and PRKAG2. Taken together, these findings provide insight into the molecular mechanisms underlying inherited cardiomyopathy. The mutations identified in this study may be further investigated in the future in order to improve the diagnosis and treatment of patients with inherited cardiomyopathy. Furthermore, our findings indicated that sequencing using the Ion Torrent PGM system is a useful approach for the identification of pathogenic mutations associated with inherited cardiomyopathy, and it may be used for the risk evaluation of individuals with a possible susceptibility to inherited cardiomyopathy.
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Evaluation of Ion Torrent sequencing technology for rapid clinical human leucocyte antigen typing.
Guerra, Sandra G; Chong, Winnie; Brown, Colin J; Navarrete, Cristina V
2018-06-05
The development of techniques to define the human leucocyte antigen (HLA) region has proven to be challenging due to its high level of polymorphism. Within a clinical laboratory, a technique for high-resolution HLA typing, which is rapid and cost effective is essential. NGS has provided a rapid, high-resolution HLA typing solution, which has reduced the number of HLA ambiguities seen with other typing methods. In this study, the One Lambda NXType NGS kit was tested on the Ion Torrent PGM platform. A total of 362 registry donors from four ethnic populations (Europeans, South Asians, Africans and Chinese) were NGS HLA typed across 9-loci (HLA-A, -B, -C, -DRB1,-DRB345 -DQB1 and -DPB1). Concordance rates of 91%-98% were obtained (for HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1) when compared to historical PCR-SSO HLA types, and the identification of uncommon alleles such as A*24:07:01 and C*04:82 were observed. A turnaround time of four days was achieved for typing 44 samples. However, some limitations were observed; primer locations did not allow all ambiguities to be resolved for HLA Class II where Exon I and IV amplification are needed (HLA-DRB1*04:07:01/04:92, HLA-DRB1*09:01:02/*09:21 and HLA-DRB1*12:01:01/*12:10). This study has demonstrated high-resolution typing by NGS can be achieved in an acceptable turnaround time for a clinical laboratory; however, the Ion Torrent workflow has some technical limitations that should be addressed. © 2018 John Wiley & Sons Ltd.
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Behera, Bijay Kumar; Baisvar, Vishwamitra Singh; Kumari, Kavita; Rout, Ajaya Kumar; Pakrashi, Sudip; Paria, Prasenjet; Rao, A R; Rai, Anil
2017-03-01
In the present study, the complete mitochondrial genome sequence of Anabas testudineusis reported using PGM sequencer (Ion Torrent, Life Technologies, La Jolla, CA). The complete mitogenome of climbing perch, A. testudineusis obtained by the de novo sequences assembly of genomic reads using the Torrent Mapping Alignment Program (TMAP), which is 16 603 bp in length. The mitogenome of A. testudineus composed of 13 protein- coding genes, two rRNA, and 22 tRNAs. Here, 20 tRNAs genes showed typical clover leaf model, and D-Loop as the control region along with gene order and organization, being closely similar to Osphronemidae and most of other Perciformes fish mitogenomes of NCBI databases. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of earlier reported A. testudineus. The phylogenetic analysis of Anabantidae depicted that their mitogenomes are closely related to each other. The complete mitogenome sequence of A. testudineus would be helpful in understanding the population genetics, phylogenetics, and evolution of Anabantidae.
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Okamoto, Nobuhiko; Nakashima, Mitsuko; Tsurusaki, Yoshinori; Miyake, Noriko; Saitsu, Hirotomo; Matsumoto, Naomichi
2013-01-01
Next-generation sequencing (NGS) combined with enrichment of target genes enables highly efficient and low-cost sequencing of multiple genes for genetic diseases. The aim of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection in autism spectrum disorder (ASD). We assessed the performance of the bench-top Ion Torrent PGM and Illumina MiSeq platforms as optimized solutions for mutation detection, using microdroplet PCR-based enrichment of 62 ASD associated genes. Ten patients with known mutations were sequenced using NGS to validate the sensitivity of our method. The overall read quality was better with MiSeq, largely because of the increased indel-related error associated with PGM. The sensitivity of SNV detection was similar between the two platforms, suggesting they are both suitable for SNV detection in the human genome. Next, we used these methods to analyze 28 patients with ASD, and identified 22 novel variants in genes associated with ASD, with one mutation detected by MiSeq only. Thus, our results support the combination of target gene enrichment and NGS as a valuable molecular method for investigating rare variants in ASD. PMID:24066114
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Genomic characterization of Zika virus isolated from Indonesia.
Yudhaputri, Frilasita A; Trimarsanto, Hidayat; Perkasa, Aditya; Yohan, Benediktus; Haryanto, Sotianingsih; Wiyatno, Ageng; Soebandrio, Amin; Myint, Khin Saw; Ledermann, Jeremy P; Rosenberg, Ronald; Powers, Ann M; Sasmono, R Tedjo
2017-10-01
Zika virus (ZIKV) JMB-185 strain was isolated from a febrile patient in Jambi, Indonesia in 2014. To understand its genetic characteristics, we performed whole genome sequencing using the Ion Torrent PGM platform on the supernatant of the first passage. The phylogenetic analysis showed that the isolate was not closely related to the Brazilian ZIKV associated with microcephaly or isolates from the recent Singapore Zika outbreak. Molecular evolution analysis indicated that JMB-185 strain may have been circulating in the Southeast Asia region, including Indonesia since 2000. We observed high nucleotide sequence identity between Indonesia, Thailand, Singapore, and American strains although unique amino acid substitutions were also observed. This report provides information on the genomic characteristics of Indonesian ZIKV which may be used for further studies. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Zhang, Suhua; Bian, Yingnan; Chen, Anqi; Zheng, Hancheng; Gao, Yuzhen; Hou, Yiping; Li, Chengtao
2017-03-01
Utilizing massively parallel sequencing (MPS) technology for SNP testing in forensic genetics is becoming attractive because of the shortcomings of STR markers, such as their high mutation rates and disadvantages associated with the current PCR-CE method as well as its limitations regarding multiplex capabilities. MPS offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. In this study, we designed a customized SNP panel that includes 273 forensically relevant identity SNPs chosen from SNPforID, IISNP, and the HapMap database as well as previously related studies and evaluated the levels of genotyping precision, sequence coverage, sensitivity and SNP performance using the Ion Torrent PGM. In a concordant study of the custom MPS-SNP panel, only four MPS callings were missing due to coverage reads that were too low (<20), whereas the others were fully concordant with Sanger's sequencing results across the two control samples, that is, 9947A and 9948. The analyses indicated a balanced coverage among the included loci, with the exception of the 16 SNPs that were used to detect an inconsistent allele balance and/or lower coverage reads among 50 tested individuals from the Chinese HAN population and the above controls. With the exception of the 16 poorly performing SNPs, the sequence coverage obtained was extensive for the bulk of the SNPs, and only three Y-SNPs (rs16980601, rs11096432, rs3900) showed a mean coverage below 1000. Analyses of the dilution series of control DNA 9948 yielded reproducible results down to 1ng of DNA input. In addition, we provide an analysis tool for automated data quality control and genotyping checks, and we conclude that the SNP targets are polymorphic and independent in the Chinese HAN population. In summary, the evaluation of the sensitivity, accuracy and genotyping performance provides strong support for the application of MPS technology in forensic SNP analysis, and the assay offers a straightforward sample-to-genotype workflow that could be beneficial in forensic casework with respect to both individual identification and complex kinship issues. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
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Diversity of bacteria in ships ballast water as revealed by next generation DNA sequencing.
Brinkmeyer, Robin
2016-06-15
The bacterial diversity in ballast water from five general cargo ships calling at the Port of Houston was determined with ion semiconductor DNA sequencing (Ion Torrent PGM) of PCR amplified 16S rRNA genes. Phylogenetic analysis revealed that the composition of bacteria in ballast water did not resemble that of typical marine habitats or even open ocean waters where BWEs occur. The predominant group of bacteria in ships conducting BWEs was the Roseobacter clade within the Alphaproteobacteria. In contrast, Gammaproteobacteria were predominant in the ship that did not conduct a BWE. All the ships contained human, fish, and terrestrial plant pathogens as well as bacteria indicative of fecal or activated sludge contamination. Most of the 60 pathogens had not been detected in ballast water previously. Among these were the human pathogens Corynebacterium diptheriae and several Legionella species and the fish pathogens Francisella piscicida and Piscirickettsia salmonis. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Seneca, Sara; Vancampenhout, Kim; Van Coster, Rudy; Smet, Joél; Lissens, Willy; Vanlander, Arnaud; De Paepe, Boel; Jonckheere, An; Stouffs, Katrien; De Meirleir, Linda
2015-01-01
Next-generation sequencing (NGS), an innovative sequencing technology that enables the successful analysis of numerous gene sequences in a massive parallel sequencing approach, has revolutionized the field of molecular biology. Although NGS was introduced in a rather recent past, the technology has already demonstrated its potential and effectiveness in many research projects, and is now on the verge of being introduced into the diagnostic setting of routine laboratories to delineate the molecular basis of genetic disease in undiagnosed patient samples. We tested a benchtop device on retrospective genomic DNA (gDNA) samples of controls and patients with a clinical suspicion of a mitochondrial DNA disorder. This Ion Torrent Personal Genome Machine platform is a high-throughput sequencer with a fast turnaround time and reasonable running costs. We challenged the chemistry and technology with the analysis and processing of a mutational spectrum composed of samples with single-nucleotide substitutions, indels (insertions and deletions) and large single or multiple deletions, occasionally in heteroplasmy. The output data were compared with previously obtained conventional dideoxy sequencing results and the mitochondrial revised Cambridge Reference Sequence (rCRS). We were able to identify the majority of all nucleotide alterations, but three false-negative results were also encountered in the data set. At the same time, the poor performance of the PGM instrument in regions associated with homopolymeric stretches generated many false-positive miscalls demanding additional manual curation of the data.
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Luo, Wei; Nie, Zhulan; Zhan, Fanbin; Wei, Jie; Wang, Weimin; Gao, Zexia
2012-11-14
Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The H(o) ranged from 0.15 to 0.83, and H(e) ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers for non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis.
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Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers
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 available under a GNU General Public License version 3.0 (GPLv3) at https://github.com/tadkeys/tabsat/ and http://demo.platomics.com/. PMID:27467908
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Dong, Jiajia; Vicente, Natallia; Chintauan-Marquier, Ioana C; Ramadi, Cahyo; Dettai, Agnès; Robillard, Tony
2017-05-15
In the present study, we report the high-coverage complete mitochondrial genome (mitogenome) of the cricket Cardiodactylus muiri Otte, 2007. The mitogenome was sequenced using a long-PCR approach on an Ion Torrent Personal Genome Machine (PGM) for next generation sequencing technology. The total length of the amplified mitogenome is 16,328 bp, representing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one noncoding region (D-loop region). The new sets of long-PCR primers reported here are invaluable resources for future comparative evolutionary genomic studies in Orthopteran insects. The new mitogenome sequence is compared with published cricket mitogenomes. In the taxonomic part, we present new records for the species and describe life-history traits, habitat and male calling song of the species; based on observation of new material, the species Cardiodactylus buru Gorochov & Robillard, 2014 is synonymized under C. muiri.
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Muzny, Donna
2018-01-15
Donna Muzny on "En route to the clinic: Diagnostic sequencing applications using the Ion Torrent" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.
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Parson, Walther; Strobl, Christina; Huber, Gabriela; Zimmermann, Bettina; Gomes, Sibylle M.; Souto, Luis; Fendt, Liane; Delport, Rhena; Langit, Reina; Wootton, Sharon; Lagacé, Robert; Irwin, Jodi
2013-01-01
Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes (mtGenomes). In forensic genetics (partial) mtGenome information can be used to assign haplotypes to their phylogenetic backgrounds, which may, in turn, have characteristic geographic distributions that would offer useful information in a forensic case. In addition and perhaps even more relevant in the forensic context, haplogroup-specific patterns of mutations form the basis for quality control of mtDNA sequences. The current method for establishing (partial) mtDNA haplotypes is Sanger-type sequencing (STS), which is laborious, time-consuming, and expensive. With the emergence of Next Generation Sequencing (NGS) technologies, the body of available mtDNA data can potentially be extended much more quickly and cost-efficiently. Customized chemistries, laboratory workflows and data analysis packages could support the community and increase the utility of mtDNA analysis in forensics. We have evaluated the performance of mtGenome sequencing using the Personal Genome Machine (PGM) and compared the resulting haplotypes directly with conventional Sanger-type sequencing. A total of 64 mtGenomes (>1 million bases) were established that yielded high concordance with the corresponding STS haplotypes (<0.02% differences). About two-thirds of the differences were observed in or around homopolymeric sequence stretches. In addition, the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of alignment software would be desirable to facilitate the application of NGS in mtDNA forensic genetics. PMID:23948325
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Genetic mutation analysis of human gastric adenocarcinomas using ion torrent sequencing platform.
Xu, Zhi; Huo, Xinying; Ye, Hua; Tang, Chuanning; Nandakumar, Vijayalakshmi; Lou, Feng; Zhang, Dandan; Dong, Haichao; Sun, Hong; Jiang, Shouwen; Zhang, Guangchun; Liu, Zhiyuan; Dong, Zhishou; Guo, Baishuai; He, Yan; Yan, Chaowei; Wang, Lu; Su, Ziyi; Li, Yangyang; Gu, Dongying; Zhang, Xiaojing; Wu, Xiaomin; Wei, Xiaowei; Hong, Lingzhi; Zhang, Yangmei; Yang, Jinsong; Gong, Yonglin; Tang, Cuiju; Jones, Lindsey; Huang, Xue F; Chen, Si-Yi; Chen, Jinfei
2014-01-01
Gastric cancer is the one of the major causes of cancer-related death, especially in Asia. Gastric adenocarcinoma, the most common type of gastric cancer, is heterogeneous and its incidence and cause varies widely with geographical regions, gender, ethnicity, and diet. Since unique mutations have been observed in individual human cancer samples, identification and characterization of the molecular alterations underlying individual gastric adenocarcinomas is a critical step for developing more effective, personalized therapies. Until recently, identifying genetic mutations on an individual basis by DNA sequencing remained a daunting task. Recent advances in new next-generation DNA sequencing technologies, such as the semiconductor-based Ion Torrent sequencing platform, makes DNA sequencing cheaper, faster, and more reliable. In this study, we aim to identify genetic mutations in the genes which are targeted by drugs in clinical use or are under development in individual human gastric adenocarcinoma samples using Ion Torrent sequencing. We sequenced 737 loci from 45 cancer-related genes in 238 human gastric adenocarcinoma samples using the Ion Torrent Ampliseq Cancer Panel. The sequencing analysis revealed a high occurrence of mutations along the TP53 locus (9.7%) in our sample set. Thus, this study indicates the utility of a cost and time efficient tool such as Ion Torrent sequencing to screen cancer mutations for the development of personalized cancer therapy.
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Chen, Hui; Luthra, Rajyalakshmi; Goswami, Rashmi S; Singh, Rajesh R; Roy-Chowdhuri, Sinchita
2015-08-28
Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.
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Singh, K M; Reddy, B; Patel, A K; Panchasara, H; Parmar, N; Patel, A B; Shah, T M; Bhatt, V D; Joshi, C G
2014-12-01
Buffalo rumen microbiome experiences a variety of diet stress and represents reservoir of Dormancy and Sporulation genes. However, the information on genomic responses to such conditions is very limited. The Ion Torrent PGM next generation sequencing technology was used to characterize general microbial diversity and the repertoire of microbial genes present, including genes associated with Dormancy and Sporulation in Mehsani buffalo rumen metagenome. The research findings revealed the abundance of bacteria at the domain level and presence of Dormancy and Sporulation genes which were predominantly associated with the Clostridia and Bacilli taxa belonging to the phyla Firmicutes. Genes associated with Sporulation cluster and Sporulation orphans were increased from 50% to 100% roughage treatment, thereby promoting sporulation all along the treatments. The spore germination is observed to be the highest in the 75% roughage treatment both in the liquid and solid rumen fraction samples with respect to the decrease in the values of the genes associated with spore core dehydration, thereby facilitating spore core hydration which is necessary for spore germination.
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Indigenous species barcode database improves the identification of zooplankton
Yang, Jianghua; Zhang, Wanwan; Sun, Jingying; Xie, Yuwei; Zhang, Yimin; Burton, G. Allen; Yu, Hongxia
2017-01-01
Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here mitochondrial cytochrome c oxidase I (COI) fragment barcodes from 910 freshwater zooplankton specimens (87 morphospecies) were recovered by a high-throughput sequencing platform, Ion Torrent PGM. Intraspecific divergence of most zooplanktons was < 5%, except Branchionus leydign (Rotifer, 14.3%), Trichocerca elongate (Rotifer, 11.5%), Lecane bulla (Rotifer, 15.9%), Synchaeta oblonga (Rotifer, 5.95%) and Schmackeria forbesi (Copepod, 6.5%). Metabarcoding data of 28 environmental samples from Lake Tai were annotated by both an indigenous database and NCBI Genbank database. The indigenous database improved the taxonomic assignment of metabarcoding of zooplankton. Most zooplankton (81%) with barcode sequences in the indigenous database were identified by metabarcoding monitoring. Furthermore, the frequency and distribution of zooplankton were also consistent between metabarcoding and morphology identification. Overall, the indigenous database improved the taxonomic assignment of zooplankton. PMID:28977035
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SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.
Mariano, Diego C B; Pereira, Felipe L; Aguiar, Edgar L; Oliveira, Letícia C; Benevides, Leandro; Guimarães, Luís C; Folador, Edson L; Sousa, Thiago J; Ghosh, Preetam; Barh, Debmalya; Figueiredo, Henrique C P; Silva, Artur; Ramos, Rommel T J; Azevedo, Vasco A C
2016-12-15
The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .
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Lim, Eileen C P; Brett, Maggie; Lai, Angeline H M; Lee, Siew-Peng; Tan, Ee-Shien; Jamuar, Saumya S; Ng, Ivy S L; Tan, Ene-Choo
2015-12-14
Next-generation sequencing (NGS) has revolutionized genetic research and offers enormous potential for clinical application. Sequencing the exome has the advantage of casting the net wide for all known coding regions while targeted gene panel sequencing provides enhanced sequencing depths and can be designed to avoid incidental findings in adult-onset conditions. A HaloPlex panel consisting of 180 genes within commonly altered chromosomal regions is available for use on both the Ion Personal Genome Machine (PGM) and MiSeq platforms to screen for causative mutations in these genes. We used this Haloplex ICCG panel for targeted sequencing of 15 patients with clinical presentations indicative of an abnormality in one of the 180 genes. Sequencing runs were done using the Ion 318 Chips on the Ion Torrent PGM. Variants were filtered for known polymorphisms and analysis was done to identify possible disease-causing variants before validation by Sanger sequencing. When possible, segregation of variants with phenotype in family members was performed to ascertain the pathogenicity of the variant. More than 97% of the target bases were covered at >20×. There was an average of 9.6 novel variants per patient. Pathogenic mutations were identified in five genes for six patients, with two novel variants. There were another five likely pathogenic variants, some of which were unreported novel variants. In a cohort of 15 patients, we were able to identify a likely genetic etiology in six patients (40%). Another five patients had candidate variants for which further evaluation and segregation analysis are ongoing. Our results indicate that the HaloPlex ICCG panel is useful as a rapid, high-throughput and cost-effective screening tool for 170 of the 180 genes. There is low coverage for some regions in several genes which might have to be supplemented by Sanger sequencing. However, comparing the cost, ease of analysis, and shorter turnaround time, it is a good alternative to exome sequencing for patients whose features are suggestive of a genetic etiology involving one of the genes in the panel.
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Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.
2014-01-01
The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021
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Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L
2014-01-01
The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.
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Pillai, Suja; Gopalan, Vinod; Lo, Chung Y; Liew, Victor; Smith, Robert A; Lam, Alfred King Y
2017-02-01
The goal of this pilot study was to develop a customized, cost-effective amplicon panel (Ampliseq) for target sequencing in a cohort of patients with sporadic phaeochromocytoma/paraganglioma. Phaeochromocytoma/paragangliomas from 25 patients were analysed by targeted next-generation sequencing approach using an Ion Torrent PGM instrument. Primers for 15 target genes (NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127, MAX, MEN1, KIF1Bβ, EPAS1, CDKN2 & PHD2) were designed using ion ampliseq designer. Ion Reporter software and Ingenuity® Variant Analysis™ software (www.ingenuity.com/variants) from Ingenuity Systems were used to analysis these results. Overall, 713 variants were identified. The variants identified from the Ion Reporter ranged from 64 to 161 per patient. Single nucleotide variants (SNV) were the most common. Further annotation with the help of Ingenuity variant analysis revealed 29 of these 713variants were deletions. Of these, six variants were non-pathogenic and four were likely to be pathogenic. The remaining 19 variants were of uncertain significance. The most frequently altered gene in the cohort was KIF1B followed by NF1. Novel KIF1B pathogenic variant c.3375+1G>A was identified. The mutation was noted in a patient with clinically confirmed neurofibromatosis. Chromosome 1 showed the presence of maximum number of variants. Use of targeted next-generation sequencing is a sensitive method for the detecting genetic changes in patients with phaeochromocytoma/paraganglioma. The precise detection of these genetic changes helps in understanding the pathogenesis of these tumours. Copyright © 2016 Elsevier Inc. All rights reserved.
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Schorn, Michelle; Zettler, Judith; Noel, Joseph P.; Dorrestein, Pieter C.; Moore, Bradley S.; Kaysser, Leonard
2013-01-01
The epoxyketone proteasome inhibitors are an established class of therapeutic agents for the treatment of cancer. Their unique α′,β′-epoxyketone pharmacophore allows binding to the catalytic β-subunits of the proteasome with extraordinary specificity. Here we report the characterization of the first gene clusters for the biosynthesis of natural peptidyl-epoxyketones. The clusters for epoxomicin, the lead compound for the anti-cancer drug Kyprolis™, and for eponemycin were identified in the actinobacterial producer strains ATCC 53904 and Streptomyces hygroscopicus ATCC 53709, respectively, using a modified protocol for Ion Torrent PGM genome sequencing. Both gene clusters code for a hybrid non-ribosomal peptide synthetase/polyketide synthase multifunctional enzyme complex and homologous redox enzymes. Epoxomicin and eponemycin were heterologously produced in Streptomyces albus J1046 via whole pathway expression. Moreover, we employed mass spectral molecular networking for a new comparative metabolomics approach in a heterologous system and discovered a number of putative epoxyketone derivatives. With this study we have definitively linked epoxyketone proteasome inhibitors and their biosynthesis genes for the first time in any organism, which will now allow for their detailed biochemical investigation. PMID:24168704
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Gomes, Sibylle M; Bodner, Martin; Souto, Luis; Zimmermann, Bettina; Huber, Gabriela; Strobl, Christina; Röck, Alexander W; Achilli, Alessandro; Olivieri, Anna; Torroni, Antonio; Côrte-Real, Francisco; Parson, Walther
2015-02-14
Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice. In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya. The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.
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Anasagasti, Ander; Barandika, Olatz; Irigoyen, Cristina; Benitez, Bruno A; Cooper, Breanna; Cruchaga, Carlos; López de Munain, Adolfo; Ruiz-Ederra, Javier
2013-11-01
Retinitis Pigmentosa (RP) involves a group of genetically determined retinal diseases caused by a large number of mutations that result in rod photoreceptor cell death followed by gradual death of cone cells. Most cases of RP are monogenic, with more than 80 associated genes identified so far. The high number of genes and variants involved in RP, among other factors, is making the molecular characterization of RP a real challenge for many patients. Although HRM has been used for the analysis of isolated variants or single RP genes, as far as we are concerned, this is the first study that uses HRM analysis for a high-throughput screening of several RP genes. Our main goal was to test the suitability of HRM analysis as a genetic screening technique in RP, and to compare its performance with two of the most widely used NGS platforms, Illumina and PGM-Ion Torrent technologies. RP patients (n = 96) were clinically diagnosed at the Ophthalmology Department of Donostia University Hospital, Spain. We analyzed a total of 16 RP genes that meet the following inclusion criteria: 1) size: genes with transcripts of less than 4 kb; 2) number of exons: genes with up to 22 exons; and 3) prevalence: genes reported to account for, at least, 0.4% of total RP cases worldwide. For comparison purposes, RHO gene was also sequenced with Illumina (GAII; Illumina), Ion semiconductor technologies (PGM; Life Technologies) and Sanger sequencing (ABI 3130xl platform; Applied Biosystems). Detected variants were confirmed in all cases by Sanger sequencing and tested for co-segregation in the family of affected probands. We identified a total of 65 genetic variants, 15 of which (23%) were novel, in 49 out of 96 patients. Among them, 14 (4 novel) are probable disease-causing genetic variants in 7 RP genes, affecting 15 patients. Our HRM analysis-based study, proved to be a cost-effective and rapid method that provides an accurate identification of genetic RP variants. This approach is effective for medium sized (<4 kb transcript) RP genes, which constitute over 80% of the total of known RP genes.
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Anasagasti, Ander; Barandika, Olatz; Irigoyen, Cristina; Benitez, Bruno A; Cooper, Breanna; Cruchaga, Carlos; López de Munain, Adolfo; Ruiz-Ederra, Javier
2013-10-24
Retinitis Pigmentosa (RP) involves a group of genetically determined retinal diseases caused by a large number of mutations that result in rod photoreceptor cell death followed by gradual death of cone cells. Most cases of RP are monogenic, with more than 80 associated genes identified so far. The high number of genes and variants involved in RP, among other factors, is making the molecular characterization of RP a real challenge for many patients. Although HRM has been used for the analysis of isolated variants or single RP genes, as far as we are concerned, this is the first study that uses HRM analysis for a high-throughput screening of several RP genes. Our main goal was to test the suitability of HRM analysis as a genetic screening technique in RP, and to compare its performance with two of the most widely used NGS platforms, Illumina and PGM-Ion Torrent technologies. RP patients (n=96) were clinically diagnosed at the Ophthalmology Department of Donostia University Hospital, Spain. We analyzed a total of 16 RP genes that meet the following inclusion criteria: 1) size: genes with transcripts of less than 4 kb; 2) number of exons: genes with up to 22 exons; and 3) prevalence: genes reported to account for, at least, 0.4 % of total RP cases worldwide. For comparison purposes, RHO gene was also sequenced with Illumina (GAII; Illumina), Ion semiconductor technologies (PGM; Life Technologies) and Sanger sequencing (ABI 3130xl platform; Applied Biosystems). Detected variants were confirmed in all cases by Sanger sequencing and tested for co-segregation in the family of affected probands. We identified a total of 65 genetic variants, 15 of which (23%) were novel, in 49 out of 96 patients. Among them, 14 (4 novel) are probable disease-causing genetic variants in 7 RP genes, affecting 15 patients. Our HRM analysis-based study, proved to be a cost-effective and rapid method that provides an accurate identification of genetic RP variants. This approach is effective for medium sized (<4 kb transcript) RP genes, which constitute over 80% of the total of known RP genes. © 2013 Published by Elsevier Ltd.
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Shin, Saeam; Kim, Yoonjung; Chul Oh, Seoung; Yu, Nae; Lee, Seung-Tae; Rak Choi, Jong; Lee, Kyung-A
2017-05-23
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA). All expected 681 single nucleotide variants, 15 small indels, and three copy number variants were correctly called, except one common variant adjacent to a rare variant on the primer-binding site. The sensitivity, specificity, false positive rate, and accuracy for detection of single nucleotide variant and small indels of S5 XL sequencing were 99.85%, 100%, 0%, and 99.99% for the Torrent Variant Caller and 99.85%, 99.99%, 0.14%, and 99.99% for NextGENe, respectively. The reproducibility of variant calling was 100%, and the precision of variant frequency also showed good performance with coefficients of variation between 0.32 and 5.29%. We obtained highly accurate data through uniform and sufficient coverage depth over all target regions and through optimization of the bioinformatics pipeline. We confirmed that our platform is accurate and practical for diagnostic BRCA1/2 testing in a clinical laboratory.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Yu, Hao; Dranchak, Patricia; Li, Zhiru
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanismmore » placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.« less
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Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X.; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing
2016-01-01
Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems. PMID:27824160
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Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing
2016-11-08
Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.
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Fassan, Matteo; Rachiglio, Anna Maria; Cappellesso, Rocco; Antonello, Davide; Amato, Eliana; Mafficini, Andrea; Lambiase, Matilde; Esposito, Claudia; Bria, Emilio; Simonato, Francesca; Scardoni, Maria; Turri, Giona; Chilosi, Marco; Tortora, Giampaolo; Fassina, Ambrogio; Normanno, Nicola
2013-01-01
Identification of driver mutations in lung adenocarcinoma has led to development of targeted agents that are already approved for clinical use or are in clinical trials. Therefore, the number of biomarkers that will be needed to assess is expected to rapidly increase. This calls for the implementation of methods probing the mutational status of multiple genes for inoperable cases, for which limited cytological or bioptic material is available. Cytology specimens from 38 lung adenocarcinomas were subjected to the simultaneous assessment of 504 mutational hotspots of 22 lung cancer-associated genes using 10 nanograms of DNA and Ion Torrent PGM next-generation sequencing. Thirty-six cases were successfully sequenced (95%). In 24/36 cases (67%) at least one mutated gene was observed, including EGFR, KRAS, PIK3CA, BRAF, TP53, PTEN, MET, SMAD4, FGFR3, STK11, MAP2K1. EGFR and KRAS mutations, respectively found in 6/36 (16%) and 10/36 (28%) cases, were mutually exclusive. Nine samples (25%) showed concurrent alterations in different genes. The next-generation sequencing test used is superior to current standard methodologies, as it interrogates multiple genes and requires limited amounts of DNA. Its applicability to routine cytology samples might allow a significant increase in the fraction of lung cancer patients eligible for personalized therapy. PMID:24236184
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The Complete Exosome Workflow Solution: From Isolation to Characterization of RNA Cargo
Schageman, Jeoffrey; Li, Mu; Barta, Tim; Lea, Kristi; Gu, Jian; Magdaleno, Susan; Setterquist, Robert; Vlassov, Alexander V.
2013-01-01
Exosomes are small (30–150 nm) vesicles containing unique RNA and protein cargo, secreted by all cell types in culture. They are also found in abundance in body fluids including blood, saliva, and urine. At the moment, the mechanism of exosome formation, the makeup of the cargo, biological pathways, and resulting functions are incompletely understood. One of their most intriguing roles is intercellular communication—exosomes function as the messengers, delivering various effector or signaling macromolecules between specific cells. There is an exponentially growing need to dissect structure and the function of exosomes and utilize them for development of minimally invasive diagnostics and therapeutics. Critical to further our understanding of exosomes is the development of reagents, tools, and protocols for their isolation, characterization, and analysis of their RNA and protein contents. Here we describe a complete exosome workflow solution, starting from fast and efficient extraction of exosomes from cell culture media and serum to isolation of RNA followed by characterization of exosomal RNA content using qRT-PCR and next-generation sequencing techniques. Effectiveness of this workflow is exemplified by analysis of the RNA content of exosomes derived from HeLa cell culture media and human serum, using Ion Torrent PGM as a sequencing platform. PMID:24205503
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Panek, Marina; Čipčić Paljetak, Hana; Barešić, Anja; Perić, Mihaela; Matijašić, Mario; Lojkić, Ivana; Vranešić Bender, Darija; Krznarić, Željko; Verbanac, Donatella
2018-03-23
The information on microbiota composition in the human gastrointestinal tract predominantly originates from the analyses of human faeces by application of next generation sequencing (NGS). However, the detected composition of the faecal bacterial community can be affected by various factors including experimental design and procedures. This study evaluated the performance of different protocols for collection and storage of faecal samples (native and OMNIgene.GUT system) and bacterial DNA extraction (MP Biomedicals, QIAGEN and MO BIO kits), using two NGS platforms for 16S rRNA gene sequencing (Ilumina MiSeq and Ion Torrent PGM). OMNIgene.GUT proved as a reliable and convenient system for collection and storage of faecal samples although favouring Sutterella genus. MP provided superior DNA yield and quality, MO BIO depleted Gram positive organisms while using QIAGEN with OMNIgene.GUT resulted in greatest variability compared to other two kits. MiSeq and IT platforms in their supplier recommended setups provided comparable reproducibility of donor faecal microbiota. The differences included higher diversity observed with MiSeq and increased capacity of MiSeq to detect Akkermansia muciniphila, [Odoribacteraceae], Erysipelotrichaceae and Ruminococcaceae (primarily Faecalibacterium prausnitzii). The results of our study could assist the investigators using NGS technologies to make informed decisions on appropriate tools for their experimental pipelines.
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Zhang, Suhua; Bian, Yingnan; Zhang, Zheren; Zheng, Hancheng; Wang, Zheng; Zha, Lagabaiyila; Cai, Jifeng; Gao, Yuzhen; Ji, Chaoneng; Hou, Yiping; Li, Chengtao
2015-01-01
SNPs, abundant in human genome with lower mutation rate, are attractive to genetic application like forensic, anthropological and evolutionary studies. Universal SNPs showing little allelic frequency variation among populations while remaining highly informative for human identification were obtained from previous studies. However, genotyping tools target only dozens of markers simultaneously, limiting their applications. Here, 124 SNPs were simultaneous tested using Ampliseq technology with Ion Torrent PGM platform. Concordance study was performed with 2 reference samples of 9947A and 9948 between NGS and Sanger sequencing. Full concordance were obtained except genotype of rs576261 with 9947A. Parameter of FMAR (%) was introduced for NGS data analysis for the first time, evaluating allelic performance, sensitivity testing and mixture testing. FMAR values for accurate heterozygotes should be range from 50% to 60%, for homozygotes or Y-SNP should be above 90%. SNPs of rs7520386, rs4530059, rs214955, rs1523537, rs2342747, rs576261 and rs12997453 were recognized as poorly performing loci, either with allelic imbalance or with lower coverage. Sensitivity testing demonstrated that with DNA range from 10 ng-0.5 ng, all correct genotypes were obtained. For mixture testing, a clear linear correlation (R2 = 0.9429) between the excepted FMAR and observed FMAR values of mixtures was observed. PMID:26691610
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He, Guanglin; Wang, Zheng; Wang, Mengge; Luo, Tao; Liu, Jing; Zhou, You; Gao, Bo; Hou, Yiping
2018-06-04
Ancestry inference based on single nucleotide polymorphism (SNP) with marked allele frequency differences in diverse populations (called ancestry-informative SNP, AISNP) is rapidly developed with the technology advancements of massively parallel sequencing (MPS). Despite the decade of exploration and broad public interest in the peopling of East-Asians, the genetic landscape of Chinese Silk Road populations based on the AISNPs is still little known. In this work, 206 unrelated individuals from Chinese Uyghur and Hui populations were firstly genotyped by 165 AISNPs (The Precision ID Ancestry Panel) using the Ion Torrent PGM system. The ethnic origin of two investigated populations and population structures and genetic relationships were subsequently investigated. The 165 AISNPs panel not only can differentiate Uyghur and Hui populations but also has potential applications in individual identification. Comprehensive population comparisons and admixture estimates demonstrated a predominantly higher European-related ancestry (36.30%) in Uyghurs than Huis (3.66%). Overall, the Precision ID Ancestry Panel can provide good resolution at the intercontinental level, but has limitations on the genetic homogeneous populations, such as the Hui and Han. Additional population-specific AISNPs remain necessary to get better-scale resolution within geographically proximate populations in East Asia. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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Paparini, Andrea; Gofton, Alexander; Yang, Rongchang; White, Nicole; Bunce, Michael; Ryan, Una M
2015-01-01
Cryptosporidium is an important enteric pathogen that infects a wide range of humans and animals. Rapid and reliable detection and characterisation methods are essential for understanding the transmission dynamics of the parasite. Sanger sequencing, and high-throughput sequencing (HTS) on an Ion Torrent platform, were compared with each other for their sensitivity and accuracy in detecting and characterising 25 Cryptosporidium-positive human and animal faecal samples. Ion Torrent reads (n = 123,857) were obtained at both 18S rRNA and actin loci for 21 of the 25 samples. Of these, one isolate at the actin locus (Cattle 05) and three at the 18S rRNA locus (HTS 10, HTS 11 and HTS 12), suffered PCR drop-out (i.e. PCR failures) when using fusion-tagged PCR. Sanger sequences were obtained for both loci for 23 of the 25 samples and showed good agreement with Ion Torrent-based genotyping. Two samples both from pythons (SK 02 and SK 05) produced mixed 18S and actin chromatograms by Sanger sequencing but were clearly identified by Ion Torrent sequencing as C. muris. One isolate (SK 03) was typed as C. muris by Sanger sequencing but was identified as a mixed C. muris and C. tyzzeri infection by HTS. 18S rRNA Type B sequences were identified in 4/6 C. parvum isolates when deep sequenced but were undetected in Sanger sequencing. Sanger was cheaper than Ion Torrent when sequencing a small numbers of samples, but when larger numbers of samples are considered (n = 60), the costs were comparative. Fusion-tagged amplicon based approaches are a powerful way of approaching mixtures, the only draw-back being the loss of PCR efficiency on low-template samples when using primers coupled to MID tags and adaptors. Taken together these data show that HTS has excellent potential for revealing the "true" composition of species/types in a Cryptosporidium infection, but that HTS workflows need to be carefully developed to ensure sensitivity, accuracy and contamination are controlled. Copyright © 2015 Elsevier Inc. All rights reserved.
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IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data.
Baez-Ortega, Adrian; Lorenzo-Diaz, Fabian; Hernandez, Mariano; Gonzalez-Vila, Carlos Ignacio; Roda-Garcia, Jose Luis; Colebrook, Marcos; Flores, Carlos
2015-09-01
We introduce IonGAP, a publicly available Web platform designed for the analysis of whole bacterial genomes using Ion Torrent sequence data. Besides assembly, it integrates a variety of comparative genomics, annotation and bacterial classification routines, based on the widely used FASTQ, BAM and SRA file formats. Benchmarking with different datasets evidenced that IonGAP is a fast, powerful and simple-to-use bioinformatics tool. By releasing this platform, we aim to translate low-cost bacterial genome analysis for microbiological prevention and control in healthcare, agroalimentary and pharmaceutical industry applications. IonGAP is hosted by the ITER's Teide-HPC supercomputer and is freely available on the Web for non-commercial use at http://iongap.hpc.iter.es. mcolesan@ull.edu.es or cflores@ull.edu.es Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Onuț-Brännström, Ioana; Benjamin, Mitchell; Scofield, Douglas G; Heiðmarsson, Starri; Andersson, Martin G I; Lindström, Eva S; Johannesson, Hanna
2018-03-13
In this study, we explored the diversity of green algal symbionts (photobionts) in sympatric populations of the cosmopolitan lichen-forming fungi Thamnolia and Cetraria. We sequenced with both Sanger and Ion Torrent High-Throughput Sequencing technologies the photobiont ITS-region of 30 lichen thalli from two islands: Iceland and Öland. While Sanger recovered just one photobiont genotype from each thallus, the Ion Torrent data recovered 10-18 OTUs for each pool of 5 lichen thalli, suggesting that individual lichens can contain heterogeneous photobiont populations. Both methods showed evidence for photobiont sharing between Thamnolia and Cetraria on Iceland. In contrast, our data suggest that on Öland the two mycobionts associate with distinct photobiont communities, with few shared OTUs revealed by Ion Torrent sequencing. Furthermore, by comparing our sequences with public data, we identified closely related photobionts from geographically distant localities. Taken together, we suggest that the photobiont composition in Thamnolia and Cetraria results from both photobiont-mycobiont codispersal and local acquisition during mycobiont establishment and/or lichen growth. We hypothesize that this is a successful strategy for lichens to be flexible in the use of the most adapted photobiont for the environment.
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Roesch, Luiz Fernando Wurdig; Silveira, Rita C; Corso, Andréa L; Dobbler, Priscila Thiago; Mai, Volker; Rojas, Bruna S; Laureano, Álvaro M; Procianoy, Renato S
2017-01-01
Administering intravenous antibiotics during labor to women at risk for transmitting Group B Streptococcus (GBS) can prevent infections in newborns. However, the impact of intrapartum antibiotic prophylaxis on mothers' microbial community composition is largely unknown. We compared vaginal microbial composition in pregnant women experiencing preterm birth at ≤ 32 weeks gestation that received intrapartum antibiotic prophylaxis with that in controls. Microbiota in vaginal swabs collected shortly before delivery from GBS positive women that received penicillin intravenously during labor or after premature rupture of membranes was compared to controls. Microbiota was analyzed by 16S rRNA sequencing using the PGM Ion Torrent to determine the effects of penicillin use during hospitalization and GBS status on its composition. Penicillin administration was associated with an altered vaginal microbial community composition characterized by increased microbial diversity. Lactobacillus sp. contributed only 13.1% of the total community in the women that received penicillin compared to 88.1% in the controls. Streptococcus sp. were present in higher abundance in GBS positive woman compared to controls, with 60% of the total vaginal microbiota in severe cases identified as Streptococcus sp. Vaginal communities of healthy pregnant women were dominated by Lactobacillus sp. and contained low diversity, while Group B Streptococcus positive women receiving intrapartum antibiotic prophylaxis had a modified vaginal microbiota composition with low abundance of Lactobacillus but higher microbial diversity.
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Complete mitogenome of Asiatic lion resolves phylogenetic status within Panthera.
Bagatharia, Snehal B; Joshi, Madhvi N; Pandya, Rohan V; Pandit, Aanal S; Patel, Riddhi P; Desai, Shivangi M; Sharma, Anu; Panchal, Omkar; Jasmani, Falguni P; Saxena, Akshay K
2013-08-23
The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability.
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Complete mitogenome of asiatic lion resolves phylogenetic status within Panthera
2013-01-01
Background The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. Results The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. Conclusion This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability. PMID:23968279
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Hinsu, Ankit T; Parmar, Nidhi R; Nathani, Neelam M; Pandit, Ramesh J; Patel, Anand B; Patel, Amrutlal K; Joshi, Chaitanya G
2017-04-01
Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Validation of an NGS mutation detection panel for melanoma.
Reiman, Anne; Kikuchi, Hugh; Scocchia, Daniela; Smith, Peter; Tsang, Yee Wah; Snead, David; Cree, Ian A
2017-02-22
Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as immunotherapy. While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential advantages in turnaround time. We describe here an Ampliseq hotspot panel for melanoma for use with the IonTorrent Personal Genome Machine (PGM) which covers the mutations currently of most clinical interest. We have validated this in 151 cases of skin and uveal melanoma from our files, and correlated the data with PCR based assessment of BRAF status. There was excellent agreement, with few discrepancies, though NGS does have greater coverage and picks up some mutations that would be missed by PCR. However, these are often rare and of unknown significance for treatment. PCR methods are rapid, less time-consuming and less expensive than NGS, and could be used as triage for patients requiring more extensive diagnostic workup. The NGS panel described here is suitable for clinical use with formalin-fixed paraffin-embedded (FFPE) samples.
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[Whole Genome Sequencing of Human mtDNA Based on Ion Torrent PGM™ Platform].
Cao, Y; Zou, K N; Huang, J P; Ma, K; Ping, Y
2017-08-01
To analyze and detect the whole genome sequence of human mitochondrial DNA （mtDNA） by Ion Torrent PGM™ platform and to study the differences of mtDNA sequence in different tissues. Samples were collected from 6 unrelated individuals by forensic postmortem examination, including chest blood, hair, costicartilage, nail, skeletal muscle and oral epithelium. Amplification of whole genome sequence of mtDNA was performed by 4 pairs of primer. Libraries were constructed with Ion Shear™ Plus Reagents kit and Ion Plus Fragment Library kit. Whole genome sequencing of mtDNA was performed using Ion Torrent PGM™ platform. Sanger sequencing was used to determine the heteroplasmy positions and the mutation positions on HVⅠ region. The whole genome sequence of mtDNA from all samples were amplified successfully. Six unrelated individuals belonged to 6 different haplotypes. Different tissues in one individual had heteroplasmy difference. The heteroplasmy positions and the mutation positions on HVⅠ region were verified by Sanger sequencing. After a consistency check by the Kappa method, it was found that the results of mtDNA sequence had a high consistency in different tissues. The testing method used in present study for sequencing the whole genome sequence of human mtDNA can detect the heteroplasmy difference in different tissues, which have good consistency. The results provide guidance for the further applications of mtDNA in forensic science. Copyright© by the Editorial Department of Journal of Forensic Medicine
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Paasinen-Sohns, Aino; Koelzer, Viktor H; Frank, Angela; Schafroth, Julian; Gisler, Aline; Sachs, Melanie; Graber, Anne; Rothschild, Sacha I; Wicki, Andreas; Cathomas, Gieri; Mertz, Kirsten D
2017-03-01
Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material. Cohort I consisted of 59 diagnostic clinical samples from the daily routine submitted for molecular testing over a 4-month time period. Cohort II consisted of 39 archival melanoma samples that were up to 15years old. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent PGM sequencer. Sequencing datasets were analyzed using the Ion Reporter software. Genomic alterations were identified and validated by orthogonal conventional assays including pyrosequencing and immunohistochemistry. Sequencing results of both cohorts, including archival formalin-fixed, paraffin-embedded material stored up to 15years, were consistent with published variant frequencies. A concordance of 100% between established assays and OFA targeted NGS was observed. The OFA workflow enabled a turnaround of 3½ days. Taken together, OFA was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics. Thus, OFA has strong potential to become an important asset for precision oncology. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
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Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.
Churchill, Jennifer D; King, Jonathan L; Chakraborty, Ranajit; Budowle, Bruce
2016-09-01
Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories.
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Genome Sequencing of Steroid Producing Bacteria Using Ion Torrent Technology and a Reference Genome.
Sola-Landa, Alberto; Rodríguez-García, Antonio; Barreiro, Carlos; Pérez-Redondo, Rosario
2017-01-01
The Next-Generation Sequencing technology has enormously eased the bacterial genome sequencing and several tens of thousands of genomes have been sequenced during the last 10 years. Most of the genome projects are published as draft version, however, for certain applications the complete genome sequence is required.In this chapter, we describe the strategy that allowed the complete genome sequencing of Mycobacterium neoaurum NRRL B-3805, an industrial strain exploited for steroid production, using Ion Torrent sequencing reads and the genome of a close strain as the reference. This protocol can be applied to analyze the genetic variations between closely related strains; for example, to elucidate the point mutations between a parental strain and a random mutagenesis-derived mutant.
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Zhang, Jin; Tang, Ying; Teng, Liumei; Lu, Minghua; Tang, Dianping
2015-06-15
A simple and low-cost DNA sensing platform based on Pb(2+)-specific DNAzyme-modified microplate was successfully developed for highly sensitive monitoring of lead ion (Pb(2+), one kind of toxic heavy metal ion) in the environmental samples coupling with a portable personal glucometer (PGM)-based detection mode. The detection cell was first prepared simply by means of immobilizing the DNAzyme on the streptavidin-modified microplate. Gold nanoparticle labeled with single-stranded DNA and invertase (Enz-AuNP-DNA) was utilized as the signal-transduction tag to produce PGM substrate (glucose). Upon addition of lead ion into the microplate, the substrate strand of the immobilized DNAzyme was catalytically cleaved by target Pb(2+), and the newly generated single-strand DNA in the microplate could hybridize again with the single-stranded DNA on the Enz-AuNP-DNA. Accompanying with the Enz-AuNP-DNA, the carried invertase could convert sucrose into glucose. The as-produced glucose could be monitored by using a widely accessible PGM for in situ amplified digital readout. Based on Enz-AuNP-DNA amplification strategy, as low as 1.0 pM Pb(2+) could be detected under the optimal conditions. Moreover, the methodology also showed good reproducibility and high selectivity toward target Pb(2+) against other metal ions because of highly specific Pb(2+)-dependent DNAzyme, and was applicable for monitoring Pb(2+) in the naturally contaminated sewage and spiked drinking water samples. Copyright © 2015 Elsevier B.V. All rights reserved.
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Roesch, Luiz Fernando Wurdig; Silveira, Rita C.; Corso, Andréa L.; Dobbler, Priscila Thiago; Mai, Volker; Rojas, Bruna S.; Laureano, Álvaro M.; Procianoy, Renato S.
2017-01-01
Background Administering intravenous antibiotics during labor to women at risk for transmitting Group B Streptococcus (GBS) can prevent infections in newborns. However, the impact of intrapartum antibiotic prophylaxis on mothers’ microbial community composition is largely unknown. We compared vaginal microbial composition in pregnant women experiencing preterm birth at ≤ 32 weeks gestation that received intrapartum antibiotic prophylaxis with that in controls. Methods Microbiota in vaginal swabs collected shortly before delivery from GBS positive women that received penicillin intravenously during labor or after premature rupture of membranes was compared to controls. Microbiota was analyzed by 16S rRNA sequencing using the PGM Ion Torrent to determine the effects of penicillin use during hospitalization and GBS status on its composition. Results Penicillin administration was associated with an altered vaginal microbial community composition characterized by increased microbial diversity. Lactobacillus sp. contributed only 13.1% of the total community in the women that received penicillin compared to 88.1% in the controls. Streptococcus sp. were present in higher abundance in GBS positive woman compared to controls, with 60% of the total vaginal microbiota in severe cases identified as Streptococcus sp. Conclusions Vaginal communities of healthy pregnant women were dominated by Lactobacillus sp. and contained low diversity, while Group B Streptococcus positive women receiving intrapartum antibiotic prophylaxis had a modified vaginal microbiota composition with low abundance of Lactobacillus but higher microbial diversity. PMID:28178310
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Spectrum of Mutations in Hypertrophic Cardiomyopathy Genes Among Tunisian Patients.
Jaafar, Nawel; Gómez, Juan; Kammoun, Ikram; Zairi, Ihsen; Amara, Wael Ben; Kachboura, Salem; Kraiem, Sondes; Hammami, Mohamed; Iglesias, Sara; Alonso, Belén; Coto, Eliecer
2016-11-01
Hypertrophic cardiomyopathy (HCM) is a common cardiac genetic disorder associated with heart failure and sudden death. Mutations in the cardiac sarcomere genes are found in approximately half of HCM patients and are more common among cases with a family history of the disease. Data about the mutational spectrum of the sarcomeric genes in HCM patients from Northern Africa are limited. The population of Tunisia is particularly interesting due to its Berber genetic background. As founder mutations have been reported in other disorders. We performed semiconductor chip (Ion Torrent PGM) next generation sequencing of the nine main sarcomeric genes (MYH7, MYBPC3, TNNT2, TNNI3, ACTC1, TNNC1, MYL2, MYL3, TPM1) as well as the recently identified as an HCM gene, FLNC, in 45 Tunisian HCM patients. We found sarcomere gene polymorphisms in 12 patients (27%), with MYBPC3 and MYH7 representing 83% (10/12) of the mutations. One patient was homozygous for a new MYL3 mutation and two were double MYBPC3 + MYH7 mutation carriers. Screening of the FLNC gene identified three new mutations, which points to FLNC mutations as an important cause of HCM among Tunisians. The mutational background of HCM in Tunisia is heterogeneous. Unlike other Mendelian disorders, there were no highly prevalent mutations that could explain most of the cases. Our study also suggested that FLNC mutations may play a role on the risk for HCM among Tunisians.
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Nessner Kavamura, Vanessa; Taketani, Rodrigo Gouvêa; Lançoni, Milena Duarte; Andreote, Fernando Dini; Mendes, Rodrigo; Soares de Melo, Itamar
2013-01-01
We used the T-RFLP technique combined with Ion Torrent (PGM) sequencing of 16S rRNA and multivariate analysis to study the structure of bulk soil and rhizosphere bacterial communities of a cactus, Cereus jamacaru, from the Brazilian Caatinga biome, which is unique to Brazil. The availability of water shapes the rhizosphere communities, resulting in different patterns during the rainy and dry seasons. Taxonomic approaches and statistical analysis revealed that the phylum Actinobacteria strongly correlated with the dry season, while samples from the rainy season exhibited a strong correlation with the phylum Proteobacteria for rhizosphere samples and with the phyla Bacteroidetes, Firmicutes, Lentisphaerae, and Tenericutes for bulk soil samples. The STAMP software also indicated that the phylum Bacteroidetes, as well as two classes in the Proteobacteria phylum (γ and δ), were the most significant ones during the rainy season. The average abundance of the phylum Actinobacteria and the genus Bacillus was significantly greater during the dry season. Some significant genera found during the dry season might reflect their tolerance to the extreme conditions found in the Caatinga biome. They may also indicate the ecological function that microorganisms play in providing plants with some degree of tolerance to water stress or in assisting in their development through mechanisms of growth promotion. Alterations in microbial communities can be due to the different abilities of native microorganisms to resist and adapt to environmental changes.
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Nessner Kavamura, Vanessa; Taketani, Rodrigo Gouvêa; Lançoni, Milena Duarte; Andreote, Fernando Dini; Mendes, Rodrigo; Soares de Melo, Itamar
2013-01-01
We used the T-RFLP technique combined with Ion Torrent (PGM) sequencing of 16S rRNA and multivariate analysis to study the structure of bulk soil and rhizosphere bacterial communities of a cactus, Cereus jamacaru, from the Brazilian Caatinga biome, which is unique to Brazil. The availability of water shapes the rhizosphere communities, resulting in different patterns during the rainy and dry seasons. Taxonomic approaches and statistical analysis revealed that the phylum Actinobacteria strongly correlated with the dry season, while samples from the rainy season exhibited a strong correlation with the phylum Proteobacteria for rhizosphere samples and with the phyla Bacteroidetes, Firmicutes, Lentisphaerae, and Tenericutes for bulk soil samples. The STAMP software also indicated that the phylum Bacteroidetes, as well as two classes in the Proteobacteria phylum (γ and δ), were the most significant ones during the rainy season. The average abundance of the phylum Actinobacteria and the genus Bacillus was significantly greater during the dry season. Some significant genera found during the dry season might reflect their tolerance to the extreme conditions found in the Caatinga biome. They may also indicate the ecological function that microorganisms play in providing plants with some degree of tolerance to water stress or in assisting in their development through mechanisms of growth promotion. Alterations in microbial communities can be due to the different abilities of native microorganisms to resist and adapt to environmental changes. PMID:24069212
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Visi, David K; D'Souza, Nandika; Ayre, Brian G; Webber Iii, Charles L; Allen, Michael S
2013-05-01
The microbial communities associated with kenaf (Hibiscus cannabinus) plant fibers during retting were determined in an effort to identify possible means of accelerating this process for industrial scale-up. Microbial communities were identified by semiconductor sequencing of 16S rRNA gene amplicons from DNA harvested from plant-surface associated samples and analyzed using an Ion Torrent PGM. The communities were sampled after 96 h from each of three different conditions, including amendments with pond water, sterilized pond water, or with a mixture of pectinolytic bacterial isolates. Additionally, plants from two different sources and having different pretreatment conditions were compared. We report that the best retting communities are dominated by members of the order Clostridiales. These bacteria appear to be naturally associated with the plant material, although slight variations between source materials were found. Additionally, heavy inoculations of pectinolytic bacteria established themselves and in addition their presence facilitated the rapid dominance of the original plant-associated Clostridiales. These data suggest that members of the order Clostridiales dominate the community and are most closely associated with efficient and effective retting. The results further suggest that establishment of the community structure is first driven by the switch to anaerobic conditions, and subsequently by possible competition for nitrogen. These findings reveal important bacterial groups involved in fiber retting, and suggest mechanisms for the manipulation of the community and retting efficiency by modifying nutrient availability.
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Tardif, Stacie; Yergeau, Étienne; Tremblay, Julien; Legendre, Pierre; Whyte, Lyle G.; Greer, Charles W.
2016-01-01
The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv. FishCreek, and Salix miyabeana cv. SX67) growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) regions were amplified and sequenced using an Ion Torrent Personal Genome Machine (PGM). Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial, and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders, and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root, and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment, and thus, protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology. PMID:27660624
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Zhao, Hui; Zhao, LingZhai; Jiang, Tao; Li, XiaoFeng; Fan, Hang; Hong, WenXin; Zhang, Yu; Zhu, Qin; Ye, Qing; Tong, YiGang; Cao, WuChun; Zhang, FuChun; Qin, ChengFeng
2014-12-01
Dengue has been well recognized as a global public health threat, but only sporadic epidemics and imported cases were reported in recent decades in China. Since July 2014, an unexpected large dengue outbreak has occurred in Guangdong province, China, resulting in more than 40000 patients including six deaths. To clarify and characterize the causative agent of this outbreak, the acute phase serum from a patient diagnosed with severe dengue was subjected to virus isolation and high-throughput sequencing (HTS). Traditional real-time RT-PCR and HTS with Ion Torrent PGM detected the presence of dengue virus serotype 2 (DENV-2). A clinical DENV-2 isolate GZ05/2014 was obtained by culturing the patient serum in mosquito C6/36 cells. The complete genome of GZ05/2014 was determined and deposited in GenBank under the access number KP012546. Phylogenetic analysis based on the complete envelope gene showed that the newly DENV-2 isolate belonged to Cosmopolitan genotype and clustered closely with other Guangdong strains isolated in the past decade. No amino acid mutations that are obviously known to increase virulence or replication were identified throughout the genome of GZ05/2014. The high homology of Guangdong DENV-2 strains indicated the possibility of establishment of local DENV-2 circulation in Guangdong, China. These results help clarify the origin of this epidemic and predict the future status of dengue in China.
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Leydet, Brian F.; Ting Liang, Fang
2015-01-01
In 1982, Borrelia burgdorferi sensu stricto (ss) was identified as the aetiological agent of Lyme disease. Since then an increasing number of Borrelia burgdorferi sensu lato (sl) species have been isolated in the United States. To date, many of these species remain understudied despite mounting evidence associating them with human illness. Borrelia bissettii is a spirochaete closely related to B. burgdorferi that has been loosely associated with human illness. Using an experimental murine infection model, we compared the infectivity and humoral immune response with a North American isolate of B. bissettii and B. burgdorferi using culture, molecular and serological methods. The original B. bissettii cultures were unable to infect immunocompetent mice, but were confirmed to be infectious after adaptation in immunodeficient animals. B. bissettii infection resulted in spirochaete burdens similar to B. burgdorferi in skin, heart and bladder whereas significantly lower burdens were observed in the joint tissues. B. bissettii induced an antibody response similar to B. burgdorferi as measured by both immunoblotting and the C6 ELISA. Additionally, this isolate of B. bissettii was sequenced on the Ion Torrent PGM, which successfully identified many genes orthologous to mammalian virulence factors described in B. burgdorferi. Similarities seen between both infections in this well-characterized murine model contribute to our understanding of the potential pathogenic nature of B. bissettii. Infection dynamics of B. bissettii, and especially the induced humoral response, are similar to B. burgdorferi, suggesting this species may contribute to the epidemiology of human borreliosis. PMID:26419825
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Jenkins, David
2018-01-10
David Jenkins on "Ion Torrent semiconductor sequencing allows rapid, low-cost sequencing of the human exome" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Jenkins, David
David Jenkins on "Ion Torrent semiconductor sequencing allows rapid, low-cost sequencing of the human exome" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.
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Yergeau, Etienne; Lawrence, John R.; Sanschagrin, Sylvie; Waiser, Marley J.; Korber, Darren R.
2012-01-01
The Athabasca oil sands deposit is the largest reservoir of crude bitumen in the world. Recently, the soaring demand for oil and the availability of modern bitumen extraction technology have heightened exploitation of this reservoir and the potential unintended consequences of pollution in the Athabasca River. The main objective of the present study was to evaluate the potential impacts of oil sands mining on neighboring aquatic microbial community structure. Microbial communities were sampled from sediments in the Athabasca River and its tributaries as well as in oil sands tailings ponds. Bacterial and archaeal 16S rRNA genes were amplified and sequenced using next-generation sequencing technology (454 and Ion Torrent). Sediments were also analyzed for a variety of chemical and physical characteristics. Microbial communities in the fine tailings of the tailings ponds were strikingly distinct from those in the Athabasca River and tributary sediments. Microbial communities in sediments taken close to tailings ponds were more similar to those in the fine tailings of the tailings ponds than to the ones from sediments further away. Additionally, bacterial diversity was significantly lower in tailings pond sediments. Several taxonomic groups of Bacteria and Archaea showed significant correlations with the concentrations of different contaminants, highlighting their potential as bioindicators. We also extensively validated Ion Torrent sequencing in the context of environmental studies by comparing Ion Torrent and 454 data sets and by analyzing control samples. PMID:22923391
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Allali, Imane; Arnold, Jason W; Roach, Jeffrey; Cadenas, Maria Belen; Butz, Natasha; Hassan, Hosni M; Koci, Matthew; Ballou, Anne; Mendoza, Mary; Ali, Rizwana; Azcarate-Peril, M Andrea
2017-09-13
Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150-199 for GS FLX+ and bases 90-99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies.
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Al-Allaf, Faisal A; Athar, Mohammad; Abduljaleel, Zainularifeen; Taher, Mohiuddin M; Khan, Wajahatullah; Ba-Hammam, Faisal A; Abalkhail, Hala; Alashwal, Abdullah
2015-07-01
Familial hypercholesterolemia (FH) is an autosomal dominant inherited disease characterized by elevated plasma low-density lipoprotein cholesterol (LDL-C). It is an autosomal dominant disease, caused by variants in Ldlr, ApoB or Pcsk9, which results in high levels of LDL-cholesterol (LDL-C) leading to early coronary heart disease. Sequencing whole genome for screening variants for FH are not suitable due to high cost. Hence, in this study we performed targeted customized sequencing of FH 12 genes (Ldlr, ApoB, Pcsk9, Abca1, Apoa2, Apoc3, Apon2, Arh, Ldlrap1, Apoc2, ApoE, and Lpl) that have been implicated in the homozygous phenotype of a proband pedigree to identify candidate variants by NGS Ion torrent PGM. Only three genes (Ldlr, ApoB, and Pcsk9) were found to be highly associated with FH based on the variant rate. The results showed that seven deleterious variants in Ldlr, ApoB, and Pcsk9 genes were pathological and were clinically significant based on predictions identified by SIFT and PolyPhen. Targeted customized sequencing is an efficient technique for screening variants among targeted FH genes. Final validation of seven deleterious variants conducted by capillary resulted to only one novel variant in Ldlr gene that was found in exon 14 (c.2026delG, p. Gly676fs). The variant found in Ldlr gene was a novel heterozygous variant derived from a male in the proband. Copyright © 2015 Elsevier B.V. All rights reserved.
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Beaton, Ainsley; Lood, Cédric; Cunningham-Oakes, Edward; MacFadyen, Alison; Mullins, Alex J; Bestawy, Walid El; Botelho, João; Chevalier, Sylvie; Dalzell, Chloe; Dolan, Stephen K; Faccenda, Alberto; Ghequire, Maarten G K; Higgins, Steven; Kutschera, Alexander; Murray, Jordan; Redway, Martha; Salih, Talal; Smith, Brian A; Smits, Nathan; Thomson, Ryan; Woodcock, Stuart; Cornelis, Pierre; Lavigne, Rob; van Noort, Vera
2018-01-01
Abstract Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline. PMID:29579234
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A NEW MASS SPECTROMETRIC TECHNIQUE FOR ...
Most organic compounds are not found in mass spectral libraries and cannot be easily identified from low resolution mass spectra. Ion Composition Elucidation (ICE) utilizes selected ion recording with a double focusing mass spectrometer in a new way to determine exact masses and relative abundances of ions more rapidly and with greater accuracy than by full scanning. These measurements are made as analytes from a complex mixture elute from a GC column into the ion source. The exact masses and relative abundances establish the elemental compositions of the ions in a mass spectrum, which limits the possible identify of the compound sufficiently to make searches of the chemical and commercial literature feasible. ICE has two facets: Mass Peak Profiling from Selected Ion Recording Data (MPPSIRD) for data acquisition and a Profile Generation Model (PGM) for automated data interpretation. NTPSIRD and the PGM will be described and several applications of ICE will be shown: tentative identification of a compound that provided a mass spectrum with I I plausible NIST library matches; confirmation of the presence of temazepam, a sedative and one of the 200 most prescribed drugs in 1999. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this T
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The removal of precious metals by conductive polymer filtration
DOE Office of Scientific and Technical Information (OSTI.GOV)
Cournoyer, M.E.
The growing demand for platinum-group metals (PGM) within the DOE complex and in industry, the need for modern and clean processes, and the increasing volume of low-grade material for secondary PGM recovery has a direct impact on the industrial practice of recovering and refining precious metals. There is a tremendous need for advanced metal ion recovery and waste minimization techniques, since the currently used method of precipitation-dissolution is inadequate. Los Alamos has an integrated program in ligand-design and separations chemistry which has developed and evaluated a series of water- soluble metal-binding polymers for recovering actinides and toxic metals from varietymore » of process streams. A natural extension of this work is to fabricate these metal-selective polymers into membrane based separation unites, i.e., hollow-fiber membranes. In the present investigation, the material for a novel hollow-fiber membrane is characterized and its selectivity for PGM reported. Energy and waste savings and economic competitiveness are also described.« less
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Heeke, Simon; Hofman, Véronique; Long-Mira, Elodie; Lespinet, Virginie; Lalvée, Salomé; Bordone, Olivier; Ribeyre, Camille; Tanga, Virginie; Benzaquen, Jonathan; Leroy, Sylvie; Cohen, Charlotte; Mouroux, Jérôme; Marquette, Charles Hugo; Ilié, Marius; Hofman, Paul
2018-03-21
Background : With the integration of various targeted therapies into the clinical management of patients with advanced lung adenocarcinoma, next-generation sequencing (NGS) has become the technology of choice and has led to an increase in simultaneously interrogated genes. However, the broader adoption of NGS for routine clinical practice is still hampered by sophisticated workflows, complex bioinformatics analysis and medical interpretation. Therefore, the performance of the novel QIAGEN GeneReader NGS system was compared to an in-house ISO-15189 certified Ion PGM NGS platform. Methods : Clinical samples from 90 patients (60 Retrospectively and 30 Prospectively) with lung adenocarcinoma were sequenced with both systems. Mutations were analyzed and EGFR , KRAS , BRAF , NRAS , ALK , PIK3CA and ERBB2 genes were compared and sampling time and suitability for clinical testing were assessed. Results : Both sequencing systems showed perfect concordance for the overlapping genes. Correlation of allele frequency was r ² = 0.93 for the retrospective patients and r ² = 0.81 for the prospective patients. Hands-on time and total run time were shorter using the PGM system, while the GeneReader platform provided good traceability and up-to-date interpretation of the results. Conclusion : We demonstrated the suitability of the GeneReader NGS system in routine practice in a clinical pathology laboratory setting.
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Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S.; Nielsen, Eva M.; Aarestrup, Frank M.
2014-01-01
Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens. PMID:24574290
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Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing
Sahoo, Malaya K.; Tan, Susanna K.; Chen, Sharon F.; Kapusinszky, Beatrix; Concepcion, Katherine R.; Kjelson, Lynn; Mallempati, Kalyan; Farina, Heidi M.; Fernández-Viña, Marcelo; Tyan, Dolly; Grimm, Paul C.; Anderson, Matthew W.; Concepcion, Waldo
2015-01-01
BK virus (BKV) infection causing end-organ disease remains a formidable challenge to the hematopoietic cell transplant (HCT) and kidney transplant fields. As BKV-specific treatments are limited, immunologic-based therapies may be a promising and novel therapeutic option for transplant recipients with persistent BKV infection. Here, we describe a whole-genome, deep-sequencing methodology and bioinformatics pipeline that identify BKV variants across the genome and at BKV-specific HLA-A2-, HLA-B0702-, and HLA-B08-restricted CD8 T-cell epitopes. BKV whole genomes were amplified using long-range PCR with four inverse primer sets, and fragmentation libraries were sequenced on the Ion Torrent Personal Genome Machine (PGM). An error model and variant-calling algorithm were developed to accurately identify rare variants. A total of 65 samples from 18 pediatric HCT and kidney recipients with quantifiable BKV DNAemia underwent whole-genome sequencing. Limited genetic variation was observed. The median number of amino acid variants identified per sample was 8 (range, 2 to 37; interquartile range, 10), with the majority of variants (77%) detected at a frequency of <5%. When normalized for length, there was no statistical difference in the median number of variants across all genes. Similarly, the predominant virus population within samples harbored T-cell epitopes similar to the reference BKV strain that was matched for the BKV genotype. Despite the conservation of epitopes, low-level variants in T-cell epitopes were detected in 77.7% (14/18) of patients. Understanding epitope variation across the whole genome provides insight into the virus-immune interface and may help guide the development of protocols for novel immunologic-based therapies. PMID:26202116
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Khoo, Jing-Jing; Chen, Fezshin; Kho, Kai Ling; Ahmad Shanizza, Azzy Iyzati; Lim, Fang-Shiang; Tan, Kim-Kee; Chang, Li-Yen; AbuBakar, Sazaly
2016-07-01
Ticks are vectors in the transmission of many important infectious diseases in human and animals. Ticks can be readily found in the semi-forested areas such as the settlements of the indigenous people in Malaysia, the Orang Asli. There is still minimal information available on the bacterial agents associated with ticks found in Malaysia. We performed a survey of the bacterial communities associated with ticks collected from domestic animals found in two Orang Asli villages in Malaysia. We collected 62 ticks, microscopically and molecularly identified as related to Haemaphysalis wellingtoni, Haemaphysalis hystricis and Haemaphysalis bispinosa. Bacterial 16s rRNA hypervariable region (V6) amplicon libraries prepared from the tick samples were sequenced on the Ion Torrent PGM platform. We detected a total of 392 possible bacterial genera after pooling and sequencing 20 samples, indicating a diverse bacterial community profile. Dominant taxa include the potential tick endosymbiont, Coxiella. Other dominant taxa include the tick-associated pathogen, Rickettsia, and environmental bacteria such as Bacillus, Mycobacterium, Sphingomonas and Pseudomonas. Other known tick-associated bacteria were also detected, including Anaplasma, Ehrlichia, Rickettsiella and Wolbachia, albeit at very low abundance. Specific PCR was performed on selected samples to identify Rickettsia and Coxiella. Sequence of Rickettsia felis, which causes spotted fever in human and cats, was identified in one sample. Coxiella endosymbionts were detected in three samples. This study provides the baseline knowledge of the microbiome of ticks in Malaysia, focusing on tick-associated bacteria affecting the Orang Asli communities. The role of the herein found Coxiella and Rickettsia in tick physiology or disease transmission merits further investigation. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.
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Thomas, Austen C; Jarman, Simon N; Haman, Katherine H; Trites, Andrew W; Deagle, Bruce E
2014-08-01
Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM(©) , we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals' diet to generate tissue correction factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected) to 14 ± 9% (TCF-corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate digestion correction factors (DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis. © 2013 John Wiley & Sons Ltd.
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Hot spot mutations in Finnish non-small cell lung cancers.
Mäki-Nevala, Satu; Sarhadi, Virinder Kaur; Rönty, Mikko; Kettunen, Eeva; Husgafvel-Pursiainen, Kirsti; Wolff, Henrik; Knuuttila, Aija; Knuutila, Sakari
2016-09-01
Non-small cell lung cancer (NSCLC) is a common cancer with a poor prognosis. The aim of this study was to screen Finnish NSCLC tumor samples for common cancer-related mutations by targeted next generation sequencing and to determine their concurrences and associations with clinical features. Sequencing libraries were prepared from DNA isolated from formalin-fixed, paraffin-embedded tumor material of 425 patients using the AmpliSeq Colon and Lung panel covering mutational hot spot regions of 22 cancer genes. Sequencing was performed with the Ion Torrent Personal Genome Machine (PGM). Data analysis of the hot spot mutations revealed mutations in 77% of the patients, with 7% having 3 or more mutations reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. Two of the most frequently mutated genes were TP53 (46%) and KRAS (25%). KRAS codon 12 mutations were the most recurrently occurring mutations. EGFR mutations were significantly associated with adenocarcinoma, female gender and never/light-smoking history; CTNNB1 mutations with light ex-smokers, PIK3CA and TP53 mutations with squamous cell carcinoma, and KRAS with adenocarcinoma. TP53 mutations were most prevalent in current smokers and ERBB2, ERBB4, PIK3CA, NRAS, NOTCH1, FBWX7, PTEN and STK11 mutations occurred exclusively in a group of ever-smokers, however the association was not statistically significant. No mutation was found that associated with asbestos exposure. Finnish NSCLC patients have a similar mutation profile as other Western patients, however with a higher frequency of BRAF mutations but a lower frequency of STK11 and ERBB2 mutations. Moreover, TP53 mutations occurred frequently with other gene mutations, most commonly with KRAS, MET, EGFR and PIK3CA mutations. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
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Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau
NASA Astrophysics Data System (ADS)
Nagano, Yuriko; Miura, Toshiko; Nishi, Shinro; Lima, Andre O.; Nakayama, Cristina; Pellizari, Vivian H.; Fujikura, Katsunori
2017-12-01
We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidium diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.
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Habtom, Habteab; Demanèche, Sandrine; Dawson, Lorna; Azulay, Chen; Matan, Ofra; Robe, Patrick; Gafny, Ron; Simonet, Pascal; Jurkevitch, Edouard; Pasternak, Zohar
2017-01-01
The ubiquity and transferability of soil makes it a resource for the forensic investigator, as it can provide a link between agents and scenes. However, the information contained in soils, such as chemical compounds, physical particles or biological entities, is seldom used in forensic investigations; due mainly to the associated costs, lack of available expertise, and the lack of soil databases. The microbial DNA in soil is relatively easy to access and analyse, having thus the potential to provide a powerful means for discriminating soil samples or linking them to a common origin. We compared the effectiveness and reliability of multiple methods and genes for bacterial characterisation in the differentiation of soil samples: ribosomal intergenic spacer analysis (RISA), terminal restriction fragment length polymorphism (TRFLP) of the rpoB gene, and five methods using the 16S rRNA gene: phylogenetic microarrays, TRFLP, and high throughput sequencing with Roche 454, Illumina MiSeq and IonTorrent PGM platforms. All these methods were also compared to long-chain hydrocarbons (n-alkanes) and fatty alcohol profiling of the same soil samples. RISA, 16S TRFLP and MiSeq performed best, reliably and significantly discriminating between adjacent, similar soil types. As TRFLP employs the same capillary electrophoresis equipment and procedures used to analyse human DNA, it is readily available for use in most forensic laboratories. TRFLP was optimized for forensic usage in five parameters: choice of primer pair, fluorescent tagging, concentrating DNA after digestion, number of PCR amplifications per sample and number of capillary electrophoresis runs per PCR amplification. This study shows that molecular microbial ecology methodologies are robust in discriminating between soil samples, illustrating their potential usage as an evaluative forensic tool. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
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Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A; Lyons, Russell E; Salin, Krishna R; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B
2016-05-07
The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world's most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.
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Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A.; Lyons, Russell E.; Salin, Krishna R.; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B.
2016-01-01
The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium. PMID:27164098
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Spatial and Temporal Comparison of DNRA Communities in New River Estuary, USA
NASA Astrophysics Data System (ADS)
Song, B.; Lisa, J.; Tobias, C. R.
2016-02-01
Dissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate respiring pathway, competing with denitrification, in various ecosystems. Studies examining the diversity and composition of DNRA communities are limited and their link to DNRA activity is unknown. We conducted a multidisciplinary investigation of sediment communities in the upper reaches of a eutrophic estuary to examine spatial and temporal variation of DNRA community structures and determine their linkage to activities. Sediment samples were collected seasonally from two study sites (AA2 and JAX) in the New River Estuary, North Carolina, USA. 15N-nitrate tracer experiments were conducted to measure potential DNRA rates while abundance of DNRA communities was measured using quantitative PCR of cytochrome C nitrite reductase genes (nrfA). Composition and diversity of DNRA communities were also examined based on next generation sequencing (NGS) of nrfA genes using an Ion Torrent PGM. Bioinformatic analysis was conducted using the FunGene pipeline and Mothur program. Higher DNRA activities were measured at JAX and associated with higher abundance of nrfA genes. Seasonal variation in DNRA rates and nrfA gene abundance was more evident at JAX than AA2. Nitrate concentration and dissolved oxygen in bottom water were significantly and positively correlated with activities and abundance of DNRA communities. The nrfA NGS analysis revealed that spatial variation of DNRA communities was much greater than temporal variation with salinity, dissolved organic carbon, and nitrate as the most important environmental variables affecting these communities. Diversity of DNRA communities was negative correlated with the DNRA rates and nrfA gene abundance, which suggests that dominant members of the DNRA community are responsible for higher rates. Thus, our multidisciplinary study clearly demonstrates the linkage between structure and activities of DNRA communities in the upper reaches of New River Estuary.
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Sharma, Poonam; Gupta, Sushim Kumar; Diene, Seydina M.
2015-01-01
For the first time, we report the whole-genome sequence analysis of Chryseobacterium oranimense G311, a multidrug-resistant bacterium, from a cystic fibrosis patient in France, including resistance to colistin. Whole-genome sequencing of C. oranimense G311 was performed using Ion Torrent PGM, and RAST, the EMBL-EBI server, and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) database were used for annotation of all genes, including antibiotic resistance (AR) genes. General features of the C. oranimense G311 draft genome were compared to the other available genomes of Chryseobacterium gleum and Chryseobacterium sp. strain CF314. C. oranimense G311 was found to be resistant to all β-lactams, including imipenem, and to colistin. The genome size of C. oranimense G311 is 4,457,049 bp in length, with 37.70% GC content. We found 27 AR genes in the genome, including β-lactamase genes which showed little similarity to the known β-lactamase genes and could likely be novel. We found the type I polyketide synthase operon followed by a zeaxanthin glycosyltransferase gene in the genome, which could impart the yellow pigmentation of the isolate. We located the O-antigen biosynthesis cluster, and we also discovered a novel capsular polysaccharide biosynthesis cluster. We also found known mutations in the orthologs of the pmrA (E8D), pmrB (L208F and P360Q), and lpxA (G68D) genes. We speculate that the presence of the capsular cluster and mutations in these genes could explain the resistance of this bacterium to colistin. We demonstrate that whole-genome sequencing was successfully applied to decipher the resistome of a multidrug resistance bacterium associated with cystic fibrosis patients. PMID:25583710
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Sharma, Poonam; Gupta, Sushim Kumar; Diene, Seydina M; Rolain, Jean-Marc
2015-03-01
For the first time, we report the whole-genome sequence analysis of Chryseobacterium oranimense G311, a multidrug-resistant bacterium, from a cystic fibrosis patient in France, including resistance to colistin. Whole-genome sequencing of C. oranimense G311 was performed using Ion Torrent PGM, and RAST, the EMBL-EBI server, and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) database were used for annotation of all genes, including antibiotic resistance (AR) genes. General features of the C. oranimense G311 draft genome were compared to the other available genomes of Chryseobacterium gleum and Chryseobacterium sp. strain CF314. C. oranimense G311 was found to be resistant to all β-lactams, including imipenem, and to colistin. The genome size of C. oranimense G311 is 4,457,049 bp in length, with 37.70% GC content. We found 27 AR genes in the genome, including β-lactamase genes which showed little similarity to the known β-lactamase genes and could likely be novel. We found the type I polyketide synthase operon followed by a zeaxanthin glycosyltransferase gene in the genome, which could impart the yellow pigmentation of the isolate. We located the O-antigen biosynthesis cluster, and we also discovered a novel capsular polysaccharide biosynthesis cluster. We also found known mutations in the orthologs of the pmrA (E8D), pmrB (L208F and P360Q), and lpxA (G68D) genes. We speculate that the presence of the capsular cluster and mutations in these genes could explain the resistance of this bacterium to colistin. We demonstrate that whole-genome sequencing was successfully applied to decipher the resistome of a multidrug resistance bacterium associated with cystic fibrosis patients. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
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Optimization of conditions to sequence long cDNAs from viruses
USDA-ARS?s Scientific Manuscript database
Fourth generation sequencing with the Minion nanopore sequencer provides opportunity to obtain deep coverage and long read for single molecules. This will benefit studies on RNA viruses. In the past, Sanger, Illumina, and Ion Torrent sequencing have been utilized to study RNA viruses. Both technique...
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The PGM3 gene encodes the major phosphoribomutase in the yeast Saccharomyces cerevisiae.
Walther, Thomas; Baylac, Audrey; Alkim, Ceren; Vax, Amélie; Cordier, Hélène; François, Jean Marie
2012-11-30
The phosphoglucomutases (PGM) Pgm1, Pgm2, and Pgm3 of the yeast Saccharomyces cerevisiae were tested for their ability to interconvert ribose-1-phosphate and ribose-5-phosphate. The purified proteins were studied in vitro with regard to their kinetic properties on glucose-1-phosphate and ribose-1-phosphate. All tested enzymes were active on both substrates with Pgm1 exhibiting only residual activity on ribose-1-phosphate. The Pgm2 and Pgm3 proteins had almost equal kinetic properties on ribose-1-phosphate, but Pgm2 had a 2000 times higher preference for glucose-1-phosphate when compared to Pgm3. The in vivo function of the PGMs was characterized by monitoring ribose-1-phosphate kinetics following a perturbation of the purine nucleotide balance. Only mutants with a deletion of PGM3 hyper-accumulated ribose-1-phosphate. We conclude that Pgm3 functions as the major phosphoribomutase in vivo. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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USDA-ARS?s Scientific Manuscript database
The characterization of genes determining compatibility or incompatibility between plant pathogenic fungi and their hosts is important for the management of crop disease. The major focus of these interactions has typically been the identification and characterization of host genes, but it is equally...
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USDA-ARS?s Scientific Manuscript database
Resistance gene analogs (RGAs) were searched bioinformatically in the sugar beet (Beta vulgaris L.) genome as potential candidates for improving resistance against different diseases. In the present study, Ion Torrent sequencing technology was used to identify mutations in 21 RGAs. The DNA samples o...
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OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data
Huang, Wenpan; Xi, Feng; Lin, Lin; Zhi, Qihuan; Zhang, Wenwei; Tang, Y. Tom; Geng, Chunyu; Lu, Zhiyuan; Xu, Xun
2014-01-01
Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller). This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST) and Alignment Optimize Structure (AOS), together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology’s Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences. PMID:24824529
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OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data.
Zhu, Pengyuan; He, Lingyu; Li, Yaqiao; Huang, Wenpan; Xi, Feng; Lin, Lin; Zhi, Qihuan; Zhang, Wenwei; Tang, Y Tom; Geng, Chunyu; Lu, Zhiyuan; Xu, Xun
2014-01-01
Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller). This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST) and Alignment Optimize Structure (AOS), together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology's Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences.
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Kyrpychova, Liubov; Carr, Richard A; Martinek, Petr; Vanecek, Tomas; Perret, Raul; Chottová-Dvořáková, Magdalena; Zamecnik, Michal; Hadravsky, Ladislav; Michal, Michal; Kazakov, Dmitry V
2017-06-01
Basal cell carcinoma (BCC) with matrical differentiation is a fairly rare neoplasm, with about 30 cases documented mainly as isolated case reports. We studied a series of this neoplasm, including cases with an atypical matrical component, a hitherto unreported feature. Lesions coded as BCC with matrical differentiation were reviewed; 22 cases were included. Immunohistochemical studies were performed using antibodies against BerEp4, β-catenin, and epithelial membrane antigen (EMA). Molecular genetic studies using Ion AmpliSeq Cancer Hotspot Panel v2 by massively parallel sequencing on Ion Torrent PGM were performed in 2 cases with an atypical matrical component (1 was previously subjected to microdissection to sample the matrical and BCC areas separately). There were 13 male and 9 female patients, ranging in age from 41 to 89 years. Microscopically, all lesions manifested at least 2 components, a BCC area (follicular germinative differentiation) and areas with matrical differentiation. A BCC component dominated in 14 cases, whereas a matrical component dominated in 4 cases. Matrical differentiation was recognized as matrical/supramatrical cells (n=21), shadow cells (n=21), bright red trichohyaline granules (n=18), and blue-gray corneocytes (n=18). In 2 cases, matrical areas manifested cytologic atypia, and a third case exhibited an infiltrative growth pattern, with the tumor metastasizing to a lymph node. BerEP4 labeled the follicular germinative cells, whereas it was markedly reduced or negative in matrical areas. The reverse pattern was seen with β-catenin. EMA was negative in BCC areas but stained a proportion of matrical/supramatrical cells. Genetic studies revealed mutations of the following genes: CTNNB1, KIT, CDKN2A, TP53, SMAD4, ERBB4, and PTCH1, with some differences between the matrical and BCC components. It is concluded that matrical differentiation in BCC in most cases occurs as multiple foci. Rare neoplasms manifest atypia in the matrical areas. Immunohistochemical analysis for BerEP4, EMA, and β-catenin can be helpful in limited biopsy specimens. From a molecular biological prospective, BCC and matrical components appear to share some of the gene mutations but have differences in others, but this observation must be validated in a large series.
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Identification of human phosphoglucomutase 3 (PGM3) as N-acetylglucosamine-phosphate mutase (AGM1).
Pang, H; Koda, Y; Soejima, M; Kimura, H
2002-03-01
We performed phenotyping of human phosphoglucomutase 3 (PGM(3)) and screening for mutations in the human N-acetylglucosamine-phosphate mutase gene (AGM(1)) to identify PGM(3) as AGM(1). By sequencing the coding region of AGM(1), two alleles containing a G or A base at nucleotide 1396, that can respectively encode aspartic acid or asparagine at codon 466, were identified. Cell extracts of COS7 cells after transfection with the pcDNA 3.1(+) plasmid containing an AGM(1) allele with 1396G or 1396A showed similar electrophoretic patterns to the PGM(3) 1 or PGM(3) 2 protein, respectively, with the isozyme detection method used for PGM(3) phenotyping. The genotypes determined by the two alleles of AGM(1) coincided exactly with the PGM(3) phenotypes in 20 individuals. We also investigated the allele frequency of the AGM(1) nucleotide polymorphism in a Japanese population by DNA sequencing and found that the frequencies of alleles 1396G and 1396A were similar to previously reported PGM(3) *1 and PGM(3) *2 frequencies. Overall, the facts that the AGM(1) gene product shows PGM activity, AGM(1) is polymorphic, the electrophoretic mobility is similar between AGM(1) allele-specific products and PGM(3) 1 and 2 proteins, PGM(3) phenotypes and AGM(1) genotypes completely coincide in 20 individuals, and AGM(1) allele frequencies are similar to those of PGM(3) *1 and PGM(3) *2 in Japanese populations, suggest that PGM(3) is identical to AGM(1).
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Draft Genome Sequence of “Cohnella kolymensis” B-2846
Kudryashova, Ekaterina B.; Ariskina, Elena V.
2016-01-01
A draft genome sequence of “Cohnella kolymensis” strain B-2846 was derived using IonTorrent sequencing technology. The size of the assembly and G+C content were in agreement with those of other species of this genus. Characterization of the genome of a novel species of Cohnella will assist in bacterial systematics. PMID:26769947
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Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers
D’Haene, Nicky; Le Mercier, Marie; De Nève, Nancy; Blanchard, Oriane; Delaunoy, Mélanie; El Housni, Hakim; Dessars, Barbara; Heimann, Pierre; Remmelink, Myriam; Demetter, Pieter; Tejpar, Sabine; Salmon, Isabelle
2015-01-01
Objective Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation. Methods We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed. Results Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%. Conclusions Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice. PMID:26366557
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Progress in ion torrent semiconductor chip based sequencing.
Merriman, Barry; Rothberg, Jonathan M
2012-12-01
In order for next-generation sequencing to become widely used as a diagnostic in the healthcare industry, sequencing instrumentation will need to be mass produced with a high degree of quality and economy. One way to achieve this is to recast DNA sequencing in a format that fully leverages the manufacturing base created for computer chips, complementary metal-oxide semiconductor chip fabrication, which is the current pinnacle of large scale, high quality, low-cost manufacturing of high technology. To achieve this, ideally the entire sensory apparatus of the sequencer would be embodied in a standard semiconductor chip, manufactured in the same fab facilities used for logic and memory chips. Recently, such a sequencing chip, and the associated sequencing platform, has been developed and commercialized by Ion Torrent, a division of Life Technologies, Inc. Here we provide an overview of this semiconductor chip based sequencing technology, and summarize the progress made since its commercial introduction. We described in detail the progress in chip scaling, sequencing throughput, read length, and accuracy. We also summarize the enhancements in the associated platform, including sample preparation, data processing, and engagement of the broader development community through open source and crowdsourcing initiatives. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Mapping mountain torrent hazards in the Hexi Corridor using an evidential reasoning approach
NASA Astrophysics Data System (ADS)
Ran, Youhua; Liu, Jinpeng; Tian, Feng; Wang, Dekai
2017-02-01
The Hexi Corridor is an important part of the Silk Road Economic Belt and a crucial channel for westward development in China. Many important national engineering projects pass through the corridor, such as highways, railways, and the West-to-East Gas Pipeline. The frequent torrent disasters greatly impact the security of infrastructure and human safety. In this study, an evidential reasoning approach based on Dempster-Shafer theory is proposed for mapping mountain torrent hazards in the Hexi Corridor. A torrent hazard map for the Hexi Corridor was generated by integrating the driving factors of mountain torrent disasters including precipitation, terrain, flow concentration processes, and the vegetation fraction. The results show that the capability of the proposed method is satisfactory. The torrent hazard map shows that there is high potential torrent hazard in the central and southeastern Hexi Corridor. The results are useful for engineering planning support and resource protection in the Hexi Corridor. Further efforts are discussed for improving torrent hazard mapping and prediction.
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Photon stimulated desorption from oxidized Al(110). [Surface hydroxyls
DOE Office of Scientific and Technical Information (OSTI.GOV)
Johnson, E.D.; Garrett, R.F.; Knotek, M.L.
1987-01-01
We have studied oxide films on Al(110) by photon stimulated desorption (PSD) on the Bell Labs U4 PGM at the National Synchrotron Light Source. Utilizing a time of flight technique we have obtained ion energy distribution (IED) and relative ion yield (RIY) data at the Al 2p and O 1s edges for oxides prepared at various temperatures. These initial studies suggest that different sites for the surface hydroxyls exist, that they can be selectively prepared, and examined by PSD. 15 refs., 9 figs.
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Mack, C L; Wilhelmi, B; Duncan, J R; Burgess, J E
2011-01-01
The process of platinum group metal (PGM) refining can be up to 99.99% efficient at best, and although it may seem small, the amount of valuable metal lost to waste streams is appreciable enough to warrant recovery. The method currently used to remove entrained metal ions from refinery wastewaters, chemical precipitation, is not effective for selective recovery of PGMs. The yeast Saccharomyces cerevisiae has been found capable of sorbing numerous precious and base metals, and is a cheap and abundant source of biomass. In this investigation, S. cerevisiae was immobilised using polyethyleneimine and glutaraldehyde to produce a suitable sorbent, capable of high platinum uptake (150-170 mg/g) at low pH (<2). The sorption mechanism was found to be a chemical reaction, which made effective desorption impossible. When applied to PGM refinery wastewater, two key wastewater characteristics limited the success of the sorption process; high inorganic ion content and complex speciation of the platinum ions. The results proved the concept principle of platinum recovery by immobilised yeast biosorption and indicated that a more detailed understanding of the platinum speciation within the wastewater is required before biosorption can be applied. Overall, the sorption of platinum by the S. cerevisiae sorbent was demonstrated to be highly effective in principle, but the complexity of the wastewater requires that pretreatment steps be taken before the successful application of this process to industrial wastewater.
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Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing.
Calmels, Nadège; Greff, Géraldine; Obringer, Cathy; Kempf, Nadine; Gasnier, Claire; Tarabeux, Julien; Miguet, Marguerite; Baujat, Geneviève; Bessis, Didier; Bretones, Patricia; Cavau, Anne; Digeon, Béatrice; Doco-Fenzy, Martine; Doray, Bérénice; Feillet, François; Gardeazabal, Jesus; Gener, Blanca; Julia, Sophie; Llano-Rivas, Isabel; Mazur, Artur; Michot, Caroline; Renaldo-Robin, Florence; Rossi, Massimiliano; Sabouraud, Pascal; Keren, Boris; Depienne, Christel; Muller, Jean; Mandel, Jean-Louis; Laugel, Vincent
2016-03-22
Deficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS). In view of the clinical overlap between NER-related disorders, as well as the existence of multiple phenotypes and the numerous genes involved, we developed a new diagnostic approach based on the enrichment of 16 NER-related genes by multiplex amplification coupled with next-generation sequencing (NGS). Our test cohort consisted of 11 DNA samples, all with known mutations and/or non pathogenic SNPs in two of the tested genes. We then used the same technique to analyse samples from a prospective cohort of 40 patients. Multiplex amplification and sequencing were performed using AmpliSeq protocol on the Ion Torrent PGM (Life Technologies). We identified causative mutations in 17 out of the 40 patients (43%). Four patients showed biallelic mutations in the ERCC6(CSB) gene, five in the ERCC8(CSA) gene: most of them had classical CS features but some had very mild and incomplete phenotypes. A small cohort of 4 unrelated classic XP patients from the Basque country (Northern Spain) revealed a common splicing mutation in POLH (XP-variant), demonstrating a new founder effect in this population. Interestingly, our results also found ERCC2(XPD), ERCC3(XPB) or ERCC5(XPG) mutations in two cases of UV-sensitive syndrome and in two cases with mixed XP/CS phenotypes. Our study confirms that NGS is an efficient technique for the analysis of NER-related disorders on a molecular level. It is particularly useful for phenotypes with combined features or unusually mild symptoms. Targeted NGS used in conjunction with DNA repair functional tests and precise clinical evaluation permits rapid and cost-effective diagnosis in patients with NER-defects.
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Cesca, Federica; Bettella, Elisa; Polli, Roberta; Cama, Elona; Scimemi, Pietro; Santarelli, Rosamaria; Murgia, Alessandra
2018-01-01
This work was aimed at establishing the molecular etiology of hearing loss in a 9-year old girl with post-lingual non-syndromic mild sensorineural hearing loss with a complex family history of clinically heterogeneous deafness. The proband's DNA was subjected to NGS analysis of a 59-targeted gene panel, with the use of the Ion Torrent PGM platform. Conventional Sanger sequencing was used for segregation analysis in all the affected relatives. The proband and all the other hearing impaired members of the family underwent a thorough clinical and audiological evaluation. A new likely pathogenic mutation in the EYA4 gene (c.1154C > T; p.Ser385Leu) was identified in the proband and in her 42-year-old father with post-lingual non-syndromic profound sensorineural hearing loss. The EYA4 mutation was also found in the proband's grandfather and uncle, both showing clinical features of Waardenburg syndrome type 1. A novel pathogenic splice-site mutation (c.321+1G > A) of the PAX3 gene was found to co-segregate with the EYA4 mutation in these two subjects. The identified novel EYA4 mutation can be considered responsible of the hearing loss observed in the proband and her father, while a dual molecular diagnosis was reached in the relatives co-segregating the EYA4 and the PAX3 mutations. In these two subjects the DFNA10 phenotype was masked by Waardenburg syndrome. The use of NGS targeted gene-panel, in combination with an extensive clinical and audiological examination led us to identify the genetic cause of the hearing loss in members of a family in which different forms of autosomal dominant deafness segregate. These results provide precise and especially important prognostic and follow-up information for the future audiologic management in the youngest affected member. Copyright © 2017 Elsevier B.V. All rights reserved.
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Nyaga, Martin M.; Stucker, Karla M.; Esona, Mathew D.; Jere, Khuzwayo C.; Mwinyi, Bakari; Shonhai, Annie; Tsolenyanu, Enyonam; Mulindwa, Augustine; Chibumbya, Julia N.; Adolfine, Hokororo; Halpin, Rebecca A.; Roy, Sunando; Stockwell, Timothy B.; Berejena, Chipo; Seheri, Mapaseka L.; Mwenda, Jason M.; Steele, A. Duncan; Wentworth, David E.
2018-01-01
Group A rotaviruses (RVAs) with distinct G and P genotype combinations have been reported globally. We report the genome composition and possible origin of seven G8P[4] and five G2P[4] human RVA strains based on the genetic evolution of all 11 genome segments at the nucleotide level. Twelve RVA ELISA positive stool samples collected in the representative countries of Eastern, Southern and West Africa during the 2007–2012 surveillance seasons were subjected to sequencing using the Ion Torrent PGM and Illumina MiSeq platforms. A reference-based assembly was performed using CLC Bio’s clc_ref_assemble_long program, and full-genome consensus sequences were obtained. With the exception of the neutralising antigen, VP7, all study strains exhibited the DS-1-like genome constellation (P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) and clustered phylogenetically with reference strains having a DS-1-like genetic backbone. Comparison of the nucleotide and amino acid sequences with selected global cognate genome segments revealed nucleotide and amino acid sequence identities of 81.7–100 % and 90.6–100 %, respectively, with NSP4 gene segment showing the most diversity among the strains. Bayesian analyses of all gene sequences to estimate the time of divergence of the lineage indicated that divergence times ranged from 16 to 44 years, except for the NSP4 gene where the lineage seemed to arise in the more distant past at an estimated 203 years ago. However, the long-term effects of changes found within the NSP4 genome segment should be further explored, and thus we recommend continued whole-genome analyses from larger sample sets to determine the evolutionary mechanisms of the DS-1-like strains collected in Africa. PMID:24952422
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HLA genotyping by next-generation sequencing of complementary DNA.
Segawa, Hidenobu; Kukita, Yoji; Kato, Kikuya
2017-11-28
Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis. We thus developed an HLA genotyping system based on next-generation sequencing of cDNA. Each HLA gene was divided into 3 or 4 target regions subjected to PCR amplification and subsequent sequencing with Ion Torrent PGM. The sequence data were then subjected to an automated analysis. The principle of the analysis was to construct candidate sequences generated from all possible combinations of variable bases and arrange them in decreasing order of the number of reads. Upon collecting candidate sequences from all target regions, 2 haplotypes were usually assigned. Cases not assigned 2 haplotypes were forwarded to 4 additional processes: selection of candidate sequences applying more stringent criteria, removal of artificial haplotypes, selection of candidate sequences with a relaxed threshold for sequence matching, and countermeasure for incomplete sequences in the HLA database. The genotyping system was evaluated using 30 samples; the overall accuracy was 97.0% at the field 3 level and 98.3% at the G group level. With one sample, genotyping of DPB1 was not completed due to short read size. We then developed a method for complete sequencing of individual molecules of the DPB1 gene, using the molecular barcode technology. The performance of the automatic genotyping system was comparable to that of systems developed in previous studies. Thus, next-generation sequencing of cDNA is a viable option for HLA genotyping.
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Nathani, Neelam M; Patel, Amrutlal K; Mootapally, Chandra Shekar; Reddy, Bhaskar; Shah, Shailesh V; Lunagaria, Pravin M; Kothari, Ramesh K; Joshi, Chaitanya G
2015-12-29
The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6 weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach. Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30 %) and carbohydrate (15-20 %) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples. Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.
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Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms.
Thomas, Andrew Maltez; Gleber-Netto, Frederico Omar; Fernandes, Gustavo Ribeiro; Amorim, Maria; Barbosa, Luisa Fernanda; Francisco, Ana Lúcia Noronha; de Andrade, Arthur Guerra; Setubal, João Carlos; Kowalski, Luiz Paulo; Nunes, Diana Noronha; Dias-Neto, Emmanuel
2014-10-03
Today there are more than 2 billion alcohol users and about 1.3 billion tobacco users worldwide. The chronic and heavy use of these two substances is at the heart of numerous diseases and may wreak havoc on the human oral microbiome. This study delves into the changes that alcohol and tobacco may cause on biofilms of the human oral microbiome. To do so, we used swabs to sample the oral biofilm of 22 subjects; including 9 control-individuals with no or very low consumption of alcohol and no consumption of tobacco, 7 who were chronic and heavy users of both substances and 6 active smokers that reported no significant alcohol consumption. DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. DNA sequences were clustered and OTUs were assigned using the ARB SILVA database and Qiime. We found no differences in species diversity and evenness among the groups. However, we found a significant decrease in species richness in only smokers and in smokers/drinkers when compared to controls. We found that Neisseria abundance was significantly decreased in both groups when compared to controls. Smokers had significant increases in Prevotella and Capnocytophaga and reductions in Granulicatella, Staphylococcus, Peptostreptococcus and Gemella when compared to the two other groups. Controls showed higher abundance of Aggregibacter, whilst smokers/drinkers had lower abundances of Fusobacteria. Samples from only smokers clustered closer together than to controls and smokers/drinkers, and also had a significant reduction in inter-group dissimilarity distances, indicating a more homogenous group than controls. Our results indicate that the continued use of tobacco or alcohol plus tobacco significantly reduces bacterial richness, which apparently leads to a reduction in inter-group variability, turning the respective biofilms into a more homogenous microenvironment in terms of bacterial community composition, with possible consequences for human oral diseases.
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Comparison of rumen bacterial communities in dairy herds of different production.
Indugu, Nagaraju; Vecchiarelli, Bonnie; Baker, Linda D; Ferguson, James D; Vanamala, Jairam K P; Pitta, Dipti W
2017-08-30
The purpose of this study was to compare the rumen bacterial composition in high and low yielding dairy cows within and between two dairy herds. Eighty five Holstein dairy cows in mid-lactation (79-179 days in milk) were selected from two farms: Farm 12 (M305 = 12,300 kg; n = 47; 24 primiparous cows, 23 multiparous cows) and Farm 9 (M305 = 9700 kg; n = 38; 19 primiparous cows, 19 multiparous cows). Each study cow was sampled once using the stomach tube method and processed for 16S rRNA gene amplicon sequencing using the Ion Torrent (PGM) platform. Differences in bacterial communities between farms were greater (Adonis: R 2 = 0.16; p < 0.001) than within farm. Five bacterial lineages, namely Prevotella (48-52%), unclassified Bacteroidales (10-12%), unclassified bacteria (5-8%), unclassified Succinivibrionaceae (1-7%) and unclassified Prevotellaceae (4-5%) were observed to differentiate the community clustering patterns among the two farms. A notable finding is the greater (p < 0.05) contribution of Succinivibrionaceae lineages in Farm 12 compared to Farm 9. Furthermore, in Farm 12, Succinivibrionaceae lineages were higher (p < 0.05) in the high yielding cows compared to the low yielding cows in both primiparous and multiparous groups. Prevotella, S24-7 and Succinivibrionaceae lineages were found in greater abundance on Farm 12 and were positively correlated with milk yield. Differences in rumen bacterial populations observed between the two farms can be attributed to dietary composition, particularly differences in forage type and proportion in the diets. A combination of corn silage and alfalfa silage may have contributed to the increased proportion of Proteobacteria in Farm 12. It was concluded that Farm 12 had a greater proportion of specialist bacteria that have the potential to enhance rumen fermentative digestion of feedstuffs to support higher milk yields.
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Grazing by Zooplankton on Diazotrophs in the Amazon River Plume and Western Tropical North Atlantic
NASA Astrophysics Data System (ADS)
Conroy, B.; Steinberg, D. K.; Song, B.; Foster, R.
2016-02-01
Organisms capable of fixing di-nitrogen (N2), known as diazotrophs, are important primary producers and a potentially significant source for new nitrogen entering the planktonic food web. However, limited evidence exists for zooplankton grazing on diazotrophs compared to other primary producers. In the western tropical North Atlantic Ocean (WTNA), the Amazon River plume creates a niche for symbiotic diatom-diazotroph associations (DDAs) which can form large blooms. In adjacent non-plume-influenced waters, the colonial cyanobacterium Trichodesmium is abundant. In order to reveal zooplankton-diazotroph grazing interactions and determine the fate of newly fixed nitrogen, gut contents of zooplankton captured in these two regions were compared based on quantitative PCR (qPCR) assay of nitrogenase genes (nifH), and their microbiomes compared using next generation sequencing (NGS) analysis of 16S rRNA genes. We sampled individual copepods from discrete depth intervals (0-25m and 25-50m) and in two size classes (0.5-1mm and 1-2mm) for analysis. A modified DNA extraction protocol was developed and 54 extracts were used as templates in nifH qPCR assays for the larger size fraction diazotrophs (>10µm): Trichodesmium, and Hemiaulus or Rhizosolenia (diatoms)-Richelia (diazotroph) associations. Copepod gut content nifH copies ranged from 1.6 to 13.6 copies individual-1 for the assay targeting the Hemiaulus-Richelia DDA and from 1.1 to 3.0 copies individual-1 for Trichodesmium. 16S NGS conducted on 35 extracts with an Ion Torrent PGM and mothur revealed that cyanobacteria sequences accounted for up to 20% of sequences per extract. Our results show that both DDAs and Trichodesmium are prey for zooplankton, and that new nitrogen moves through the food web via these grazing interactions. These interactions should be considered in future explorations of the global ocean nitrogen cycle.
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Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data
2014-01-01
Background The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms. Results In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established. Conclusions A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark procedure can be used to evaluate existing or in-development mappers as well as to optimize parameters of a chosen mapper for any application and any sequencing platform. PMID:24708189
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[Impacts of malathion on population genetic structure of Oxya chinensis].
Lu, Fu-Ping; Li, Cui-Lan; Duan, Yi-Hao; Guo, Ya-Ping; Ma, En-Bo
2004-09-01
Allozyme electrophoresis was employed to compare the difference in mortality among the genotypes at two polymorphic loci of Pgm and Me of grasshopper Oxya chinensis individuals acutely exposed to 1.5g/L malathion which resulted in 56% mortality in 24 hours. The selective lethal effects were observed among the genotypes at Pgm locus but not at Me locus. It is noted that the genotype Pgm-ab experienced the highest mortality (80%), whereas Pgm-bb and Pgm-bc were 49%, lower than the average. The chi(2) tests showed significant difference in morality between Pgm-bb and Pgm-cc. After exposure the allele frequency of Pgm-b showed a notable increase among surviving individuals. The cluster analysis based on Roger's genetic distance indicated that the acute exposure to malathion can cause differentiation in genetic composition at population level in Oxya chinensis. Because malathion is commonly used as the insecticide for grasshopper control, the data obtained in this study suggest that the similar genotype-mortality effects may occur in crop fields.
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Bacterial diversity and composition of an alkaline uranium mine tailings-water interface.
Khan, Nurul H; Bondici, Viorica F; Medihala, Prabhakara G; Lawrence, John R; Wolfaardt, Gideon M; Warner, Jeff; Korber, Darren R
2013-10-01
The microbial diversity and biogeochemical potential associated with a northern Saskatchewan uranium mine water-tailings interface was examined using culture-dependent and -independent techniques. Morphologically-distinct colonies from uranium mine water-tailings and a reference lake (MC) obtained using selective and non-selective media were selected for 16S rRNA gene sequencing and identification, revealing that culturable organisms from the uranium tailings interface were dominated by Firmicutes and Betaproteobacteria; whereas, MC organisms mainly consisted of Bacteroidetes and Gammaproteobacteria. Ion Torrent (IT) 16S rRNA metagenomic analysis carried out on extracted DNA from tailings and MC interfaces demonstrated the dominance of Firmicutes in both of the systems. Overall, the tailings-water interface environment harbored a distinct bacterial community relative to the MC, reflective of the ambient conditions (i.e., total dissolved solids, pH, salinity, conductivity, heavy metals) dominating the uranium tailings system. Significant correlations among the physicochemical data and the major bacterial groups present in the tailings and MC were also observed. Presence of sulfate reducing bacteria demonstrated by culture-dependent analyses and the dominance of Desulfosporosinus spp. indicated by Ion Torrent analyses within the tailings-water interface suggests the existence of anaerobic microenvironments along with the potential for reductive metabolic processes.
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qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles
Song, Sarah; Nones, Katia; Miller, David; Harliwong, Ivon; Kassahn, Karin S.; Pinese, Mark; Pajic, Marina; Gill, Anthony J.; Johns, Amber L.; Anderson, Matthew; Holmes, Oliver; Leonard, Conrad; Taylor, Darrin; Wood, Scott; Xu, Qinying; Newell, Felicity; Cowley, Mark J.; Wu, Jianmin; Wilson, Peter; Fink, Lynn; Biankin, Andrew V.; Waddell, Nic; Grimmond, Sean M.; Pearson, John V.
2012-01-01
Tumour cellularity, the relative proportion of tumour and normal cells in a sample, affects the sensitivity of mutation detection, copy number analysis, cancer gene expression and methylation profiling. Tumour cellularity is traditionally estimated by pathological review of sectioned specimens; however this method is both subjective and prone to error due to heterogeneity within lesions and cellularity differences between the sample viewed during pathological review and tissue used for research purposes. In this paper we describe a statistical model to estimate tumour cellularity from SNP array profiles of paired tumour and normal samples using shifts in SNP allele frequency at regions of loss of heterozygosity (LOH) in the tumour. We also provide qpure, a software implementation of the method. Our experiments showed that there is a medium correlation 0.42 (-value = 0.0001) between tumor cellularity estimated by qpure and pathology review. Interestingly there is a high correlation 0.87 (-value 2.2e-16) between cellularity estimates by qpure and deep Ion Torrent sequencing of known somatic KRAS mutations; and a weaker correlation 0.32 (-value = 0.004) between IonTorrent sequencing and pathology review. This suggests that qpure may be a more accurate predictor of tumour cellularity than pathology review. qpure can be downloaded from https://sourceforge.net/projects/qpure/. PMID:23049875
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NASA Astrophysics Data System (ADS)
Qiu, Tian; Guo, Huiqin; Zhao, Huan; Wang, Luhua; Zhang, Zhihui
2015-06-01
Identification of multi-gene variations has led to the development of new targeted therapies in lung adenocarcinoma patients, and identification of an appropriate patient population with a reliable screening method is the key to the overall success of tumor targeted therapies. In this study, we used the Ion Torrent next-generation sequencing (NGS) technique to screen for mutations in 89 cases of lung adenocarcinoma metastatic lymph node specimens obtained by fine-needle aspiration cytology (FNAC). Of the 89 specimens, 30 (34%) were found to harbor epidermal growth factor receptor (EGFR) kinase domain mutations. Seven (8%) samples harbored KRAS mutations, and three (3%) samples had BRAF mutations involving exon 11 (G469A) and exon 15 (V600E). Eight (9%) samples harbored PIK3CA mutations. One (1%) sample had a HRAS G12C mutation. Thirty-two (36%) samples (36%) harbored TP53 mutations. Other genes including APC, ATM, MET, PTPN11, GNAS, HRAS, RB1, SMAD4 and STK11 were found each in one case. Our study has demonstrated that NGS using the Ion Torrent technology is a useful tool for gene mutation screening in lung adenocarcinoma metastatic lymph node specimens obtained by FNAC, and may promote the development of new targeted therapies in lung adenocarcinoma patients.
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Habjanec, Lidija; Frkanec, Ruza; Halassy, Beata; Tomasić, Jelka
2006-01-01
The adjuvant activity of liposomes and immunostimulating peptidoglycan monomer (PGM) in different formulations has been studied in mice model using ovalbumin (OVA) as an antigen. PGM is a natural compound of bacterial origin with well-defined chemical structure: GlcNAc-MurNAc-L-Ala-D-isoGln-mesoDpm(epsilonNH2)-D-Ala-D-Ala. It is a non-toxic, non-pyrogenic, and water-soluble immunostimulator. The aim of this study was to investigate the influence of different liposomal formulations of OVA, with or without PGM, on the production of total IgG, as well as of IgG1 and IgG2a subclasses of OVA-specific antibodies (as indicators of Th2 and Th1 type of immune response, respectively). CBA mice were immunized s.c. with OVA mixed with liposomes, OVA with PGM mixed with liposomes, OVA encapsulated into liposomes and OVA with PGM encapsulated into liposomes. Control groups were OVA in saline, OVA with PGM in saline, and OVA in CFA/IFA adjuvant formulation. The entrapment efficacy of OVA was monitored by HPLC method. The adjuvant activity of the mixture of OVA and empty liposomes, the mixture of OVA, PGM, and liposomes and PGM encapsulated with OVA into liposomes on production of total anti-OVA IgG was demonstrated. The mixture of PGM and liposomes exhibited additive immunostimulating effect on the production of antigen-specific IgGs. The analysis of IgG subclasses revealed that encapsulation of OVA into liposomes favors the stimulation of IgG2a antibodies, indicating the switch toward the Th1 type of immune response. When encapsulated into liposomes or mixed with liposomes, PGM induced a switch from Th1 to Th2 type of immune response. It could be concluded that appropriate formulations of antigen, PGM, and liposomes differently affect the humoral immune response and direct the switch in the type of immune response (Th1/Th2).
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BitPredator: A Discovery Algorithm for BitTorrent Initial Seeders and Peers
DOE Office of Scientific and Technical Information (OSTI.GOV)
Borges, Raymond; Patton, Robert M; Kettani, Houssain
2011-01-01
There is a large amount of illegal content being replicated through peer-to-peer (P2P) networks where BitTorrent is dominant; therefore, a framework to profile and police it is needed. The goal of this work is to explore the behavior of initial seeds and highly active peers to develop techniques to correctly identify them. We intend to establish a new methodology and software framework for profiling BitTorrent peers. This involves three steps: crawling torrent indexers for keywords in recently added torrents using Really Simple Syndication protocol (RSS), querying torrent trackers for peer list data and verifying Internet Protocol (IP) addresses from peermore » lists. We verify IPs using active monitoring methods. Peer behavior is evaluated and modeled using bitfield message responses. We also design a tool to profile worldwide file distribution by mapping IP-to-geolocation and linking to WHOIS server information in Google Earth.« less
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NASA Astrophysics Data System (ADS)
Prichard, H. M.; Barnes, Stephen J.; Dale, C. W.; Godel, B.; Fisher, P. C.; Nowell, G. M.
2017-11-01
Chromitite from the Harold's Grave locality in the mantle section of the Shetland ophiolite complex is extremely enriched in Ru, Os and Ir, at μg/g concentrations. High-resolution X-ray computed tomography on micro-cores from these chromitites was used to determine the location, size, distribution and morphology of the platinum-group minerals (PGM). There are five generations of PGM in these chromitites. Small (average 5 μm in equivalent sphere diameter, ESD) euhedral laurites, often with Os-Ir alloys, are totally enclosed in the chromite and are likely to have formed first by direct crystallisation from the magma as the chromite crystallised. Also within the chromitite there are clusters of larger (50 μm ESD) aligned elongate crystals of Pt-, Rh-, Ir-, Os- and Ru-bearing PGM that have different orientations in different chromite crystals. These may have formed either by exsolution, or by preferential nucleation of PGMs in boundary layers around particular growing chromite grains. Thirdly there is a generation of large (100 μm ESD) composite Os-Ir-Ru-rich PGM that are all interstitial to the chromite grains and sometimes form in clusters. It is proposed that Os, Ir and Ru in this generation were concentrated in base metal sulfide droplets that were then re-dissolved into a later sulfide-undersaturated magma, leaving PGM interstitial to the chromite grains. Fourthly there is a group of almost spherical large (80 μm ESD) laurites, hosting minor Os-Ir-Ru-rich PGM that form on the edge or enclosed in chromite grains occurring in a sheet crosscutting a chromitite layer. These may be hosted in an annealed late syn- or post magmatic fracture. Finally a few of the PGM have been deformed in localised shear zones through the chromitites. The vast majority of the PGM - including small PGM enclosed within chromite, larger interstitial PGM and elongate aligned PGM - have Os isotope compositions that give Re-depletion model ages approximately equal to the age of the ophiolite at ∼492 Ma. A number of other PGM - not confined to a single textural group - fall to more or less radiogenic values, with four PGM giving anomalously unradiogenic Os corresponding to an older age of ∼1050 Ma. The 187Os/188Os isotopic ratios for PGM from Cliff and Quoys, from the same ophiolite section, are somewhat more radiogenic than those at Harold's Grave. This may be due to a distinct mantle source history or possibly the assimilation of radiogenic crustal Os.
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Ono, N; Yamasaki, Y; Yamamoto, N; Sunami, A; Miyake, H
1986-11-01
The possible mechanism of the anti-inflammatory activity of proglumetacin maleate (PGM), a new indomethacin (IND) derivative interacting with arachidonic acid (AA) metabolism, was investigated to elucidate the contributions of PGM itself and its two major metabolites, desproglumideproglumetacin maleate (DPP) and IND. PGM caused much less inhibition of PGE2 formation by sheep seminal vesicle microsomes (IC50 = 310 microM) and TXB2 formation by a washed rabbit platelet suspension (IC50 = 6.3 microM) than IND. DPP also caused less inhibition of cyclooxygenase than IND. Moreover, PGM had less effect on sodium arachidonate (SAA)-induced rat platelet aggregation ex vivo and AA-induced sudden death in rabbits than IND. These results show that PGM has anti-inflammatory activity after its conversion to the active metabolite IND. However, the inhibitory effects of PGM and DPP were as strong as that of IND on SAA- or collagen-induced rabbit platelet aggregation in vitro. These activities are considered to be associated with platelet membrane interaction. Moreover, unlike IND, PGM (IC50 = 1.5 microM) and DPP (IC50 = 16.3 microM) strongly inhibited 5-HETE formation by the cytosol of guinea pig polymorphonuclear leukocytes. This unique activity of PGM on 5-lipoxygenase may contribute to its anti-inflammatory activity.
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Liu, Jing-Jing; Zhang, Guo-Chang; Kong, In Iok; Yun, Eun Ju; Zheng, Jia-Qi; Kweon, Dae-Hyuk; Jin, Yong-Su
2018-05-15
The probiotic yeast Saccharomyces boulardii has been extensively studied for the prevention and treatment of diarrheal diseases, and it is now commercially available in some countries. S. boulardii displays notable phenotypic characteristics, such as a high optimal growth temperature, high tolerance against acidic conditions, and the inability to form ascospores, which differentiate S. boulardii from Saccharomyces cerevisiae The majority of prior studies stated that S. boulardii exhibits sluggish or halted galactose utilization. Nonetheless, the molecular mechanisms underlying inefficient galactose uptake have yet to be elucidated. When the galactose utilization of a widely used S. boulardii strain, ATCC MYA-796, was examined under various culture conditions, the S. boulardii strain could consume galactose, but at a much lower rate than that of S. cerevisiae While all GAL genes were present in the S. boulardii genome, according to analysis of genomic sequencing data in a previous study, a point mutation (G1278A) in PGM2 , which codes for phosphoglucomutase, was identified in the genome of the S. boulardii strain. As the point mutation resulted in the truncation of the Pgm2 protein, which is known to play a pivotal role in galactose utilization, we hypothesized that the truncated Pgm2 might be associated with inefficient galactose metabolism. Indeed, complementation of S. cerevisiae PGM2 in S. boulardii restored galactose utilization. After reverting the point mutation to a full-length PGM2 in S. boulardii by Cas9-based genome editing, the growth rates of wild-type (with a truncated PGM2 gene) and mutant (with a full-length PGM2 ) strains with glucose or galactose as the carbon source were examined. As expected, the mutant (with a full-length PGM2 ) was able to ferment galactose faster than the wild-type strain. Interestingly, the mutant showed a lower growth rate than that of the wild-type strain on glucose at 37°C. Also, the wild-type strain was enriched in the mixed culture of wild-type and mutant strains on glucose at 37°C, suggesting that the truncated PGM2 might offer better growth on glucose at a higher temperature in return for inefficient galactose utilization. Our results suggest that the point mutation in PGM2 might be involved in multiple phenotypes with different effects. IMPORTANCE Saccharomyces boulardii is a probiotic yeast strain capable of preventing and treating diarrheal diseases. However, the genetics and metabolism of this yeast are largely unexplored. In particular, molecular mechanisms underlying the inefficient galactose metabolism of S. boulardii remain unknown. Our study reports that a point mutation in PGM2 , which codes for phosphoglucomutase, is responsible for inferior galactose utilization by S. boulardii After correction of the mutated PGM2 via genome editing, the resulting strain was able to use galactose faster than a parental strain. While the PGM2 mutation made the yeast use galactose slowly, investigation of the genomic sequencing data of other S. boulardii strains revealed that the PGM2 mutation is evolutionarily conserved. Interestingly, the PGM2 mutation was beneficial for growth at a higher temperature on glucose. We speculate that the PGM2 mutation was enriched due to selection of S. boulardii in the natural habitat (sugar-rich fruits in tropical areas). Copyright © 2018 American Society for Microbiology.
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Biswas et al. describe an “exceptional responder” lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for 7 years while undergoing single or combination ERBB2-directed therapies. Whole-genome, whole-exome, and high-coverage ion-torrent targeted sequencing were used to demonstrate extreme genomic heterogeneity between the lung and lymph node metastatic
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Butler, Kimberly S; Young, Megan Y L; Li, Zhihua; Elespuru, Rosalie K; Wood, Steven C
2016-02-01
Next-Generation Sequencing is a rapidly advancing technology that has research and clinical applications. For many cancers, it is important to know the precise mutation(s) present, as specific mutations could indicate or contra-indicate certain treatments as well as be indicative of prognosis. Using the Ion Torrent Personal Genome Machine and the AmpliSeq Cancer Hotspot panel v2, we sequenced two pancreatic cancer cell lines, BxPC-3 and HPAF-II, alone or in mixtures, to determine the error rate, sensitivity, and reproducibility of this system. The system resulted in coverage averaging 2000× across the various amplicons and was able to reliably and reproducibly identify mutations present at a rate of 5%. Identification of mutations present at a lower rate was possible by altering the parameters by which calls were made, but with an increase in erroneous, low-level calls. The panel was able to identify known mutations in these cell lines that are present in the COSMIC database. In addition, other, novel mutations were also identified that may prove clinically useful. The system was assessed for systematic errors such as homopolymer effects, end of amplicon effects and patterns in NO CALL sequence. Overall, the system is adequate at identifying the known, targeted mutations in the panel. Published by Elsevier Inc.
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Dynamic light-scattering study of gelatin and aggregation of gastric mucin
NASA Astrophysics Data System (ADS)
Bansil, Rama; Cao, Xingxiang; Bhaskar, K. Ramakrishnan; LaMont, Jeffrey T.
1997-05-01
Dynamic light scattering studies show that concentration and pH play important roles in determining pig gastric mucin's (PGM) ability to aggregate and gel. At low concentrations, PGM macromolecules exist in solution predominantly in the form of monomers. At high concentrations, PGM macromolecules aggregate to form supra-macromolecular clusters. When the pH of the high concentration PGM solution is changed from 7.0 to 2.0, the system undergoes a sol-gel transition: from a solution of polydisperse aggregates to a gel. This pH and concentration dependent sol-gel transition of PGM solution may provide a mechanism for the mammalian stomach to protect itself against being digested by the gastric juice.
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2016-06-12
Particle Size in Discrete Element Method to Particle Gas Method (DEM_PGM) Coupling in Underbody Blast Simulations Venkatesh Babu, Kumar Kulkarni, Sanjay...buried in soil viz., (1) coupled discrete element & particle gas methods (DEM-PGM) and (2) Arbitrary Lagrangian-Eulerian (ALE), are investigated. The...DEM_PGM and identify the limitations/strengths compared to the ALE method. Discrete Element Method (DEM) can model individual particle directly, and
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NASA Astrophysics Data System (ADS)
Fonseca, Raúl O. C.; Brückel, Karoline; Bragagni, Alessandro; Leitzke, Felipe P.; Speelmanns, Iris M.; Wainwright, Ashlea N.
2017-11-01
Although Earth's continental crust is thought to derive from melting of the Earth's mantle, how the crust has formed and the timing of its formation are not well understood. The main difficulty in understanding how the crust was extracted from the Earth's mantle is that most isotope systems recorded in mantle rocks have been disturbed by crustal recycling, metasomatic activity and dilution of the signal by mantle convection. In this regard, important age constraints can be obtained from Re-Os model ages in platinum group minerals (PGM), as Re-poor and Os-rich PGM show evidence of melting events up to 4.1 Ga. To constrain the origin of the Re-Os fractionation and Os isotope systematics of natural PGM, we have investigated the linkage between sulfide and PGM grains of variable composition via a series of high-temperature experiments carried out at 1 bar. We show that with the exception of laurite, all experimentally-produced PGM, in particular Pt3Fe (isoferroplatinum) and Pt-Ir metal grains, are systematically richer in Re than their sulfide precursors and will develop radiogenic 187Os /188Os signatures over time relative to their host base metal sulfides. Cooling of an PGM-saturated sulfide assemblage shows a tendency to amplify the extent of Re-Os fractionation between PGM and the different sulfide phases present during cooling. Conversely, laurite grains (RuS2) are shown to accept little to no Re in them and their Os isotope composition changes little over time as a result. Laurite is therefore the PGM that provides the most robust Re-depletion ages in mantle lithologies. Our results are broadly consistent with observations made on natural PGM, where laurites are systematically less radiogenic than Pt-rich PGM. These experimental results highlight the need for the acquisition of large datasets for both mantle materials and ophiolite-derived detrital grains that include measurements of the Os isotope composition of minerals rich in highly siderophile elements at the grain scale (i.e. PGM and base metal sulfides). Only with such datasets is it possible to identify past episodes of mantle melting.
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Zhou, Jiangsheng; Bai, Yang; Dai, Rujuan; Guo, Xiaoli; Liu, Zhong-Hua; Yuan, Sheng
2018-05-09
Coprinopsis polysaccharides exhibit hypoglycemic and antioxidant activities. In this report, increases in polysaccharide production by homologous co-overexpression or individual homologous overexpression of phosphoglucomutase and UDP glucose pyrophosphorylase gene in Coprinopsis cinerea, which participate in polysaccharide biosynthesis. The transcription levels of the target genes were upregulated significantly in the oePGM-UGP strain when compared with the oePGM or oeUGP strain. The maximum intracellular polysaccharide content obtained in the oePGM-UGP strain was 1.49-fold higher than that of the WT strain, whereas a slight improvement in polysaccharide production was obtained in the oePGM and oeUGP strains. Extracellular polysaccharide production was enhanced by 75% in the oePGM-UGP strain when compared with that of the WT strain, whereas improvements of 30% and 16% were observed for the oePGM and oeUGP strains, respectively. These results show that multiple interventions in polysaccharide biosynthesis pathways of Basidiomycetes might improve polysaccharide yields when compared with that of single interventions.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Dennis, B.R.; Lawton, R.G.; Kolar, J.D.
The well-logging operations performed in the Miravalles Geothermal Field in Costa Rica were conducted during two separate field trips. The Phase I program provided the deployment of a suite of high-temperature borehole instruments, including the temperature/rabbit, fluid sampler, and three-arm caliper in Well PGM-3. These same tools were deployed in Well PGM-10 along with an additional survey run with a combination fluid velocity/temperature/pressure instrument used to measure thermodynamic properties under flowing well conditions. The Phase II program complemented Phase I with the suite of tools deployed in Wells PGM-5, PGM-11, and PGM-12. 4 refs., 25 figs., 1 tab.
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Mattos, Bianca Braz; Montebianco, Caroline; Romanel, Elisson; da Franca Silva, Tatiane; Bernabé, Renato Barroso; Simas-Tosin, Fernanda; Souza, Lauro M; Sassaki, Guilherme L; Vaslin, Maite F S; Barreto-Bergter, Eliana
2018-05-01
Cladosporium herbarum is a plant pathogen associated with passion fruit scab and mild diseases in pea and soybean. In this study, a peptidogalactomannan (pGM) of C. herbarum mycelium was isolated and structurally characterized, and its role in plant-fungus interactions was evaluated. C. herbarum pGM is composed of carbohydrates (76%) and contains mannose, galactose and glucose as its main monosaccharides (molar ratio, 52:36:12). Methylation and 13 C-nuclear magnetic resonance ( 13 C-NMR) spectroscopy analysis have shown the presence of a main chain containing (1 → 6)-linked α-D-Manp residues, and β-D-Galf residues are present as (1 → 5)-interlinked side chains. β-Galactofuranose containing similar structures were characterized by our group in A. fumigatus, A. versicolor, A. flavus and C. resinae. Tobacco BY-2 cells were used as a model system to address the question of the role of C. herbarum pGM in cell viability and induction of the expression of plant defense-related genes. Native and partially acid hydrolyzed pGMs (lacking galactofuranosyl side-chain residues) were incubated with BY-2 cell suspensions at different concentrations. Cell viability drastically decreased after exposure to more than 400 μg ml -1 pGM; however no cell viability effect was observed after exposure to a partially acid hydrolyzed pGM. BY-2 cell contact with pGM strongly induce the expression of plant defense-related genes, such as phenylalanine ammonia lyase (PAL) and lipoxygenase (LOX), as well as the pathogen-related PR-1a, PR-2 and PR-3 genes, suggesting that pGM activates defense responses in tobacco cells. Interestingly, contact with partially hydrolyzed pGM also induced defense-related gene expression at earlier times than native pGM. These results show that the side chains of the (1 → 5)-linked β-D-galactofuranosyl units from pGM play an important role in the first line fungus-plant interactions mediating plant responses against C. herbarum. In addition, it was observed that pGM and/or C. herbarum conidia are able to induced HR when in contact with tobacco leaves and in vitro plantlets roots, producing necrotic lesions and peroxidase and NO burst, respectively. Copyright © 2018 Elsevier Masson SAS. All rights reserved.
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Bertolini, Francesca; Scimone, Concetta; Geraci, Claudia; Schiavo, Giuseppina; Utzeri, Valerio Joe; Chiofalo, Vincenzo; Fontanesi, Luca
2015-01-01
Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources. PMID:26151450
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Bertolini, Francesca; Scimone, Concetta; Geraci, Claudia; Schiavo, Giuseppina; Utzeri, Valerio Joe; Chiofalo, Vincenzo; Fontanesi, Luca
2015-01-01
Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.
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Duarte, S M B; Stefano, J T; Miele, L; Ponziani, F R; Souza-Basqueira, M; Okada, L S R R; de Barros Costa, F G; Toda, K; Mazo, D F C; Sabino, E C; Carrilho, F J; Gasbarrini, A; Oliveira, C P
2018-04-01
The aim of the study was to compare the gut microbiomes from obese and lean patients with or without NASH to outline phenotypic differences. We performed a cross-sectional pilot study comprising biopsy-proven NASH patients grouped according to BMI. Microbiome DNA was extracted from stool samples, and PCR amplification was performed using primers for the V4 region of the 16S rRNA gene. The amplicons were sequenced using the Ion PGM Torrent platform, and data were analyzed using QIIME software. Macronutrient consumption was analyzed by a 7-day food record. Liver fibrosis ≥ F2 was associated with increased abundance of Lactobacilli (p = 0.0007). NASH patients showed differences in Faecalibacterium, Ruminococcus, Lactobacillus and Bifidobacterium abundance compared with the control group. Lean NASH patients had a 3-fold lower abundance of Faecalibacterium and Ruminococcus (p = 0.004), obese NASH patients were enriched in Lactobacilli (p = 0.002), and overweight NASH patients had reduced Bifidobacterium (p = 0.018). Moreover, lean NASH patients showed a deficiency in Lactobacillus compared with overweight and obese NASH patients. This group also appeared similar to the control group with regard to gut microbiome alpha diversity. Although there were qualitative differences between lean NASH and overweight/obese NASH, they were not statistically significant (p = 0.618). The study limitations included a small sample size, a food questionnaire that collected only qualitative and semi-quantitative data, and variations in group gender composition that may influence differences in FXR signaling, bile acids metabolism and the composition of gut microbiota. Our preliminary finding of a different pathogenetic process in lean NASH patients needs to be confirmed by larger studies, including those with patient populations stratified by sex and dietary habits. Copyright © 2017 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.
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Enhanced leavening ability of baker's yeast by overexpression of SNR84 with PGM2 deletion.
Lin, Xue; Zhang, Cui-Ying; Bai, Xiao-Wen; Xiao, Dong-Guang
2015-06-01
Dough-leavening ability is one of the main aspects considered when selecting a baker's yeast strain for baking industry. Generally, modification of maltose metabolic pathway and known regulatory networks of maltose metabolism were used to increase maltose metabolism to improve leavening ability in lean dough. In this study, we focus on the effects of PGM2 (encoding for the phosphoglucomutase) and SNR84 (encoding for the H/ACA snoRNA) that are not directly related to both the maltose metabolic pathway and known regulatory networks of maltose metabolism on the leavening ability of baker's yeast in lean dough. The results show that the modifications on PGM2 and/or SNR84 are effective ways in improving leavening ability of baker's yeast in lean dough. Deletion of PGM2 decreased cellular glucose-1-phosphate and overexpression of SNR84 increased the maltose permease activity. These changes resulted in 11, 19 and 21% increases of the leavening ability for PGM2 deletion, SNR84 overexpression and SNR84 overexpression combining deleted PGM2, respectively.
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Agm1/Pgm3-Mediated Sugar Nucleotide Synthesis Is Essential for Hematopoiesis and Development▿
Greig, Kylie T.; Antonchuk, Jennifer; Metcalf, Donald; Morgan, Phillip O.; Krebs, Danielle L.; Zhang, Jian-Guo; Hacking, Douglas F.; Bode, Lars; Robb, Lorraine; Kranz, Christian; de Graaf, Carolyn; Bahlo, Melanie; Nicola, Nicos A.; Nutt, Stephen L.; Freeze, Hudson H.; Alexander, Warren S.; Hilton, Douglas J.; Kile, Benjamin T.
2007-01-01
Carbohydrate modification of proteins includes N-linked and O-linked glycosylation, proteoglycan formation, glycosylphosphatidylinositol anchor synthesis, and O-GlcNAc modification. Each of these modifications requires the sugar nucleotide UDP-GlcNAc, which is produced via the hexosamine biosynthesis pathway. A key step in this pathway is the interconversion of GlcNAc-6-phosphate (GlcNAc-6-P) and GlcNAc-1-P, catalyzed by phosphoglucomutase 3 (Pgm3). In this paper, we describe two hypomorphic alleles of mouse Pgm3 and show there are specific physiological consequences of a graded reduction in Pgm3 activity and global UDP-GlcNAc levels. Whereas mice lacking Pgm3 die prior to implantation, animals with less severe reductions in enzyme activity are sterile, exhibit changes in pancreatic architecture, and are anemic, leukopenic, and thrombocytopenic. These phenotypes are accompanied by specific rather than wholesale changes in protein glycosylation, suggesting that while universally required, the functions of certain proteins and, as a consequence, certain cell types are especially sensitive to reductions in Pgm3 activity. PMID:17548465
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Garcia Sanchez, Rosa; Hahn-Hägerdal, Bärbel; Gorwa-Grauslund, Marie F
2010-09-01
Overexpression of the PGM2 gene encoding phosphoglucomutase (Pgm2p) has been shown to improve galactose utilization both under aerobic and under anaerobic conditions. Similarly, xylose utilization has been improved by overexpression of genes encoding xylulokinase (XK), enzymes from the non-oxidative pentose phosphate pathway (non-ox PPP) and deletion of the endogenous aldose reductase GRE3 gene in engineered Saccharomyces cerevisiae strains carrying either fungal or bacterial xylose pathways. In the present study, we investigated how the combination of these traits affect xylose and galactose utilization in the presence or absence of glucose in S. cerevisiae strains engineered with the xylose reductase (XR)-xylitol dehydrogenase (XDH) pathway. In the absence of PGM2 overexpression, the combined overexpression of XK, the non-ox PPP and deletion of the GRE3 gene significantly delayed aerobic growth on galactose, whereas no difference was observed between the control strain and the xylose-engineered strain when the PGM2 gene was overexpressed. Under anaerobic conditions, the overexpression of the PGM2 gene increased the ethanol yield and the xylose consumption rate in medium containing xylose as the only carbon source. The possibility of Pgm2p acting as a xylose isomerase (XI) could be excluded by measuring the XI activity in both strains. The additional copy of the PGM2 gene also resulted in a shorter fermentation time during the co-consumption of galactose and xylose. However, the effect was lost upon addition of glucose to the growth medium. PGM2 overexpression was shown to benefit xylose and galactose fermentation, alone and in combination. In contrast, galactose fermentation was impaired in the engineered xylose-utilizing strain harbouring extra copies of the non-ox PPP genes and a deletion of the GRE3 gene, unless PGM2 was overexpressed. These cross-reactions are of particular relevance for the fermentation of mixed sugars from lignocellulosic feedstock.
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Reiman, Anne; Pandey, Sarojini; Lloyd, Kate L; Dyer, Nigel; Khan, Mike; Crockard, Martin; Latten, Mark J; Watson, Tracey L; Cree, Ian A; Grammatopoulos, Dimitris K
2016-11-01
Background Detection of disease-associated mutations in patients with familial hypercholesterolaemia is crucial for early interventions to reduce risk of cardiovascular disease. Screening for these mutations represents a methodological challenge since more than 1200 different causal mutations in the low-density lipoprotein receptor has been identified. A number of methodological approaches have been developed for screening by clinical diagnostic laboratories. Methods Using primers targeting, the low-density lipoprotein receptor, apolipoprotein B, and proprotein convertase subtilisin/kexin type 9, we developed a novel Ion Torrent-based targeted re-sequencing method. We validated this in a West Midlands-UK small cohort of 58 patients screened in parallel with other mutation-targeting methods, such as multiplex polymerase chain reaction (Elucigene FH20), oligonucleotide arrays (Randox familial hypercholesterolaemia array) or the Illumina next-generation sequencing platform. Results In this small cohort, the next-generation sequencing method achieved excellent analytical performance characteristics and showed 100% and 89% concordance with the Randox array and the Elucigene FH20 assay. Investigation of the discrepant results identified two cases of mutation misclassification of the Elucigene FH20 multiplex polymerase chain reaction assay. A number of novel mutations not previously reported were also identified by the next-generation sequencing method. Conclusions Ion Torrent-based next-generation sequencing can deliver a suitable alternative for the molecular investigation of familial hypercholesterolaemia patients, especially when comprehensive mutation screening for rare or unknown mutations is required.
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Wang, Huiqiang; Han, Hongliang; Ma, Zhanfang
2017-04-01
In this work, a new conductive hydrogel was prepared by a simple cross-linking coordination method using 1,3,5-benzenetricarboxylic acid as the ligand and Fe 3+ as the metal ion. The hydrogel film was formed on a glassy carbon electrode (GCE) by a drop coating method, which can dramatically facilitate the transport of electrons. A sensitive label-free electrochemical immunosensor was fabricated following electrodeposition of gold nanoparticles (AuNPs) on a hydrogel film and immobilization of an antibody. Neuron-specific enolase (NSE), a lung cancer biomarker, was used as the model analyte to be detected. The proposed immunosensor exhibited a wide linear detection range of 1pgmL -1 to 200ngmL -1 and a limit of detection of 0.26pgmL -1 (the ratio of signal to noise (S/N)=3). Moreover, the detection of NSE in human serum samples showed satisfactory accuracy compared with the data determined by enzyme-linked immunosorbent assay (ELISA), indicating good analytical performance of the immunoassay. Copyright © 2016 Elsevier B.V. All rights reserved.
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Ding, Yu; Li, Niu; Chang, Gouying; Li, Juan; Yao, Ruen; Shen, Yiping; Wang, Jian; Huang, Xiaodong; Wang, Xiumin
2018-06-02
The phosphoglucomutase 1 (PGM1) enzyme plays a central role in glucose homeostasis by catalyzing the inter-conversion of glucose 1-phosphate and glucose 6-phosphate. Recently, PGM1 deficiency has been recognized as a cause of the congenital disorders of glycosylation (CDGs). Two Chinese Han pediatric patients with recurrent hypoglycemia, hepatopathy and growth retardation are described in this study. Targeted gene sequencing (TGS) was performed to screen for causal genetic variants in the genome of the patients and their parents to determine the genetic basis of the phenotype. DNA sequencing identified three variations of the PGM1 gene (NM_002633.2). Patient 1 had a novel homozygous mutation (c.119delT, p.Ile40Thrfs*28). In patient 2, we found a compound heterozygous mutation of c.1172G>T(p.Gly391Val) (novel) and c.1507C>T(p.Arg503*) (known pathogenic). This report deepens our understanding of the clinical features of PGM1 mutation. The early molecular genetic analysis and multisystem assessment were here found to be essential to the diagnosis of PGM1-CDG and the provision of timely and proper treatment.
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Training alignment parameters for arbitrary sequencers with LAST-TRAIN.
Hamada, Michiaki; Ono, Yukiteru; Asai, Kiyoshi; Frith, Martin C
2017-03-15
LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. the source code is freely available at http://last.cbrc.jp/. mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
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ERIC Educational Resources Information Center
Eckes, Thomas
2017-01-01
This paper presents an approach to standard setting that combines the prototype group method (PGM; Eckes, 2012) with a receiver operating characteristic (ROC) analysis. The combined PGM-ROC approach is applied to setting cut scores on a placement test of English as a foreign language (EFL). To implement the PGM, experts first named learners whom…
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Pearson, Claire L.; Loshon, Charles A.; Pedersen, Lotte B.; Setlow, Barbara; Setlow, Peter
2000-01-01
A Bacillus subtilis gene termed yhfR encodes the only B. subtilis protein with significant sequence similarity to 2,3-diphosphoglycerate-dependent phosphoglycerate mutases (dPGM). This gene is expressed at a low level during growth and sporulation, but deletion of yhfR had no effect on growth, sporulation, or spore germination and outgrowth. YhfR was expressed in and partially purified from Escherichia coli but had little if any PGM activity and gave no detectable PGM activity in B. subtilis. These data indicate that B. subtilis does not require YhfR and most likely does not require a dPGM. PMID:10869096
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After the revolution? Ethical and social challenges in 'personalized genomic medicine'
Juengst, Eric T; Settersten, Richard A; Fishman, Jennifer R; McGowan, Michelle L
2012-06-01
Personalized genomic medicine (PGM) is a goal that currently unites a wide array of biomedical initiatives, and is promoted as a 'new paradigm for healthcare' by its champions. Its promissory virtues include individualized diagnosis and risk prediction, more effective prevention and health promotion, and patient empowerment. Beyond overcoming scientific and technological hurdles to realizing PGM, proponents may interpret and rank these promises differently, which carries ethical and social implications for the realization of PGM as an approach to healthcare. We examine competing visions of PGM's virtues and the directions in which they could take the field, in order to anticipate policy choices that may lie ahead for researchers, healthcare providers and the public.
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Frkanec, Ruza; Noethig-Laslo, Vesna; Vranesić, Branka; Mirosavljević, Krunoslav; Tomasić, Jelka
2003-04-01
The interaction of immunostimulating compounds, the peptidoglycan monomer (PGM) and structurally related adamantyltripeptides (AdTP1 and AdTP2), respectively, with phospholipids in liposomal bilayers were investigated by electron paramagnetic resonance spectroscopy. (1). The fatty acids bearing the nitroxide spin label at different positions along the acyl chain were used to investigate the interaction of tested compounds with negatively charged multilamellar liposomes. Electron spin resonance (ESR) spectra were studied at 290 and 310 K. The entrapment of the adamantyltripeptides affected the motional properties of all spin labelled lipids, while the entrapment of PGM had no effect. (2). Spin labelled PGM was prepared and the novel compound bearing the spin label attached via the amino group of diaminopimelic acid was chromatographically purified and chemically characterized. The rotational correlation time of the spin labelled molecule dissolved in buffer at pH 7.4 was studied as a function of temperature. The conformational change was observed above 300 K. The same effect was observed with the spin labelled PGM incorporated into liposomes. Such effect was not observed when the spin labelled PGM was studied at alkaline pH, probably due to the hydrolysis of PGM molecule. The study of possible interaction with liposomal membrane is relevant to the use of tested compounds incorporated into liposomes, as adjuvants in vivo.
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Recurrent mutation in the crystallin alpha A gene associated with inherited paediatric cataract.
Javadiyan, Shari; Craig, Jamie E; Souzeau, Emmanuelle; Sharma, Shiwani; Lower, Karen M; Pater, John; Casey, Theresa; Hodson, Trevor; Burdon, Kathryn P
2016-02-11
Cataract is a major cause of childhood blindness worldwide. The purpose of this study was to determine the genetic cause of paediatric cataract in a South Australian family with a bilateral lamellar paediatric cataract displaying variable phenotypes. Fifty-one genes implicated in congenital cataract in human or mouse were sequenced in an affected individual from an Australian (Caucasian) family using a custom Ampliseq library on the Ion Torrent Personal Genome Machine. Reads were mapped against the human genome (hg19) and variants called with the Torrent Suite software. Variants were annotated to dbSNP 137 using Ion Reporter (IR 1.6.2) and were prioritised for validation if they were novel or rare and were predicted to be protein changing. We identified a previously reported oligomerization disrupting mutation, c.62G > A (p.R21Q), in the Crystallin alpha A (CRYAA) gene segregating in this three generation family. No other novel or rare coding mutations were detected in the known cataract genes sequenced. Microsatellite markers were used to compare the haplotypes between the family reported here and a previously published family with the same segregating mutation. Haplotype analysis indicated a potential common ancestry between the two South Australian families with this mutation. The work strengthens the genotype-phenotype correlations between this functional mutation in the crystallin alpha A (CRYAA) gene and paediatric cataract. The p.R21Q mutation is the most likely cause of paediatric cataract in this family. The recurrence of this mutation in paediatric cataract families is likely due to a familial relationship.
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Aoki, Motoki; Wakuno, Ai; Kushiro, Asuka; Mae, Naomi; Kakizaki, Masashi; Nagata, Shun-Ichi; Ohta, Minoru
2017-12-22
Anesthetic and cardiorespiratory effects of total intravenous anesthesia (TIVA) technique using propofol-guaifenesin-medetomidine (PGM) and alfaxalone-guaifenesin-medetomidine (AGM) were preliminarily evaluated in Thoroughbred horses undergoing castration. Twelve male Thoroughbred horses were assigned randomly into two groups. After premedication with intravenous (IV) administrations of medetomidine (5.0 µg/kg) and butorphanol (0.02 mg/kg), anesthesia was induced with guaifenesin (10 mg/kg IV), followed by either propofol (2.0 mg/kg IV) (group PGM: n=6) or alfaxalone (1.0 mg/kg IV) (group AGM: n=6). Surgical anesthesia was maintained for 60 min at a constant infusion of either propofol (3.0 mg/kg/hr) (group PGM) or alfaxalone (1.5 mg/kg/hr) (group AGM), in combination with guaifenesin (80 mg/kg/hr) and medetomidine (3.0 µg/kg/hr). Responses to surgical stimuli, cardiorespiratory values, and induction and recovery characteristics were recorded throughout anesthesia. During anesthesia induction, one horse paddled in group PGM. All horses from group AGM were maintained at adequate anesthetic depth for castration. In group PGM, 3 horses showed increased cremaster muscle tension and one showed slight movement requiring additional IV propofol to maintain surgical anesthesia. No horse exhibited apnea, although arterial oxygen tension decreased in group AGM to less than 60 mmHg. Recovery quality was good to excellent in both groups. In conclusion, TIVA using PGM and AGM infusion was available for 60 min anesthesia in Thoroughbred horses. TIVA techniques using PGM and AGM infusion provided clinically acceptable general anesthesia with mild cardiorespiratory depression. However, inspired air should be supplemented with oxygen to prevent hypoxemia during anesthesia.
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AOKI, Motoki; WAKUNO, Ai; KUSHIRO, Asuka; MAE, Naomi; KAKIZAKI, Masashi; NAGATA, Shun-ichi; OHTA, Minoru
2017-01-01
Anesthetic and cardiorespiratory effects of total intravenous anesthesia (TIVA) technique using propofol-guaifenesin-medetomidine (PGM) and alfaxalone-guaifenesin-medetomidine (AGM) were preliminarily evaluated in Thoroughbred horses undergoing castration. Twelve male Thoroughbred horses were assigned randomly into two groups. After premedication with intravenous (IV) administrations of medetomidine (5.0 µg/kg) and butorphanol (0.02 mg/kg), anesthesia was induced with guaifenesin (10 mg/kg IV), followed by either propofol (2.0 mg/kg IV) (group PGM: n=6) or alfaxalone (1.0 mg/kg IV) (group AGM: n=6). Surgical anesthesia was maintained for 60 min at a constant infusion of either propofol (3.0 mg/kg/hr) (group PGM) or alfaxalone (1.5 mg/kg/hr) (group AGM), in combination with guaifenesin (80 mg/kg/hr) and medetomidine (3.0 µg/kg/hr). Responses to surgical stimuli, cardiorespiratory values, and induction and recovery characteristics were recorded throughout anesthesia. During anesthesia induction, one horse paddled in group PGM. All horses from group AGM were maintained at adequate anesthetic depth for castration. In group PGM, 3 horses showed increased cremaster muscle tension and one showed slight movement requiring additional IV propofol to maintain surgical anesthesia. No horse exhibited apnea, although arterial oxygen tension decreased in group AGM to less than 60 mmHg. Recovery quality was good to excellent in both groups. In conclusion, TIVA using PGM and AGM infusion was available for 60 min anesthesia in Thoroughbred horses. TIVA techniques using PGM and AGM infusion provided clinically acceptable general anesthesia with mild cardiorespiratory depression. However, inspired air should be supplemented with oxygen to prevent hypoxemia during anesthesia. PMID:29057764
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Precision glass molding: Toward an optimal fabrication of optical lenses
NASA Astrophysics Data System (ADS)
Zhang, Liangchi; Liu, Weidong
2017-03-01
It is costly and time consuming to use machining processes, such as grinding, polishing and lapping, to produce optical glass lenses with complex features. Precision glass molding (PGM) has thus been developed to realize an efficient manufacture of such optical components in a single step. However, PGM faces various technical challenges. For example, a PGM process must be carried out within the super-cooled region of optical glass above its glass transition temperature, in which the material has an unstable non-equilibrium structure. Within a narrow window of allowable temperature variation, the glass viscosity can change from 105 to 1012 Pas due to the kinetic fragility of the super-cooled liquid. This makes a PGM process sensitive to its molding temperature. In addition, because of the structural relaxation in this temperature window, the atomic structure that governs the material properties is strongly dependent on time and thermal history. Such complexity often leads to residual stresses and shape distortion in a lens molded, causing unexpected changes in density and refractive index. This review will discuss some of the central issues in PGM processes and provide a method based on a manufacturing chain consideration from mold material selection, property and deformation characterization of optical glass to process optimization. The realization of such optimization is a necessary step for the Industry 4.0 of PGM.
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Yomano, L P; Scopes, R K; Ingram, L O
1993-01-01
Phosphoglycerate mutase is an essential glycolytic enzyme for Zymomonas mobilis, catalyzing the reversible interconversion of 3-phosphoglycerate and 2-phosphoglycerate. The pgm gene encoding this enzyme was cloned on a 5.2-kbp DNA fragment and expressed in Escherichia coli. Recombinants were identified by using antibodies directed against purified Z. mobilis phosphoglycerate mutase. The pgm gene contains a canonical ribosome-binding site, a biased pattern of codon usage, a long upstream untranslated region, and four promoters which share sequence homology. Interestingly, adhA and a D-specific 2-hydroxyacid dehydrogenase were found on the same DNA fragment and appear to form a cluster of genes which function in central metabolism. The translated sequence for Z. mobilis pgm was in full agreement with the 40 N-terminal amino acid residues determined by protein sequencing. The primary structure of the translated sequence is highly conserved (52 to 60% identity with other phosphoglycerate mutases) and also shares extensive homology with bisphosphoglycerate mutases (51 to 59% identity). Since Southern blots indicated the presence of only a single copy of pgm in the Z. mobilis chromosome, it is likely that the cloned pgm gene functions to provide both activities. Z. mobilis phosphoglycerate mutase is unusual in that it lacks the flexible tail and lysines at the carboxy terminus which are present in the enzyme isolated from all other organisms examined. Images PMID:8320209
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Li, Wenli; Turner, Amy; Aggarwal, Praful; Matter, Andrea; Storvick, Erin; Arnett, Donna K; Broeckel, Ulrich
2015-12-16
Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. The Ion AmpliSeq Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq. To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton). We analyzed standard reference RNA samples and RNA samples obtained from human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs). Using published data from two standard RNA reference samples, we observed a strong concordance of log2 fold change for all genes when comparing AmpliSeq to Illumina HiSeq (Pearson's r = 0.92) and Ion Torrent Proton (Pearson's r = 0.92). We used ROC, Matthew's correlation coefficient and RMSD to determine the overall performance characteristics. All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations. Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy.
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Issues to be resolved in Torrents—Future Revolutionised File Sharing
NASA Astrophysics Data System (ADS)
Thanekar, Sachin Arun
2010-11-01
Torrenting is a highly popular peer to peer file sharing activity that allows participants to send and receive files from other computers. As it is an advantageous technique as compare to traditional client server file sharing in terms of time, cost and speed, some drawbaks are also there. Content unavailability, lack of anonymity, leechers, cheaters and download speed consistency are the major problems to sort out. Efforts are needed to resolve these problems and to make this better application. Legal issues are also one of the measure factors of consideration. BitTorrent metafiles themselves do not store copyrighted data. Whether the publishers of BitTorrent metafiles violate copyrights by linking to copyrighted material is controversial. Various countries have taken legal action against websites that host BitTorrent trackers. Eg. Supernova.org, Torrentspy. Efforts are also needed to make such a useful protocol legal.
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Argentina set for privatization
DOE Office of Scientific and Technical Information (OSTI.GOV)
Chynoweth, E.
Buyers are lining up for Argentina's two big state-controlled petrochemical groups, Buenos Aires-based Petroquimica General Mosconi (PGM) and Petroquimica Bahia Blance (PBB). However, feedstock supply contracts with government-owned oil group Yacientos Petroliferos Fiscales (YPG) and gas group Gas del Estado hold the key to both sales. Shell Compania Argentina Petroleo SA (CAPSA), Perez Companc, and Global Petroleum have already bought PGM tender documentation. Shell says it will bid for PGM if the feedstock contract with YPF is acceptable. In addition to price and volume, Shell says the length is critical; it wants a 15-year deal, but would settle for 11.more » YPF initially sought a five-year contract. PGM, which produces 300,000 m.t./year of aromatics, plus oxo alcohols, methanol, and methyl tert-butyl ether, has sales of $150 million/year.« less
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Adjuvant activity of peptidoglycan monomer and its metabolic products.
Halassy, Beata; Krstanović, Marina; Frkanec, Ruza; Tomasić, Jelka
2003-02-14
Peptidoglycan monomer (PGM) is a natural compound of bacterial origin. It is a non-toxic, non-pyrogenic, water-soluble immunostimulator potentiating humoral immune response to ovalbumin (OVA) in mice. It is fast degraded and its metabolic products-the pentapeptide (PP) and the disaccharide (DS)-are excreted from the mammalian organism upon parenteral administration. The present study investigates: (a). whether PGM could influence the long-living memory generation; (b). whether metabolic products retain adjuvant properties of the parent compound and contribute to its adjuvanticity. We report now that mice immunised twice with OVA+PGM had significantly higher anti-OVA IgG levels upon challenge with antigen alone 6 months later in comparison to control group immunised with OVA only. PP and DS were prepared enzymatically in vitro as apyrogenic and chemically pure compounds. When mice were immunised with OVA plus PP and DS, respectively, the level of anti-OVA IgGs in sera was not higher than in mice immunised with OVA alone, while PGM raised the level of specific antibodies. Results implicate that the adjuvant active molecule, capable of enhancing long-living memory generation, is PGM itself, and none of its metabolic products.
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A better sequence-read simulator program for metagenomics.
Johnson, Stephen; Trost, Brett; Long, Jeffrey R; Pittet, Vanessa; Kusalik, Anthony
2014-01-01
There are many programs available for generating simulated whole-genome shotgun sequence reads. The data generated by many of these programs follow predefined models, which limits their use to the authors' original intentions. For example, many models assume that read lengths follow a uniform or normal distribution. Other programs generate models from actual sequencing data, but are limited to reads from single-genome studies. To our knowledge, there are no programs that allow a user to generate simulated data following non-parametric read-length distributions and quality profiles based on empirically-derived information from metagenomics sequencing data. We present BEAR (Better Emulation for Artificial Reads), a program that uses a machine-learning approach to generate reads with lengths and quality values that closely match empirically-derived distributions. BEAR can emulate reads from various sequencing platforms, including Illumina, 454, and Ion Torrent. BEAR requires minimal user input, as it automatically determines appropriate parameter settings from user-supplied data. BEAR also uses a unique method for deriving run-specific error rates, and extracts useful statistics from the metagenomic data itself, such as quality-error models. Many existing simulators are specific to a particular sequencing technology; however, BEAR is not restricted in this way. Because of its flexibility, BEAR is particularly useful for emulating the behaviour of technologies like Ion Torrent, for which no dedicated sequencing simulators are currently available. BEAR is also the first metagenomic sequencing simulator program that automates the process of generating abundances, which can be an arduous task. BEAR is useful for evaluating data processing tools in genomics. It has many advantages over existing comparable software, such as generating more realistic reads and being independent of sequencing technology, and has features particularly useful for metagenomics work.
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ElectroCat: DOE's approach to PGM-free catalyst and electrode R&D
Thompson, Simon T.; Wilson, Adria R.; Zelenay, Piotr; ...
2018-02-03
The successful development of high-performance, durable platinum group metal-free (PGM-free) electrocatalysts and electrodes for polymer electrolyte membrane fuel cells (PEMFCs) will ultimately improve the cost-competiveness of fuel cells in a wide range of applications. This is considered to be a critical development especially for automotive fuel cell applications in order to bring the system cost of an automotive fuel cell system down to the $30/kW cost target set by the U.S. Department of Energy (DOE). The platinum group metal (PGM) electrocatalysts are a major contributor to the system cost. Addressing the technical challenges to PGM-free electrocatalyst and electrode development, therefore,more » represents one of DOE's most pressing research and development (R&D) priorities. ElectroCat was formed by the DOE as part of the Energy Materials Network (EMN) in early 2016, and shares with other EMN consortia the goal of decreasing the time to market for advanced materials related to clean energy technologies, in the context of increasing U.S. fuel cell electric vehicle (FCEV) manufacturing competitiveness. To accomplish this, the consortium performs core research and development and provides universities and companies streamlined access to the unique, world-class set of tools and expertise relevant to early-stage applied PGM-free catalyst R&D of the member national laboratories. Moreover, ElectroCat fosters a systematic methodology by which prospective catalysts and electrodes are prepared and analyzed rapidly and comprehensively using high-throughput, combinatorial methods. Catalyst discovery is augmented by theory as well as foundational electrocatalysis and materials knowledge at the participating national laboratories. Furthermore, ElectroCat has developed a data sharing framework, requisite of all EMN consortia, for disseminating its findings to the public via a searchable database, to further expedite incorporation of PGM-free electrocatalysts into next-generation fuel cells by advancing the general understanding of the PGM-free electrocatalyst field.« less
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ElectroCat: DOE's approach to PGM-free catalyst and electrode R&D
DOE Office of Scientific and Technical Information (OSTI.GOV)
Thompson, Simon T.; Wilson, Adria R.; Zelenay, Piotr
The successful development of high-performance, durable platinum group metal-free (PGM-free) electrocatalysts and electrodes for polymer electrolyte membrane fuel cells (PEMFCs) will ultimately improve the cost-competiveness of fuel cells in a wide range of applications. This is considered to be a critical development especially for automotive fuel cell applications in order to bring the system cost of an automotive fuel cell system down to the $30/kW cost target set by the U.S. Department of Energy (DOE). The platinum group metal (PGM) electrocatalysts are a major contributor to the system cost. Addressing the technical challenges to PGM-free electrocatalyst and electrode development, therefore,more » represents one of DOE's most pressing research and development (R&D) priorities. ElectroCat was formed by the DOE as part of the Energy Materials Network (EMN) in early 2016, and shares with other EMN consortia the goal of decreasing the time to market for advanced materials related to clean energy technologies, in the context of increasing U.S. fuel cell electric vehicle (FCEV) manufacturing competitiveness. To accomplish this, the consortium performs core research and development and provides universities and companies streamlined access to the unique, world-class set of tools and expertise relevant to early-stage applied PGM-free catalyst R&D of the member national laboratories. Moreover, ElectroCat fosters a systematic methodology by which prospective catalysts and electrodes are prepared and analyzed rapidly and comprehensively using high-throughput, combinatorial methods. Catalyst discovery is augmented by theory as well as foundational electrocatalysis and materials knowledge at the participating national laboratories. Furthermore, ElectroCat has developed a data sharing framework, requisite of all EMN consortia, for disseminating its findings to the public via a searchable database, to further expedite incorporation of PGM-free electrocatalysts into next-generation fuel cells by advancing the general understanding of the PGM-free electrocatalyst field.« less
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Edrees, Burhan M; Athar, Mohammad; Abduljaleel, Zainularifeen; Al-Allaf, Faisal A; Taher, Mohiuddin M; Khan, Wajahatullah; Bouazzaoui, Abdellatif; Al-Harbi, Naffaa; Safar, Ramzia; Al-Edressi, Howaida; Alansary, Khawala; Anazi, Abulkareem; Altayeb, Naji; Ahmed, Muawia A
2016-12-01
A targeted customized sequencing of genes implicated in autosomal recessive polycystic kidney disease (ARPKD) phenotype was performed to identify candidate variants using the Ion torrent PGM next-generation sequencing. The results identified four potential pathogenic variants in PKHD1 gene [c.4870C > T, p.(Arg1624Trp), c.5725C > T, p.(Arg1909Trp), c.1736C > T, p.(Thr579Met) and c.10628T > G, p.(Leu3543Trp)] among 12 out of 18 samples. However, one variant c.4870C > T, p.(Arg1624Trp) was common among eight patients. Some patient samples also showed few variants in autosomal dominant polycystic kidney disease (ADPKD) disease causing genes PKD1 and PKD2 such as c.12433G > A, p.(Val4145Ile) and c.1445T > G, p.(Phe482Cys), respectively. All causative variants were validated by capillary sequencing and confirmed the presence of a novel homozygous variant c.10628T > G, p.(Leu3543Trp) in a male proband. We have recently published the results of these studies (Edrees et al., 2016). Here we report for the first time the effect of the common mutation p.(Arg1624Trp) found in eight samples on the protein structure and function due to the specific amino acid changes of PKHD1 protein using molecular dynamics simulations. The computational approaches provide tool predict the phenotypic effect of variant on the structure and function of the altered protein. The structural analysis with the common mutation p.(Arg1624Trp) in the native and mutant modeled protein were also studied for solvent accessibility, secondary structure and stabilizing residues to find out the stability of the protein between wild type and mutant forms. Furthermore, comparative genomics and evolutionary analyses of variants observed in PKHD1 , PKD1 , and PKD2 genes were also performed in some mammalian species including human to understand the complexity of genomes among closely related mammalian species. Taken together, the results revealed that the evolutionary comparative analyses and characterization of PKHD1 , PKD1 , and PKD2 genes among various related and unrelated mammalian species will provide important insights into their evolutionary process and understanding for further disease characterization and management.
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NASA Astrophysics Data System (ADS)
Loye, Alexandre; Jaboyedoff, Michel; Theule, Joshua Isaac; Liébault, Frédéric
2016-06-01
Debris flows have been recognized to be linked to the amounts of material temporarily stored in torrent channels. Hence, sediment supply and storage changes from low-order channels of the Manival catchment, a small tributary valley with an active torrent system located exclusively in sedimentary rocks of the Chartreuse Massif (French Alps), were surveyed periodically for 16 months using terrestrial laser scanning (TLS) to study the coupling between sediment dynamics and torrent responses in terms of debris flow events, which occurred twice during the monitoring period. Sediment transfer in the main torrent was monitored with cross-section surveys. Sediment budgets were generated seasonally using sequential TLS data differencing and morphological extrapolations. Debris production depends strongly on rockfall occurring during the winter-early spring season, following a power law distribution for volumes of rockfall events above 0.1 m3, while hillslope sediment reworking dominates debris recharge in spring and autumn, which shows effective hillslope-channel coupling. The occurrence of both debris flow events that occurred during the monitoring was linked to recharge from previous debris pulses coming from the hillside and from bedload transfer. Headwater debris sources display an ambiguous behaviour in sediment transfer: low geomorphic activity occurred in the production zone, despite rainstorms inducing debris flows in the torrent; still, a general reactivation of sediment transport in headwater channels was observed in autumn without new debris supply, suggesting that the stored debris was not exhausted. The seasonal cycle of sediment yield seems to depend not only on debris supply and runoff (flow capacity) but also on geomorphic conditions that destabilize remnant debris stocks. This study shows that monitoring the changes within a torrent's in-channel storage and its debris supply can improve knowledge on recharge thresholds leading to debris flow.
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A mountain river sediment cascade and its controls: the Schöttlbach torrent, Styria
NASA Astrophysics Data System (ADS)
Lutzmann, Silke; Stangl, Johannes; Sass, Oliver
2017-04-01
Steep alpine headwater torrents are characterized by episodic heavy floods and bedload pulses triggered by local high-intensity mountain rainstorms. They frequently pose serious risks and damage in the densely populated East Alpine Region. It is important to understand where critical sediments are mobilized, how much bedload is delivered to the outlet and what controls the variability. We present a concept to quantify the sediment cascade's components and influencing factors for the Schöttlbach torrent - a 71 km2 non-glaciated catchment in the Niedere Tauern mountain Range in Styria, Austria. Geomorphic mapping is used to identify primary bedload sources on slope as well as patterns of lithology, slope-channel coupling and vegetation conditioning erosion intensity. We apply modern near-range measuring techniques (TLS, Structure from Motion) to monitor erosion rates from representative erosion sites and sediment delivery rates at the outlet since 2014. These measurements are interpreted based on the geomorphic map to derive a catchment-wide seasonal sediment budget. To explain seasonal variations we evaluate precipitation and discharge data from a dense station network as storm precipitation and runoff events are the main triggers of torrent sediment mobilization. Torrent reaches in instable glaciofluvial sediments of the last glaciation show high average erosion rates of ca. 0.08 m/a from 2014 to 2016 surpassing rates in deeply weathered bedrock reaches by an order of magnitude (approx. 0.006 m/a). We model a torrent-wide erosion volume of 2000 m3/a opposing an output of 7000 m3/a in that period. We attribute parts of this discrepancy to a sediment wave reworking signal of an extreme flood event in 2011.
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Influences of animal mucins on lysozyme activity in solution and on hydroxyapatite surfaces.
Park, Won-Kyu; Chung, Jin-Woo; Kim, Young-Ku; Chung, Sung-Chang; Kho, Hong-Seop
2006-10-01
The purpose of this study was to investigate the influence of animal mucins on lysozyme activity in solution and on the surface of hydroxyapatite (HA) beads. The effects of animal mucins on lysozyme activity in solution were examined by incubating porcine gastric mucin (PGM) or bovine submaxillary mucin (BSM) with hen egg-white lysozyme (HEWL) or salivary samples. HA-immobilised animal mucins or lysozyme were used to determine the influence of animal mucins on lysozyme activity on HA surfaces. Lysozyme activity was determined by turbidity measurement of a Micrococcus lysodeikticus substrate suspension. Protein concentration was determined by ninhydrin assay. PGM inhibited the activity of HEWL and salivary lysozyme in solution. The amount of inhibition was dependent on mucin concentration, incubation time and temperature, and the structural integrity of the mucin. The inhibition of salivary lysozyme activity by PGM was greater in submandibular/sublingual saliva than in parotid saliva. The inhibition of lysozyme activity by PGM was markedly dependent on pH. However, BSM did not inhibit the in-solution lysozyme activities of HEWL and clarified saliva. Both PGM and BSM bound to HA surfaces, and HA-adsorbed animal mucins increased the subsequent adsorption of lysozyme. When HA beads were exposed to a mixture of HEWL and PGM or BSM, lysozyme activity on the HA surfaces was significantly increased. The results suggest that animal mucins affect lysozyme activity, and the effects are different on HA surfaces compared with in solution. Further research is needed to determine the effect of animal mucins on lysozyme activity in vivo.
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The relief formed by the descent phenomenon in the north-east part of Kosova.
Bulliqi, Shpejtim; Isufi, Florim; Ramadani, Ibrahim; Gashi, Gani
2012-04-01
In the diverse relief of north-east part of Kosova a relatively wide range occupies the relief modelled by the descent phenomenon, which is conditioned by morph-structural and climatic factors quite suitable for their development. The morphogenesis activity of descent phenomenon is conditioned by the types of rocks, tectonic process of this region and climatic conditions. These factors condition horizontal and vertical relief fragmentation, slope, especially in Gollaku mountains and in SE part of Kopaonik mountain. Along the tectonic descents, the steepness is detaching and the detaching lines consisting of magmatic rocks show overthrows, demolitions and stony torrents, but the Teri gene composition formations are modelled by sliding and muddy torrents, depending upon the presence of clayey and alevrolite belts on these Teri gene ones. The impact of factors and conditions on the relief of this part, the phenomena like demolitions, overthrows, sliding, muddy torrents, stony torrents, etc, operate here, which play an important morphological role in the modelling of relief.
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Wang, Xueping; Xu, Rui; Sun, Xu; Wang, Yaoguang; Ren, Xiang; Du, Bin; Wu, Dan; Wei, Qin
2017-10-15
An ultrasensitive sandwich-type photoelectrochemical (PEC) immunosensor was constructed for the detection of prostate specific antigen (PSA). In this work, Au-nanoparticle-loaded tungsten oxide (WO 3 -Au) hybrid composites was applied as PEC sensing platform, while Ca ions doped CdSe equipped on the conducting framework of reduced graphene oxide (rGO-Ca:CdSe) nanocomposites were employed as the signal amplification probe. As for WO 3 -Au, massive Au nanoparticles were formed on the surface of WO 3 without any additional reducing agent, providing a novel nanocarriers for anchoring plenty of the primary antibodies due to the large specific surface area and good biocompatibility by chemical bonding between Au nanoparticles and -NH 2 of antibodies. Besides, the incorporation of the rGO and the doping of Ca ions could improve the conductivity and hinder the recombination of electron-hole pairs of CdSe nanoparticles effectively, thereby enhancing the photocurrent conversion efficiency. Based on the sandwich immunoreaction, the primary antibody was immobilized onto WO 3 -Au substrate, after the formed rGO-Ca:CdSe labels were captured onto the electrode surface via the specific antibody-antigen interaction, the photocurrent intensity could be further enhanced due to the sensitization effect. Under the optimal conditions, the proposed PEC immunosensor shows a linear relationship between photocurrent variation and the logarithm of PSA concentration in the wide range of 5pgmL -1 to 50ngmL -1 with a low detection limit of 2.6pgmL -1 (S/N=3). Moreover, it also presented good stability and acceptable specificity, indicating the potential applications in clinical diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.
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Toscana Virus Genome Stability: Data from a Meningoencephalitis Case in Mantua, Italy
Baggieri, Melissa; Gattuso, Gianni; Fortuna, Claudia; Remoli, Maria Elena; Vaccari, Gabriele; Zaccaria, Guendalina; Marchi, Antonella; Bucci, Paola; Benedetti, Eleonora; Fiorentini, Cristiano; Nicoletti, Loredana
2014-01-01
Abstract In July of 2013, samples from a patient with a neurological syndrome were collected from Mantua hospital and sent to the National Reference Laboratory for Arboviruses (National Institute of Health, Rome). On the basis of the symptoms, serological and molecular assays were performed to diagnose either West Nile virus (WNV) or Toscana virus (TOSV) infection. Molecular and serological tests confirmed TOSV infection. Virus isolation was obtained from cerebrospinal fluid. A full genome sequence was determined from this TOSV strain with next-generation sequencing using Ion Torrent technology. Nucleotide and amino acidic sequences grouped phylogenetically with lineage TOSV A and showed a low genome variability. PMID:25514123
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Bai, Hanwen
2011-01-01
The majority of understanding of root gravity responses comes from the study of primary roots, even though lateral roots make a far greater contribution to root system architecture. The focus of this report is the analysis of gravitropic responses in lateral roots of wild-type background and pgm-1 mutants. Despite the significant reduction in gravitropic response of primary roots of pgm-1 mutants, the lateral roots of this mutant demonstrate wild-type rates of gravitropism, suggesting a significant difference in gravity signal transduction between primary and lateral roots. PMID:21921698
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Gonzales, Ivana; Artyushkova, Kateryna; Atanassov, Plamen
2018-03-13
Here, we discuss perspectives and challenges in applying density functional theory for the calculation of spectroscopic properties of platinum group metal (PGM)-free electrocatalysts for oxygen reduction. More specifically, we discuss recent advances in the density functional theory calculations of core-level shifts in binding energies of N 1s electrons as measured by X-ray photoelectron spectroscopy. The link between the density functional theory calculations, the electrocatalytic performance of the catalysts, and structural analysis using modern spectroscopic techniques is expected to significantly increase our understanding of PGM-free catalysts at the molecular level.
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Bai, Hanwen; Wolverton, Chris
2011-10-01
The majority of understanding of root gravity responses comes from the study of primary roots, even though lateral roots make a far greater contribution to root system architecture. The focus of this report is the analysis of gravitropic responses in lateral roots of wild-type background and pgm-1 mutants. Despite the significant reduction in gravitropic response of primary roots of pgm-1 mutants, the lateral roots of this mutant demonstrate wild-type rates of gravitropism, suggesting a significant difference in gravity signal transduction between primary and lateral roots.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gonzales, Ivana; Artyushkova, Kateryna; Atanassov, Plamen
Here, we discuss perspectives and challenges in applying density functional theory for the calculation of spectroscopic properties of platinum group metal (PGM)-free electrocatalysts for oxygen reduction. More specifically, we discuss recent advances in the density functional theory calculations of core-level shifts in binding energies of N 1s electrons as measured by X-ray photoelectron spectroscopy. The link between the density functional theory calculations, the electrocatalytic performance of the catalysts, and structural analysis using modern spectroscopic techniques is expected to significantly increase our understanding of PGM-free catalysts at the molecular level.
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Iannino, Florencia; Herrmann, Claudia K; Roset, Mara S; Briones, Gabriel
2015-05-05
Zoonoses that affect human and animal health have an important economic impact. In the study now presented, a bivalent vaccine has been developed that has the potential for preventing the transmission from cattle to humans of two bacterial pathogens: Brucella abortus and Shiga toxin-producing Escherichia coli (STEC). A 66kDa chimeric antigen, composed by EspA, Intimin, Tir, and H7 flagellin (EITH7) from STEC, was constructed and expressed in B. abortus Δpgm vaccine strain (BabΔpgm). Mice orally immunized with BabΔpgm(EITH7) elicited an immune response with the induction of anti-EITH7 antibodies (IgA) that clears an intestinal infection of E. coli O157:H7 three times faster (t=4 days) than mice immunized with BabΔpgm carrier strain (t=12 days). As expected, mice immunized with BabΔpgm(EITH7) strain also elicited a protective immune response against B. abortus infection. A Brucella-based vaccine platform is described capable of eliciting a combined protective immune response against two bacterial pathogens with diverse lifestyles-the intracellular pathogen B. abortus and the intestinal extracellular pathogen STEC. Copyright © 2015 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Coggon, J. A.; Nowell, G.; Pearson, G.; Oberthür, T.; Lorand, J.; Melcher, F.; Parman, S. W.
2010-12-01
Discrete platinum-group minerals (PGM) occur as accessory phases in mafic-ultamafic intrusions and ophiolitic chromitites, as well as numerous detrital deposits globally. The 190Pt-186Os decay system, measured by laser ablation MC-ICPMS (LA-MC-ICPMS) provides a useful geochronometric tool for direct dating of PGM. Here we present two examples that verify the accuracy of the technique in geologically well constrained situations and demonstrate the potential for using the 190Pt-186Os PGM method to accurately date layered mafic intrusions, ophiolitic chromitites and detrital PGM deposits. Fifty PGM grains from three different horizons within the Bushveld complex yield a Pt-Os isochron age of 2012 ± 47 Ma (2σ, MSWD = 1.19, 186Os/188Osi = 0.119818 ± 0.000006). This is consistent with the published U-Pb zircon age of 2054 Ma (Scoates and Friedman, 2008). The younger PGM isochron age is not likely to be a function of difference in blocking temperatures in the different systems. Pt-Os model ages are possible in high pt grains because initial 186Os/188Os can be well constrained. Using this approach we obtained Pt-Os model ages of 2113 ± 106 Ma and 2042 ± 102 Ma for a Bushveld Pt-Fe alloy and sperrylite respectively. Detrital PGM derived from the Meratus ophiolite, southeast Borneo yield a 190Pt-186Os isochron age of 202.5 Ma ± 8.3 Ma (2σ, n = 260, MSWD = 0.90, 186Os/188Osi = 0.119830 ± 0.000003), consistent with radiometric and biostratigraphic age constraints (Wakita et al., 1998). We interpret this as the age of formation of the PGM grains in during chromitite genesis in the lower oceanic lithosphere. Our combined data demonstrate the utility of the LA-MC-ICPMS method as a tool for accurate Pt-Os dating of detrital PGM as well as their igneous parent bodies. We can constrain Pt/Os fractionation at the ablation site as being < 2.5%, while within-grain heterogeneity is ultimately one of the strongest controls on isochron and single-grain ages given the partial sampling represented by laser ablation. Scoates, J.S. and Friedman, R.M. 2008. Precise age of the platiniferous Merensky reef, Bushveld Complex, South Africa, by the U-Pb zircon chemical abrasion ID-TIMS technique; Economic Geology 103, p. 465-471. Wakita, K., Miyazaki, K., Zulkarnain, I., Sopaheluwakan, J. and Sanyoto, P. 1998. Tectonic implications of new age data for the Meratus complex of south Kalimantan, Indonesia; Island Arc 7, p. 202-222.
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Mountain torrents: Quantifying vulnerability and assessing uncertainties
Totschnig, Reinhold; Fuchs, Sven
2013-01-01
Vulnerability assessment for elements at risk is an important component in the framework of risk assessment. The vulnerability of buildings affected by torrent processes can be quantified by vulnerability functions that express a mathematical relationship between the degree of loss of individual elements at risk and the intensity of the impacting process. Based on data from the Austrian Alps, we extended a vulnerability curve for residential buildings affected by fluvial sediment transport processes to other torrent processes and other building types. With respect to this goal to merge different data based on different processes and building types, several statistical tests were conducted. The calculation of vulnerability functions was based on a nonlinear regression approach applying cumulative distribution functions. The results suggest that there is no need to distinguish between different sediment-laden torrent processes when assessing vulnerability of residential buildings towards torrent processes. The final vulnerability functions were further validated with data from the Italian Alps and different vulnerability functions presented in the literature. This comparison showed the wider applicability of the derived vulnerability functions. The uncertainty inherent to regression functions was quantified by the calculation of confidence bands. The derived vulnerability functions may be applied within the framework of risk management for mountain hazards within the European Alps. The method is transferable to other mountain regions if the input data needed are available. PMID:27087696
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Nancy E. Karraker; Lisa M. Ollivier; Garth R. Hodgson
2005-01-01
Oviposition sites and reproductive ecology of the southern-torrent salamander (Rhyacotriton variegatus) remain poorly documented. This species oviposits in cryptic locations making the detection of eggs difficult. Here we describe the discovery of 1 clutch of eggs of R. variegatus from northern California, which further expands our...
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USDA-ARS?s Scientific Manuscript database
The Pregnant Gilt Model (PGM) is substantially complete and has provided substantive deliverables for the swine industry in Canada and beyond. The success of the PGM was largely dependent on a team of more than 30 researchers, students and technicians, along with external collaborators and instituti...
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Evaluation of Brucella abortus Phosphoglucomutase (pgm) Mutant as a New Live Rough-Phenotype Vaccine
Ugalde, Juan Esteban; Comerci, Diego José; Leguizamón, M. Susana; Ugalde, Rodolfo Augusto
2003-01-01
Brucella abortus S19 is the vaccine most frequently used against bovine brucellosis. Although it induces good protection levels, it cannot be administered to pregnant cattle, revaccination is not advised due to interference in the discrimination between infected and vaccinated animals during immune-screening procedures, and the vaccine is virulent for humans. Due to these reasons, there is a continuous search for new bovine vaccine candidates that may confer protection levels comparable to those conferred by S19 but without its disadvantages. A previous study characterized the phenotype associated with the phosphoglucomutase (pgm) gene disruption in Brucella abortus S2308, as well as the possible role for the smooth lipopolysaccharide (LPS) in virulence and intracellular multiplication in HeLa cells (J. E. Ugalde, C. Czibener, M. F. Feldman, and R. A. Ugalde, Infect. Immun. 68:5716-5723, 2000). In this report, we analyze the protection, proliferative response, and cytokine production induced in BALB/c mice by a Δpgm deletion strain. We show that this strain synthesizes O antigen with a size of approximately 45 kDa but is rough. This is due to the fact that the Δpgm strain is unable to assemble the O side chain in the complete LPS. Vaccination with the Δpgm strain induced protection levels comparable to those induced by S19 and generated a proliferative splenocyte response and a cytokine profile typical of a Th1 response. On the other hand, we were unable to detect a specific anti-O-antigen antibody response by using the fluorescence polarization assay. In view of these results, the possibility that the Δpgm mutant could be used as a vaccination strain is discussed. PMID:14573645
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Morris, V L; Jackson, D P; Grattan, M; Ainsworth, T; Cuppels, D A
1995-04-01
Pseudomonas syringae pv. tomato DC3481, a Tn5-induced mutant of the tomato pathogen DC3000, cannot grow and elicit disease symptoms on tomato seedlings. It also cannot grow on minimal medium containing malate, citrate, or succinate, three of the major organic acids found in tomatoes. We report here that this mutant also cannot use, as a sole carbon and/or energy source, a wide variety of hexoses and intermediates of hexose catabolism. Uptake studies have shown that DC3481 is not deficient in transport. A 3.8-kb EcoRI fragment of DC3000 DNA, which complements the Tn5 mutation, has been cloned and sequenced. The deduced amino acid sequences of two of the three open reading frames (ORFs) present on this fragment, ORF2 and ORF3, had no significant homology with sequences in the GenBank databases. However, the 510-amino-acid sequence of ORF1, the site of the Tn5 insertion, strongly resembled the deduced amino acid sequences of the Bacillus subtilis and Zea mays genes encoding 2,3-diphosphoglycerate (DPG)-independent phosphoglyceromutase (PGM) (52% identity and 72% similarity and 37% identity and 57% similarity, respectively). PGMs not requiring the cofactor DPG are usually found in plants and algae. Enzyme assays confirmed that P. syringae PGM activity required an intact ORF1. Not only is DC3481 the first PGM-deficient pseudomonad mutant to be described, but the P. syringae pgm gene is the first gram-negative bacterial gene identified that appears to code for a DPG-independent PGM. PGM activity appears essential for the growth and pathogenicity of P. syringae pv. tomato on its host plant.
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NASA Astrophysics Data System (ADS)
Kapsiotis, Argirios; Grammatikopoulos, Tassos A.; Tsikouras, Basilios; Hatzipanagiotou, Konstantin; Zaccarini, Federica; Garuti, Giorgio
2011-01-01
The Pindos ophiolite complex, located in the northwestern part of continental Greece, hosts various chromite deposits of both metallurgical (high-Cr) and refractory (high-Al) type. The Pefki chromitites are banded and sub-concordant to the surrounding serpentinized dunites. The Cr# [Cr/(Cr + Al)] of magnesiochromite varies between 0.75 and 0.79. The total PGE grade ranges from 105.9 up to 300.0 ppb. IPGE are higher than PPGE, typical of mantle hosted ophiolitic chromitites. The PGM assemblage in chromitites comprises anduoite, ruarsite, laurite, irarsite, sperrylite, hollingworthite, Os-Ru-Ir alloys including osmium and rutheniridosmine, Ru-bearing oxides, braggite, paolovite, platarsite, cooperite, vysotskite, and palladodymite. Iridarsenite and omeiite were also observed as exsolutions in other PGM. Rare electrum and native Ag are recovered in concentrates. This PGM assemblage is of great petrogenetic importance because it is significantly different from that commonly observed in podiform mantle-hosted and banded crustal-hosted ophiolitic chromitites. PGE chalcogenides of As and S are primary, and possibly crystallized directly from a progressively enriched in As boninitic melt before or during magnesiochromite precipitation. The presence of Ru-bearing oxides implies simultaneous desulfurization and dearsenication processes. Chemically zoned laurite and composite paolovite-electrum intergrowths are indicative of the relatively high mobility of certain PGE at low temperatures under locally oxidizing conditions. The PGM assemblage and chemistry, in conjunction with geological and petrologic data of the studied chromitites, indicate that it is characteristic of chromitites found within or close to the petrologic Moho. Furthermore, the strikingly different PGM assemblages between the high-Cr chromitites within the Pindos massif is suggestive of non-homogeneous group of ores.
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Loewenthal, Neta; Haim, Alon; Parvari, Ruti; Hershkovitz, Eli
2015-12-01
Phosphoglucomutase 1 (PGM1, EC 5.4.2.2) plays a critical role in glucose homeostasis and is also essential for protein N-glycosylation. The main clinical manifestations of PGM1 deficiency (MIM 614921) reported in 19 patients from different ethnic backgrounds include the following: cleft uvula/palate, Pierre Robin sequence, muscle weakness, dilated cardiomyopathy, growth retardation, elevated serum transaminases, hypoglycemia, and various endocrine abnormalities. We report the variable clinical picture of seven patients with PGM1 deficiency from a consanguineous family. Medical records of the patients were reviewed for clinical details and endocrine evaluation. Whole exome sequencing (WES) was performed. Seven patients aged 2-29 years were included, one patient died at 13 years old when getting off the school bus. All patients have an abnormal palatine structure (cleft palate, bifid uvula) and elevated serum transaminases, 4/7 have short stature (<-2 SDS) and one was diagnosed with growth hormone deficiency. Recurrent episodes of ketotic hypoglycemia were present in 6/7 patients. In two patients, hypoglycemic episodes have spontaneously resolved later on. Four out of seven patients have deteriorating adrenal function with abnormally low cortisol and ACTH levels during hypoglycemia and subnormal response of cortisol to low dose ACTH test . Serum electrolytes were within normal range. Hydrocortisone replacement therapy improved, but not entirely eliminated hypoglycemic episodes. WES revealed a previously described homozygous mutation c.112A>T, p.Asn38Tyr in the PGM1 gene. The clinical picture of PGM1 deficiency is variable among patients with the same mutation and genetic background. ACTH deficiency should be considered in any PGM1 deficient patient with hypoglycemia. © 2015 Wiley Periodicals, Inc.
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Morris, V L; Jackson, D P; Grattan, M; Ainsworth, T; Cuppels, D A
1995-01-01
Pseudomonas syringae pv. tomato DC3481, a Tn5-induced mutant of the tomato pathogen DC3000, cannot grow and elicit disease symptoms on tomato seedlings. It also cannot grow on minimal medium containing malate, citrate, or succinate, three of the major organic acids found in tomatoes. We report here that this mutant also cannot use, as a sole carbon and/or energy source, a wide variety of hexoses and intermediates of hexose catabolism. Uptake studies have shown that DC3481 is not deficient in transport. A 3.8-kb EcoRI fragment of DC3000 DNA, which complements the Tn5 mutation, has been cloned and sequenced. The deduced amino acid sequences of two of the three open reading frames (ORFs) present on this fragment, ORF2 and ORF3, had no significant homology with sequences in the GenBank databases. However, the 510-amino-acid sequence of ORF1, the site of the Tn5 insertion, strongly resembled the deduced amino acid sequences of the Bacillus subtilis and Zea mays genes encoding 2,3-diphosphoglycerate (DPG)-independent phosphoglyceromutase (PGM) (52% identity and 72% similarity and 37% identity and 57% similarity, respectively). PGMs not requiring the cofactor DPG are usually found in plants and algae. Enzyme assays confirmed that P. syringae PGM activity required an intact ORF1. Not only is DC3481 the first PGM-deficient pseudomonad mutant to be described, but the P. syringae pgm gene is the first gram-negative bacterial gene identified that appears to code for a DPG-independent PGM. PGM activity appears essential for the growth and pathogenicity of P. syringae pv. tomato on its host plant. PMID:7896694
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Mineral resource of the month: platinum-group metals
Hilliard, Henry
2003-01-01
The precious metals commonly referred to as platinum-group metals (PGM) include iridium, osmium, palladium, platinum, rhodium and ruthenium. PGM are among the rarest of elements, and their market values — particularly for palladium, platinum and rhodium — are the highest of all precious metals.
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Wideband radar cross section reduction using two-dimensional phase gradient metasurfaces
DOE Office of Scientific and Technical Information (OSTI.GOV)
Li, Yongfeng; Qu, Shaobo; Wang, Jiafu
2014-06-02
Phase gradient metasurface (PGMs) are artificial surfaces that can provide pre-defined in-plane wave-vectors to manipulate the directions of refracted/reflected waves. In this Letter, we propose to achieve wideband radar cross section (RCS) reduction using two-dimensional (2D) PGMs. A 2D PGM was designed using a square combination of 49 split-ring sub-unit cells. The PGM can provide additional wave-vectors along the two in-plane directions simultaneously, leading to either surface wave conversion, deflected reflection, or diffuse reflection. Both the simulation and experiment results verified the wide-band, polarization-independent, high-efficiency RCS reduction induced by the 2D PGM.
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Koo, Kwang M.; Jung, Sera; Lee, Beom S.; Kim, Jin-Baek; Jo, Yeong D.; Choi, Hong-Il; Kang, Si-Yong; Chung, Gook-H.; Jeong, Won-Joong; Ahn, Joon-Woo
2017-01-01
The focus of this study was the mechanism of starch accumulation in Chlamydomonas reinhardtii high-starch mutants. Three C. reinhardtii mutants showing high-starch content were generated using gamma irradiation. When grown under nitrogen-deficient conditions, these mutants had more than twice as much starch than a wild-type control. The mechanism of starch over-accumulation in these mutants was studied with comparative transcriptome analysis. In all mutants, induction of phosphoglucomutase 1 (PGM1) expression was detected; PGM1 catalyzes the inter-conversion of glucose 1-phosphate and glucose 6-phosphate in both starch biosynthetic and glycolytic pathway. Interestingly, transcript levels of phosphoglucose isomerase 1 (PGI1), fructose 1,6-bisphosphate aldolase 1 and 2 (FBA1 and FBA2) were down-regulated in all mutants; PGI1, FBA1, and FBA2 act on downstream of glucose 6-phosphate conversion in glycolytic pathway. Therefore, down-regulations of PGI1, FBA1, and FBA2 may lead to accumulation of upstream metabolites, notably glucose 6-phosphate, resulting in induction of PGM1 expression through feed-forward regulation and that PGM1 overexpression caused starch over-accumulation in mutants. These results suggest that PGI1, FBA1, FBA2, and PGM1 correlate with each other in terms of coordinated transcriptional regulation and play central roles for starch over-accumulation in C. reinhardtii. PMID:28588557
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Potential Risk Assessment of Mountain Torrent Disasters on Sloping Fields in China
NASA Astrophysics Data System (ADS)
GAO, X.
2017-12-01
China's sloping fields have the problems of low production and serious soil erosion, and mountain torrent disasters will bring more serious soil and water loss to traditional extensive exploitation of sloping field resources. In this paper, China's sloping fields were classified into three grades, such as slightly steep, steep and very steep grade. According to the geological hazards prevention and control regulation, the historical data of China's mountain torrent disasters were spatially interpolated and divided into five classes, such as extremely low, low, middle, high and extremely high level. And the risk level map of mountain torrents was finished in ArcGIS. By using overlaying analysis on sloping fields and risk level map, the potential risk regionalization map of sloping fields in various slope grades was obtained finally. The results shows that the very steep and steep sloping fields are mainly distributed in the first or second stage terraces in China. With the increase of hazard risk level, the area of sloping fields decreases rapidly and the sloping fields in extremely low and low risk levels of mountain torrents reach 98.9%. With the increase of slope grade, the area of sloping fields in various risk levels also declines sharply. The sloping fields take up approximately 60 65% and 26 30% in slightly steep and steep grade areas separately at different risk level. The risk regionalization map can provide effective information for returning farmland to forests or grassland and reducing water and soil erosion of sloping fields in the future.
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Global exploration and production capacity for platinum-group metals from 1995 through 2015
Wilburn, David R.
2012-01-01
Platinum-group metals (PGMs) are required in a variety of commercial, industrial, and military applications for many existing and emerging technologies, yet the United States is highly dependent on foreign sources of PGMs. Information on global exploration for PGMs since 1995 has been used in this study as a basis for identifying locations where the industry has determined that exploration has provided data sufficient to warrant development of a new mine or expansion of an existing operation or where a significant increase in capacity for PGMs is anticipated by 2015. Discussions include an overview of the industry and the selected sites, factors affecting mineral supply, and circumstances leading to the development of mineral properties with the potential to affect mineral supply. Of the 52 sites or regional operations that were considered in this analysis, 16 sites were producing before 1995, 28 sites commenced production from 1995 through 2010, and 8 sites were expected to begin production from 2011 through 2015 if development plans came to fruition. The United States imports PGMs primarily from Canada, Russia, South Africa, and Zimbabwe to meet increasing demand for these materials in a variety of specialized and high-tech applications. Feed sources of PGMs are changing in South Africa and Russia, which together accounted for about 89 percent of platinum production and 82 percent of palladium production in 2009. A greater amount of South African PGM capacity is likely to come from deeper, higher cost Upper Group Reef seam 2 deposits and deposits in the Eastern Bushveld area. Future Russian PGM capacity is likely to come from ore zones with generally lower PGM content and different platinum-to-palladium ratios than the nickel-rich ore that dominated PGM supply in the 1990s. Because PGM supply from Canada and Russia is derived as a byproduct of copper and nickel mining, the PGM supply from these countries is influenced by economic, environmental, political, and technological factors affecting exploration for and development of copper and nickel, as well as factors affecting the PGM industry. The recovery of PGMs from mill tailings since 2004 and the recycling of PGMs from catalytic converters, electrical components, and jewelry has increased since 1995 so that recycled PGMs recovered from these products accounted for about 30 percent of the supply of platinum worldwide and 29 percent of the supply of palladium worldwide in 2010. Economic and geopolitical conditions have influenced PGM supply and demand. The global recession of 2008 and 2009 temporarily decreased demand for PGMs and constrained PGM mine exploration and development, at least through 2010. Legislation regulating the structure of the mining sector has affected mining in Russia, South Africa, and Zimbabwe. Stricter vehicle emissions standards in established markets since the 1980s have led to mandatory use of pollution control devices, such as catalytic converters, that contain PGMs and are required on vehicles in expanding markets, such as China and India. It is expected that South Africa, Russia, Canada, and Zimbabwe will continue to be the principal sources of PGM at least for the next decade. Based on this review of the PGM industry, the world’s platinum capacity, expressed in terms of recoverable platinum metal, increased from 1995 through 2010 by 77,000 kilograms (kg) in South Africa, 9,000 kg in Zimbabwe, 6,000 kg in Russia, 2,000 kg in Botswana, and 2,000 kg in Canada. For the same period, palladium capacity worldwide increased by 44,000 kg in South Africa, 22,000 kg in Russia, 8,000 kg in Canada, 8,000 kg in the United States, 7,000 kg in Zimbabwe, and 3,000 kg in Botswana. Platinum capacity worldwide is expected to further increase by 24,000 kg in South Africa, 9,000 kg in Russia, 3,000 kg in Canada, and 2,000 kg in Zimbabwe from 2011 through 2015. Palladium capacity worldwide is likewise expected to increase an additional 16,000 kg in Russia, 14,000 kg in South Africa, 4,000 kg in Zimbabwe, and 1,000 kg in Canada if new or expanded mine and associated processing capacity comes into production as planned. It is likely that the magnitude of these changes in PGM capacity has been influenced by such factors as the global economy, electrical capacity shortages and mine safety concerns in South Africa, and geopolitical conditions in the major PGM producing countries.
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Metagenome changes in the biogas producing community during anaerobic digestion of rice straw.
Pore, Soham D; Shetty, Deepa; Arora, Preeti; Maheshwari, Sneha; Dhakephalkar, Prashant K
2016-08-01
The present investigation was undertaken to study the microbial community succession in a sour and healthy digester. Ion torrent next-generation sequencing (NGS)-based metagenomic approach indicated abundance of hydrolytic bacteria and exclusion of methanogens and syntrophic bacteria in sour digester. Functional gene analysis revealed higher abundance of enzymes involved in acidogenesis and lower abundance of enzymes associated with methanogenesis like Methyl coenzyme M-reductase, F420 dependent reductase and Formylmethanofuran dehydrogenase in sour digester. Increased abundance of methanogens (Methanomicrobia) and genes involved in methanogenesis was observed in the restored/healthy digester highlighting revival of pH sensitive methanogenic community. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Peer-Group Mentoring as a Tool for Teacher Development
ERIC Educational Resources Information Center
Geeraerts, Kendra; Tynjälä, Päivi; Heikkinen, Hannu L. T.; Markkanen, Ilona; Pennanen, Matti; Gijbels, David
2015-01-01
Peer-group mentoring (PGM) is a new model designed to support the professional development of teachers in Finland. This study examines the experiences of mentees participating in PGM and potential differences in the experiences of teachers in general education and vocational education. It also addresses the mentees' perceptions of the results of…
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Isozyme variation in lychee (Litchi chinensis Sonn.)
USDA-ARS?s Scientific Manuscript database
A genetic diversity analysis involving 49 lychee (Litchi chinensis SOM.) accessions using eight enzyme systems encoding 12 loci (Zdh-I, Zdh-2, Mdh-2, Per-l, Pgi-2, Pgm-1, Pgm-2, Sk& Tpi-1, Tpi-2, Ugpp-1, and Ugpp-2) revealed moderate to high levels of genetic variability. Cluster analysis of the iso...
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Inactivation of avirulent pgm+ and delta pgm Yersinia pestis by ultraviolet light (UV-C)
USDA-ARS?s Scientific Manuscript database
Yersinia pestis is the causative agent of bubonic plague. Though not considered a foodborne pathogen, Y. pestis can survive, and even grow, in some foods, and the foodborne route of transmission is not without precedent. As such, concerns exist over the possible intentional contamination of foods wi...
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NASA Astrophysics Data System (ADS)
Malitch, K. N.; Anikina, E. V.; Badanina, I. Yu.; Belousova, E. A.; Pushkarev, E. V.; Khiller, V. V.
2016-01-01
The isotopic and geochemical characteristics of PGE mineralization in high-Mg chromitite from the banded dunite-wehrlite-clinopyroxenite complex of the Nurali lherzolite massif, the South Urals, Russia is characterized for the first time. Electron microprobe analysis and LA MC-ICP-MS mass spectrometry are used for studying Cr-spinel and platinum-group minerals (PGM). Two processes synchronously develop in high-Mg chromitite subject to metamorphism: (1) the replacement of Mg-Al-rich Cr-spinel, orthopyroxene, and diopside by chromite, Cr-amphibole, chlorite, and garnet; (2) the formation of a secondary mineral assemblage consisting of finely dispersed ruthenium or Ru-hexaferrum aggregate and silicate-oxide or silicate matter on the location of primary Ru-Os-sulfides of the laurite-erlichmanite solid solution series. Similar variations of Os-isotopic composition in both primary and secondary PGM assemblages are evidence for the high stability of the Os isotope system in PGM and for the possibility of using model 187Os/188Os ages in geodynamic reconstructions.
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Geopotential Model Improvement Using POCM_4B Dynamic Ocean Topography Information: PGM2000A
NASA Technical Reports Server (NTRS)
Pavlis, N. K.; Chinn, D. S.; Cox, C. M.; Lemoine, Frank G.; Smith, David E. (Technical Monitor)
2000-01-01
The two-year mean (1993-1994) Dynamic Ocean Topography (DOT) field implied by the POCM_4B circulation model was used to develop normal equations for DOT, in a surface spherical harmonic representation. These normal equations were combined with normal equations from satellite tracking data, surface gravity data, and altimeter data from TOPEX/Poseidon and ERS-1. Several least-squares combination solutions were developed in this fashion, by varying parameters such as the maximum degree of the estimated DOT and the relative weights of the different data. The solutions were evaluated in terms of orbit fit residuals, GPS/Leveling-derived undulations, and independent DOT information from in situ WOCE hydrographic data. An optimal solution was developed in this fashion which was originally presented at the 1998 EGS meeting in Nice, France. This model, designated here PGM2000A, maintains the orbit and land geoid modeling performance of EGM96, while improving its marine geoid modeling capability. In addition, PGM2000A's error spectrum is considerably more realistic than those of other contemporary gravitational models and agrees well with the error spectrum of EGM96. We will present the development and evaluation of PGM2000A, with particular emphasis on the weighting of the DOT information implied by POCM_4B. We will also present an inter-comparison of PGM2000A with the GRIM5-C1 and TEG-4 models. Directions for future work and problematic areas will be identified.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hess, Becky M.; Kaiser, Brooke LD; Sydor, Michael A.
ABSTRACT Aims To develop and optimize an assay to determine viability status of Bacillus anthracis Sterne and Yersinia pestis pgm- strains in the presence of white powders by coupling propidium monoazide (PMA) treatment with real-time PCR (qPCR) analysis. Methods and Results PMA selectively enters nonviable cells and binds DNA, thereby increasing qPCR assay cycle threshold (CT) values compared to untreated samples. Dye concentration, cell number and fitness, incubation time, inactivation methods, and assay buffer were optimized for B. anthracis Sterne and Y. pestis pgm-. Differences in CT values in nonviable cells compared to untreated samples were consistently > 9 formore » both B. anthracis Sterne vegetative cells and Y. pestis pgm- in the presence and absence of three different white powders. Our method eliminates the need for a DNA extraction step prior to detection by qPCR. Conclusions The developed assay enables simultaneous identification and viability assessment for B. anthracis Sterne and Y. pestis pgm- under laboratory conditions, even in the presence of white powders. Eliminating the DNA extraction step that is typically used reduces total assay time and labor requirements for sample analysis. Significance and Impact of the Study The method developed for simultaneous detection and viability assessment for B. anthracis and Y. pestis can be employed in forming decisions about the severity of a biothreat event or the safety of food. Keywords Bacillus anthracis, Yersinia pestis, Propidium Monoazide, qPCR, White Powders, Rapid Viability Detection« less
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Energetic Coupling between Ligand Binding and Dimerization in E. coli Phosphoglycerate Mutase
Gardner, Nathan W.; Monroe, Lyman K.; Kihara, Daisuke; Park, Chiwook
2016-01-01
Energetic coupling of two molecular events in a protein molecule is ubiquitous in biochemical reactions mediated by proteins, such as catalysis and signal transduction. Here, we investigate energetic coupling between ligand binding and folding of a dimer using a model system that shows three-state equilibrium unfolding in an exceptional quality. The homodimeric E. coli cofactor-dependent phosphoglycerate mutase (dPGM) was found to be stabilized by ATP in a proteome-wide screen, although dPGM does not require or utilize ATP for enzymatic function. We investigated the effect of ATP on the thermodynamic stability of dPGM using equilibrium unfolding. In the absence of ATP, dPGM populates a partially unfolded, monomeric intermediate during equilibrium unfolding. However, addition of 1.0 mM ATP drastically reduces the population of the intermediate by selectively stabilizing the native dimer. Using a computational ligand docking method, we predicted ATP binds to the active site of the enzyme using the triphosphate group. By performing equilibrium unfolding and isothermal titration calorimetry with active-site variants of dPGM, we confirmed that active-site residues are involved in ATP binding. Our findings show that ATP promotes dimerization of the protein by binding to the active site, which is distal from the dimer interface. This cooperativity suggests an energetic coupling between the active-site and the dimer interface. We also propose a structural link to explain how ligand binding to the active site is energetically coupled with dimerization. PMID:26919584
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The EGM2008 Global Gravitational Model
NASA Astrophysics Data System (ADS)
Pavlis, N. K.; Holmes, S. A.; Kenyon, S. C.; Factor, J. K.
2008-12-01
The development of a new Earth Gravitational Model (EGM) to degree 2160 has been completed. This model, designated EGM2008, is the product of the final re-iteration of our modelling and estimation approach. Our multi-year effort has produced several Preliminary Gravitational Models (PGM) of increasingly improved performance. One of these models (PGM2007A) was provided for evaluation to an independent Evaluation Working Group, sponsored by the International Association of Geodesy (IAG). In an effort to address certain shortcomings of PGM2007A, we have considered the feedback that we received from this Working Group. As part of this effort, EGM2008 incorporates an improved version of our 5'x5' global gravity anomaly database and has benefited from the latest GRACE based satellite-only solutions (e.g., ITG- GRACE03S). EGM2008 incorporates an improved ocean-wide set of altimetry-derived gravity anomalies that were estimated using PGM2007B (a variant of PGM2007A) and its associated Dynamic Ocean Topography (DOT) model as reference models in a "Remove-Compute-Restore" fashion. For the Least Squares Collocation estimation of our final global 5'x5' area-mean gravity anomaly database, we have used consistently PGM2007B as our reference model to degree 2160. We have developed and used a formulation that predicts area-mean gravity anomalies that are effectively band-limited to degree 2160, thereby minimizing aliasing effects during the harmonic analysis process. We have also placed special emphasis on the refinement and "calibration" of the error estimates that accompany our final combination solution EGM2008. We present the main aspects of the model's development and evaluation. This evaluation was accomplished primarily through the comparison of various model derived quantities with independent data and models (e.g., geoid undulations derived from GPS positioning and spirit levelling, astronomical deflections of the vertical, etc.). We will also present comparisons of our model-implied Dynamic Ocean Topography with other contemporary estimates (e.g., from ECCO).
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Gagnon, Zofia E; Patel, Amit
2007-02-15
Recent data show that platinum group metals (PGMs), primarily platinum (Pt), palladium (Pd) and rhodium (Rd), from automobile catalytic converters are being deposited in the environment. We investigated the PGM neurotoxicity and tolerance mechanism by induction of metallothionein (MT) in developing chick embryos. Chick embryos were injected on the 7th and 14th days of incubation with different concentrations of Pt and mixture of Pt, Pd and Rh (PGM mix) solutions. It is documented that induction of MT by zinc (Zn+2) protects against metal and non-metal hepatotoxicity. In this study the MT induction was examined through pretreatment of the two highest Pt(IV) exposure levels with exogenous Zn2+ on the 4th and 11th days of incubation. SDS-PAGE assay and digital image system were used to identify and quantify MT in homogenized brain and liver tissues. Quantitative analysis revealed an increase of MT in the 5 ppm Pt exposure as compared to controls. The 10 ppm Pt treatment was a lethal dose for exposed embryos. There was increased mortality at the 1.0 PGM mix level. The interaction of Pt, Pd and Rh in the mixture seems to favor metal accumulation and MT induction in the liver but not the brain. Pretreatment with exogenous Zn2+ increased chick survival. These results indicate that induction of MT plays a protective role against PGM toxicity. Metal analysis using atomic absorption spectrometer in graphite furnace mode (GFAAS) revealed PGM accumulation in chick embryo liver and brain tissues proportional to exposure concentration. Our results may imply that MT has an important role as a tolerance mechanism against PGM toxicity. The presence of Pt(IV) in brain tissue suggests that the undeveloped blood-brain barrier is permeable to PGMs. This raises concerns regarding the implication of these metals on neural injury.
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NASA Astrophysics Data System (ADS)
Janu, Stefan; Mehlhorn, Susanne; Moser, Markus
2013-04-01
Analysis and reconstructed modelling of the debris flow event of the 21st of July 2012 of St. Lorenzen (Styria, Austria) Authors: Stefan Janu, Susanne Mehlhorn, Markus Moser The village of St. Lorenzen, in the Styrian Palten valley is situated on the banks of the Lorenz torrent, in which a debris flow event occurred in the early morning hours of the 21st of July 2012, causing catastrophic damage to residential buildings and other infrastructural facilities. In the ministry-approved hazard zone map of 2009, the flood water discharge and bedload volume associated with a 150-year event was estimated at 34 m³/s and 25,000 m³ respectively for the 5.84 km² catchment area. The bedload transport capacity of the torrent was classified as ranging from 'heavy' to 'capable of producing debris flows'. The dominant process type of the mass movement event may be described as a fine-grained debris flow. The damage in the residential area of St.Lorenzen was caused by a debris flow pulse in the lower reach of the Lorenz torrent. This debris flow pulse was in turn caused by numerous landslides along the middle reaches of the torrent, some of which caused blockages, ultimately leading to an outburst event in the main torrent. Discharge cross-sections ranging from 65 - 90 m², and over 100 m² in a few instances, were measured upstream of the St. Lorenzen residential area. Back-calculations of velocities yielded an average debris flow velocity along the middle reaches of the torrent between 11 and 16 m/s. An average velocity of 9 m/s was calculated for the debris flow at the neck of the alluvial fan directly behind the center of the village. Due to both the high discharge values as well as to the height of the mass movement deposits, the natural hazard event of 21 July 2012 in St. Lorenzen is clearly to be described as having had an extreme intensity. A total of 67 buildings were damaged along the Lorenz torrent, 7 of were completely destroyed. According to the Austrian Service for Torrent and Avalanche Control, a great number of protection measures have in the past been realized in the Lorenz torrent, which with certainty contributed significantly to an even greater amount of damage in the St. Lorenz residential area having been prevented. Attempts at reconstructing the event processes as well simulating the debris flow in 2D were undertaken in the course of the event documentation and analysis. The thus obtained discharge heights, flow velocities and impact pressure values corresponded with the well documented event. The two dimensional simulations were carried out with the program FLO-2D, which is capable of simulating debris flows. The rheological parameters of the debris flow material were determined with the aid of a viscometer and a debris rotation drum. The debris flow hydrograph, bedload and bedload ratio were reconstructed using data from the event documentation, such as difference models, geological mapping, wetted perimeters, witness's statements, etc. The aim of the very detailed event documentation and analysis was to reconstruct the extreme process sequence along with the damaging effects that they had in the build-up area of St. Lorenzen. There was a large media interest in this event. The results should therefore serve to answer the multitude of questions about this event that lie in the public as well political interests. Additional and substantial protection measures were also planned for the village of St. Lorenzen on the basis of these event analysis results. These are comprised of two debris flow barriers in the lower gorge streches with a capacity of 15,000 m³ each as well as a bedload retention basin directly above, with a capacity of 30,000 m³. Construction of these technical protection measures has already begun. Authoŕs adresses: DI Stefan Janu Fachbereich Wildbachprozesse Austrian Service for Torrent and Avalanche Control, GBL Ennstal und Salzatal Schönaustraße 50 8940 Liezen Dipl.Geogr. Susanne Mehlhorn Fachbereich Wildbachprozesse Austrian Service for Torrent and Avalanche Control, BMLFUW Abt. IV/5 Marxergasse 2 1030 Wien DI Markus Moser Fachbereich Wildbachprozesse Austrian Service for Torrent and Avalanche Control, GBL Lungau Johann Löcker Str. 3 5580 Tamsweg
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Hereditary Hemochromatosis Restores the Virulence of Plague Vaccine Strains
Quenee, Lauriane E.; Hermanas, Timothy M.; Ciletti, Nancy; Louvel, Helene; Miller, Nathan C.; Elli, Derek; Blaylock, Bill; Mitchell, Anthony; Schroeder, Jay; Krausz, Thomas; Kanabrocki, Joseph; Schneewind, Olaf
2012-01-01
Nonpigmented Yersinia pestis (pgm) strains are defective in scavenging host iron and have been used in live-attenuated vaccines to combat plague epidemics. Recently, a Y. pestis pgm strain was isolated from a researcher with hereditary hemochromatosis who died from laboratory-acquired plague. We used hemojuvelin-knockout (Hjv−/−) mice to examine whether iron-storage disease restores the virulence defects of nonpigmented Y. pestis. Unlike wild-type mice, Hjv−/− mice developed lethal plague when challenged with Y. pestis pgm strains. Immunization of Hjv−/− mice with a subunit vaccine that blocks Y. pestis type III secretion generated protection against plague. Thus, individuals with hereditary hemochromatosis may be protected with subunit vaccines but should not be exposed to live-attenuated plague vaccines. PMID:22896664
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After the revolution? Ethical and social challenges in ‘personalized genomic medicine’
Juengst, Eric T; Settersten, Richard A; Fishman, Jennifer R; McGowan, Michelle L
2013-01-01
Personalized genomic medicine (PGM) is a goal that currently unites a wide array of biomedical initiatives, and is promoted as a ‘new paradigm for healthcare’ by its champions. Its promissory virtues include individualized diagnosis and risk prediction, more effective prevention and health promotion, and patient empowerment. Beyond overcoming scientific and technological hurdles to realizing PGM, proponents may interpret and rank these promises differently, which carries ethical and social implications for the realization of PGM as an approach to healthcare. We examine competing visions of PGM’s virtues and the directions in which they could take the field, in order to anticipate policy choices that may lie ahead for researchers, healthcare providers and the public. PMID:23662108
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NASA Astrophysics Data System (ADS)
Jaafar, Nardiah Rizwana; Bakar, Farah Diba Abu; Murad, Abdul Munir Abdul; Mahadi, Nor Muhammad
2015-09-01
The conversion of 3-phosphoglycerate to 2-phosphoglycerate during glycolysis and gluconeogenesis is catalyzed by phosphoglycerate mutase (PGM). Better understanding of metabolic reactions performed by this enzyme has been studied extensively in prokaryotes and eukaryotes. Here, we report a phosphoglycerate mutase from the psychrophilic yeast, Glaciozyma antarctica. cDNA encoding for PGM from G. antarctica PI12, a psychrophilic yeast isolated from sea ice at Casey Station, Antarctica was amplified. The gene was then cloned into a cloning vector and sequenced, which verified its identity as the gene putatively encoding for PGM. The recombinant protein was expressed in Escherichia coli BL21 (DE3) as inclusion bodies and this was confirmed by SDS-PAGE and Western blot.
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2014-01-01
Background Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. Results We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. Conclusions The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel. PMID:24669946
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Bertolini, Francesca; Ghionda, Marco Ciro; D'Alessandro, Enrico; Geraci, Claudia; Chiofalo, Vincenzo; Fontanesi, Luca
2015-01-01
The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine) for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon) as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43%) in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97) and lower for avian species (0.70). PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.
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Kai, Wataru; Nomura, Kazuharu; Fujiwara, Atushi; Nakamura, Yoji; Yasuike, Motoshige; Ojima, Nobuhiko; Masaoka, Tetsuji; Ozaki, Akiyuki; Kazeto, Yukinori; Gen, Koichiro; Nagao, Jiro; Tanaka, Hideki; Kobayashi, Takanori; Ototake, Mitsuru
2014-03-26
Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.
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Bertolini, Francesca; Ghionda, Marco Ciro; D’Alessandro, Enrico; Geraci, Claudia; Chiofalo, Vincenzo; Fontanesi, Luca
2015-01-01
The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine) for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon) as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43%) in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97) and lower for avian species (0.70). PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures. PMID:25923709
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Luo, Gang; Angelidaki, Irini
2014-09-01
The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier Ltd. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Komini Babu, Siddharth; Chung, Hoon T.; Zelenay, Piotr
This paper reports on the characterization of polymer electrolyte fuel cell (PEFC) cathodes featuring a platinum group metal-free (PGM-free) catalyst using nano-scale resolution X-ray computed tomography (nano-CT) and morphological analysis. PGM-free PEFC cathodes have gained significant interest in the past decade since they have the potential to dramatically reduce PEFC costs by eliminating the large platinum (Pt) raw material cost. However, several challenges remain before they are commercially viable. Since these catalysts have lower volumetric activity, the PGM-free cathodes are thicker and are subject to increased gas and proton transport resistances that reduce the performance. To better understand the efficacymore » of the catalyst and improve electrode performance, a detailed understanding the correlation between electrode fabrication, morphology, and performance is crucial. In this work, the pore/solid structure and the ionomer distribution was resolved in three dimensions (3D) using nano-CT for three PGM-free electrodes of varying Nafion® loading. The associated transport properties were evaluated from pore/particlescale simulations within the nano-CT imaged structure. These characterizations are then used to elucidate the microstructural origins of the dramatic changes in fuel cell performance with varying Nafion® ionomer loading. We show that this is primarily a result of distinct changes in ionomer’s spatial distribution. The significant impact of electrode morphology on performance highlights the importance of PGM-free electrode development in concert with efforts to improve catalyst activity and durability.« less
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Komini Babu, Siddharth; Chung, Hoon T.; Zelenay, Piotr; ...
2016-11-02
This paper reports on the characterization of polymer electrolyte fuel cell (PEFC) cathodes featuring a platinum group metal-free (PGM-free) catalyst using nano-scale resolution X-ray computed tomography (nano-CT) and morphological analysis. PGM-free PEFC cathodes have gained significant interest in the past decade since they have the potential to dramatically reduce PEFC costs by eliminating the large platinum (Pt) raw material cost. However, several challenges remain before they are commercially viable. Since these catalysts have lower volumetric activity, the PGM-free cathodes are thicker and are subject to increased gas and proton transport resistances that reduce the performance. To better understand the efficacymore » of the catalyst and improve electrode performance, a detailed understanding the correlation between electrode fabrication, morphology, and performance is crucial. In this work, the pore/solid structure and the ionomer distribution was resolved in three dimensions (3D) using nano-CT for three PGM-free electrodes of varying Nafion® loading. The associated transport properties were evaluated from pore/particlescale simulations within the nano-CT imaged structure. These characterizations are then used to elucidate the microstructural origins of the dramatic changes in fuel cell performance with varying Nafion® ionomer loading. We show that this is primarily a result of distinct changes in ionomer’s spatial distribution. The significant impact of electrode morphology on performance highlights the importance of PGM-free electrode development in concert with efforts to improve catalyst activity and durability.« less
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NASA Astrophysics Data System (ADS)
Kurt-Karakus, Perihan Binnur; Ugranli-Cicek, Tugba; Sofuoglu, Sait C.; Celik, Halil; Gungormus, Elif; Gedik, Kadir; Sofuoglu, Aysun; Okten, Hatice Eser; Birgul, Askın; Alegria, Henry; Jones, Kevin C.
2018-03-01
Atmospheric levels of 43 PCBs, 22 OCPs, and 14 PBDEs were determined in 16 cities at urban and rural sites by passive sampling to generate the first large-scale nationwide dataset of POP residues in Turkey's atmosphere. Sampling campaign was performed from May 2014 to April 2015 with three-month sampling periods at locations on east-west and north-south transects through the country to investigate seasonal and spatial variations, including long range atmospheric transport (LRAT). Factor analysis was conducted to infer on the potential sources. Overall average Σ43PCBs concentration was 108 ± 132 pg/m3. PCB-118 (26.3 ± 44.6 pg/m3) was the top congener, and penta-CBs had the highest contribution with 54.3%. ΣDDTs had the highest annual mean concentration with 134 ± 296 pg/m3 among the OCP groups among which the highest concentration compound was p'p-DDE (97.6 ± 236 pg/m3). Overall average concentration of Σ14PBDEs was 191 ± 329 pg/m3 with the highest contribution from BDE-190 (42%). Comparison of OCPs and PCBs concentrations detected at temperatures which were above and below annual average temperature indicated higher concentrations in the warmer periods, hence significance of secondary emissions for several OCPs and Σ43PCBs, as well as inference as LRAT from secondary emissions. The first nationwide POPs database constructed in this study, point to current use, local secondary emissions, and LRAT for different individual compounds, and indicate the need for regular monitoring.
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Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution.
Kuang, Meihua Christina; Kominek, Jacek; Alexander, William G; Cheng, Jan-Fang; Wrobel, Russell L; Hittinger, Chris Todd
2018-05-21
Repeated evolutionary events imply underlying genetic constraints that can make evolutionary mechanisms predictable. Morphological traits are thought to evolve frequently through cis-regulatory changes because these mechanisms bypass constraints in pleiotropic genes that are reused during development. In contrast, the constraints acting on metabolic traits during evolution are less well studied. Here we show how a metabolic bottleneck gene has repeatedly adopted similar cis-regulatory solutions during evolution, likely due to its pleiotropic role integrating flux from multiple metabolic pathways. Specifically, the genes encoding phosphoglucomutase activity (PGM1/PGM2), which connect GALactose catabolism to glycolysis, have gained and lost direct regulation by the transcription factor Gal4 several times during yeast evolution. Through targeted mutations of predicted Gal4-binding sites in yeast genomes, we show this galactose-mediated regulation of PGM1/2 supports vigorous growth on galactose in multiple yeast species, including Saccharomyces uvarum and Lachancea kluyveri. Furthermore, the addition of galactose-inducible PGM1 alone is sufficient to improve the growth on galactose of multiple species that lack this regulation, including Saccharomyces cerevisiae. The strong association between regulation of PGM1/2 by Gal4 even enables remarkably accurate predictions of galactose growth phenotypes between closely related species. This repeated mode of evolution suggests that this specific cis-regulatory connection is a common way that diverse yeasts can govern flux through the pathway, likely due to the constraints imposed by this pleiotropic bottleneck gene. Since metabolic pathways are highly interconnected, we argue that cis-regulatory evolution might be widespread at pleiotropic genes that control metabolic bottlenecks and intersections.
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Consani, Sirio; Carbone, Cristina; Dinelli, Enrico; Balić-Žunić, Tonci; Cutroneo, Laura; Capello, Marco; Salviulo, Gabriella; Lucchetti, Gabriella
2017-06-01
Metal-polluted mine waters represent a major threat to the quality of waters and sediments in a downstream basin. At the confluence between acidic mine waters and the unpolluted waters of the Gromolo Torrent (Liguria, North-West Italy), the massive formation of an ochreous amorphous precipitate takes place. This precipitate forms a soft blanket that covers the torrent bed and can be observed down to its mouth in the sea. The aim of this work is to evaluate the dispersion of metals in the Gromolo Torrent basin from the abandoned Cu-Fe sulphide mine of Libiola to the Ligurian Sea and to assess the metal remobilisation from the amorphous precipitates. The mineralogy of the superficial sediments collected in the torrent bed and the concentrations of different elements of environmental concern (Cu, Zn, Cd, Co, Cr, Mn, Ni, Pb, As, and Sb) were therefore analysed. The results showed that the precipitates contain high concentration of Fe, Al, Cu, and Zn, significantly modifying the bulk chemistry of the Gromolo Torrent sediments. In order to evaluate the possible remobilisation of ecotoxic elements from the amorphous precipitates, bulk leaching tests were performed with both deionised and seawater. Bulk leaching tests with deionised water mobilised primarily high Pb amounts, but also relatively high concentrations of Fe, Al, Cu, and Zn are released in the leachate. In seawater tests, Fe, Al, Cu, and Zn were released in smaller amounts, while other elements like Mn, Cd, Co, and Ni increased in the released fraction. Pb was still strongly released as in deionised water experiments. The results show that the interaction of precipitates and seawater can remobilise high concentrations of metals, thus affecting the surrounding environment.
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Domestic Production Issues in Chromium and Platinum-Group Metals
1988-09-01
iridium, and minor amounts of osmium. 12 Uses. Platinum-group metals (PGM) are critical as catalysts in fossil fuel processing and electronic...metals (PGM) were then described as critical in fossil fuel production, and in electronic and electrical components. The international market is...this research process . ii Table of Contents Page Preface.. .............. ii List of Figures ................ vi List of Tables ................ vi
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Zhou, Dong-Jie; Pan, Jiang; Yu, Hui-Lei; Zheng, Gao-Wei; Xu, Jian-He
2013-07-01
A new strain, Enterobacter sp. ECU1107, was identified among over 200 soil isolates using a two-step screening strategy for the enantioselective synthesis of (2S,3R)-3-phenylglycidate methyl ester (PGM), a key intermediate for production of a potent anticancer drug Taxol®. An organic-aqueous biphasic system was employed to reduce spontaneous hydrolysis of the substrate PGM and isooctane was found to be the most suitable organic solvent. The temperature and pH optima of the whole cell-mediated bioreaction were 40 °C and 6.0, respectively. Under these reaction conditions, the enantiomeric excess (ee(s)) of (2S,3R)-PGM recovered was greater than 99 % at approximately 50 % conversion. The total substrate loading in batch reaction could reach 600 mM. By using whole cells of Enterobacter sp. ECU1107, (2S,3R)-PGM was successfully prepared in decagram scale in a 1.0-l mechanically stirred reactor, affording the chiral epoxy ester in >99 % ee s and 43.5 % molar yield based on the initial load of racemic substrate.
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Gradient metasurface for four-direction anomalous reflection in terahertz
NASA Astrophysics Data System (ADS)
Wang, Jiao; Jiang, Yannan
2018-06-01
In this paper, a four-direction anomalous reflection metasurface is proposed. The basic cells comprise of squares and circles, which are designed at various sizes and arranged in a super cell at regular spacing. Then, properly combining super cells molds a square phase gradient metasurface (PGM). It is mounted on an optical thickness gold mirror, which inhibits all light transmission. Markedly different from previously reported metasurfaces, the square PGM is characterized by four-direction reflection beams. It takes into consideration the normal incidence and the oblique incidence. For the normal incidence, that the degrees of the four reflection angles are identical is due to the x, - x, y and - y directional discontinuous phase gradients, and lies on the symmetric structure in the xoy plane, which is then revealed by the surface current distribution. Incident angles varying from -20° to 20°, the reflection angles are demonstrated in the oblique incidence. Moreover, the PGM is polarization-independent. The performance is attributed to the symmetry of structure, which is verified by Radar cross section. Simulated results prove that our method offers a simple and effective strategy for metasurface design in terahertz. The proposed PGM can aid in focused beams, steering beams, and shaped beams.
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Genetic Pd, Pt, Au, Ag, and Rh mineralogy in Noril'sk sulfide ores
NASA Astrophysics Data System (ADS)
Spiridonov, E. M.; Kulagov, E. A.; Serova, A. A.; Kulikova, I. M.; Korotaeva, N. N.; Sereda, E. V.; Tushentsova, I. N.; Belyakov, S. N.; Zhukov, N. N.
2015-09-01
The undeformed ore-bearing intrusions of the Noril'sk ore field (NOF) cut through volcanic rocks of the Late Permian-Early Triassic trap association folded in brachysynclines. Due to the nonuniform load on the roof of intrusive bodies, most sulfide melts were squeezed, up to the tops of ore-bearing intrusions; readily fusible Ni-Fe-Cu sulfide melts were almost completely squeezed. In our opinion, not only one but two stages of mineralization developed at the Noril'sk deposits: (i) syntrap magmatic and (ii) epigenetic post-trap metamorphic-hydrothermal. All platinum-group minerals (PGM) and minerals of gold are metasomatic in the Noril'sk ores. They replaced sulfide solid solutions and exsolution structures. All types of PGM and Au minerals occur in the ores, varying in composition from pyrrhotite to chalcopyrite, talnakhite, mooihoekite, and rich in galena; they are localized in the inner and outer contact zones and differ only in the quantitative proportions of ore minerals. The aureoles of PGM and Au-Ag minerals are wider than the contours of sulfide bodies and coincide with halos of fluid impact on orebodies and adjacent host rocks. The pneumatolytic PGM and Au-Ag minerals are correlated in abundance with the dimensions of sulfide bodies. Their amounts are maximal in veins of late fusible ore composed of eutectic PbS ss and iss intergrowths, as well as at their contacts. The Pd and Pt contents in eutectic sulfide ores of NOF are the world's highest. In the process of noble-metal mineral formation, the fluids supply Pd, Pt, Au, As, Sb, Sn, Bi, and a part of Te, whereas Fe, Ni, Cu, Pb, Ag, Rh, a part of Te and Pd are leached from the replaced sulfide minerals. The pneumatolytic PGM of the early stage comprises Pd and Pt intermetallic compounds enriched in Au along with Pd-Pt-Fe-Ni-Cu-Sn-Pb(As) and (Pd,Pt,Au)(Sn,Sb,Bi,Te,As) solid solutions. Pneumatolytic PGM and Au minerals of the middle stage are products of solid-phase transformation and recrystallization of early PGM in combination with the newly formed mineral species Sb-paolovite-insizwaite-geversite-maslovite, niggliite, tetraferroplatinum, rustenburgite-atokite-zvyagintsevite, moncheite, majakite, plumbopalladinite, polarite in association with altaite. The late minerals of the middle stage include stannopalladinite, tatianaite-taimyrite, Ag-Pd-Pt tetraauricupride, and cuproauride. PGM and Au-Ag minerals of the late stage are represented by sobolevskite-sudburyite-kotulskite, maslovite-michenerite, low-Sb paolovite, hessite, cabriite, Au-Ag minerals with fineness of 870-003, froodite, Sb-free insizwaite, Bi-free geversite, and Sb-free niggliite. Electrum and küstelite in PGM aggregates are not zoned. Crystals of Au-Ag minerals that grow over PGM minerals are smoothly zoned. Their zoning may be direct (crystal margins are enriched in Ag), inverse, oscillatory, and complex. Despite favorable annealing conditions, exsolution structures are not identified in Au-Ag minerals from the Noril'sk ores. Sperrylite—the latest of pneumatolytic PGM—occurs as metacrysts up to 14 cm in size. Sperrylite, which replaces high-Sb minerals, contains up to 11 wt % Sb. Pneumatolytic noble-metal minerals originated under the effect of the fluids released during crystallization of sulfide melts in an extremely reductive setting and at extremely low fS2; temperature drops from ~450 to ~350°C. Metamorphic-hydrothermal Ag mineralization (native silver, Hg-silver, sulfides and selenides, chalcopyrite-lenaite solid solutions, argentopentlandite), Pd mineralization (vysotskite, palladoarsenide, vincentite, Sb-free Ag-paolovite, malyshevite, native palladium), and Pt mineralization (kharaelakhite, cooperite, native platinum) develop in those parts of orebodies that are affected by low-grade metamorphism.
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Mittermeier, Thomas; Madkikar, Pankaj; Wang, Xiaodong; Gasteiger, Hubert A.; Piana, Michele
2017-01-01
In this experimental study, we investigate various transition-metal silicides as platinum-group-metal-(PGM)-free electrocatalysts for the hydrogen oxidation reaction (HOR), and for the hydrogen evolution reaction (HER) in acidic environment for the first time. Using cyclic voltammetry in 0.1 M HClO4, we first demonstrate that the tested materials exhibit sufficient stability against dissolution in the relevant potential window. Further, we determine the HOR and HER activities for Mo, W, Ta, Ni and Mo-Ni silicides in rotating disk electrode experiments. In conclusion, for the HOR only Ni2Si shows limited activity, and the HER activity of the investigated silicides is considerably lower compared to other PGM-free HER catalysts reported in the literature. PMID:28773022
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Rose, Karsten; Steinbüchel, Alexander
2002-06-04
A non-rubber degrading mutant of the polyisoprene rubber degrading bacterium Micromonospora aurantiaca W2b lacking the capability to form halos on latex overlay agar plates was isolated after N-methyl-N-nitro-N-nitrosoguanidine mutagenesis. A 10.3-kb shuttle cosmid vector pGM446 was constructed from the Streptomyces cloning vectors pGM160 and pOJ446. This vector was transferred by conjugation from Escherichia coli to M. aurantiaca W2b. The frequency of formation of exconjugants with pGM446 was 3.6 x 10(-3). This vector could be useful for shotgun cloning of genes into the non-rubber degrading mutant L1 from M. aurantiaca W2b.
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Environmental constraints and call evolution in torrent-dwelling frogs.
Goutte, Sandra; Dubois, Alain; Howard, Samuel D; Marquez, Rafael; Rowley, Jodi J L; Dehling, J Maximilian; Grandcolas, Philippe; Rongchuan, Xiong; Legendre, Frédéric
2016-04-01
Although acoustic signals are important for communication in many taxa, signal propagation is affected by environmental properties. Strong environmental constraints should drive call evolution, favoring signals with greater transmission distance and content integrity in a given calling habitat. Yet, few empirical studies have verified this prediction, possibly due to a shortcoming in habitat characterization, which is often too broad. Here we assess the potential impact of environmental constraints on the evolution of advertisement call in four groups of torrent-dwelling frogs in the family Ranidae. We reconstruct the evolution of calling site preferences, both broadly categorized and at a finer scale, onto a phylogenetic tree for 148 species with five markers (∼3600 bp). We test models of evolution for six call traits for 79 species with regard to the reconstructed history of calling site preferences and estimate their ancestral states. We find that in spite of existing morphological constraints, vocalizations of torrent-dwelling species are most probably constrained by the acoustic specificities of torrent habitats and particularly their high level of ambient noise. We also show that a fine-scale characterization of calling sites allows a better perception of the impact of environmental constraints on call evolution. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.
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NASA Astrophysics Data System (ADS)
Nyssen, Jan; Gebreslassie, Seifu; Assefa, Romha; Deckers, Jozef; Guyassa, Etefa; Poesen, Jean; Frankl, Amaury
2017-04-01
Many thousands of gabion check dams have been installed to control gully erosion in Ethiopia, but several challenges still remain, such as the issue of gabion failure in ephemeral streams with coarse bed load, that abrades at the chute step. As an alternative for gabion check dams in torrents with coarse bed load, boulder-faced log dams were conceived, installed transversally across torrents and tested (n = 30). For this, logs (22-35 cm across) were embedded in the banks of torrents, 0.5-1 m above the bed and their upstream sides were faced with boulders (0.3-0.7 m across). Similar to gabion check dams, boulder-faced log dams lead to temporary ponding, spreading of peak flow over the entire channel width and sediment deposition. Results of testing under extreme flow conditions (including two storms with return periods of 5.6 and 7 years) show that 18 dams resisted strong floods. Beyond certain flood thresholds, represented by proxies such as Strahler's stream order, catchment area, D95 or channel width), 11 log dams were completely destroyed. Smallholder farmers see much potential in this type of structure to control first-order torrents with coarse bed load, since the technique is cost-effective and can be easily installed.
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NASA Astrophysics Data System (ADS)
Rudaz, Benjamin; Loye, Alexandre; Mazotti, Benoit; Bardou, Eric; Jaboyedoff, Michel
2013-04-01
The Materosion project, conducted between the swiss canton of Valais (CREALP) and University of Lausanne (CRET) aims at forecasting sediment transfer in alpine torrents using the sediment cascade concept. The study site is the high Anniviers valley, around the village of Zinal (Valais). The torrents are divided in homogeneous reaches, to and from which sediments are transported by debris flows and bedload transport events. The model runs simulations of 100 years, with a 1-month time step, each with a given a random meteorological event ranging from no activity up to high magnitude debris flows. These events are calibrated using local rain data and observed corresponding debris flow frequencies. The model is applied to ten torrent systems with variable geological context, watershed geometries and sediment supplies. Given the high number of possible event scenarios, 10'000 simulations per torrent are performed, giving a statistical distribution of cumulated volumes and an event size distribution. A way to visualize the complex results data is proposed, and a back-analysis of the internal sediment cascade dynamic is performed. The back-analysis shows that the results' distribution stabilize after ~5'000 simulations. The model results, especially the range of debris flow volumes are crucial to maintain mitigation measures such as retention dams, and give clues for future sediment cascade modeling.
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Corno, Antonio F; Kocica, Mladen J; Torrent-Guasp, Francisco
2006-04-01
The new concepts of cardiac anatomy and physiology, based on the observations made by Francisco Torrent-Guasp's discovery of the helical ventricular myocardial band, can be useful in the context of the surgical strategies currently used to manage patients with congenital heart defects. The potential impact of the Torrent-Guasp's Heart on congenital heart defects have been analyzed in the following settings: ventriculo-arterial discordance (transposition of the great arteries), double (atrio-ventricular and ventriculo-arterial) discordance (congenitally corrected transposition of the great arteries), Ebstein's anomaly, pulmonary valve regurgitation after repair of tetralogy of Fallot, Ross operation, and complex intra-ventricular malformations. The functional interaction of right and left ventricles occurs not only through their arrangements in series but also thanks to the structural spiral features. Changes in size and function of either ventricle may influence the performance of the other ventricle. The variety and complexity of congenital heart defects make the recognition of the relationship between form and function a vital component, especially when compared to acquired disease. The new concepts of cardiac anatomy and function proposed by Francisco Torrent-Guasp, based on his observations, should stimulate further investigations of alternative surgical strategies by individuals involved with the management of patients with congenital heart defects.
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Platinum-group minerals in the LG and MG chromitites of the eastern Bushveld Complex, South Africa
NASA Astrophysics Data System (ADS)
Oberthür, Thomas; Junge, Malte; Rudashevsky, Nikolay; de Meyer, Eveline; Gutter, Paul
2016-01-01
The chromitites of the Bushveld Complex in South Africa contain vast resources of platinum-group elements (PGE); however, except for the economic upper group (UG)-2 chromitite seam, information on the distribution of the PGE in the ores and on the mineralogical nature, assemblages, and proportions of platinum-group minerals (PGM) is essentially missing. In the present geochemical and mineralogical study, PGE concentrates originating from the lower group (LG)-6 and middle group (MG)-1/2 chromitites were investigated with the intention to fill this gap of knowledge. Chondrite-normalized PGE patterns of bulk rock and concentrates are characterized by a positive slope from Os to Rh, a slight drop to Pt, and an increase to Pd again. The pronounced similarities of the PGE patterns indicate similar primary processes of PGE concentration in the chromitites, namely "sulfide control" of the PGE mineralization, i.e., co-precipitation of chromite and sulfide. Further, the primary control of PGE concentration in chromitites appears to be dual in character: (i) base-level concentrations of IPGE (up to ˜500 ppb) hosted within chromite and (ii) co-precipitation of chromite and sulfide, the latter containing virtually the entire remaining PGE budget. Sulfides (chalcopyrite, pentlandite, and pyrite; pyrrhotite is largely missing) are scarce within the chromitites and occur mainly interstitial to chromite grains. Pd and Rh contents in pentlandite are low and erratic. Essentially, the whole PGE inventory of the ores occurs in the form of discrete PGM. The PGM are almost always associated with sulfides. The dominant PGM are various Pt-Pd-Rh sulfides (cooperite/braggite [(Pt,Pd)S] and malanite/cuprorhodsite [CuPt2S4]/[CuRh2S4]), laurite [RuS2], the main carrier of the IPGE (Os, Ir, Ru), sulfarsenides [(Rh,Pt,Ir)AsS], sperrylite [PtAs2], Pt-Fe alloys, and a large variety of mainly Pd-rich PGM. The LG and MG chromitites have many characteristics in common and define a general, "typical" PGM spectrum of Bushveld chromitites. This PGM assemblage is characterized by the predominance of PGE-sulfides including elevated proportions of malanite, variable proportions of (sulf) arsenides, and Pt-Fe alloys in conjunction with a paucity of (bismutho)tellurides. The formation of this specific PGM spectrum is related to the distinct chromitite environment and its depositional and post-depositional history, whereby desulfurization reactions have probably played an important role. The LG-6 samples have higher contents of PGE-sulfides, including extraordinary high proportions of malanite but low PGE-arsenide and PGE-sulfarsenide contents compared to the MG-1/2 samples. This indicates a higher availability of arsenic either in the stratigraphically higher MG-1/2 samples (compared to the LG-6) or regionally in the chromitites south of the Steelpoort lineament.
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Guo, Fei; Zhou, Yishu; Song, He; Zhao, Jinling; Shen, Hongying; Zhao, Bin; Liu, Feng; Jiang, Xianhua
2016-11-01
The HID-Ion AmpliSeq™ Identity Panel (the HID Identity Panel) is designed to detect 124-plex single nucleotide polymorphisms (SNPs) with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 90 individual identification SNPs (IISNPs) on autosomal chromosomes and 34 lineage informative SNPs (LISNPs) on Y chromosome. In this study, we evaluated performance for the HID Identity Panel to provide a reference for NGS-SNP application, focusing on locus strand balance, locus coverage balance, heterozygote balance, and background signals. Besides, several experiments were carried out to find out improvements and limitations of this panel, including studies of species specificity, repeatability and concordance, sensitivity, mixtures, case-type samples and degraded samples, population genetics and pedigrees following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. In addition, Southern and Northern Chinese Han were investigated to assess applicability of this panel. Results showed this panel led to cross-reactivity with primates to some extent but rarely with non-primate animals. Repeatable and concordant genotypes could be obtained in triplicate with one exception at rs7520386. Full profiles could be obtained from 100pg input DNA, but the optimal input DNA would be 1ng-200pg with 21 initial PCR cycles. A sample with ≥20% minor contributor could be considered as a mixture by the number of homozygotes, and full profiles belonging to minor contributors could be detected between 9:1 and 1:9 mixtures with known reference profiles. Also, this assay could be used for case-type samples and degraded samples. For autosomal SNPs (A-SNPs), F ST across all 90loci was not significantly different between Southern and Northern Chinese Han or between male and female samples. All A-SNP loci were independent in Chinese Han population. Except for 18loci with H e <0.4, most of the A-SNPs in the HID Identity Panel presented high polymorphisms. Forensic parameters were calculated as >99.999% for combined discrimination power (CDP), 0.999999724 for combined power of exclusion (CPE), 1.390×10 11 for combined likelihood ratio (CLR) of trios, and 2.361×10 6 for CLR of motherless duos. For Y-SNPs, a total of 8 haplotypes were observed with the value of 0.684 for haplotype diversity. As a whole, the HID Identity Panel is a well-performed, robust, reliable and high informative NGS-SNP assay and it can fully meet requirements for individual identification and paternity testing in forensic science. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
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Dry deposition of gaseous oxidized mercury in Western Maryland.
Castro, Mark S; Moore, Chris; Sherwell, John; Brooks, Steve B
2012-02-15
The purpose of this study was to directly measure the dry deposition of gaseous oxidized mercury (GOM) in western Maryland. Annual estimates were made using passive ion-exchange surrogate surfaces and a resistance model. Surrogate surfaces were deployed for seventeen weekly sampling periods between September 2009 and October 2010. Dry deposition rates from surrogate surfaces ranged from 80 to 1512 pgm(-2)h(-1). GOM dry deposition rates were strongly correlated (r(2)=0.75) with the weekly average atmospheric GOM concentrations, which ranged from 2.3 to 34.1 pgm(-3). Dry deposition of GOM could be predicted from the ambient air concentrations of GOM using this equation: GOM dry deposition (pgm(-2)h(-1))=43.2 × GOM concentration-80.3. Dry deposition velocities computed using GOM concentrations and surrogate surface GOM dry deposition rates, ranged from 0.2 to 1.7 cms(-1). Modeled dry deposition rates were highly correlated (r(2)=0.80) with surrogate surface dry deposition rates. Using the overall weekly average surrogate surface dry deposition rate (369 ± 340 pg m(-2)h(-1)), we estimated an annual GOM dry deposition rate of 3.2 μg m(-2)year(-1). Using the resistance model, we estimated an annual GOM dry deposition rate of 3.5 μg m(-2)year(-1). Our annual GOM dry deposition rates were similar to the dry deposition (3.3 μg m(-2)h(-1)) of gaseous elemental mercury (GEM) at our site. In addition, annual GOM dry deposition was approximately 1/2 of the average annual wet deposition of total mercury (7.7 ± 1.9 μg m(-2)year(-1)) at our site. Total annual mercury deposition from dry deposition of GOM and GEM and wet deposition was approximately 14.4 μg m(-2)year(-1), which was similar to the average annual litterfall deposition (15 ± 2.1 μg m(-2)year(-1)) of mercury, which was also measured at our site. Copyright © 2012 Elsevier B.V. All rights reserved.
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Duran, C.J.; Barnes, S-J.; Pleše, P.; Prašek, M. Kudrna; Zientek, Michael L.; Pagé, P.
2017-01-01
The distribution of platinum-group elements (PGE) within zoned magmatic ore bodies has been extensively studied and appears to be controlled by the partitioning behavior of the PGE during fractional crystallization of magmatic sulfide liquids. However, other chalcophile elements, especially TABS (Te, As, Bi, Sb, and Sn) have been neglected despite their critical role in forming platinum-group minerals (PGM). TABS are volatile trace elements that are considered to be mobile so investigating their primary distribution may be challenging in magmatic ore bodies that have been somewhat altered. Magmatic sulfide ore bodies from the Noril’sk-Talnakh mining district (polar Siberia, Russia) offer an exceptional opportunity to investigate the behavior of TABS during fractional crystallization of sulfide liquids and PGM formation as the primary features of the ore bodies have been relatively well preserved. In this study, new petrographic (2D and 3D) and whole-rock geochemical data from Cu-poor to Cu-rich sulfide ores of the Noril’sk-Talnakh mining district are integrated with published data to consider the role of fractional crystallization in generating mineralogical and geochemical variations across the different ore types (disseminated to massive). Despite textural variations in Cu-rich massive sulfides (lenses, veins, and breccias), these sulfides have similar chemical compositions, which suggests that Cu-rich veins and breccias formed from fractionated sulfide liquids that were injected into the surrounding rocks. Numerical modeling using the median disseminated sulfide composition as the initial sulfide liquid composition and recent DMSS/liq and DISS/liq predicts the compositional variations observed in the massive sulfides, especially in terms of Pt, Pd, and TABS. Therefore, distribution of these elements in the massive sulfides was likely controlled by their partitioning behavior during sulfide liquid fractional crystallization, prior to PGM formation. Our observations indicate that in the Cu-poor massive sulfides the PGM formed as the result of exsolution from sulfide minerals whereas in the Cu-rich massive sulfides the PGM formed by crystallization from late-stage fractionated sulfide liquids. We suggest that the significant amount of Sn-bearing PGM may be related to crustal contamination from granodiorite, whereas As, Bi, Te, and Sb were likely added to the magma along with S from sedimentary rocks. Large PGM that are scarce and randomly distributed may account for most of the whole-rock Pt budget. Based on our results, we propose a holistic genetic model for the formation of the magmatic sulfide ore bodies of the Noril’sk-Talnakh mining district.
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NASA Astrophysics Data System (ADS)
Prichard, Hazel M.; Mondal, Sisir K.; Mukherjee, Ria; Fisher, Peter C.; Giles, Nicolas
2018-04-01
Palladium concentrations of 1-3 ppm with an average Pt/Pd ratio of 0.15 have been located for the first time in a magnetitite layer in the Nuasahi Massif in Orissa India. This layer occurs at a high stratigraphic level in the complex and is nearly 4-km long and 5-12-m thick. The sections of the Pd-rich zone identified to date extend over a distance of 1 km at the southern end of the layer. Several phases of mineralization are evident. The first, primary assemblage of platinum-group minerals (PGM) contains Pd-sulfides (vysotskite), Pd-Pb alloys (zvyagintsevite), and a Pd-In alloy, a mineral probably new to mineralogy. These PGM are confined to central magnetite grains in the magnetitites. The magnetite grains with exsolved fine laths of ilmenite at centers are referred to as central magnetite grains. These central magnetite grains are commonly surrounded by blebs of ilmenite and magnetite that contain the majority of the PGM. These are dominated by Pd-antimonides, variably altered to Pd-oxides, and other PGM including PtAs2 (sperrylite), RuS2 (laurite), and IrRhAsS (irarsite/hollingwothite). Many of these PGM also occur in the interstitial silicates, with rare occurrences in the central magnetite grains. We propose that the platinum-group elements (PGE) crystallized during a minor sulfide saturation event that occurred as the magnetitites crystallized. This event produced the minor Cu-sulfides in these magnetitites. Later introduction of antimony and arsenic, during the alteration event that produced the blebby ilmenite and magnetite, led to the more primary PGM being succeeded by the main PGM assemblage, dominated by Pd-antimonides. These are associated with secondary Cu minerals and sperrylite. Subsequent oxidation during weathering in the hot wet Indian climate produced the Pd-oxides. The Nuasahi Massif is a sill-like Archean layered ultramafic-mafic intrusion genetically linked to high-Mg siliceous basalt or boninites and is characterized by unusually thick layers of chromitite. PGE are concentrated in these chromitites and in the base metal sulfide-bearing breccias in the overlying gabbro. The Pd in the magnetitites described here indicates the presence of a third level where PGE are concentrated and a magma that crystallized to produce PGE concentrations at three stratigraphic levels in the massif. This indicates that similar thin sill-like intrusions, hosting unusually thick chromitites, may also have PGE concentrations at a number of stratigraphic levels.
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Lv, Chao; Hong, Yang; Fu, Zhiqiang; Lu, Ke; Cao, Xiaodan; Wang, Tao; Zhu, Chuangang; Li, Hao; Xu, Rui; Jia, Bingguang; Han, Qian; Dou, Xuefeng; Shen, Yuanxi; Zhang, Zuhang; Zai, Jinli; Feng, Jintao; Lin, Jiaojiao
2016-03-09
Schistosomiasis is a huge threat to human and animal health. Apart from bovines, goats play an important role in the transmission of schistosomiasis in some endemic areas of China. An accessible, quality-assured goat schistosomiasis diagnostic technique is needed. Recently, our laboratory identified two recombinant diagnostic antigens, SjPGM and SjRAD23 via an immuno-proteomic method. The application of these two recombinant antigens to develop a higher sensitivity and specificity technique for the sheep schistosomiasis diagnosis is urgently needed. Epitopes of SjPGM and SjRAD23 were predicted and three polypeptides, two from SjRAD23 and one from SjPGM, were selected. Recombinant plasmids containing two to three DNA sequences encoding predicted polypeptides or large hydrophilic region of Sj23 (LHD-Sj23) were constructed and expressed. Eight recombinant schistosome antigens including four multi-epitope proteins and four recombinant single-molecule antigens as well as SEA, were assessed by ELISA in 91 sera from schistosome-infected goats, 44 sera from non-infected goats, 37 sera from Orientobilharzia-infected goats, and 12 from Haemonchus contortus-infected goats. ELISA tests showed that three multi-epitope proteins had higher sensitivity than the four single-molecule antigens (rSjRAD23, rSjPGM, rBSjRAD23-1, rBSj23) and the multi-epitope protein rBSjPGM-BSjRAD23-1-BSj23 had the highest sensitivity (97.8 %, 89/91) and maintained good specificity (100 %, 44/44) as well as low cross-reactivity with haemonchosis (8.33 %, 3/12) and orientobilharziasis (13.51 %, 5/37) in the diagnosis of goat schistosomiasis. In contrast, when SEA was applied as a diagnosis antigen, it had 100 % (91/91) sensitivity, 75 % (33/44) specificity, 25 and 83.78 % cross-reactivity with haemonchosis (3/12) and orientobilharziasis (31/37), respectively. The application of recombinant multi-epitope proteins may increase the sensitivity of diagnosis technique and retain high specificity of single-molecule antigens for schistosomiasis, and the recombinant antigen rBSjPGM-BSjRAD23-1-BSj23 has the potential to be used as a diagnosis antigen for goat schistosomiasis.
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Mohamed, Sameera; van der Merwe, Elizabet M; Altermann, Wladyslaw; Doucet, Frédéric J
2016-04-01
Mine tailings can represent untapped secondary resources of non-ferrous, ferrous, precious, rare and trace metals. Continuous research is conducted to identify opportunities for the utilisation of these materials. This preliminary study investigated the possibility of extracting major elements from South African tailings associated with the mining of Platinum Group Metals (PGM) at the Two Rivers mine operations. These PGM tailings typically contain four major elements (11% Al2O3; 12% MgO; 22% Fe2O3; 34% Cr2O3), with lesser amounts of SiO2 (18%) and CaO (2%). Extraction was achieved via thermochemical treatment followed by aqueous dissolution, as an alternative to conventional hydrometallurgical processes. The thermochemical treatment step used ammonium sulphate, a widely available, low-cost, recyclable chemical agent. Quantification of the efficiency of the thermochemical process required the development and optimisation of the dissolution technique. Dissolution in water promoted the formation of secondary iron precipitates, which could be prevented by leaching thermochemically-treated tailings in 0.6M HNO3 solution. The best extraction efficiencies were achieved for aluminium (ca. 60%) and calcium (ca. 80%). 35% iron and 32% silicon were also extracted, alongside chromium (27%) and magnesium (25%). Thermochemical treatment using ammonium sulphate may therefore represent a promising technology for extracting valuable elements from PGM tailings, which could be subsequently converted to value-added products. However, it is not element-selective, and major elements were found to compete with the reagent to form water-soluble sulphate-metal species. Further development of this integrated process, which aims at achieving the full potential of utilisation of PGM tailings, is currently underway. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Eumorphic Plastic Surgery: Expectation Versus Satisfaction in Body Dysmorphic Disorder.
Morselli, Paolo Giovanni; Micai, Alessandro; Boriani, Filippo
2016-08-01
Eumorphic Plastic Surgery aims at improving the severe psychosocial pain caused by a deformity. Dysmorphopathology is an increasingly relevant problem facing the plastic surgeon. The aim of this study is to describe the perioperative questionnaires created by the senior author and to present a cohort of plastic surgery patients suffering from dysmorphopathies. These patients were prospectively followed and evaluated with the proposed questionnaires through their surgical pathway to explore the degree of satisfaction or disappointment compared to expectations. All candidates for plastic surgery procedures between April 2011 and June 2013 were included in the study. Preoperatively, all patients completed the Patient Expectation Questionnaire (E-pgm). Twelve months postoperatively, they completed the Patient Satisfaction Questionnaire (S-pgm). The E-pgm and S-pgm were compared to evaluate the consistency between the patient's preoperative expectations and postoperative evaluations. A total of 158 patients were included in the study. Out of them, 79 % experienced an improvement or no variation between preoperative expectations and postoperative satisfaction. With regard to the motivation for undergoing surgery, 91 % showed that the surgical procedure met the motivation. An overall positive perioperative change in life was experienced by 93 % of patients. The E-pgm questionnaire proved to be a valid and reliable tool for the selection of suitable candidates for surgery and for identification of dysmorphophobic patients. Enhancing the doctor-patient relationship and communication can reduce ambiguity and avoid troublesome misunderstandings, litigation and other legal implications. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .
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Weathering of PGE sulfides and Pt-Fe alloys in the Freetown Layered Complex, Sierra Leone
NASA Astrophysics Data System (ADS)
Bowles, John F. W.; Suárez, Saioa; Prichard, Hazel M.; Fisher, Peter C.
2017-12-01
Fresh and weathered rocks and saprolite from Horizon B of the Freetown Layered Complex contain platinum-group minerals (PGM). The PGM in the fresh rocks are 1-7 μm across, including cooperite (PtS), isoferroplatinum (Pt3Fe), minor tetraferroplatinum (PtFe), tulameenite (Pt2FeCu), Os-bearing laurite (RuS2), and other base metal-sulfide (BMS)-bearing PGM. The weathered rocks contain fewer of those PGM but a high proportion of disordered Cu-(±Pd)-bearing Pt-Fe alloys. The saprolite hosts scarce, smaller (1-3 μm) ordered PtFe and disordered PtFe3. The Pt-Fe alloys became increasingly Fe rich as weathering proceeded. Pt-Fe oxides appeared during weathering. Copper sulfides associated with the primary PGM and cooperite (with <3% Pd) were destroyed to provide the minor Cu and Pd found in some of the disordered Pt-Fe alloys. Platinum- and Pd-bearing saprolites have retained the original rock fabric and, to a depth of about 2 m, surround residual rocks that show progressive weathering (corestones). Ground water passing through the saprolite has transported Pt and Pd (and probably Au) in solution down slope into saprolite over unmineralized rocks. Transport is marked by changes in the Pt/Pd ratio indicating that the metals have moved independently. Palladium is present in marginally higher concentrations in the deeper saprolite than in the corestones suggesting some retention of Pd in the deeper saprolite. Platinum and Pd are less concentrated in the upper saprolite than the deeper saprolite indicating surface leaching. Alteration occurred over a long period in an organic and microbial rich environment that may have contributed to the leaching and transport of PGE.
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Massively parallel sequencing-enabled mixture analysis of mitochondrial DNA samples.
Churchill, Jennifer D; Stoljarova, Monika; King, Jonathan L; Budowle, Bruce
2018-02-22
The mitochondrial genome has a number of characteristics that provide useful information to forensic investigations. Massively parallel sequencing (MPS) technologies offer improvements to the quantitative analysis of the mitochondrial genome, specifically the interpretation of mixed mitochondrial samples. Two-person mixtures with nuclear DNA ratios of 1:1, 5:1, 10:1, and 20:1 of individuals from different and similar phylogenetic backgrounds and three-person mixtures with nuclear DNA ratios of 1:1:1 and 5:1:1 were prepared using the Precision ID mtDNA Whole Genome Panel and Ion Chef, and sequenced on the Ion PGM or Ion S5 sequencer (Thermo Fisher Scientific, Waltham, MA, USA). These data were used to evaluate whether and to what degree MPS mixtures could be deconvolved. Analysis was effective in identifying the major contributor in each instance, while SNPs from the minor contributor's haplotype only were identified in the 1:1, 5:1, and 10:1 two-person mixtures. While the major contributor was identified from the 5:1:1 mixture, analysis of the three-person mixtures was more complex, and the mixed haplotypes could not be completely parsed. These results indicate that mixed mitochondrial DNA samples may be interpreted with the use of MPS technologies.
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Zientek, M.L.
1992-01-01
Platinum-group minerals occur in significant proportions in placer deposits in several localities in South Kalimantan. They consist of Pt-Fe alloy that may be intergrown with or contain inclusions of Ir-Os-Ru alloy, laurite and chromite. Alluvial PGM found along Sungai Tambanio are in part derived from chromatite schlieren in dunitic bodies intruded into clinopyroxene cumulates that may be part of an Alaskan-type ultramafic complex. A chromitite schlieren in serpentinite from one of these dunitic bodies is anomalous in PGE. The chondrite-normalized PGE pattern for this rock, pan concentrates from this area, and PGM concentrates from diamond-Au-PGM placer deposits have an "M'-shaped pattern enriched in Ir and Pt that is typical of PGE-mineralization associated with Alaskan-type ultramafic complexes. -Authors
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Unbiased, scalable sampling of protein loop conformations from probabilistic priors.
Zhang, Yajia; Hauser, Kris
2013-01-01
Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion.
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Unbiased, scalable sampling of protein loop conformations from probabilistic priors
2013-01-01
Background Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Results Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Conclusion Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion. PMID:24565175
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Tang, Juan; Huang, Yapei; Zhang, Cengceng; Liu, Huiqiong; Tang, Dianping
2016-12-15
A new impedimetric immunosensor for the fast determination of ochratoxin A (OTA) in food samples was developed based on the instant catalyst as enhancer. Initially, the signal tags were prepared via co-immobilization of anti-OTA antibody and amine-terminated dendrimer (PAMAM) on the graphene oxide nanosheets through the covalent interaction, which were utilized as a good platform for combining manganese ion (anti-OTA-GO-PAMAM-Mn(2+)). Upon target OTA introduction, a competitive-type immunoreaction was implemented between the analyte and the immobilized OTA-BSA on the electrode for the anti-OTA antibody on the graphene oxide nanosheets labels. After a competitive immunoassay format, the anti-OTA-GO-PAMAM-Mn(2+) were captured onto the electrode surface, which could induce the in situ formation of MnO2via classical redox reaction between Mn(2+) and KMnO4 on the immunesensing platform. Moreover, the generated MnO2 nanoparticles act as efficient catalyst could catalyze the 4-chloro-1-naphthol (4-CN) oxidation without H2O2 to generate an insoluble precipitation on the platform. Under the optimal conditions, the instant catalyst based impedimetric immunosensor displayed a wide dynamic working range between 0.1pgmL(-1) and 30ngmL(-1). The detection limit (LOD) of the assay was 0.055pgmL(-1). The developed method exhibited high selectivity and can be used for the determination of OTA in real red wine samples. Copyright © 2016 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Vickers, H.; Baddeley, L.
2011-11-01
RF heating of the F region plasma at high latitudes has long been known to produce electron temperature increases that can vary from tens to hundreds of percent above the background, unperturbed level. In contrast, artificial ionospheric modification experiments conducted using the Space Plasma Exploration by Active Radar (SPEAR) heating facility on Svalbard have often failed to produce obvious enhancements in the electron temperatures when measured using the European Incoherent Scatter Svalbard radar (ESR), colocated with the heater. Contamination of the ESR ion line spectra by the zero-frequency purely growing mode (PGM) feature is known to persist at varying amplitudes throughout SPEAR heating, and such spectral features can lead to significant temperature underestimations when the incoherent scatter spectra are analyzed using conventional methods. In this study, we present the first results of applying a recently developed technique to correct the PGM-contaminated spectra to SPEAR-enhanced ESR spectra and derive an alternative estimate of the SPEAR-heated electron temperature. We discuss how the effectiveness of the spectrum corrections can be affected by the data variance, estimated over the integration period. The subsequent electron temperatures, inferred from corrected spectra, range from a few tens to a few hundred Kelvin above the average background temperature. These temperatures are found to be in reasonable agreement with the theoretical “enhanced” temperature, calculated for the peak of the stationary temperature perturbation profile, when realistic absorption effects are accounted for.
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USDA-ARS?s Scientific Manuscript database
Detection of human norovirus (HuNoV) usually relies on molecular biology techniques, such as qRT PCR. Since histo-blood group antigens (HBGAs) are the functional receptors for HuNoV, HuNoV can bind to porcine gastric mucin (PGM), which contains HBGA-like antigens. In this study, PGM conjugated magn...
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Essumang, D K
2010-06-01
Tissues from Manta birostris caught by fishermen from Dixcove in the western part of Ghana were analyzed for their Platinum, palladium and rhodium concentrations (PGM). The use of chondrichthyan fish has permitted the study of trace levels of Platinum group metals (PGMs) which have travelled very far into the sea. The analysis showed that Ghana's coastline is fairly polluted with these platinum group metals (PGMs). PGM concentration in manta ray recorded a range of (0.15-0.85) microg/g for Pt, (0.033-0.67) microg/g for Pd and (0.007-0.145) microg/g for Rh. Comparing these values to the UK dietary intake of 0.2 microg/day for Pt and Rh and 1.0 microg/day for Pd, its indicates that the values obtained from the analysis for Pt was above the required level. This is the first study to show the accumulation of PGM in chondrichthyan fish, although the sources of this pollution are not clear as manta birostris is migratory and therefore need to be investigated further. The presence of the PGM is very significant, since manta ray meat is consumed in Ghana. This may presents a health risk, due to a possible accumulation of PGMs in humans.
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Engelsdorf, Timo; Will, Cornelia; Hofmann, Jörg; Schmitt, Christine; Merritt, Brian B; Rieger, Leonie; Frenger, Marc S; Marschall, André; Franke, Rochus B; Pattathil, Sivakumar; Voll, Lars M
2017-01-01
Penetration resistance represents the first level of plant defense against phytopathogenic fungi. Here, we report that the starch-deficient Arabidopsis thaliana phosphoglucomutase (pgm) mutant has impaired penetration resistance against the hemibiotrophic fungus Colletotrichum higginsianum. We could not determine any changes in leaf cutin and epicuticular wax composition or indolic glucosinolate levels, but detected complex alterations in the cell wall monosaccharide composition of pgm. Notably, other mutants deficient in starch biosynthesis (adg1) or mobilization (sex1) had similarly affected cell wall composition and penetration resistance. Glycome profiling analysis showed that both overall cell wall polysaccharide extractability and relative extractability of specific pectin and xylan epitopes were affected in pgm, suggesting extensive structural changes in pgm cell walls. Screening of mutants with alterations in content or modification of specific cell wall monosaccharides indicated an important function of pectic polymers for penetration resistance and hyphal growth of C. higginsianum during the biotrophic interaction phase. While mutants with affected pectic rhamnogalacturonan-I (mur8) were hypersusceptible, penetration frequency and morphology of fungal hyphae were impaired on pmr5 pmr6 mutants with increased pectin levels. Our results reveal a strong impact of starch metabolism on cell wall composition and suggest a link between carbohydrate availability, cell wall pectin and penetration resistance.
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Influence of forest management on headwater stream amphibians at multiple spatial scales
Stoddard, Margo; Hayes, John P.; Erickson, Janet L.
2004-01-01
Background Amphibians are important components of headwater streams in forest ecosystems of the Pacific Northwest (PNW). They comprise the highest vertebrate biomass and density in these systems and are integral to trophic dynamics both as prey and as predators. The most commonly encountered amphibians in PNW headwater streams include the Pacific giant salamander (Dicamptodon tenebrosus), the tailed frog (Ascaphus truei), the southern torrent salamander (Rhyacotriton variegatus), and the Columbia torrent salamander (R. kezeri).
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Lee, Preston V; Dinu, Valentin
2015-11-04
Our publication of the BitTorious portal [1] demonstrated the ability to create a privatized distributed data warehouse of sufficient magnitude for real-world bioinformatics studies using minimal changes to the standard BitTorrent tracker protocol. In this second phase, we release a new server-side specification to accept anonymous philantropic storage donations by the general public, wherein a small portion of each user's local disk may be used for archival of scientific data. We have implementated the server-side announcement and control portions of this BitTorrent extension into v3.0.0 of the BitTorious portal, upon which compatible clients may be built. Automated test cases for the BitTorious Volunteer extensions have been added to the portal's v3.0.0 release, supporting validation of the "peer affinity" concept and announcement protocol introduced by this specification. Additionally, a separate reference implementation of affinity calculation has been provided in C++ for informaticians wishing to integrate into libtorrent-based projects. The BitTorrent "affinity" extensions as provided in the BitTorious portal reference implementation allow data publishers to crowdsource the extreme storage prerequisites for research in "big data" fields. With sufficient awareness and adoption of BitTorious Volunteer-based clients by the general public, the BitTorious portal may be able to provide peta-scale storage resources to the scientific community at relatively insignificant financial cost.
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Disastrous torrential floods in mountain areas in Serbia
NASA Astrophysics Data System (ADS)
Gavrilovic, Z.
2009-04-01
In Serbia, the relief is predominantly hilly and mountainous, intersected with numerous rivers. The greatest number of watercourses are small torrents; however the proportionally large rivers also have a distinctive torrential character. The highest parts of the catchments are at the altitudes above 1500 m, while their confluences are at the altitudes of 200 - 300 m. The catchment and channel slopes are extremely steep. So, as the initial natural preconditions are satisfied, torrential floods are the consequence. Although the Južna Morava catchments were regulated by erosion control works, during the last decades there were numerous torrential floods. Some of the floods had disastrous proportions, not recorded in Serbia or in Europe. The flood of river Vlasina in 1988 was presented to the professional public several times. This flood was not an isolated case. Many large-scale torrential floods occurred in Serbia from 1994 to 2007. As there were floods also in 2007, the causes of the recorded floods had to be analysed. The analysis pointed out a series of scenarios which were the causes of disastrous torrential floods, and also the disadvantages of the actual system of torrent and erosion control. Special attention was focused on the floods which resulted from sudden snow melting. This paper will present the results of the analyses of the extreme torrential floods of the rivers Nišava and Vlasina. Key words: Flood, torrents, torrent control, erosion control
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Chinese Lessons from Other Peoples’ Wars
2011-11-01
have a unified center for lessons learned (key U.S. examples are the Joint Center for Operational Analy- 8 sis, the Center for Army Lessons Learned...complete publicly available docu- mentary and analytical record in Chinese on the wars might present. Readers are advised to bear these chal- lenges...guided missiles (PGM). Indeed, there are 14 many PLA studies about the PGM and its employment in the U.S. joint and integrated operations in the
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Zema, Demetrio Antonio; Bombino, Giuseppe; Denisi, Pietro; Lucas-Borja, Manuel Esteban; Zimbone, Santo Marcello
2018-06-12
In mountain streams possible negative impacts of check dams on soil, water and riparian vegetation due to check dam installation can be noticed. In spite of the ample literature on the qualitative effects of engineering works on channel hydrology, morphology, sedimentary effects and riparian vegetation characteristics, quantitative evaluations of the changes induced by check dams on headwater characteristics are rare. In order to fill this gap, this study has evaluated the effects of check dams located in headwaters of Calabria (Southern Italy) on hydrological and geomorphological processes and on the response of riparian vegetation to these actions. The analysis has compared physical and vegetation indicators in transects identified around check dams (upstream and downstream) and far from their direct influence (control transects). Check dams were found to influence significantly unit discharge, surface and subsurface sediments (both upstream and downstream), channel shape and transverse distribution of riparian vegetation (upstream) as well as cover and structure of riparian complexes (downstream). The actions of the structures on torrent longitudinal slope and biodiversity of vegetation were less significant. The differences on bed profile slope were significant only between upstream and downstream transects. The results of the Agglomerative Hierarchical Cluster analysis confirmed the substantial similarity between upstream and control transects, thus highlighting that the construction of check dams, needed to mitigate the hydro-geological risks, has not strongly influenced the torrent functioning and ecology before check dam construction. Moreover, simple and quantitative linkages between torrent hydraulics, geomorphology and vegetation characteristics exist in the analysed headwaters; these relationships among physical adjustments of channels and most of the resulting characteristics of the riparian vegetation are specific for the transect locations with respect of check dams. Conversely, the biodiversity of the riparian vegetation basically eludes any quantitative relations with the physical and other vegetal characteristics of the torrent transects. Copyright © 2018 Elsevier B.V. All rights reserved.
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Polyglycerol-opioid conjugate produces analgesia devoid of side effects.
González-Rodríguez, Sara; Quadir, Mohiuddin A; Gupta, Shilpi; Walker, Karolina A; Zhang, Xuejiao; Spahn, Viola; Labuz, Dominika; Rodriguez-Gaztelumendi, Antonio; Schmelz, Martin; Joseph, Jan; Parr, Maria K; Machelska, Halina; Haag, Rainer; Stein, Christoph
2017-07-04
Novel painkillers are urgently needed. The activation of opioid receptors in peripheral inflamed tissue can reduce pain without central adverse effects such as sedation, apnoea, or addiction. Here, we use an unprecedented strategy and report the synthesis and analgesic efficacy of the standard opioid morphine covalently attached to hyperbranched polyglycerol (PG-M) by a cleavable linker. With its high-molecular weight and hydrophilicity, this conjugate is designed to selectively release morphine in injured tissue and to prevent blood-brain barrier permeation. In contrast to conventional morphine, intravenous PG-M exclusively activated peripheral opioid receptors to produce analgesia in inflamed rat paws without major side effects such as sedation or constipation. Concentrations of morphine in the brain, blood, paw tissue, and in vitro confirmed the selective release of morphine in the inflamed milieu. Thus, PG-M may serve as prototype of a peripherally restricted opioid formulation designed to forego central and intestinal side effects.
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Wang, Zhenzhen; Chen, Zhaowei; Gao, Nan; Ren, Jinsong; Qu, Xiaogang
2015-10-07
Herein, for the first time, we presented a simple and general approach by using personal glucose meters (PGM) for portable and ultrasensitive detection of microbial pathogens. Upon addition of pathogenic bacteria, glucoamylase-quaternized magnetic nanoparticles (GA-QMNPS) conjugates were disrupted by the competitive multivalent interactions between bacteria and QMNPS, resulting in the release of GA. After magnetic separation, the free GA could catalyze the hydrolysis of amylose into glucose for quantitative readout by PGM. In such way, PGM was transmuted into a bacterial detection device and extremely low detection limits down to 20 cells mL(-1) was achieved. More importantly, QMNPS could inhibit the growth of the bacteria and destroy its cellular structure, which enabled bacteria detection and inhibition simultaneously. The simplicity, portability, sensitivity and low cost of presented work make it attractive for clinical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Binder, Andrew J.; Toops, Todd J.; Unocic, Raymond R.
Platinum group metal (PGM) catalysts are the current standard for control of pollutants in automotive exhaust streams. Aside from their high cost, PGM catalysts struggle with CO oxidation at low temperatures (<200 °C) due to inhibition by hydrocarbons in exhaust streams. Here we present a ternary mixed oxide catalyst composed of copper oxide, cobalt oxide, and ceria (dubbed CCC) that outperforms synthesized and commercial PGM catalysts for CO oxidation in simulated exhaust streams while showing no signs of inhibition by propene. Diffuse reflectance IR (DRIFTS) and light-off data both indicate low interaction between propene and the CO oxidation active sitemore » on this catalyst, and a separation of adsorption sites is proposed as the cause of this inhibition resistance. In conclusion, this catalyst shows great potential as a low-cost component for low temperature exhaust streams that are expected to be a characteristic of future automotive systems.« less
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Eliminating NVA Requirements & Improving the Inspection System
2011-01-27
Wg ISPR Blood Pgm QA JTAC Stan/Eval Formal Joint Comm AAAHC SCI Security Pgm Review Pathologists WII Ed & Dev Inter vent. Servi ces FDA Pubs...his/her tour Balanced mix of scheduled & no-notice inspections Units will be inspected for Readiness and Compliance every 24 months Readiness...a whole IG Team Chiefs drive team effectiveness, are the most visible direct representatives of MAJCOM CCs & should be selected by CIP or a board
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Airborne Chlordane Contamination in Houses Treated for Termites at a Midwestern Air Force Base
1981-02-01
to provide entry authorization. Inside air temperature and relative humidity were measured with a sling psychrometer at the time of sampling...of the houses had chlordane concentrations 21.0 Pg/m3. No correlation could be made between chlordane concentration and year of treatment except for...from 14.5 to 37.8 pg/m8, were found in houses treated in 1970. Correlation of chlordane concentration could not be made with barometric pressure
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Komini Babu, Siddharth; Chung, Hoon Taek; Zelenay, Piotr; ...
2017-08-04
Here, this paper presents a two-dimensional (2D) computational model of a polymer electrolyte fuel cell (PEFC) with a platinum group metal-free (PGM-free) catalyst cathode that can significantly reduce PEFC costs by eliminating the need for expensive platinum catalysts. Due to their comparatively low volumetric activity, PGM-free cathodes are an order of magnitude thicker than their Pt-based counterpart. The resulting need for greater electrode thickness to achieve sufficient power density requires careful attention to the transport losses across the thicker cathodes. The presented model is used to correlate the composition and morphology of the cathode to PEFC performance. The model ismore » a complete cell, continuum model that includes an advanced agglomerate model for a microstructurally consistent representation of the cathode. A unique feature of the approach is the integration of morphology and transport parameter statistics extracted from nano-scale resolution X-ray computed tomography (nano-CT) imaging of PGM-free cathodes. The model was validated with experimental results of PGM-free cathodes with varying Nafion loading. Lastly, our key findings are a need for increased cathode hydrophobicity and increased ionomer conductivity through either reduced tortuosity or increased bulk conductivity. We further use the model to evaluate targets for the volumetric activity and active site density for future catalysts.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Komini Babu, Siddharth; Chung, Hoon Taek; Zelenay, Piotr
Here, this paper presents a two-dimensional (2D) computational model of a polymer electrolyte fuel cell (PEFC) with a platinum group metal-free (PGM-free) catalyst cathode that can significantly reduce PEFC costs by eliminating the need for expensive platinum catalysts. Due to their comparatively low volumetric activity, PGM-free cathodes are an order of magnitude thicker than their Pt-based counterpart. The resulting need for greater electrode thickness to achieve sufficient power density requires careful attention to the transport losses across the thicker cathodes. The presented model is used to correlate the composition and morphology of the cathode to PEFC performance. The model ismore » a complete cell, continuum model that includes an advanced agglomerate model for a microstructurally consistent representation of the cathode. A unique feature of the approach is the integration of morphology and transport parameter statistics extracted from nano-scale resolution X-ray computed tomography (nano-CT) imaging of PGM-free cathodes. The model was validated with experimental results of PGM-free cathodes with varying Nafion loading. Lastly, our key findings are a need for increased cathode hydrophobicity and increased ionomer conductivity through either reduced tortuosity or increased bulk conductivity. We further use the model to evaluate targets for the volumetric activity and active site density for future catalysts.« less
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Engelsdorf, Timo; Will, Cornelia; Hofmann, Jörg; Schmitt, Christine; Merritt, Brian B.; Rieger, Leonie; Frenger, Marc S.; Marschall, André; Franke, Rochus B.; Pattathil, Sivakumar
2017-01-01
Abstract Penetration resistance represents the first level of plant defense against phytopathogenic fungi. Here, we report that the starch-deficient Arabidopsis thaliana phosphoglucomutase (pgm) mutant has impaired penetration resistance against the hemibiotrophic fungus Colletotrichum higginsianum. We could not determine any changes in leaf cutin and epicuticular wax composition or indolic glucosinolate levels, but detected complex alterations in the cell wall monosaccharide composition of pgm. Notably, other mutants deficient in starch biosynthesis (adg1) or mobilization (sex1) had similarly affected cell wall composition and penetration resistance. Glycome profiling analysis showed that both overall cell wall polysaccharide extractability and relative extractability of specific pectin and xylan epitopes were affected in pgm, suggesting extensive structural changes in pgm cell walls. Screening of mutants with alterations in content or modification of specific cell wall monosaccharides indicated an important function of pectic polymers for penetration resistance and hyphal growth of C. higginsianum during the biotrophic interaction phase. While mutants with affected pectic rhamnogalacturonan-I (mur8) were hypersusceptible, penetration frequency and morphology of fungal hyphae were impaired on pmr5 pmr6 mutants with increased pectin levels. Our results reveal a strong impact of starch metabolism on cell wall composition and suggest a link between carbohydrate availability, cell wall pectin and penetration resistance. PMID:28204541
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NASA Astrophysics Data System (ADS)
Badanina, Inna Yu.; Malitch, Kreshimir N.; Lord, Richard A.; Meisel, Thomas C.
2013-12-01
In this paper we present textural and mineral chemistry data for a PGM inclusion assemblage and whole-rock platinum-group element (PGE) concentrations of chromitite from Harold's Grave, which occurrs in a dunite pod in a mantle tectonite at Unst in the Shetland Ophiolite Complex (SOC), Scotland. The study utilized a number of analytical techniques, including acid digestion and isotope dilution (ID) ICP-MS, hydroseparation and electron microprobe analysis. The chromitite contains a pronounced enrichment of refractory PGE (IPGE: Os, Ir and Ru) over less refractory PGE (PPGE: Rh, Pt and Pd), typical of mantle hosted `ophiolitic' chromitites. A `primary' magmatic PGM assemblage is represented by euhedrally shaped (up to 60 μm in size) single and composite inclusions in chromite. Polyphase PGM grains are dominated by laurite and osmian iridium, with subordinate laurite + osmian iridium + iridian osmium and rare laurite + Ir-Rh alloy + Rh-rich sulphide (possibly prassoite). The compositional variability of associated laurite and Os-rich alloys at Harold's Grave fit the predicted compositions of experiment W-1200-0.37 of Andrews and Brenan (Can Mineral 40: 1705-1716, 2002) providing unequivocal information on conditions of their genesis, with the upper thermal stability of laurite in equilibrium with Os-rich alloys estimated at 1200-1250 °C and f(S2) of 10-0.39-10-0.07.
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A regional analysis of elements at risk exposed to mountain hazards in the Eastern European Alps
NASA Astrophysics Data System (ADS)
Fuchs, Sven; Zischg, Andreas
2014-05-01
We present a method to quantify the number and value of buildings exposed to torrents and snow avalanches in the Austrian Alps, as well as the number of exposed people. Based on a unique population and building register dataset, a relational SQL database was developed that allows in combination with GIS data a rule-based nation-wide automated analysis. Furthermore, possibilities and challenges are discussed with respect to the use of such data in vulnerability assessment and with respect to resilience measures. We comprehensively address the challenge of data accuracy, scale and uncertainties. From the total of approximately 2.4 million buildings with a clearly attributable geographical location, around 120,000 are exposed to torrent processes (5 %) and snow avalanches (0.4 %); exposition was defined here as located within the digitally available hazard maps of the Austrian Torrent and Avalanche Control Service. Around 5 % of the population (360,000 out of 8.5 million inhabitants), based on those people being compulsory listed in the population register, are located in these areas. The analysis according to the building category resulted in 2.05 million residential buildings in Austria (85 %), 93,000 of which (4.5 %) are exposed to these hazards. In contrast, 37,300 buildings (1.6 %) throughout the country belong to the category of accommodation facilities, 5,600 of which are exposed (15 %). Out of the 140,500 commercial buildings, 8,000 (5 %) are exposed. A considerable spatial variation was detectable within the communities and Federal States. In general, an above-average exposition of buildings to torrent process and snow avalanches was detectable in communities located in the Federal State of Salzburg, Styria and Vorarlberg (torrents), and Tyrol and Vorarlberg (snow avalanches). In the alpine part of Austria, the share of exposed accommodation buildings was two times (Salzburg) and three times (Vorarlberg) higher than the regional average of exposed buildings, and the share of agricultural buildings was around 50 % lower than on the national level. A significantly higher share of people is exposed in Salzburg (torrents) and Tyrol and Vorarlberg (snow avalanches); nevertheless, there is a need for a further in-depth local analysis. The results clearly indicate that an assessment using nation-wide data on buildings and population has advantages in vulnerability assessment compared to traditional approaches. However, the data has some limits if information on the large scale of individual catchments is needed, which restricts the application when an increase in resilience towards mountain hazards is targeted.
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Hazard assessment for small torrent catchments - lessons learned
NASA Astrophysics Data System (ADS)
Eisl, Julia; Huebl, Johannes
2013-04-01
The documentation of extreme events as a part of the integral risk management cycle is an important basis for the analysis and assessment of natural hazards. In July 2011 a flood event occurred in the Wölzer-valley in the province of Styria, Austria. For this event at the "Wölzerbach" a detailed event documentation was carried out, gathering data about rainfall, runoff and sediment transport as well as information on damaged objects, infrastructure or crops using various sources. The flood was triggered by heavy rainfalls in two tributaries of the Wölzer-river. Though a rain as well as a discharge gaging station exists for the Wölzer-river, the torrents affected by the high intensity rainfalls are ungaged. For these ungaged torrent catchments the common methods for hazard assessment were evaluated. The back-calculation of the rainfall event was done using a new approach for precipitation analysis. In torrent catchments especially small-scale and high-intensity rainfall events are mainly responsible for extreme events. Austria's weather surveillance radar is operated by the air traffic service "AustroControl". The usually available dataset is interpreted and shows divergences especially when it comes to high intensity rainfalls. For this study the raw data of the radar were requested and analysed. Further on the event was back-calculated with different rainfall-runoff models, hydraulic models and sediment transport models to obtain calibration parameters for future use in hazard assessment for this region. Since there are often problems with woody debris different scenarios were simulated. The calibrated and plausible results from the runoff models were used for the comparison with empirical approaches used in the practical sector. For the planning of mitigation measures of the Schöttl-torrent, which is one of the affected tributaries of the Wölzer-river, a physical scale model was used in addition to the insights of the event analysis to design a check dam for sediment retention. As far as the transport capacity of the lower reaches is limited a balance had to be found between protection on the one hand and sediment connectivity to the Wölzer-river on the other. The lessons learned kicked off discussions for future hazard assessment especially concerning the use of rainfall data and design precipitation values for small torrent catchments. Also the comparison with empirical values showed the need for differentiated concepts for hazard analysis. Therefor recommendations for the use of spatial rainfall reduction factors as well as the demarcation of hazard maps using different event scenarios are proposed.
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2007-11-01
athankelijkheden, de hoeveelheid situatie? Auteur (s) ir. P.L.H. Cleophas drs. M.H.M. Delmee PROGRAMMA PROJECT drs. S. Hoesmans drs. P.G.M. van Scheepstal drs...hiertussen een aanvullende belangrijke schakel. In theorie worden binnen de CLAS en CZSK verschillende methoden voor het plannen van een operatie gehanteerd...J.H.A.Blokker MCM drs P.G.M. van Scheepstal Afdelingshoofd Auteur 72/72 TNO-rapport I TNO-DV 2007 A452 TNO-rapport I TNO-DV 2007 A452 Bijlage A 11/4 A Fysiek
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The trickle before the torrent-diffraction data from X-ray lasers.
Maia, Filipe R N C; Hajdu, Janos
2016-08-01
Today Scientific Data launched a collection of publications describing data from X-ray free-electron lasers under the theme 'Structural Biology Applications of X-ray Lasers'. The papers cover data on nanocrystals, single virus particles, isolated cell organelles, and living cells. All data are deposited with the Coherent X-ray Imaging Data Bank (CXIDB) and available to the scientific community to develop ideas, tools and procedures to meet challenges with the expected torrents of data from new X-ray lasers, capable of producing billion exposures per day.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, Hanguang; Hwang, Sooyeon; Wang, Maoyu
It remains a grand challenge to replace platinum group metal (PGM) catalysts with earth-abundant materials for the oxygen reduction reaction (ORR) in acidic media, which is crucial for large-scale deployment of proton exchange membrane fuel cells (PEMFCs). Here, we report a high-performance atomic Fe catalyst derived from chemically Fe-doped zeolitic imidazolate frameworks (ZIFs) by directly bonding Fe ions to imidazolate ligands within 3D frameworks. Although the ZIF was identified as a promising precursor, the new synthetic chemistry enables the creation of well-dispersed atomic Fe sites embedded into porous carbon without the formation of aggregates. The size of catalyst particles ismore » tunable through synthesizing Fe-doped ZIF nanocrystal precursors in a wide range from 20 to 1000 nm followed by one-step thermal activation. Similar to Pt nanoparticles, the unique size control without altering chemical properties afforded by this approach is able to increase the number of PGM-free active sites. The best ORR activity is measured with the catalyst at a size of 50 nm. Further size reduction to 20 nm leads to significant particle agglomeration, thus decreasing the activity. Using the homogeneous atomic Fe model catalysts, we elucidated the active site formation process through correlating measured ORR activity with the change of chemical bonds in precursors during thermal activation up to 1100 °C. The critical temperature to form active sites is 800 °C, which is associated with a new Fe species with a reduced oxidation number (from Fe3+ to Fe2+) likely bonded with pyridinic N (FeN4) embedded into the carbon planes. Further increasing the temperature leads to continuously enhanced activity, linked to the rise of graphitic N and Fe–N species. The new atomic Fe catalyst has achieved respectable ORR activity in challenging acidic media (0.5 M H2SO4), showing a half-wave potential of 0.85 V vs RHE and leaving only a 30 mV gap with Pt/C (60 μgPt/cm2). Enhanced stability is attained with the same catalyst, which loses only 20 mV after 10 000 potential cycles (0.6–1.0 V) in O2 saturated acid. The high-performance atomic Fe PGM-free catalyst holds great promise as a replacement for Pt in future PEMFCs.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, Hanguang; Hwang, Sooyeon; Wang, Maoyu
It remains a grand challenge to replace platinum group metal (PGM) catalysts with earth-abundant materials for the oxygen reduction reaction (ORR) in acidic media, which is crucial for large-scale deployment of proton exchange membrane fuel cells (PEMFCs). We report a high-performance atomic Fe catalyst derived from chemically Fe-doped zeolitic imidazolate frameworks (ZIFs) by directly bonding Fe ions to imidazolate ligands within 3D frameworks. Although the ZIF was identified as a promising precursor, the new synthetic chemistry enables the creation of well-dispersed atomic Fe sites embedded into porous carbon without the formation of aggregates. The size of catalyst particles is tunablemore » through synthesizing Fe-doped ZIF nanocrystal precursors in a wide range from 20 to 1000 nm followed by one-step thermal activation. Similar to Pt nanoparticles, the unique size control without altering chemical properties afforded by this approach is able to increase the number of PGM-free active sites. The best ORR activity is measured with the catalyst at a size of 50 nm. Further size reduction to 20 nm leads to significant particle agglomeration, thus decreasing the activity. In using the homogeneous atomic Fe model catalysts, we elucidated the active site formation process through correlating measured ORR activity with the change of chemical bonds in precursors during thermal activation up to 1100 °C. The critical temperature to form active sites is 800 °C, which is associated with a new Fe species with a reduced oxidation number (from Fe 3+ to Fe 2+) likely bonded with pyridinic N (FeN 4) embedded into the carbon planes. Further increasing the temperature leads to continuously enhanced activity, linked to the rise of graphitic N and Fe–N species. The new atomic Fe catalyst has achieved respectable ORR activity in challenging acidic media (0.5 M H 2SO 4), showing a half-wave potential of 0.85 V vs RHE and leaving only a 30 mV gap with Pt/C (60 μg Pt/cm 2). Finally, enhanced stability is attained with the same catalyst, which loses only 20 mV after 10 000 potential cycles (0.6–1.0 V) in O 2 saturated acid. The high-performance atomic Fe PGM-free catalyst holds great promise as a replacement for Pt in future PEMFCs.« less
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Zhang, Hanguang; Hwang, Sooyeon; Wang, Maoyu; ...
2017-09-13
It remains a grand challenge to replace platinum group metal (PGM) catalysts with earth-abundant materials for the oxygen reduction reaction (ORR) in acidic media, which is crucial for large-scale deployment of proton exchange membrane fuel cells (PEMFCs). We report a high-performance atomic Fe catalyst derived from chemically Fe-doped zeolitic imidazolate frameworks (ZIFs) by directly bonding Fe ions to imidazolate ligands within 3D frameworks. Although the ZIF was identified as a promising precursor, the new synthetic chemistry enables the creation of well-dispersed atomic Fe sites embedded into porous carbon without the formation of aggregates. The size of catalyst particles is tunablemore » through synthesizing Fe-doped ZIF nanocrystal precursors in a wide range from 20 to 1000 nm followed by one-step thermal activation. Similar to Pt nanoparticles, the unique size control without altering chemical properties afforded by this approach is able to increase the number of PGM-free active sites. The best ORR activity is measured with the catalyst at a size of 50 nm. Further size reduction to 20 nm leads to significant particle agglomeration, thus decreasing the activity. In using the homogeneous atomic Fe model catalysts, we elucidated the active site formation process through correlating measured ORR activity with the change of chemical bonds in precursors during thermal activation up to 1100 °C. The critical temperature to form active sites is 800 °C, which is associated with a new Fe species with a reduced oxidation number (from Fe 3+ to Fe 2+) likely bonded with pyridinic N (FeN 4) embedded into the carbon planes. Further increasing the temperature leads to continuously enhanced activity, linked to the rise of graphitic N and Fe–N species. The new atomic Fe catalyst has achieved respectable ORR activity in challenging acidic media (0.5 M H 2SO 4), showing a half-wave potential of 0.85 V vs RHE and leaving only a 30 mV gap with Pt/C (60 μg Pt/cm 2). Finally, enhanced stability is attained with the same catalyst, which loses only 20 mV after 10 000 potential cycles (0.6–1.0 V) in O 2 saturated acid. The high-performance atomic Fe PGM-free catalyst holds great promise as a replacement for Pt in future PEMFCs.« less
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NASA Astrophysics Data System (ADS)
Hasani, M.; Khodadadi, A.; Koleini, S. M. J.; Saeedi, A. H.; Meléndez, A. M.
2017-01-01
Dissolution of platinum group metals (PGM; herein Pt, Pd and Rh) in different chloride-based leaching systems from spent auto catalysts was performed. Response surface methodology and a five-level-five-factor central composite design were used to evaluate the effects of 1) temperature, 2) liquid-to-solid ratio, 3) stirring speed, 4) acid concentration and 5) particle size on extraction yield of PGM by aqua regia. Analysis of variance was used to determine the optimum conditions and most significant factors affecting the overall metal extraction. In the optimum conditions, leaching of Pt, Pd and Rh was 91.58%, 93.49% and 60.15%, respectively. The effect of different oxidizing agents on the PGM dissolution in chloride medium was studied comparatively in the following leaching systems: a) aqua regia/sulfuric acid mixture, b) hydrogen peroxide in sulfuric acid (piranha solution), c) sodium hypochlorite and d) copper(II). Dissolution of Rh is increased in both aqua regia and hydrogen peroxide/hydrochloric acid solutions by adding sulfuric acid.
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Binder, Andrew J.; Toops, Todd J.; Unocic, Raymond R.; ...
2015-09-11
Platinum group metal (PGM) catalysts are the current standard for control of pollutants in automotive exhaust streams. Aside from their high cost, PGM catalysts struggle with CO oxidation at low temperatures (<200 °C) due to inhibition by hydrocarbons in exhaust streams. Here we present a ternary mixed oxide catalyst composed of copper oxide, cobalt oxide, and ceria (dubbed CCC) that outperforms synthesized and commercial PGM catalysts for CO oxidation in simulated exhaust streams while showing no signs of inhibition by propene. Diffuse reflectance IR (DRIFTS) and light-off data both indicate low interaction between propene and the CO oxidation active sitemore » on this catalyst, and a separation of adsorption sites is proposed as the cause of this inhibition resistance. In conclusion, this catalyst shows great potential as a low-cost component for low temperature exhaust streams that are expected to be a characteristic of future automotive systems.« less
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Polychlorinated biphenyls (PCBs) in the atmosphere of sub-alpine northern Italy.
Castro-Jiménez, J; Dueri, S; Eisenreich, S J; Mariani, G; Skejo, H; Umlauf, G; Zaldívar, J M
2009-03-01
The main objective of this work was to assess the atmospheric concentrations and seasonal variations of selected POPs in a sub-alpine location where few data are available. A monitoring and research station was set up at the JRC Ispra EMEP site (Italy). We present and discuss a one-year data set (2005-2006) on PCB air concentrations. Sigma 7PCBs monthly averaged concentration varied from 31 to 76 pgm(-3). Concentrations in the gas phase (21-72 pgm(-3)) were higher than those in the particulate phase (3-10 pgm(-3)). Advection of air masses and re-volatilization from local sources seem to play a dominant role as drivers of PCB atmospheric concentrations in the area. Indications of seasonal variation affecting PCB congener patterns and the gas/particulate partitioning were found. Modeling calculations suggest a predominant importance of the wet deposition in this region (1 microgm(-2)yr(-1) Sigma 7PCBs yearly total wet deposition flux; 650-2400 pgL(-1) rainwater concentrations).
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Lee, Sang-Kyu; Eom, Joon-Seob; Hwang, Seon-Kap; Shin, Dongjin; An, Gynheung; Okita, Thomas W.; Jeon, Jong-Seong
2016-01-01
To elucidate the starch synthesis pathway and the role of this reserve in rice pollen, we characterized mutations in the plastidic phosphoglucomutase, OspPGM, and the plastidic large subunit of ADP-glucose (ADP-Glc) pyrophosphorylase, OsAGPL4. Both genes were up-regulated in maturing pollen, a stage when starch begins to accumulate. Progeny analysis of self-pollinated heterozygous lines carrying the OspPGM mutant alleles, osppgm-1 and osppgm-2, or the OsAGPL4 mutant allele, osagpl4-1, as well as reciprocal crosses between the wild type (WT) and heterozygotes revealed that loss of OspPGM or OsAGPL4 caused male sterility, with the former condition rescued by the introduction of the WT OspPGM gene. While iodine staining and transmission electron microscopy analyses of pollen grains from homozygous osppgm-1 lines produced by anther culture confirmed the starch null phenotype, pollen from homozygous osagpl4 mutant lines, osagpl4-2 and osagpl4-3, generated by the CRISPR/Cas system, accumulated small amounts of starch which were sufficient to produce viable seed. Such osagpl4 mutant pollen, however, was unable to compete against WT pollen successfully, validating the important role of this reserve in fertilization. Our results demonstrate that starch is mainly polymerized from ADP-Glc synthesized from plastidic hexose phosphates in rice pollen and that starch is an essential requirement for successful fertilization in rice. PMID:27588462
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Brauner, Katrin; Hörmiller, Imke; Nägele, Thomas; Heyer, Arnd G
2014-07-01
The knock-out mutation of plastidial phosphoglucomutase (pgm) causes a starchless phenotype in Arabidopsis thaliana, and results in a severe growth reduction of plants cultivated under diurnal conditions. It has been speculated that high soluble sugar levels accumulating during the light phase in leaf mesophyll might cause a reduction of photosynthetic activity or that shortage of reduced carbon during the night is the reason for the slow biomass gain of pgm. Separate simultaneous measurements of leaf net photosynthesis and root respiration demonstrate that photosynthetic activity per unit fresh weight is not reduced in pgm, whereas root respiration is strongly elevated. Comparison with a mutant defective in the dominating vacuolar invertase (AtβFruct4) revealed that high sucrose concentration in the cytosol, but not in the vacuole, of leaf cells is responsible for elevated assimilate transport to the root. Increased sugar supply to the root, as observed in pgm mutants, forces substantial respiratory losses. Because root respiration accounts for 80% of total plant respiration under long-day conditions, this gives rise to retarded biomass formation. In contrast, reduced vacuolar invertase activity leads to reduced net photosynthesis in the shoot and lowered root respiration, and affords an increased root/shoot ratio. The results demonstrate that roots have very limited capacity for carbon storage but exert rigid control of supply for their maintenance metabolism. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.
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Analysis of an ordinary bedload transport event in a mountain torrent (Rio Vanti, Verona, Italy)
NASA Astrophysics Data System (ADS)
Pastorello, Roberta; D'Agostino, Vincenzo
2016-04-01
The correct simulation of the sediment-transport response of mountain torrents both for extreme and ordinary flood events is a fundamental step to understand the process, but also to drive proper decisions on the protection works. The objective of this research contribution is to reconstruct the 'ordinary' flood event with the associated sediment-graph of a flood that caused on the 14th of October, 2014 the formation of a little debris cone (about 200-210 m3) at the junction between the 'Rio Vanti' torrent catchment and the 'Selva di Progno' torrent (Veneto Region, Prealps, Verona, Italy). To this purpose, it is important to notice that a great part of equations developed for the computation of the bedload transport capacity, like for example that of Schoklitsch (1962) or Smart and Jaeggi (1983), are focused on extraordinary events heavily affecting the river-bed armour. These formulas do not provide reliable results if used on events, like the one under analysis, not too far from the bankfull conditions. The Rio Vanti event was characterized by a total rainfall depth of 36.2 mm and a back-calculated peak discharge of 6.12 m3/s with a return period of 1-2 years. The classical equations to assess the sediment transport capacity overestimate the total volume of the event of several orders of magnitude. By the consequence, the following experimental bedload transport equation has been applied (D'Agostino and Lenzi, 1999), which is valid for ordinary flood events (q: unit water discharge; qc: unit discharge of bedload transport initiation; qs: unit bedload rate; S: thalweg slope): -qs-˜= 0,04ṡ(q- qc) S3/2 In particular, starting from the real rainfall data, the hydrograph and the sediment-graph have been reconstructed. Then, comparing the total volume calculated via the above cited equation to the real volume estimated using DoD techniques on post-event photogrammetric survey, a very satisfactory agreement has been obtained. The result further supports the thesis that the bedload transport in boulder-bed torrents is characterised by an important threshold, which corresponds to a high variation of the sediment discharge due to the bed-armour breaking.
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NASA Astrophysics Data System (ADS)
Saha, Shibely
High cost and limited abundance of Platinum (Pt) have hindered effective commercialization of Proton Exchange Membrane Fuel Cell and Electrolyzer. Efforts have been undertaken to reduce precious group metal (PGM) requirement for these devices without compromising the activity of the catalyst by using transition metal carbides (TMC) as non-PGM support thanks to their similar electronic and geometric structures as Pt. In this work Mo2C was selected as non-PGM support and Pt was used as the PGM of interest. We hypothesize that the hollow nanotube morphology of Mo2C support combined with Pt nano particles deposited on it via atomic layer deposition (ALD) technique would allow increased interaction between them which may increase the activity of Pt and Mo2C as well as maximize the Pt active surface area. Specifically, a rotary ALD equipment was used to grow Pt particles from atomic level to 2--3 nanometers by simply adjusting number of ALD cycles in order to probe the interaction between the deposited Pt nanoparticles and Mo2C nanotube support. Interaction between the Pt and Mo2 C was analyzed via surface characterization and electrochemical characterization. Interaction between Pt and Mo2C arises due to the lattice mismatch between Pt and Mo2C as well as electron migration between them. Lattice spacing analysis using high resolution transmission electron microscopy (HRTEM) images, combined with Pt binding energy shift in XPS results, clearly showed strong bonding between Pt nanoparticles and the Mo2C nanotube support in all the resultant Pt/Mo2C samples. We postulate that this strong interaction is responsible for the significantly enhanced durability observed in our constant potential electrolysis (CPE) and accelerated degradation testing (ADT). Of the three samples from different ALD cycles (15, 50 and 100), Mo2C nanotubes modified by 50 (1.07 wt% Pt loading) and 100 cycles (4.4 wt% Pt) of Pt deposition, showed higher HER and HOR activity per Pt mass than commercial 20% Pt supported on carbon black. Finally, we report the systematic investigation of the feasibility of this nanoscale Pt/Mo 2C catalyst in a practical device setting. The ORR activity of 100 Pt/Mo 2C was determined using the catalyst in the cathode of the MEA. Performance of this catalyst led the Pt utilization to be 10.35kWgPt-1 outperforming the target set by DOE for 2017--2020 by 30%.
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How the environment shapes animal signals: a test of the acoustic adaptation hypothesis in frogs.
Goutte, S; Dubois, A; Howard, S D; Márquez, R; Rowley, J J L; Dehling, J M; Grandcolas, P; Xiong, R C; Legendre, F
2018-01-01
Long-distance acoustic signals are widely used in animal communication systems and, in many cases, are essential for reproduction. The acoustic adaptation hypothesis (AAH) implies that acoustic signals should be selected for further transmission and better content integrity under the acoustic constraints of the habitat in which they are produced. In this study, we test predictions derived from the AAH in frogs. Specifically, we focus on the difference between torrent frogs and frogs calling in less noisy habitats. Torrents produce sounds that can mask frog vocalizations and constitute a major acoustic constraint on call evolution. We combine data collected in the field, material from scientific collections and the literature for a total of 79 primarily Asian species, of the families Ranidae, Rhacophoridae, Dicroglossidae and Microhylidae. Using phylogenetic comparative methods and including morphological and environmental potential confounding factors, we investigate putatively adaptive call features in torrent frogs. We use broad habitat categories as well as fine-scale habitat measurements and test their correlation with six call characteristics. We find mixed support for the AAH. Spectral features of torrent frog calls are different from those of frogs calling in other habitats and are related to ambient noise levels, as predicted by the AAH. However, temporal call features do not seem to be shaped by the frogs' calling habitats. Our results underline both the complexity of call evolution and the need to consider multiple factors when investigating this issue. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.
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Gauging Flash-Floods: Automated Measurement of Flood Events in Mountain Torrents
NASA Astrophysics Data System (ADS)
Liechti, Katharina; Boss, Stefan; Fritschi, Bruno; Zappa, Massimiliano
2017-04-01
Rating curves contain uncertainties, especially in their upper range of higher discharge. This is due to more uncertainties in the measurements and also the typically lower number of measurements of high discharge events. However, it is the upper part of a rating curve that is of interest if it comes to dimensioning protection measures against floods and flash floods. For small municipalities who plan mitigation measures like a dam for protection against flash floods of small mountain torrent a rating curve as accurate as possible can be of great interest. It helps to reduce costs that can be caused by both under- and overdimensioning of a protective structure. We therefore invented a mobile discharge measurement station that is set up to construct a rating curve for small turbulent mountain torrents. It operates with salt dilution method and works in its current setup up to about 10 m3/s. The salt is injected automatically to the torrent when an event of desired magnitude takes place. Further downstream a conductivity measuring sensor records the change in salt concentration of the stream water. This mechanism is guided by automatic continuous observation of radar quantitative precipitation estimates (QPE) and a water pressure sensor. Measurements at a first test site gave promising results. The system does event measurements independent of the time of day and day of the week. The measuring equipment at the field site is only activated in case of an event. Therefore it has a low power consumption and can be run by only two solar panels.
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NASA Astrophysics Data System (ADS)
Mikkonen, Anu; Yläranta, Kati; Tiirola, Marja; Romantschuk, Martin; Sinkkonen, Aki
2016-04-01
Pentachlorophenol (PCP) is a priority pollutant of exclusively anthropogenic origin. Formerly used commonly in timber preservatives, PCP has persisted at polluted groundwater sites decades after its use was banned, typically as the last detectable contaminant component. Notorious for its toxicity and poor biodegradability, little is known about the genetic potential and pathways for PCP degradation in the environment. The only fully characterized mineralization pathway is initiated by the enzyme coded by chromosomal pcpB gene, previously detected in PCP degrading Sphingomonadaceae bacteria isolated at two continents. However, there is no information about the abundance or diversity of any PCP degradation related gene at contaminated sites in situ. Our aim was to assess whether pcpB and/or sphingomonads seem to play a role in in situ degradation of PCP, by studying whether pcpB i) is detectable at chlorophenol-polluted groundwater sediments, ii) responds to PCP concentration changes, and iii) shows correlation with the abundance of sphingomonads or a specific sphingomonad genus. Novel protocols for quantification and profiling of pcpB, with primers covering full known diversity, were developed and tested at two sites in Finland with well-documented long-term chlorophenol contamination history: Kärkölä and Pursiala. High throughput sequencing complemented characterization of the total bacterial community and pcpB gene pool. The relative abundance of pcpB in bacterial community was associated with spatial variability in groundwater PCP concentration in Pursiala, and with temporal differences in groundwater PCP concentration in Kärkölä. T-RFLP fingerprinting results indicated and Ion Torrent PGM and Sanger sequencing confirmed the presence of a single phylotype of pcpB at both geographically distant, historically contaminated sites, matching the one detected previously in Canadian bioreactor clones and Kärkölä bioreactor isolates. Sphingomonad abundance generally correlated positively with pcpB abundance. Sphingomonad and pcpB ranges in the same sample were comparable regardless of differences in sphingomonad community composition between different groundwater wells. These first cultivation-independent results of pcpB abundance and diversity at contaminated sites indicate that pcpB confers competitive advantage in environments contaminated with the priority pollutant PCP and may be related to its degradation in situ; its relative abundance amongst bacteria reflected PCP concentration, and it seemed to be widely shared among various sphingomonad genera. Interestingly, decades under contamination pressure have led to no diversification of pcpB gene at these sites, suggesting constrained distribution and evolution of genetic potential for PCP degradation. It remains open whether the present form of the gene or pathway is the single most efficient one in these environments, or whether inoculation with diverse degrader strains isolated elsewhere could further enhance PCP bioremediation.
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Barkholtz, Heather M.; Liu, Di -Jia
2016-11-14
Over the past several years, metal-organic framework (MOF)-derived platinum group metal free (PGM-free) electrocatalysts have gained considerable attention due to their high efficiency and low cost as potential replacement for platinum in catalyzing oxygen reduction reaction (ORR). In this review, we summarize the recent advancements in design, synthesis and characterization of MOF-derived ORR catalysts and their performances in acidic and alkaline media. As a result, we also discuss the key challenges such as durability and activity enhancement critical in moving forward this emerging electrocatalyst science.
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NASA Astrophysics Data System (ADS)
Yadav, Ishwar Chandra; Devi, Ningombam Linthoingmabi; Li, Jun; Zhang, Gan
2017-07-01
Elevated level of brominated- and chlorinated-flame retardants (FRs) have been accounted in ambient air across the globe. Despite what might be expected, restricted information is available on PBDEs and other halogenated FR contained indoor air in whole of Indian sub-continent especially in case of Nepal, sandwiched between two most populous countries i.e. India and China. It was conjectured that the level of halogenated flame retardant (HFRs) in Nepalese air would be high because they have not been liable to control in Nepal; and henceforth there is more plausibility of HFRs to be available in a diverse array of goods and consumer products. This study therefore aims to measure the occurrence, spatial distributions and sources of 15 brominated- and 2 chlorinated-FRs in indoor air from four major cities of Nepal. The overall concentrations of HFRs ranged from 16.1 to 6750 pg/m3 (median 334 pg/m3). The total concentrations of novel brominated fire retardants (NBFRs) were 20 and 100 times (13.2-6270 pg/m3) higher than PBDEs (2.2-353 pg/m3) and DPs (0.67-129 pg/m3), respectively indicating much higher usages of NBFRs in Nepal. The level of ∑PBDEs in air is identified with utilization of wide variety of consumers products and building materials containing FRs in Nepalese houses, while higher concentration of BDE-209 were subject to emission from materials containing deca-BDE formulation. Significantly higher concentrations of DBDPE than BDE-209 in air demonstrated a move to more prominent use of DBDPE as alternative to BDE-209. The lower fanti ratios suggests the DP level in this study was essentially affected by the long range atmospheric transport from remote DP source instead of commercial products. The exposure to BDE-47, -99, -153, -209 and HBB via inhalation was 3-4 orders of magnitude lower than corresponding RfD values, suggesting insignificant risk to Nepalese population. However, other modes of human exposure might still be significant in Nepal.
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de la Torre, A; Barbas, B; Sanz, P; Navarro, I; Artíñano, B; Martínez, M A
2018-07-15
Urban ambient air samples, including gas-phase (PUF), total suspended particulates (TSP), PM 10 , PM 2.5 and PM 1 airborne particle fractions were collected to evaluate gas-particle partitioning and size particle distribution of traditional and novel halogenated flame retardants. Simultaneously, passive air samplers (PAS) were deployed in the same location. Analytes included 33 polybrominated diphenyl ether (PBDE), 2,2',4,4',5,5'-hexabromobiphenyl (BB-153), hexabromobenzene (HBB), pentabromoethylbenzene (PBEB), 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE), decabromodiphenyl ethane (DBDPE), dechloranes (Dec 602, 603, 604, 605 or Dechorane plus (DP)) and chlordane plus (CP). Clausius-Clapeyron equation, gas-particle partition coefficient (K p ), fraction partitioned onto particles (φ) and human respiratory risk assessment were used to evaluate local or long-distance transport sources, gas-particle partitioning sorption mechanisms, and implications for health, respectively. PBDEs were the FR with the highest levels (13.9pgm -3 , median TSP+PUF), followed by DP (1.56pgm -3 ), mirex (0.78pgm -3 ), PBEB (0.05pgm -3 ), and BB-153 (0.04pgm -3 ). PBDE congener pattern in particulate matter was dominated by BDE-209, while the contribution of more volatile congeners, BDE-28, -47, -99, and -100 was higher in gas-phase. Congener contribution increases with particle size and bromination degree, being BDE-47 mostly bounded to particles≤PM 1 , BDE-99 to > PM 1 and BDE-209 to > PM 2.5 . No significant differences were found for PBDE and DP concentrations obtained with passive and active samplers, demonstrating the ability of the formers to collect particulate material. Deposition efficiencies and fluxes on inhaled PBDEs and DP in human respiratory tract were calculated. Contribution in respiratory track was dominated by head airway (2.16 and 0.26pgh -1 , for PBDE and DP), followed by tracheobronchial (0.12 and 0.02pgh -1 ) and alveoli (0.01-0.002pgh -1 ) regions. Finally, hazard quotient values on inhalation were proposed (6.3×10 -7 and 1.1×10 -8 for PBDEs and DP), reflecting a low cancer risk through inhalation. Copyright © 2018 Elsevier B.V. All rights reserved.
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Hodges, P W; Kippers, V; Richardson, C A
1997-01-01
Fine-wire electromyography is primarily utilised for the recording of activity of the deep musculature, however, due to the location of these muscles, accurate electrode placement is difficult. Real-time ultrasound imaging (RTUI) of muscle tissue has been used for the guidance of the needle insertion for the placement of electrodes into the muscles of the abdominal wall. The validity of RTUI guidance of needle insertion into the deep muscles has not been determined. A cadaveric study was conducted to evaluate the accuracy with which RTUI can be used to guide fine-wire electrode placement using the posterior fibres of gluteus medius (PGM) as an example. Pilot studies revealed that the ultrasound resolution of cadaveric tissue is markedly reduced making it impossible to directly evaluate the technique, therefore, three studies were conducted. An initial study involved the demarcation of the anatomical boundaries of PGM using RTUI to define a technique based on an anatomical landmark that was consisent with the in vivo RTUI guided needle placement technique. This anatomical landmark was then used as the guide for the cadaveric needle insertion. Once the needle was positioned 0.05 ml of dye was introduced and the specimen dissected. The dye was accurately placed in PGM in 100% of the specimens. Finally, fine-wire electrodes were inserted into the PGM of five volunteers and manoeuvres performed indicating the accuracy of placement. This study supports the use of ultrasound imaging for the accurate guidance of needle insertion for fine-wire and needle EMG electrodes.
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Frederiks, T M; Christopher, J T; Harvey, G L; Sutherland, M W; Borrell, A K
2012-09-01
Cereal crops can suffer substantial damage if frosts occur at heading. Identification of post-head-emergence frost (PHEF) resistance in cereals poses a number of unique and difficult challenges. Many decades of research have failed to identify genotypes with PHEF resistance that could offer economically significant benefit to growers. Research and breeding gains have been limited by the available screening systems. Using traditional frost screening systems, genotypes that escape frost injury in trials due to spatial temperature differences and/or small differences in phenology can be misidentified as resistant. We believe that by improving techniques to minimize frost escapes, such 'false-positive' results can be confidently identified and eliminated. Artificial freezing chambers or manipulated natural frost treatments offer many potential advantages but are not yet at the stage where they can be reliably used for frost screening in breeding programmes. Here we describe the development of a novel photoperiod gradient method (PGM) that facilitates screening of genotypes of different phenology under natural field frosts at matched developmental stages. By identifying frost escapes and increasing the efficiency of field screening, the PGM ensures that research effort can be focused on finding genotypes with improved PHEF resistance. To maximize the likelihood of identifying PHEF resistance, we propose that the PGM form part of an integrated strategy to (i) source germplasm;(ii) facilitate high throughput screening; and (iii) permit detailed validation. PGM may also be useful in other studies where either a range of developmental stages and/or synchronized development are desired.
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Zhang, Yu; Yu, Xiaomin; Ichikawa, Mie; Lyons, Jonathan J.; Datta, Shrimati; Lamborn, Ian T.; Jing, Huie; Kim, Emily S.; Biancalana, Matthew; Wolfe, Lynne A.; DiMaggio, Thomas; Matthews, Helen F.; Kranick, Sarah M.; Stone, Kelly D.; Holland, Steven M.; Reich, Daniel S.; Hughes, Jason D.; Mehmet, Huseyin; McElwee, Joshua; Freeman, Alexandra F.; Freeze, Hudson H.; Su, Helen C.; Milner, Joshua D.
2014-01-01
Background Identifying genetic syndromes that lead to significant atopic disease can open new pathways for investigation and intervention in allergy. Objective To define a genetic syndrome of severe atopy, elevated serum IgE, immune deficiency, autoimmunity, and motor and neurocognitive impairment. Methods Eight patients from two families who had similar syndromic features were studied. Thorough clinical evaluations, including brain MRI and sensory evoked potentials, were performed. Peripheral lymphocyte flow cytometry, antibody responses, and T cell cytokine production were measured. Whole exome sequencing was performed to identify disease-causing mutations. Immunoblotting, qRT-PCR, enzymatic assays, nucleotide sugar and sugar phosphate analyses along with MALDI-TOF mass spectrometry of glycans were used to determine the molecular consequences of the mutations. Results Marked atopy and autoimmunity were associated with increased TH2 and TH17 cytokine production by CD4+ T cells. Bacterial and viral infection susceptibility were noted along with T cell lymphopenia, particularly of CD8+ T cells, and reduced memory B cells. Apparent brain hypomyelination resulted in markedly delayed evoked potentials and likely contributed to neurological abnormalities. Disease segregated with novel autosomal recessive mutations in a single gene, phosphoglucomutase 3 (PGM3). Although PGM3 protein expression was variably diminished, impaired function was demonstrated by decreased enzyme activity and reduced UDP-GlcNAc, along with decreased O- and N-linked protein glycosylation in patients’ cells. These results define a new Congenital Disorder of Glycosylation. Conclusions Autosomal recessive, hypomorphic PGM3 mutations underlie a disorder of severe atopy, immune deficiency, autoimmunity, intellectual disability and hypomyelination. PMID:24589341
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Avagyan, Rozanna; Sadiktsis, Ioannis; Bergvall, Christoffer; Westerholm, Roger
2014-10-01
Urban particulate matter (PM), asphalt, and tire samples were investigated for their content of benzothiazole and benzothiazole derivates. The purpose of this study was to examine whether wear particles, i.e., tire tread wear or road surface wear, could contribute to atmospheric concentrations of benzothiazole derivatives. Airborne particulate matter (PM10) sampled at a busy street in Stockholm, Sweden, contained on average 17 pg/m(3) benzothiazole and 64 pg/m(3) 2-mercaptobenzothiazole, and the total suspended particulate-associated benzothiazole and 2-mercaptobenzothiazole concentrations were 199 and 591 pg/m(3), respectively. This indicates that tire tread wear may be a major source of these benzothiazoles to urban air PM in Stockholm. Furthermore, 2-mercaptobenzothiazole was determined in urban air particulates for the first time in this study, and its presence in inhalable PM10 implies that the human exposure to this biocide is underestimated. This calls for a revision of the risk assessments of 2-mercaptobenzothiazole exposure to humans which currently is limited to occupational exposure.
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Folding and Aggregation of Mucin Domains.
NASA Astrophysics Data System (ADS)
Urbanc, Brigita; Bansil, Rama; Turner, Bradley
2007-03-01
Mucin glycoproteins consist of tandem repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in polymerization of mucin via disulfide bonds and play an important role in the pH dependent gelation of gastric mucin, which is essential to protecting the stomach from autodigestion. We have examined the folding and aggregation of the non-repetitive sequence of von Willebrand factor vWF-C1 domain (67 amino acids) and PGM 2X (242 amino acids) using Discrete Molecular Dynamics (four-bead protein model with hydrogen bonding and amino acid-specific hydrophobic/hydrophilic and electrostatic interactions of side chains). Simulations of vWF C1 show 4-6 β-strands separated by turns/loops with more loops at lower pH. A simulation of several vWF C1 proteins at low pH shows aggregates still with a high content of β-strands and enhanced turn/loop regions. For the PGM 2X simulation the contact map shows several salt bridges enclosing hairpin turns. The implications of these simulations for describing the aggregation/gelation of PGM will be discussed.
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August 2014 Hiroshima landslide disaster and its societal impact
NASA Astrophysics Data System (ADS)
Fukuoka, Hiroshi; Sassa, Kyoji; Wang, Chunxiang
2015-04-01
In the early morning of August 20, 2014, Hiroshima city was hit by a number of debris flows along a linear rain band which caused extreme downpour. This disaster claimed 74 death, although this city experienced very similar disaster in 1999, claiming more than 30 residents lives. In the most severely affected debris flow torrent, more than 50 residents were killed. Most of the casualties arose in the wooden, vulnerable houses constructed in front of the exit of torrents. Points and lessons learnt from the disaster are as follows: 1. Extreme rainfall events : geology and geomorphology does not much affect the distribution of landslides initiation sites. 2. Area of causative extreme rainfall is localized in 2 km x 10 km along the rain band. 3. Authors collected two types of sands from the source scar of the initial debris slides which induced debris flows. Tested by the ring shear apparatus under pore-pressure control condition, clear "Sliding surface liquefaction" was confirmed for both samples even under small normal stress, representing the small thickness of the slides. These results shows even instant excess pore pressure could initiate the slides and trigger slide-induced debris flow by undrained loading onto the torrent deposits. 4. Apparently long-term land-use change affected the vulnerability of the community. Residential area had expanded into hill-slope (mountainous / semi-mountainous area) especially along the torrents. Those communities were developed on the past debris flow fan. 5. As the devastated area is very close to downtown of Hiroshima city, it gave gigantic societal impact to the Japanese citizens. After 1999 Hiroshima debris flow disaster, the Landslide disaster reduction law which intends to promote designation of landslide potential risk zones, was adopted in 2000. Immediately after 2014 disaster, national diet approved revision of the bill.
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Recovery of precious metals from space
NASA Technical Reports Server (NTRS)
Freiser, Henry
1991-01-01
The overall objective is to develop efficient and economical separation and recovery methods for the platinum group and other precious metals. The separation of Pd(II) from Pt(II), Ir(III), and Rh(III) with trioctylphosphine oxide (TOPO) in heptane using centrifugal partition chromatography (CPC) was investigated. Activities to achieve this objective focussed on selection and evaluation of extraction systems for the PGM and modification of selected systems for multistage operation with a view to scaling up to desired macro levels. On the basis of preliminary evaluation of a series of simple metal complexing agents and chelating agents, the TOPO in heptane was selected as a likely system for isolating of Pd(II) and Pt(II) from the other PGM. A multistage apparatus capable of configuration as a simple rugged device, a centrifugal partition chromatograph (CPC), was shown to be effective. The extraction of Pd(II) was studied by CPC and batch solvent extraction. The distribution ratios for Pd(II) determined by both methods agree well. In low HCl concentrations (less than 0.1 M), the extracted species was PdCl2.(TOPO)2, irrespective of the chloride concentration, while at acid concentrations above 0.1 M, the Pd was extracted as the ion pair, 2(TOPO.H+).(PdCl4)2-. Base line separation of Pd(II) and Pt(II) in CPC was obtained under a variety of chloride and HCl concentration. It was demonstrated that the efficiency of CPC for metal separation was limited by chemical kinetic factors rather than instrumental factors, strongly suggesting that dramatic improvements can be achieved by studying reaction kinetics of formation and dissociation of the extractable metal complex.
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Xie, Fan; Zhao, Lili
2018-01-01
Ganoderma lucidum is a medicinal mushroom that has been widely used in East Asia for the treatment of various diseases. The pharmacological activity of this fungus is primarily attributable to the polysaccharides and triterpenoids. In this study, to obtain the fruit bodies with improved content of active constituents, we examined the effect of salicylic acid (SA) and calcium ion on the biosynthesis of polysaccharides and triterpenoids by spraying the chemicals during the fruiting. To explore the underlying mechanisms for the variation, the transcripts of related genes involved in the polysaccharide and triterpenoid biosynthesis were measured. Results showed that Ca2+ had no effect on production of polysaccharides and triterpenoids, whereas SA increased triterpenoid content by 23.32%, compared to the control, but it had little influence on polysaccharide production. Interestingly, the combined induction increased polysaccharide and triterpenoid content by 9.02% and 13.61%, respectively, compared to the control. Under Ca2+ induction, the transcript of ugp gene in the polysaccharide biosynthetic pathway up-regulated in all three stages (mycelium, primordium, and fruit body), while pgm and gls gave no response in the mycelium and primordium stages, and up-regulated in the fruit body stage. Differently, six key triterpenoid biosynthetic genes including hmgr, hmgs, mvd, fps, sqs, and ls did not respond to the induction. In the case of SA and combined induction, pgm and ugp were up-regulated in all three stages, while gls showed an increased expression in the primordium stage and no response in other stages. The six triterpenoid biosynthetic genes were up-regulated in all three stages. The present study provides a useful approach to producing G. lucidum fruit bodies with high polysaccharide and triterpenoid content. This is important to the G. lucidum industry. PMID:29694432
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, Hanguang; Hwang, Sooyeon; Wang, Maoyu
To significantly reduce the cost of proton exchange membrane (PEM) fuel cells, current Pt must be replaced by platinum-metal-group (PGM)-free catalysts for the oxygen reduction reaction (ORR) in acid. We report here a new class of high-performance atomic iron dispersed carbon catalysts through controlled chemical doping of iron ions into zinc-zeolitic imidazolate framework (ZIF), a type of metal-organic framework (MOF). The novel synthetic chemistry enables accurate size control of Fe-doped ZIF catalyst particles with a wide range from 20 to 1000 nm without changing chemical properties, which provides a great opportunity to increase the density of active sites that ismore » determined by the particle size. We elucidated the active site formation mechanism by correlating the chemical and structural changes with thermal activation process for the conversion from Fe-N4 complex containing hydrocarbon networks in ZIF to highly active FeNx sites embedded into carbon. A temperature of 800oC was identified as the critical point to start forming pyridinic nitrogen doping at the edge of the graphitized carbon planes. Further increasing heating temperature to 1100oC leads to increase of graphitic nitrogen, generating possible synergistic effect with FeNx sites to promote ORR activity. The best performing catalyst, which has well-defined particle size around 50 nm and abundance of atomic FeNx sites embedded into carbon structures, achieve a new performance milestone for the ORR in acid including a half-wave potential of 0.85 V vs RHE and only 20 mV loss after 10,000 cycles in O2 saturated H2SO4 electrolyte. The new class PGM-free catalyst with approaching activity to Pt holds great promise for future PEM fuel cells.« less
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Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
Kaas, Rolf S; Leekitcharoenphon, Pimlapas; Aarestrup, Frank M; Lund, Ole
2014-01-01
Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.
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Measuring Sister Chromatid Cohesion Protein Genome Occupancy in Drosophila melanogaster by ChIP-seq.
Dorsett, Dale; Misulovin, Ziva
2017-01-01
This chapter presents methods to conduct and analyze genome-wide chromatin immunoprecipitation of the cohesin complex and the Nipped-B cohesin loading factor in Drosophila cells using high-throughput DNA sequencing (ChIP-seq). Procedures for isolation of chromatin, immunoprecipitation, and construction of sequencing libraries for the Ion Torrent Proton high throughput sequencer are detailed, and computational methods to calculate occupancy as input-normalized fold-enrichment are described. The results obtained by ChIP-seq are compared to those obtained by ChIP-chip (genomic ChIP using tiling microarrays), and the effects of sequencing depth on the accuracy are analyzed. ChIP-seq provides similar sensitivity and reproducibility as ChIP-chip, and identifies the same broad regions of occupancy. The locations of enrichment peaks, however, can differ between ChIP-chip and ChIP-seq, and low sequencing depth can splinter broad regions of occupancy into distinct peaks.
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Morrison, Cheryl L.; Springmann, Marcus J.; Iwanowicz, Deborah D.; Wade, Christopher M.
2015-01-01
A suite of tetra-nucleotide microsatellite loci were developed for the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822, from Ion Torrent next-generation sequencing data. Ten of the 96 primer sets tested amplified consistently in 30 snails from Miami, Florida, plus 12 individuals representative of their native East Africa, Indian and Pacific Ocean regions. The loci displayed moderate levels of allelic diversity (average 5.6 alleles/locus) and heterozygosity (average 42 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring among regional samples. The invasive A. fulica can cause extensive damage to important food crops and natural resources, including native flora and fauna. The loci characterized here will be useful for determining the origins and tracking the spread of invasions, detecting fine-scale spatial structuring and estimating demographic parameters.
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Vargas-Caro, Carolina; Bustamante, Carlos; Bennett, Michael B; Ovenden, Jennifer R
2016-01-01
The yellownose skate Zearaja chilensis is endemic to South America. The species is the target of a valuable commercial fishery in Chile, but is highly susceptible to over-exploitation. The complete mitochondrial genome was described from 694,593 sequences obtained using Ion Torrent Next Generation Sequencing. The total length of the mitogenome was 16,909 bp, comprising 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Comparison between the proposed mitogenome and one previously described from "raw fish fillets from a skate speciality restaurant in Seoul, Korea" resulted in 97.4% similarity, rather than approaching 100% similarity as might be expected. The 2.6% dissimilarity may indicate the presence of two separate stocks or two different species of, ostensibly, Z. chilensis in South America and highlights the need for caution when using genetic resources without a taxonomic reference or a voucher specimen.
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Miller, Mark P.; Haig, Susan M.; Wagner, R.S.
2006-01-01
The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.
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Kocica, Mladen J; Corno, Antonio F; Carreras-Costa, Francesc; Ballester-Rodes, Manel; Moghbel, Mark C; Cueva, Clotario N C; Lackovic, Vesna; Kanjuh, Vladimir I; Torrent-Guasp, Francisco
2006-04-01
We are currently witnessing the advent of new diagnostic tools and therapies for heart diseases, but, without serious scientific consensus on fundamental questions about normal and diseased heart structure and function. During the last decade, three successive, international, multidisciplinary symposia were organized in order to setup fundamental research principles, which would allow us to make a significant step forward in understanding heart structure and function. Helical ventricular myocardial band of Torrent-Guasp is the revolutionary new concept in understanding global, three-dimensional, functional architecture of the ventricular myocardium. This concept defines the principal, cumulative vectors, integrating the tissue architecture (i.e. form) and net forces developed (i.e. function) within the ventricular mass. Here we expose the compendium of Torrent-Guasp's half-century long functional anatomical investigations in the light of ongoing efforts to define the integrative approach, which would lead to new understanding of the ventricular form and function by linking across multiple scales of biological organization, as defined in ongoing Physiome project. Helical ventricular myocardial band of Torrent-Guasp may also, hopefully, allow overcoming some difficulties encountered in contemporary efforts to create a comprehensive mathematical model of the heart.
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NASA Astrophysics Data System (ADS)
Curry, B. B.
2014-12-01
Unprecedented age control on many last glacial stratigraphic units and morainal ice-margin positions are interpreted from AMS radiocarbon ages of tundra plant macrofossils archived in low-relief ice-walled lake plain (IWLP) deposits the Lake Michigan Lobe (south-central Laurentide Ice Sheet). IWLPs are periglacial features that formed on morainal dead-ice permafrost. Lacustrine sediment, and the fossils contained therein, had physical and temporal proximity to the glacier which formed the underlying moraine. In modern ice-walled lakes, as the lake's ice cover begins to melt, moats form which allows access of sloughing tundra-mantled active layer sediment (soil) into the lakes. Multiple AMS ages from two sites with proglacial sediment buried by glacial max LIS diamicton, and IWLPs reveal evidence of episodic plant growth and sedimentation including ca. 24.0 to 24.4 ka (post Shelby Phase), 22.5 to 21.1 ka (post Livingston Phase), 18.1 to 17.4 ka (post Woodstock Phase). Although presently based on negative evidence, the associated nonconformities (listed in title) indicate periods when cold conditions did not promote development of the estival moat. Although the evidence does not preclude tundra growth during the cold summers, there was little landscape modification due to limited thawing of the active layer. At approximately the onset of the 19.2-18.5 "warm" period, at least two large deglacial discharge events flooded the Fox and Kankakee tributary valleys of the Illinois River. The latter, known as the Kankakee Torrent, occurred at 19.05 - 18.85 ka (σ1 range) at the Oswego channel complex. The temporal coincidence of the torrents and sedimentation in ice-walled lakes suggests that the post-Livingston Phase nonconformity (21.1 - 19.2 ka) was a period of lessened meltwater discharge through subglacial conduits (tunnel valleys) as the frozen toe promoted formation of subglacial lakes, buildup of pore-water pressures, and the release of subglacial water as "torrents". In the case of the Fox and Kankakee torrents, ice-marginal discharge first flowed into proglacial lakes which ultimately breached moraines, resulting in catastrophic "torrents". Hence, present knowledge does not allow determination of the nature of the subglacial release (catastrophic vs. large, steady discharge).
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Physical modelling of sediment transport in mountain torrents upstream of open check dams
NASA Astrophysics Data System (ADS)
Schwindt, Sebastian; Franca, Mario J.; Schleiss, Anton J.
2015-04-01
Dynamic morphological processes in mountain torrents do not only attract the attention of many contemporary researchers, but are also a relevant issue for the design of flood protection measures in the downstream sections where dwellers may be threatened by the important potential of flows with high concentration of sediments. Events which have a morphodynamic effect are simulated at the Laboratory of Hydraulic Constructions (LCH) in order to optimize the design of a flood protection measure, notably open check dams. Different scenarios with a fix bed consisting of boulders as well as mobile beds are studied and the influence of flow constrictions, i.e. distinct geometric configurations of open check dams are analysed. Three varying water pumped discharges in the order of 5 to 20 l/s are tested with progressively increasing solid discharges of 1, 3 and 6 % of the liquid discharge according to the transport capacity. The moistened sediments are introduced via a system of conveyor belts and are then mixed with the liquid discharge in an about 3 m long rough trapezoidal channel with a base width of 24 cm. The mean diameter Dm of the injected sediments is 0.86 cm and the dimensionless grain size distribution is in line with a normalized shape derived from over 60 streams in the Alps. A wide range of frequent floods in morphologically diverging types of mountain torrents is covered, in particular regarding the sediment availability in the catchment area and along the river. A basic assumption here is considering that the frequent floods are floods with return periods between 1 to 5 years and are the most important process in terms of amounts of sediment transport. This may be arguable for some mountain torrents and landscape effective processes which are driven by floods with return periods of more than several decades. In order to identify benchmarks for hydraulic parameters which lead to the obstruction of flow restrictions at mountain torrents, the water depth is evaluated using ultrasonic probes, the flow velocity is derived by particle image velocimetry (PIV) and the occurrence of sediment depositions as well as the sediment outflow are observed. The results are in particular analysed in the moment when the flow constriction causes rising back water effects.
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NASA Astrophysics Data System (ADS)
Fukuoka, H.; Wang, C.
2015-12-01
Hiroshima city was hit by swarm debris flows along a narrow, and linear-shaped rain band of 2 km x 10 km which appeared in the early morning of August 20, 2014. Most of the flows were induced by shallow slide in the upstream. This disaster claimed 74 death, although this city experienced very similar disaster in 1999, claiming more than 30 residents lives. In the most severely affected debris flow torrent, more than 50 residents were killed. Most of the casualties arose in the wooden, vulnerable houses constructed in front of the exit of torrents. Points and lessons learnt from the disaster are as follows:1. Authors collected two types of sands from the source scar of the initial debris slides which induced debris flows. Tested by the ring shear apparatus under pore-pressure control condition, clear "Sliding surface liquefaction" was confirmed for both samples even under small normal stress, representing the small thickness of the slides. These results shows even instant excess pore pressure could initiate the slides and trigger slide-induced debris flow byundrained loading onto the torrent deposits.2. Apparently long-term land-use change since 1945 affected and raised the vulnerability of the community. Residential area had expanded into hill-slope (mountainous / semi-mountainous area) especially along the torrents. Those communities were developed on the past debris flow fan.3. As the devastated area is very close to downtown of Hiroshima city, it gave large societal impact to the Japanese citizens. After 1999 Hiroshima debris flow disaster, the Landslide disaster reduction law which intends to promote designation of landslide potential risk zones, was adopted in 2000. Immediately after 2014 disaster, national diet approved revision of the bill to promote rapid completion of the designation over the national territory. MLIT (Ministry of Land, Infrastructure, Tranportation and Tourism) decided to install X-band rain radars at more sites to cover whole city zones of the country. However, narrow extreme rain bands or spots which can not be detected effectively, often appear these years. It means more rain gauges conncted to the net should be implemented at upstreams of the communities facing torrent exits and on debris fan.
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DiCaprio, Erin; Phantkankum, Nuttapong; Culbertson, Doug; Ma, Yuanmei; Hughes, John H; Kingsley, David; Uribe, Roberto M; Li, Jianrong
2016-09-02
Human norovirus (NoV) is a major cause of fresh produce-associated outbreaks and human NoV in irrigation water can potentially lead to viral internalization in fresh produce. Therefore, there is a need to develop novel intervention strategies to target internalized viral pathogens while maintaining fresh produce quality. In this study electron beam (E-beam) and gamma radiation were evaluated for efficacy against a human NoV GII.4 strain and Tulane virus (TV). Virus survival following ionizing radiation treatments was determined using direct quantitative reverse transcriptase PCR (RT-qPCR), the porcine gastric mucin magnetic bead (PGM-MB) binding assay followed by RT-qPCR, and plaque assay. In simple media, a high dose of E-beam treatment was required to completely abolish the receptor binding ability of human NoV (35.3kGy) and TV (19.5-24.1kGy), as assessed using the PGM-MB binding assay. Both human NoV and TV were more susceptible to gamma irradiation than E-beam, requiring 22.4kGy to achieve complete inactivation. In whole strawberries, no human NoV or TV RNA was detected following 28.7kGy of E-beam treatment using the PGM-MB binding assay. Overall, human NoV and TV are highly resistant to ionizing radiation and therefore the technology may not be suitable to eliminate viruses in fresh produce at the currently approved levels. In addition, the PGM-MB binding assay is an improved method to detect viral infectivity compared to direct RT-qPCR. Copyright © 2016. Published by Elsevier B.V.
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Wu, Q; Baek, S-Y; Fang, M; Chang, Y-S
2010-06-01
Polybrominated diphenyl ethers (PBDEs) are considered harmful to human health because of their toxicities and persistence in environments. In the current study, the distribution and fate of PBDEs in classrooms and computer rooms in 17 elementary schools in South Korea have been described. Eight congeners (brominated diphenyl ether-28, -47, -99, -100, -153, -154, -183, and -209) in air, floor dust, and product surface dust were measured. While Sigma(8)PBDEs in the air in classrooms showed considerable variations (0.659-1600 pg/m(3), arithmetic mean +/- s.d.: 377 +/- 441 pg/m(3)), those in computer rooms were somewhat similar (134-220 pg/m(3), arithmetic mean +/- s.d.: 169 +/- 40 pg/m(3)). Sigma(8)PBDEs in floor dust varied over a wide range, from 453 to 45,700 ng/g, for all rooms. Based on congener patterns, two groups were created--CL-1 that is dominated by high-brominated congeners and CL-2 primarily comprising low-brominated congeners--for both air and floor dust of classrooms. Surface dust had low concentrations, ranged from ND to 181, from ND to 128, and from ND to 256 pg/cm(2) for desk/chair sets, lockers, and playing tools, respectively. Pearson correlation coefficients were calculated individually for air, floor dust, and surface dust. The results indicate that both surface dust and floor dust may act as a secondary source of PBDEs in indoor environments after emission from facilities. Children have been estimated to have a higher potential exposure to PBDEs than adults. Since children spend most of their day time at school, PBDE distributions in school environments should be a matter of great concern.
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Pal, Sunil Kumar; Liput, Magdalena; Piques, Maria; Ishihara, Hirofumi; Obata, Toshihiro; Martins, Marina C.M.; Sulpice, Ronan; van Dongen, Joost T.; Fernie, Alisdair R.; Yadav, Umesh Prasad; Lunn, John E.; Usadel, Björn; Stitt, Mark
2013-01-01
Growth is driven by newly fixed carbon in the light, but at night it depends on reserves, like starch, that are laid down in the light. Unless plants coordinate their growth with diurnal changes in the carbon supply, they will experience acute carbon starvation during the night. Protein synthesis represents a major component of cellular growth. Polysome loading was investigated during the diurnal cycle, an extended night, and low CO2 in Arabidopsis (Arabidopsis thaliana) Columbia (Col-0) and in the starchless phosphoglucomutase (pgm) mutant. In Col-0, polysome loading was 60% to 70% in the light, 40% to 45% for much of the night, and less than 20% in an extended night, while in pgm, it fell to less than 25% early in the night. Quantification of ribosomal RNA species using quantitative reverse transcription-polymerase chain reaction revealed that polysome loading remained high for much of the night in the cytosol, was strongly light dependent in the plastid, and was always high in mitochondria. The rosette sucrose content correlated with overall and with cytosolic polysome loading. Ribosome abundance did not show significant diurnal changes. However, compared with Col-0, pgm had decreased and increased abundance of plastidic and mitochondrial ribosomes, respectively. Incorporation of label from 13CO2 into protein confirmed that protein synthesis continues at a diminished rate in the dark. Modeling revealed that a decrease in polysome loading at night is required to balance protein synthesis with the availability of carbon from starch breakdown. Costs are also reduced by using amino acids that accumulated in the previous light period. These results uncover a tight coordination of protein synthesis with the momentary supply of carbon. PMID:23674104
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Seasonal and spatial distributions of atmospheric polychlorinated naphthalenes in Shanghai, China.
Die, Qingqi; Nie, Zhiqiang; Fang, Yanyan; Yang, Yufei; Gao, Xingbao; Tian, Yajun; He, Jie; Liu, Feng; Huang, Qifei; Tian, Shulei
2016-02-01
Air samples were collected in Shanghai during summer and winter 2013, and the gas and particulate concentrations of polychlorinated naphthalenes (PCNs) were measured. All 75 congeners were quantified and the corresponding toxic equivalents (TEQs) were calculated. PCN concentrations were higher in summer than winter, at 8.22-102 pg/m(3) (average of 61.3 pg/m(3)) in summer and 16.5-61.1 pg/m(3) (average of 37.7 pg/m(3)) in winter. Their seasonal TEQ values were in contrast, at 1.35-7.31 fg/m(3) (average of 3.84 fg/m(3)) in summer and 4.08-23.3 fg/m(3) (average of 8.80 fg/m(3)) in winter, because of the seasonal change in congener profiles. Tri-CNs were the predominant homologs in both the summer and winter samples. However, the major congeners in summer were PCNs containing less chlorine, but these decreased over winter. Air mass back trajectories suggested that wind direction over various sites was similar in the summer and winter seasons, yet there were clear seasonal variations in atmospheric PCN concentrations. Ratios of several characteristic congeners were calculated and the results indicated that the ratios varied only to a limited extent with PCN emissions profile from industrial thermal sources, but varied strongly with profiles of technical PCN and PCN contaminants in polychlorinated biphenyl mixtures. The results of principal component analysis suggest that local industrial thermal emissions (thermal processes containing waste incineration and secondary metal smelting processes) still play a considerable role in influencing the atmospheric PCNs in Shanghai. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Howley, Eimear; Bestwick, Michael; Fradley, Rosa; Harrison, Helen; Leveridge, Mathew; Okada, Kengo; Fieldhouse, Charlotte; Farnaby, Will; Canning, Hannah; Sykes, Andy P; Merchant, Kevin; Hazel, Katherine; Kerr, Catrina; Kinsella, Natasha; Walsh, Louise; Livermore, David G; Hoffman, Isaac; Ellery, Jonathan; Mitchell, Phillip; Patel, Toshal; Carlton, Mark; Barnes, Matt; Miller, David J
2017-11-01
Irregular N-methyl-D-aspartate receptor (NMDAR) function is one of the main hypotheses employed to facilitate understanding of the underlying disease state of schizophrenia. Although direct agonism of the NMDAR has not yielded promising therapeutics, advances have been made by modulating the NMDAR co-agonist site which is activated by glycine and D-serine. One approach to activate the co-agonist site is to increase synaptic D-serine levels through inhibition of D-amino acid oxidase (DAO), the major catabolic clearance pathway for this and other D-amino acids. A number of DAO inhibitors have been developed but most have not entered clinical trials. One exception to this is sodium benzoate which has demonstrated efficacy in small trials of schizophrenia and Alzheimer's disease. Herein we provide data on the effect of sodium benzoate and an optimised Takeda compound, PGM030756 on ex vivo DAO enzyme occupancy and cerebellar D-serine levels in mice. Both compounds achieve high levels of enzyme occupancy; although lower doses of PGM030756 (1, 3 and 10 mg/kg) were required to achieve this compared to sodium benzoate (300, 1000 mg/kg). Cerebellar D-serine levels were increased by both agents with a delay of approximately 6 h after dosing before the peak effect was achieved. Our data and methods may be useful in understanding the effects of sodium benzoate that have been seen in clinical trials of schizophrenia and Alzheimer's disease and to support the potential clinical assessment of other DAO inhibitors, such as PGM030756, which demonstrate good enzyme occupancy and D-serine increases following administration of low oral doses.
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Asymmetric Signature of Glacial Antarctic Intermediate Water in the Central South Pacific
NASA Astrophysics Data System (ADS)
Tapia, R.; Nuernberg, D.; Ho, S. L.; Lamy, F.; Ullermann, J.; Gersonde, R.; Tiedemann, R.
2017-12-01
Southern Ocean Intermediate Waters (SOIWs) play a key role in modulating the global climate on glacial-interglacial time scales as they connect the Southern Ocean and the tropics. Despite their importance, the past evolution of the SOIWs in the central South Pacific is largely unknown due to a dearth of sedimentary archives. Here we compare Mg/Ca-temperature, stable carbon and oxygen isotope records from surface-dwelling (G. bulloides) and deep-dwelling (G. inflata) planktic foraminifera at site PS75/059-2 (54°12.9' S, 125°25.53' W; recovery 13.98 m; 3.613 m water depth), located north of the modern Subantarctic Front. Our study focuses on the temperature and salinity variability controlled by SOIWs, which were subducted at the Subantarctic Front during the Last Glacial Maximum (LGM; 29-17ka BP) and the Penultimate Glacial Maximum (PGM; 180-150ka BP). During both glacial periods conditions at the subsurface ocean were colder and fresher relative to the Holocene (<10ka) suggesting an enhanced presence of SOIWs. In spite of the comparable subsurface cooling during both glacial, the subsurface ocean during the PGM was saltier and 0.35‰ more depleted in δ13C in comparison to the LGM. Interestingly, the mean δ13C value of the PGM is comparable to the Carbon Isotope Minimum Events, which might suggests a larger contribution of "old" low δ13C deep waters to the study site during the PGM. A Latitudinal comparison of subsurface proxies suggests glacial asymmetries in the advection of SOIWs into the central Pacific, plausibly related to glacial changes in the convection depth of SOIWs at the South Antarctic Front area rather than changes in production of the SOIWs.
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A Study of Iron-Nitrogen-Carbon Fuel Cell Catalysts: Chemistry - Nanostructure - Performance
NASA Astrophysics Data System (ADS)
Workman, Michael J., Jr.
Fuel cells have the potential to be a pollution-free, low-cost, and energy efficient alternative to the internal combustion engine for transportation and small-scale stationary power applications. The current state of fuel cell technology has already achieved two of these three lofty goals. The remaining barrier to wide-scale deployment is the high cost, which is primarily caused by dependence on large amounts of platinum to catalyze the energy conversion reactions. To overcome this barrier and facilitate the integration of fuel cells into mainstream applications, research into a new class of catalyst materials that do not require platinum is needed. There has been a significant amount of research effort directed toward the development of platinum-group metal free (PGM-free) catalysts, yet there is a lack of consensus on both the engineering parameters necessary to improve the technology and the fundamental science that would facilitate rational design. I have engaged in research on PGM-free catalysts based on inexpensive and abundant reagents, specifically: nicarbazin and iron. Catalysts made from these precursors have previously proven to be among the best PGM-free catalysts, but their continued advancement suffered from the same lack of understanding that besets all catalysts in this class. The work I have performed address both engineering concerns and fundamental underlying principles. I present results demonstrating correlations between physical structure, chemical speciation, and synthesis parameters, as well as addressing active site chemistry and likely locations. My research presented herein introduces new morphology analysis techniques and elucidates several key structure-to-property characteristics of catalysts derived from iron and nicarbazin. I discuss the development and application of a new length-scale specific surface analysis technique that allows for analysis of well-defined size ranges from a few nm to several microns. The existing technique of focused ion beam tomography is modified and optimized for platinum-group metal free catalyst layers, facilitating direct observation of catalyst integration into catalyst layers. I present evidence supporting the hypothesis that atomically dispersed iron coordinated with nitrogen are the dominant active sites in these catalysts. Further, that the concentration of surface oxides in the carbon structure, which can be directly influenced by synthesis parameters, correlates with both the concentration of active sites in the material and with fuel cell performance. Catalyst performance is hindered by the addition of carbon nanotubes and by the presence of metallic iron. Evidence consistent with the catalytic active sites residing in the graphitic plane is also presented.
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The X-ray microscopy beamline UE46-PGM2 at BESSY
NASA Astrophysics Data System (ADS)
Follath, R.; Schmidt, J. S.; Weigand, M.; Fauth, K.
2010-06-01
The Max Planck Institute for Metal Physics in Stuttgart and the Helmholtz Center Berlin operate a soft X-ray microscopy beamline at the storage ring BESSY II. A collimated PGM serves as monochromator for a scanning X-ray microscope and a full field X-ray microscope at the helical undulator UE46. The selection between both instruments is accomplished via two switchable focusing mirrors. The scanning microscope (SM) is based on the ALS STXM microscope and fabricated by the ACCEL company. The full field microscope (FFM) is currently in operation at the U41-SGM beamline and will be relocated to its final location this year.
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Develop high activity, low cost non-PGM fuel cell electrocatalyst and stable supports
DOE Office of Scientific and Technical Information (OSTI.GOV)
Colon-Mercado, H. R.; Elvington, M. C.; Garcia-Diaz, B. L.
2016-09-28
A unique approach has been developed to probe the non-PGM catalyst active site for the Oxygen Reduction Reaction (ORR) for PEMFC. Iron based functionalities have been engineered into Metallic Organic Framework (MOF) catalysts to evaluate their impact on activity for the ORR. A series of FePhen@MOF catalysts have been synthesized with varying [Fe] to investigate the effect on electrochemical and electrocatalytic properties. The magnitude of the Fe II/III redox couple and the electrochemical surface area are analyzed to determine if there is a correlation between [Fe] and the ORR onset potential and/or the relative number of active sites.
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Fang, Deyu; Gao, Guanyue; Yu, Yuan; Shen, Jie; Zhi, Jinfang
2016-05-10
In this study, a new method for acute biotoxicity assessment was proposed by measuring the glucose consumption of microbes with a personal glucose meter (PGM). To obtain an ideal biotoxicity assessment performance, an appropriate microbe was selected first, and then the relevant parameters, such as temperature and microbial concentration were optimized. Under the optimized parameters, the acute biotoxicity of four environmental pollutants (As(3+), Ni(2+), 4-chlorophenol, and 2,4-dichlorophenol), three wastewater samples and three soil samples were evaluated. This technology breakthrough will help us develop a low cost, easy to use water-environmental early-warning kit.
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Krstanović, Marina; Frkanec, Ruza; Vranesić, Branka; Ljevaković, Durdica; Sporec, Vesna; Tomasić, Jelka
2002-06-25
The reversed-phase HPLC method using UV detection was developed for the determination of (a) immunostimulating peptidoglycan monomers represented by the basic structure GlcNAc-MurNAc-L-Ala-D-isoGln-meso-DAP(omegaNH(2))-D-Ala-D-Ala (PGM) and two more lipophilic derivatives, Boc-Tyr-PGM and (Ada-1-yl)-CH(2)-CO-PGM, (b) two diastereomeric immunostimulating adamantyltripeptides L- and D-(adamant-2-yl)-Gly-L-Ala-D-isoGln and (c) peptides obtained by the enzyme hydrolyses of peptidoglycans and related peptides. The enzymes used, N-acetylmuramyl-L-alanine amidase and an L,D-aminopeptidase are present in mammalian sera and are involved in the metabolism of peptidoglycans and related peptides. Appropriate solvent systems were chosen with regard to structure and lipophilicity of each compound. As well, different gradient systems within the same solvent system had to be applied in order to achieve satisfactory separation and retention time. HPLC separation was developed with the aim to use this method for the study of the stability of the tested compounds, the purity during preparation and isolation and for following the enzyme hydrolyses.
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Sebastián, David; Serov, Alexey; Artyushkova, Kateryna; Gordon, Jonathan; Atanassov, Plamen; Aricò, Antonino S; Baglio, Vincenzo
2016-08-09
Direct methanol fuel cells (DMFCs) offer great advantages for the supply of power with high efficiency and large energy density. The search for a cost-effective, active, stable and methanol-tolerant catalyst for the oxygen reduction reaction (ORR) is still a great challenge. In this work, platinum group metal-free (PGM-free) catalysts based on Fe-N-C are investigated in acidic medium. Post-treatment of the catalyst improves the ORR activity compared with previously published PGM-free formulations and shows an excellent tolerance to the presence of methanol. The feasibility for application in DMFC under a wide range of operating conditions is demonstrated, with a maximum power density of approximately 50 mW cm(-2) and a negligible methanol crossover effect on the performance. A review of the most recent PGM-free cathode formulations for DMFC indicates that this formulation leads to the highest performance at a low membrane-electrode assembly (MEA) cost. Moreover, a 100 h durability test in DMFC shows suitable applicability, with a similar performance-time behavior compared to common MEAs based on Pt cathodes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Zhang, Jingshu; Everson, Mark P; Wallington, Timothy J; Field, Frank R; Roth, Richard; Kirchain, Randolph E
2016-07-19
Platinum-group metals (PGMs) are technological and economic enablers of many industrial processes. This important role, coupled with their limited geographic availability, has led to PGMs being labeled as "critical materials". Studies of future PGM flows have focused on trends within material flows or macroeconomic indicators. We complement the previous work by introducing a novel technoeconomic model of substitution among PGMs within the automotive sector (the largest user of PGMs) reflecting the rational response of firms to changing prices. The results from the model support previous conclusions that PGM use is likely to grow, in some cases strongly, by 2030 (approximately 45% for Pd and 5% for Pt), driven by the increasing sales of automobiles. The model also indicates that PGM-demand growth will be significantly influenced by the future Pt-to-Pd price ratio, with swings of Pt and Pd demand of as much as 25% if the future price ratio shifts higher or lower even if it stays within the historic range. Fortunately, automotive catalysts are one of the more effectively recycled metals. As such, with proper policy support, recycling can serve to meet some of this growing demand.
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Azmi, Kifaya; Schonian, Gabriele; Schnur, Lionel F.; Nasereddin, Abedelmajeed; Ereqat, Suheir; Abdeen, Ziad
2013-01-01
Background/Objectives Palestinian strains of L.tropica characterized by multilocus enzyme electrophoresis (MLEE) fall into two zymodemes, either MON-137 or MON-307. Methodology/Principle Findings Assays employing PCR and subsequent RFLP were applied to sequences found in the Hexokinase (HK) gene, an enzyme that is not used in MLEE, and the Phosphoglucomutase (PGM) gene, an enzyme that is used for MLEE, to see if they would facilitate consigning local strains of L.tropica to either zymodeme MON-137 or zymodeme MON-307. Following amplification and subsequent double digestion with the restriction endonucleases MboI and HaeIII, variation in the restriction patterns of the sequence from the HK gene distinguished strains of L.tropica, L.major and L.infantum and also exposed two genotypes (G) among the strains of L.tropica: HK-LtG1, associated with strains of L.tropica of the zymodemes MON-137 and MON-265, and HK-LtG2, associated with strains of L.tropica of the zymodemes MON-307, MON-288, MON-275 and MON-54. Following amplification and subsequent digestion by the restriction endonuclease MboI, variation in the sequence from the PGM gene also exposed two genotypes among the strains of L.tropica: PGM-G1, associated only with strains of L.tropica of the zymodeme MON-137; and PGM-G2, associated with strains of L.tropica of the zymodemes MON-265, MON-307, MON-288, MON-275 and MON-54, and, also, with six strains of L.major, five of L.infantum and one of L.donovani. The use of the HK and PGM gene sequences enabled distinction the L.tropica strains of the zymodeme MON-137 from those of the zymodeme MON-265. This genotyping system ‘correctly’ identified reference strains of L.tropica of known zymodemal affiliation and also from clinical samples, with a level of sensitivity down to <1 fg in the case of the former and to 1 pg of DNA in the case of the latter. Conclusions/Significance Both assays proved useful for identifying leishmanial parasites in clinical samples without resource to culture and MLEE. PMID:24086789
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Miller, M.P.; Haig, S.M.; Wagner, R.S.
2006-01-01
The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders. ?? The American Genetic Association. 2006. All rights reserved.
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NASA Astrophysics Data System (ADS)
Wing-Yuen Chow, Candace; Bründl, Michael; Keiler, Margreth
2017-04-01
In mountain regions, high economic losses have increased significantly in the past decades due to severe hazard processes, in spite of notable investments in hazard management. Assessing the vulnerability of built structures to high magnitude torrent events is a part of consequence analysis, where hazard intensity is related to the degree of loss sustained. While vulnerability curves have been developed for different countries, the presented work contributes new data from Swiss-based case studies that address a known gap associated with the consequences of high magnitude events. Data for this stage of the investigation communicates the degree of loss associated with affected structures and has been provided by local authorities dealing with natural hazards (e.g. Amt für Wald des Kantons Bern (KAWA) and cantonal insurance providers). Information used for the empirical quantification of vulnerability to torrent processes is derived from detailed post-event documentation and the loss database and verified with field visits. Building the initial database supports data sharing and the systematic inclusion of additional case studies as they become available. The collection of this new data is fundamental to the development of a local vulnerability curve based on observed sediment deposition heights, a proxy for describing hazard intensity. The result will then be compared to curves derived from Austrian and Italian datasets.
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NASA Astrophysics Data System (ADS)
Moser, Markus; Mehlhorn, Susanne; Rudolf-Miklau, Florian; Suda, Jürgen
2017-04-01
Since the beginning of systematic torrent control in Austria 130 years ago, barriers are constructed for protection purposes. Until the end of the 1960s, solid barriers were built at the exits of depositional areas to prevent dangerous debris flows from reaching high consequence areas. The development of solid barriers with large slots or slits to regulate sediment transport began with the use of reinforced concrete during the 1970s (Rudolf-Miklau, Suda 2011). In order to dissipate the energy of debris flows debris flow breakers have been designed since the 1980s. By slowing and depositing the surge front of the debris flow, downstream reaches of the stream channel and settlement areas should be exposed to considerably lower dynamic impact. In the past, the technological development of these constructions was only steered by the experiences of the engineering practice while an institutionalized process of standardization comparable to other engineering branches was not existent. In future all structures have to be designed and dimensioned according to the EUROCODE standards. This was the reason to establish an interdisciplinary working group (ON-K 256) at the Austrian Standards Institute (ASI), which has managed to developed comprehensive new technical standards for torrent control engineering, including load models, design, dimensioning and life cycle assessment of torrent control works (technical standard ONR 24800 - series). Extreme torrential events comprise four definable displacement processes floods; fluvial solid transport; hyper-concentrated solid transport (debris floods) and debris flow (stony debris flow or mud-earth flow). As a rule, the design of the torrential barriers has to follow its function (Kettl, 1984). Modern protection concepts in torrent control are scenario-oriented and try to optimize different functions in a chain of protections structures (function chain). More or less the first step for the designing the optimal construction type is the definition of the displacement processes for each torrent section. The criteria for each process are defined in the technical standard ONR 24800 - series in Austria. According to ONR 24800 the functions of torrential barriers can be divided in process control functional types (retention; dosing and filtering; energy dissipation). The last step is the designing of the construction type. Bedload and debris events in Austria showed the functionality of the barriers. On the basis of these findings and results, some recommendations were derived to improve the function fulfilment of the technical protection measures.
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Damiati, E; Borsani, G; Giacopuzzi, Edoardo
2016-05-01
The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants.
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Miyazaki, Celina M; Mishra, Rohit; Kinahan, David J; Ferreira, Marystela; Ducrée, Jens
2017-10-01
Antibody immobilization on polymeric substrates is a key manufacturing step for microfluidic devices that implement sample-to-answer automation of immunoassays. In this work, a simple and versatile method to bio-functionalize poly(methylmethacrylate) (PMMA), a common material of such "Lab-on-a-Chip" systems, is proposed; using the Layer-by-Layer (LbL) technique, we assemble nanostructured thin films of poly(ethylene imine) (PEI) and graphene oxide (GO). The wettability of PMMA surfaces was significantly augmented by the surface treatment with (PEI/GO) 5 film, with an 81% reduction of the contact angle, while the surface roughness increased by 600%, thus clearly enhancing wettability and antibody binding capacity. When applied to enzyme-linked immunosorbent assays (ELISAs), the limit of detection of PMMA surface was notably improved from 340pgmL -1 on commercial grade polystyrene (PS) and 230pgmL -1 on plain PMMA surfaces to 130pgmL -1 on (PEI/GO) 5 treated PMMA. Furthermore, the accelerated antibody adsorption kinetics on the LbL films of GO allowed to substantially shorten incubation times, e.g. for anti-rat IgG adsorption from 2h down to 15min on conventional and treated surfaces, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.
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Roark, Shaun A; Kelble, Mary A; Nacci, Diane; Champlin, Denise; Coiro, Laura; Guttman, Sheldon I
2005-03-01
The present study was conducted to evaluate evidence of genetic adaptation to local contaminants in populations of the migratory marine fish Menidia menidia residing seasonally in reference sites or an industrial harbor contaminated with dioxin-like compounds (DLCs). For this purpose, we compared DLC sensitivity and genetic patterns of populations sampled from sites both inside and outside New Bedford Harbor (NBH; MA, USA), a U.S. Environmental Protection Agency Superfund site with extreme polychlorinated biphenyl (PCB) contamination. Offspring of M. menidia collected from NBH were significantly less sensitive regarding embryonic exposure to the dioxin-like PCB congener 3,3',4,4',5-pentachlorobiphenyl (PCB 126) than offspring of M. menidia from a reference site. Analysis of 10 polymorphic enzymatic loci indicated little genetic differentiation among populations in the study area. However, genotype frequencies of juveniles from both NBH and an adjacent site in Massachusetts exhibited significant deviations from Hardy-Weinberg equilibrium expectations at one locus, phosphoglucomutase (PGM*). Genetic analysis of survivors of embryonic laboratory exposure to PCB 126 indicated that genotypes at PGM* were related to survivorship. Although a relationship was identified between DLC tolerance and PGM* genotype, regional mixing of M. menidia populations during migration and absence of multigeneration exposure at contaminated sites may limit localized adaptation.
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Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius
Cabañes, F. Javier; Sanseverino, Walter; Castellá, Gemma; ...
2015-03-13
In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a resequencing approach in a whole fungal genome (36 Mbp), a non-ochratoxin A producing strain of Aspergillus carbonarius. Ochratoxin A (OTA) is a potent nephrotoxin which is found mainly in cereals and their products, but it also occurs in a variety of common foods and beverages. Due to the fact that this strain does not produce OTA, we focused some of the bioinformatics analyses in genes involvedmore » in OTA biosynthesis, using a reference genome of an OTA producing strain of the same species. This study revealed that in the atoxigenic strain there is a high accumulation of nonsense and missense mutations in several genes. Importantly, a two fold increase in gene mutation ratio was observed in PKS and NRPS encoding genes which are suggested to be involved in OTA biosynthesis.« less
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Single-Cell Semiconductor Sequencing
Kohn, Andrea B.; Moroz, Tatiana P.; Barnes, Jeffrey P.; Netherton, Mandy; Moroz, Leonid L.
2014-01-01
RNA-seq or transcriptome analysis of individual cells and small-cell populations is essential for virtually any biomedical field. It is especially critical for developmental, aging, and cancer biology as well as neuroscience where the enormous heterogeneity of cells present a significant methodological and conceptual challenge. Here we present two methods that allow for fast and cost-efficient transcriptome sequencing from ultra-small amounts of tissue or even from individual cells using semiconductor sequencing technology (Ion Torrent, Life Technologies). The first method is a reduced representation sequencing which maximizes capture of RNAs and preserves transcripts’ directionality. The second, a template-switch protocol, is designed for small mammalian neurons. Both protocols, from cell/tissue isolation to final sequence data, take up to 4 days. The efficiency of these protocols has been validated with single hippocampal neurons and various invertebrate tissues including individually identified neurons within a simpler memory-forming circuit of Aplysia californica and early (1-, 2-, 4-, 8-cells) embryonic and developmental stages from basal metazoans. PMID:23929110
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Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius
DOE Office of Scientific and Technical Information (OSTI.GOV)
Cabañes, F. Javier; Sanseverino, Walter; Castellá, Gemma
In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a resequencing approach in a whole fungal genome (36 Mbp), a non-ochratoxin A producing strain of Aspergillus carbonarius. Ochratoxin A (OTA) is a potent nephrotoxin which is found mainly in cereals and their products, but it also occurs in a variety of common foods and beverages. Due to the fact that this strain does not produce OTA, we focused some of the bioinformatics analyses in genes involvedmore » in OTA biosynthesis, using a reference genome of an OTA producing strain of the same species. This study revealed that in the atoxigenic strain there is a high accumulation of nonsense and missense mutations in several genes. Importantly, a two fold increase in gene mutation ratio was observed in PKS and NRPS encoding genes which are suggested to be involved in OTA biosynthesis.« less
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NASA Astrophysics Data System (ADS)
Anenburg, Michael; Mavrogenes, John A.
2016-11-01
Platinum group element (PGE) nanonuggets are a nuisance in experimental studies designed to measure solubility or partitioning of noble metals in silicate melts. Instead of treating nanonuggets as experimental artifacts, we studied their behaviour motivated by recent discoveries of PGE nanonuggets in a variety of natural settings. We used an experimental setup consisting of AgPd, Pt or AuPd capsules and Fe(-Ti) oxide-saturated hydrous peralkaline silicate melts to maximise nanonugget production. TABS (Te, As, Bi, Sb, Sn) commonly occur in PGM (platinum group minerals), prompting addition of Bi to our experiments to investigate its properties as well. Three-dimensional optical examination by 100× objective and immersion oil reveals variable colour which correlates with nanonugget size and shape due to plasmon resonance effects. We observe two textural types: (1) intermediate-sized nanonuggets dispersed in the glass and adhering to oxides, and (2) abundant fine nanonuggets dispersed in the glass with coarse euhedral crystals in contact with oxides. Slow cooling removes dispersed nanonuggets and greatly coarsens existing oxide-associated metal crystals. Nanonugget-free halos are commonly observed around oxide grains. All metal phases are composed of major (Ag, Pd) and trace (Pt, Ir, Au) capsule material. Our results show reduction processes, imposed by growing oxides, causing local metal saturation in the oxide rich zones with preferential nucleation on smaller oxide grains. The redox gradient then blocks additional metals from diffusing into oxide rich zones, forming halos. As the entire experimental charge is reduced throughout the run, nanonuggets form in the distal glass. Bismuth contents of metal phases do not depend on Bi2O3 amounts dissolved in the melt. Further PGM crystallisation consumes nanonuggets as feedstock. We conclude that the appearance of metallic PGE phases happens in two stages: first as nanonuggets and then as larger PGM. Once formed, nanonuggets cannot be removed by oxidation or dissolution, but only by PGM coarsening. Sulfur-poor PGE ore deposits commonly contain more PGE than permitted by existing estimates of equilibrium solubility in silicate melts. This is commonly explained by initial scavenging of PGE by sulfide liquids followed by S-loss, but evidence for S-loss is not conclusive. We suggest that nanonuggets may be a means to transport PGE from source regions to form ore deposits, followed by direct PGM crystallisation from silicate melt without intermediate concentration by sulfide liquids.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Holby, Edward F.; Zelenay, Piotr
Atomic-scale structures of oxygen reduction reaction (ORR) active sites in non-platinum group metal (non-PGM) catalysts, made from pyrolysis of carbon, nitrogen, and transition-metal (TM) precursors have been the subject of continuing discussion in the fuel cell electrocatalysis research community. We found that quantum chemical modeling is a path forward for understanding of these materials and how they catalyze the ORR. Here, we demonstrate through literature examples of how such modeling can be used to better understand non-PGM ORR active site relative stability and activity and how such efforts can also aid in the interpretation of experimental signatures produced by thesemore » materials.« less
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Holby, Edward F.; Zelenay, Piotr
2016-05-17
Atomic-scale structures of oxygen reduction reaction (ORR) active sites in non-platinum group metal (non-PGM) catalysts, made from pyrolysis of carbon, nitrogen, and transition-metal (TM) precursors have been the subject of continuing discussion in the fuel cell electrocatalysis research community. We found that quantum chemical modeling is a path forward for understanding of these materials and how they catalyze the ORR. Here, we demonstrate through literature examples of how such modeling can be used to better understand non-PGM ORR active site relative stability and activity and how such efforts can also aid in the interpretation of experimental signatures produced by thesemore » materials.« less
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Geomorphological and ecological effects of check dams in mountain torrents of Southern Italy
NASA Astrophysics Data System (ADS)
Zema, Demetrio Antonio; Bombino, Giuseppe; Denisi, Pietro; Tamburino, Vincenzo; Marcello Zimbone, Santo
2017-04-01
It is known that installation of check dams noticeably influences torrent morphology and ecology. However, the effects of check dams on channel section and riparian vegetation of torrents are not yet completely understood. This paper provides a further contribution to a better comprehension of the actions played by check dams on hydrological and geomorphological processes in headwaters and their effects on riparian ecosystem. Field surveys on channel morphology, bed material and riparian vegetation were carried out close to five check dams in each of four mountain reaches of Calabria (Southern Italy). For each check dam three transects (one upstream, one downstream and one far from the check dam, located in the undisturbed zone and adopted as control) were identified; at each transect, a set of geomorphological and ecological indicators were surveyed as follows. Channel section morphology was assessed by the width/depth ratio (w/d); the median particle size (D50) and the finer sediment fraction (%fines) were chosen to characterize channel bed material; the specific discharge (q, the discharge per channel unit width) was assumed as measure of the flow regime. Vegetation cover and structure were evaluated by Global Canopy Cover (GCC) and Weighted Canopy Height (WCH) respectively (Bombino et al., 2008); the index of alpha-diversity (H-alpha, Hill, 1973) and the ratio between the number of alien species and the number of native species (NSA/NSN) were chosen as indicators of species richness/abundance and degree of vegetation integrity, respectively. Compared to the control transects, the values of w/d were higher upstream of check dams and lower downstream; conversely, q was lower upstream and higher in downstream sites. Upstream of the check dams D50 of bed material was lower and %fines was higher compared to the control transects; vice versa, the downstream transects showed higher D50 and lower %fines. The differences in the riparian vegetation among transects were found as the torrent ecological response to the strong contrasts surveyed in hydrological (q) and geomorphological (w/d, D50 and %fines) characteristics. Compared to control transects, vegetation was more extensive (higher GCC) and developed (higher WCH) in the upstream zones; the reverse pattern was noticed in the downstream transects (lower GCC and WCH). The indexes H-alpha and NSA/NSN were higher upstream of check dams: the presence of the check dams induced higher species richness and evenness, with alien species prevailing over native ones in the sedimentation wedge. Conversely, downstream of check dams H-alpha and NSA/NSN were lower: here, riparian vegetation lost some herbaceous species and assumed a terrestrial character. Overall, this study confirms on a quantitative approach that check dams have far reaching effects on geomorphology and ecology of mountain torrent channels; as a consequence, important and complex changes occur not only in the extent and development of riparian vegetation, but also in the species diversity and distribution. REFERENCES - Bombino G., Gurnell A.M., Tamburino V., Zema D.A., Zimbone S.M. 2008. Sediment size variation in torrents with check-dams: effects on riparian vegetation. Ecological Engineering 32(2), 166-177. - Hill MO. 1973. Diversity and evenness: a unifying notation and its consequences. Ecology 54: 427-431.
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Peruvian perovskite Between Transition-metal to PGM/PlatinumGroupMetal Catalytic Fusion
NASA Astrophysics Data System (ADS)
Maksoed, Wh-
2016-11-01
Strongly correlated electronic materials made of simple building blocks, such as a transition-metal ion in an octahedral oxygen cage forming a perovskite structure- Dagotto & Tokura for examples are the high-temperature superconductivity & the CMR/Colossal Magnetoresistance . Helium-4 denotes from LC Case,ScD: "Catalytic Fusion of Deuterium into Helium-4"- 1998 dealt with gaseous D2- "contacted with a supported metallic catalyst at superatmospheric pressure". The catalyst is a platinum-group metal, at about 0.5% - 1% by weight, on activated C. Accompanies Stephen J Geier, 2010 quotes "transition metal complexes", the Energy thus produced is enormous, and because the deuterium is very cheap in the form of heavy water (less than US 1/g), the fuel cost is very low (<<1 %/KwH). "The oceans contain enough deuterium to satisfy the Earth's energy needs for many millions of year" to keep "maria"/Latin name of seas &Deuteronomy to be eternally preserves. Heartfelt Gratitudes to HE. Mr. Prof. Ir. HANDOJO.
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Saeki, Ikuyo; Hirao, Akira S; Kenta, Tanaka
2015-06-01
Twelve microsatellite markers were developed and characterized in a threatened maple species, Acer miyabei (Sapindaceae), for use in population genetic analyses. Using Ion Personal Genome Machine (PGM) sequencing, we developed microsatellite markers with perfect di- and trinucleotide repeats. These markers were tested on a total of 44 individuals from two natural populations of A. miyabei subsp. miyabei f. miyabei in Hokkaido Island, Japan. The number of alleles per locus ranged from two to eight. The observed and expected heterozygosities per locus ranged from 0.05 to 0.75 and from 0.05 to 0.79, respectively. Some of the markers were successfully transferred to the closely related species A. campestre, A. platanoides, and A. pictum. The developed markers will be useful in characterizing the genetic structure and diversity of A. miyabei and will help to understand its spatial genetic variation, levels of inbreeding, and patterns of gene flow, thereby providing a basis for conservation.
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TP53, PIK3CA, FBXW7 and KRAS Mutations in Esophageal Cancer Identified by Targeted Sequencing.
Zheng, Huili; Wang, Yan; Tang, Chuanning; Jones, Lindsey; Ye, Hua; Zhang, Guangchun; Cao, Weihai; Li, Jingwen; Liu, Lifeng; Liu, Zhencong; Zhang, Chao; Lou, Feng; Liu, Zhiyuan; Li, Yangyang; Shi, Zhenfen; Zhang, Jingbo; Zhang, Dandan; Sun, Hong; Dong, Haichao; Dong, Zhishou; Guo, Baishuai; Yan, H E; Lu, Qingyu; Huang, Xue; Chen, Si-Yi
2016-01-01
Esophageal cancer (EC) is a common malignancy with significant morbidity and mortality. As individual cancers exhibit unique mutation patterns, identifying and characterizing gene mutations in EC that may serve as biomarkers might help predict patient outcome and guide treatment. Traditionally, personalized cancer DNA sequencing was impractical and expensive. Recent technological advancements have made targeted DNA sequencing more cost- and time-effective with reliable results. This technology may be useful for clinicians to direct patient treatment. The Ion PGM and AmpliSeq Cancer Panel was used to identify mutations at 737 hotspot loci of 45 cancer-related genes in 64 EC samples from Chinese patients. Frequent mutations were found in TP53 and less frequent mutations in PIK3CA, FBXW7 and KRAS. These results demonstrate that targeted sequencing can reliably identify mutations in individual tumors that make this technology a possibility for clinical use. Copyright© 2016, International Institute of Anticancer Research (Dr. John G. Delinasios), All rights reserved.
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NASA Astrophysics Data System (ADS)
Capello, Marco; Tolotti, Raffaella; Bernabè, Dimitri; Carbone, Cristina; Consani, Sirio; Vagge, Greta; Cutroneo, Laura
2016-04-01
Mineral content and physico-chemical properties of the freshwaters are the main factors affecting both algal assemblages and distributions, while presence of dissolved silicon, low water conductivity, and rocky-mountain habitats host benthic diatom assemblages of high species richness. It is shown that diatoms are sensible to the freshwater acidification (used as pH indicators in acid waters), environmental and climate changes, river organic load, and heavy metal water pollution. For this characteristic, diatoms are among the major biological markers for a variety of environmental and stratigraphic applications. In particular, qualitative and quantitative analyses (assemblage analyses) together with biotic indices as well as morphological and ultrastructure parameterisation provide tools for detailed environmental control and paleo-environmental reconstructions. Severe environmental problems are typically caused by "abandoned mine" and are consequences of the cessation of the mining activity with a lack in infrastructure maintenance. The mine waters which flow into the Gromolo Torrent are almost acidic (pH varying from 2.4 to 5) and enriched in heavy metals and SO42-. This pollution is caused by Acid Mine Drainage (AMD) processes that interest the Libiola mining area, known as a typical example of active AMD processes. The aim of this work is: 1) to characterise the local benthic diatom assemblages along the acidic mine effluents that discharge from Libiola mine, the entire Gromolo torrent course, and in the marine area off the torrent mouth; 2) to identify the main diatom biomarker taxa; 3) to highlight striking situations of equilibrium-disequilibrium in the algal communities, and 4) to point out types and frequency of some teratologies affecting specific diatom taxa as a response to environmental stressors (such as metal-metalloid enrichment). A total of 17 diatom samples was collected and examined, including some marine samples. Diatoms were collected in the riverbed from the hard surface of selected cobblestone by scraping. In laboratory all the samples were washed (by digestion with hydrogen peroxide) and mounted according to the protocol used by the DISTAV Laboratories (University of Genoa). Identification and enumeration of diatom valves was performed using an LM Reichert Jung-Polyvar microscope with 1000x oil-immersion lens. Moreover, a representative subsample of each preparation was observed using SEM images providing an interesting iconographic dataset. Preliminary results show that diatom assemblages are characteristic (in both quality and quantity) in the three different environmental conditions highlighted: a) in AMD environment diatoms are quantitatively scarcely, represented by both typically pioneer and highly tolerant species; b) in the Gromolo torrent diatoms are well represented with fairly well-structured communities, but present specific types and different frequencies in teratological frustula, whereas c) in marine environment they are very poorly represented.
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On the measure of large woody debris in an alpine catchment
NASA Astrophysics Data System (ADS)
D'Agostino, V.; Bertoldi, G.; Rigon, E.
2012-04-01
The management of large woody debris (LWD) in Alpine torrents is a complex and ambiguous task. On one side the presence of LWD contributes to in-channel and floodplain morphological processes and plays an important role in landscape ecology and biodiversity. On the other side LWD increases considerably flood hazards when some river cross-sections result critical for the human interface (e.g. culverts, bridges, artificial channels). Only few studies provide quantitative data of LWD volumes in Alpine torrents. Research is needed both at basin scale processes (LWD recruiting from hillslopes) and at channel scale processes (feeding from river bank, storage/transport/deposition of LWD along the river bed). Our study proposes an integrate field survey methodology to assess the overall LWD amount which can be entrained by a flood. This knowledge is mandatory for the scientific research, for the implementation of LWD transport models, and for a complete hazard management in mountain basins. The study site is the high-relief basin of the Cordevole torrent (Belluno Province, Central Alps, Italy) whose outlet is located at the Saviner village (basin area of 109 square kilometers). In the November 1966 an extreme flood event occurred and some torrent reaches were heavily congested by LWD enhancing the overall damages due to long-duration overflows. Currently, the LWD recruitment seems to be strictly correlated with bank erosion and hillslope instability and the conditions of forest stand suggest LWD hazard is still high. Previous studies on sub-catchments of the Cordevole torrent have also shown an inverse relation between the drainage area and the LWD storage in the river-bed. Present contribution analyzes and quantifies the presence of LWD in the main valley channel of the Cordevole basin. A new sampling methodology was applied to integrate surveys of riparian vegetation and LWD storage. Data inventory confirms the previous relationship between LWD volumes and drainage area and indicates the floating as primary origin of LWD presence in the river bed. The total amount of LWD at the basin outlet resulted 1300 cubic meters corresponding to about 12 cubic meters per square kilometer of drainage area. Additional data about in-channel dynamics and threshold discharges to move LWD are in progress. These will be obtained through an innovative monitoring approach based on active transponders (RFID, Radio Frequency Identification). 70 transponder have been inserted in selected LWD samples and 70 transponders will be inserted in standardized artificial LWD to carry out experiments during the snowmelt season. A fixed antenna is located at the outlet section on a check-dam together with a video-camera and a hydrometer. The overall arrangement of the LWD monitoring system under test is then presented.
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Risk watershed analysis: a new approach to manage torrent control structures
NASA Astrophysics Data System (ADS)
Quefféléan, Yann; Carladous, Simon; Deymier, Christian; Marco, Olivier
2017-04-01
Torrential check dams have been built in French public forests since the 19th century, applying the Restoration and conservation of Mountainous Areas (RTM) laws (1860, 1864, 1882). The RTM department of the National Forestry Office (ONF) helps the government to decide on protective actions to implement within these areas. While more than 100 000 structures were registered in 1964, more than 14 000 check dams are currently registered and maintained within approximatively 380 000 ha of RTM public forests. The RTM department officers thus have a long experience in using check dams for soil restoration, but also in implementing other kinds of torrential protective structures such as sediment traps, embankments, bank protection, and so forth. As a part of the ONF, they are also experienced in forestry engineering. Nevertheless, some limits in torrent control management have been highlighted: - as existing protective structures are ageing, their effectiveness to protect elements at risk must be assessed but it is a difficult task ; - as available budget for maintenance is continuously decreasing, priorities have to be made but decisions are difficult : what are the existing check dams functions? what is their expected effect on torrential hazard? is maintenance cost too important given this expected effect to protect elements at risk? Given these questions, a new policy has been engaged by the RTM department since 2012. A technical overview at the torrential watershed scale is now needed to help better maintenance decisions: it has been called a Risk Watershed Analysis (Etude de Bassin de Risque in French, EBR) and is funded by the government. Its objectives are to: - recall initial objectives of protective structures : therefore, a detailed archive analysis is made ; - describe current elements at risk to protect ; - describe natural hazards at the torrential watershed scale and their evolution since protective structures implementation ; - describe civil engineering and forestry works that have been implemented within the watershed, including their cost ; - decide on current protective works to implement (maintenance and new investment). For each EBR, a multidisciplinary team is involved with specialists in geomorphology, hydrology, hydraulics, geology, civil engineering and forestry. Approximatively 1 100 EBRs should be implemented at the national scale, including other natural phenomena such as snow avalanches and rock falls. Since 2012, approximatively 10 % have been realized in areas with the most significant elements at risk. From a practical point of view, these studies have helped a better understanding of torrential watershed conditions and of torrent control expected effect over years. An analysis of these studies will be performed soon to have a first overview of torrent control effect. We claim that these EBRs could be a significant source of information to help a comprehensive evaluation of long-term effectiveness of torrent control.
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Testing seismic amplitude source location for fast debris-flow detection at Illgraben, Switzerland
NASA Astrophysics Data System (ADS)
Walter, Fabian; Burtin, Arnaud; McArdell, Brian W.; Hovius, Niels; Weder, Bianca; Turowski, Jens M.
2017-06-01
Heavy precipitation can mobilize tens to hundreds of thousands of cubic meters of sediment in steep Alpine torrents in a short time. The resulting debris flows (mixtures of water, sediment and boulders) move downstream with velocities of several meters per second and have a high destruction potential. Warning protocols for affected communities rely on raising awareness about the debris-flow threat, precipitation monitoring and rapid detection methods. The latter, in particular, is a challenge because debris-flow-prone torrents have their catchments in steep and inaccessible terrain, where instrumentation is difficult to install and maintain. Here we test amplitude source location (ASL) as a processing scheme for seismic network data for early warning purposes. We use debris-flow and noise seismograms from the Illgraben catchment, Switzerland, a torrent system which produces several debris-flow events per year. Automatic in situ detection is currently based on geophones mounted on concrete check dams and radar stage sensors suspended above the channel. The ASL approach has the advantage that it uses seismometers, which can be installed at more accessible locations where a stable connection to mobile phone networks is available for data communication. Our ASL processing uses time-averaged ground vibration amplitudes to estimate the location of the debris-flow front. Applied to continuous data streams, inversion of the seismic amplitude decay throughout the network is robust and efficient, requires no manual identification of seismic phase arrivals and eliminates the need for a local seismic velocity model. We apply the ASL technique to a small debris-flow event on 19 July 2011, which was captured with a temporary seismic monitoring network. The processing rapidly detects the debris-flow event half an hour before arrival at the outlet of the torrent and several minutes before detection by the in situ alarm system. An analysis of continuous seismic records furthermore indicates that detectability of Illgraben debris flows of this size is unaffected by changing environmental and anthropogenic seismic noise and that false detections can be greatly reduced with simple processing steps.
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Chander, M; Setlow, P; Lamani, E; Jedrzejas, M J
1999-06-15
Phosphoglycerate mutase (PGM), an important enzyme in the glycolytic pathway, catalyzes the transfer of a phosphate group between the 2 and the 3 positions of glyceric acid. The gene coding for the 2, 3-diphosphoglycerate independent monomeric PGM from Bacillus stearothermophilus (57 kDa), whose activity is extremely pH sensitive and has an absolute and specific requirement for Mn2+, has been cloned and the enzyme overexpressed and purified to homogeneity. Circular dichroism studies showed at most only small secondary structure changes in the enzyme upon binding to Mn2+ or its 3-phosphoglycerate substrate, but thermal unfolding analyses revealed that Mn2+ but not 3-phosphoglycerate caused a large increase in the enzyme's stability. Diffraction-quality crystals of the enzyme were obtained at neutral pH in the presence of 3-phosphoglyceric acid with ammonium sulfate as the precipitating agent; these crystals diffract X rays to beyond 2.5-A resolution and belong to the orthorhombic space group C2221 with unit cell dimensions, a = 58.42, b = 206.08, c = 124.87 A, and alpha = beta = gamma = 90.0 degrees. The selenomethionyl version of the B. stearothermophilus protein has also been overexpressed, purified, and crystallized. Employing these crystals, the determination of the three-dimensional structure of this PGM by the multiwavelength anomalous dispersion method is in progress. Copyright 1999 Academic Press.
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Jiang, Yanfen; Kulkarni, Raveendra R; Parreira, Valeria R; Prescott, John F
2009-09-01
This study identified and assessed secreted proteins of Clostridium perfringens additional to those previously described for their ability to protect broiler chickens against necrotic enteritis (NE). Secreted proteins of virulent and avirulent C. perfringens were electrophoretically separated and reacted with serum of chickens immune to NE. Three immunoreactive protein bands unique to the virulent C. perfringens were identified by mass spectrometry as the toxin C. perfringens large cytotoxin (TpeL), endo-beta-N-acetylglucosaminidase (Naglu), and phosphoglyceromutase (Pgm). The genes encoding Naglu and Pgm proteins were cloned, and their gene products were purified as histidine-tagged recombinant proteins from Escherichia coli and used in immunizing chickens. Immunized and nonimmunized control broiler chickens were then challenged with two different strains (CP1, CP4) of C. perfringens and assessed for the development of NE. Of the two immunogens, Pgm immunization showed significant protection of broiler chickens against experimental NE, although protection reduced as challenge severity increased. However, birds immunized with Naglu were protected from challenge only with strain CP4. Birds immunized with these proteins had antigen-specific antibodies when tested in an enzyme-linked immunosorbent assay. In conclusion, this study demonstrated the partial efficacy of additional secreted proteins in immunity of broiler chickens to NE. The study also showed that there may be differences in the protective ability of immunogens depending on the infecting C. perfringens strain.
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NASA Technical Reports Server (NTRS)
Guan, Changhui; Rosen, Elizabeth S.; Boonsirichai, Kanokporn; Poff, Kenneth L.; Masson, Patrick H.
2003-01-01
The arl2 mutants of Arabidopsis display altered root and hypocotyl gravitropism, whereas their inflorescence stems are fully gravitropic. Interestingly, mutant roots respond like the wild type to phytohormones and an inhibitor of polar auxin transport. Also, their cap columella cells accumulate starch similarly to wild-type cells, and mutant hypocotyls display strong phototropic responses to lateral light stimulation. The ARL2 gene encodes a DnaJ-like protein similar to ARG1, another protein previously implicated in gravity signal transduction in Arabidopsis seedlings. ARL2 is expressed at low levels in all organs of seedlings and plants. arl2-1 arg1-2 double mutant roots display kinetics of gravitropism similar to those of single mutants. However, double mutants carrying both arl2-1 and pgm-1 (a mutation in the starch-biosynthetic gene PHOSPHOGLUCOMUTASE) at the homozygous state display a more pronounced root gravitropic defect than the single mutants. On the other hand, seedlings with a null mutation in ARL1, a paralog of ARG1 and ARL2, behave similarly to the wild type in gravitropism and other related assays. Taken together, the results suggest that ARG1 and ARL2 function in the same gravity signal transduction pathway in the hypocotyl and root of Arabidopsis seedlings, distinct from the pathway involving PGM.
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Spatial Distribution and Air-Water Exchange of Organic Flame Retardants in the Lower Great Lakes.
McDonough, Carrie A; Puggioni, Gavino; Helm, Paul A; Muir, Derek; Lohmann, Rainer
2016-09-06
Organic flame retardants (OFRs) such as polybrominated diphenyl ethers (PBDEs) and novel halogenated flame retardants (NHFRs) are ubiquitous, persistent, and bioaccumulative contaminants that have been used in consumer goods to slow combustion. In this study, polyethylene passive samplers (PEs) were deployed throughout the lower Great Lakes (Lake Erie and Lake Ontario) to measure OFRs in air and water, calculate air-water exchange fluxes, and investigate spatial trends. Dissolved Σ12BDE was greatest in Lake Ontario near Toronto (18 pg/L), whereas gaseous Σ12BDE was greatest on the southern shoreline of Lake Erie (11 pg/m(3)). NHFRs were generally below detection limits. Air-water exchange was dominated by absorption of BDEs 47 and 99, ranging from -964 pg/m(2)/day to -30 pg/m(2)/day. Σ12BDE in air and water was significantly correlated with surrounding population density, suggesting that phased-out PBDEs continued to be emitted from population centers along the Great Lakes shoreline in 2012. Correlation with dissolved Σ12BDE was strongest when considering population within 25 km while correlation with gaseous Σ12BDE was strongest when using population within 3 km to the south of each site. Bayesian kriging was used to predict dissolved Σ12BDE over the lakes, illustrating the utility of relatively highly spatially resolved measurements in identifying potential hot spots for future study.
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Granada, Camille E; Vargas, Luciano K; Sant'Anna, Fernando Hayashi; Balsanelli, Eduardo; Baura, Valter Antonio de; Oliveira Pedrosa, Fábio de; Souza, Emanuel Maltempi de; Falcon, Tiago; Passaglia, Luciane M P
2018-05-17
Lupinus albescens is a resistant cover plant that establishes symbiotic relationships with bacteria belonging to the Bradyrhizobium genus. This symbiosis helps the development of these plants in adverse environmental conditions, such as the ones found in arenized areas of Southern Brazil. This work studied three Bradyrhizobium sp. (AS23, NAS80 and NAS96) isolated from L. albescens plants that grow in extremely poor soils (arenized areas and adjacent grasslands). The genomes of these three strains were sequenced in the Ion Torrent platform using the IonXpress library preparation kit, and presented a total number of bases of 1,230,460,823 for AS23, 1,320,104,022 for NAS80, and 1,236,105,093 for NAS96. The genome comparison with closest strains Bradyrhizobium japonicum USDA6 and Bradyrhizobium diazoefficiens USDA110 showed important variable regions (with less than 80% of similarity). Genes encoding for factors for resistance/tolerance to heavy metal, flagellar motility, response to osmotic and oxidative stresses, heat shock proteins (present only in the three sequenced genomes) could be responsible for the ability of these microorganisms to survive in inhospitable environments. Knowledge about these genomes will provide a foundation for future development of an inoculant bioproduct that should optimize the recovery of degraded soils using cover crops.
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Evaluating Hydrogen Evolution and Oxidation in Alkaline Media to Establish Baselines
Alia, Shaun M.; Pivovar, Bryan S.
2018-04-28
This paper fills a significant gap in the literature for alkaline hydrogen evolution (HER) and oxidation (HOR) baseline performance, while reviewing the different variables that influence observed properties. Although high-performing HER-HOR catalysts in acidic electrolytes are too active to measure kinetic in rotating disk electrode (RDE) half-cells, under alkaline conditions RDE kinetics evaluations are relevant and half-cell performances are comparable to hydrogen pump data. This paper focuses on best practices to ensure that half-cell tests don't unnecessarily lower platinum group metal (PGM) performance or improve non-PGM performance. Specific aspects examined include experiments on PGMs minimizing the impact of impurities (electrolyte,more » cell material) and experiments on non-PGMs minimizing the impact from test protocols (counter electrode).« less
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Morselli, Paolo Giovanni; Micai, Alessandro; Giorgini, Federico Armando
2016-08-01
The "Lull pgm system" is a closed system for purifying harvested fat. It processes the collected tissue safely without any additional cost. The system was conceived by referring to the targets described in the literature with the aim of creating a simple system that guarantees a high standard of purification and requires minimal equipment that is available in every operating room. Cost must be always considered: even the most prosperous hospitals must keep within tight annual budgets. "Lull" can be used instead of expensive devices or disposable kits, without substantially increasing the operating time. The system has been used in clinical practice for many plastic reconstructive procedures and has obtained positive results and patient satisfaction, and no contraindications or disadvantages have been observed.
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Evaluating Hydrogen Evolution and Oxidation in Alkaline Media to Establish Baselines
DOE Office of Scientific and Technical Information (OSTI.GOV)
Alia, Shaun M.; Pivovar, Bryan S.
This paper fills a significant gap in the literature for alkaline hydrogen evolution (HER) and oxidation (HOR) baseline performance, while reviewing the different variables that influence observed properties. Although high-performing HER-HOR catalysts in acidic electrolytes are too active to measure kinetic in rotating disk electrode (RDE) half-cells, under alkaline conditions RDE kinetics evaluations are relevant and half-cell performances are comparable to hydrogen pump data. This paper focuses on best practices to ensure that half-cell tests don't unnecessarily lower platinum group metal (PGM) performance or improve non-PGM performance. Specific aspects examined include experiments on PGMs minimizing the impact of impurities (electrolyte,more » cell material) and experiments on non-PGMs minimizing the impact from test protocols (counter electrode).« less
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Sophisticated Communication in the Brazilian Torrent Frog Hylodes japi.
de Sá, Fábio P; Zina, Juliana; Haddad, Célio F B
2016-01-01
Intraspecific communication in frogs plays an important role in the recognition of conspecifics in general and of potential rivals or mates in particular and therefore with relevant consequences for pre-zygotic reproductive isolation. We investigate intraspecific communication in Hylodes japi, an endemic Brazilian torrent frog with territorial males and an elaborate courtship behavior. We describe its repertoire of acoustic signals as well as one of the most complex repertoires of visual displays known in anurans, including five new visual displays. Previously unknown in frogs, we also describe a bimodal inter-sexual communication system where the female stimulates the male to emit a courtship call. As another novelty for frogs, we show that in addition to choosing which limb to signal with, males choose which of their two vocal sacs will be used for visual signaling. We explain how and why this is accomplished. Control of inflation also provides additional evidence that vocal sac movement and color must be important for visual communication, even while producing sound. Through the current knowledge on visual signaling in Neotropical torrent frogs (i.e. hylodids), we discuss and highlight the behavioral diversity in the family Hylodidae. Our findings indicate that communication in species of Hylodes is undoubtedly more sophisticated than we expected and that visual communication in anurans is more widespread than previously thought. This is especially true in tropical regions, most likely due to the higher number of species and phylogenetic groups and/or to ecological factors, such as higher microhabitat diversity.
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Sophisticated Communication in the Brazilian Torrent Frog Hylodes japi
de Sá, Fábio P.; Zina, Juliana; Haddad, Célio F. B.
2016-01-01
Intraspecific communication in frogs plays an important role in the recognition of conspecifics in general and of potential rivals or mates in particular and therefore with relevant consequences for pre-zygotic reproductive isolation. We investigate intraspecific communication in Hylodes japi, an endemic Brazilian torrent frog with territorial males and an elaborate courtship behavior. We describe its repertoire of acoustic signals as well as one of the most complex repertoires of visual displays known in anurans, including five new visual displays. Previously unknown in frogs, we also describe a bimodal inter-sexual communication system where the female stimulates the male to emit a courtship call. As another novelty for frogs, we show that in addition to choosing which limb to signal with, males choose which of their two vocal sacs will be used for visual signaling. We explain how and why this is accomplished. Control of inflation also provides additional evidence that vocal sac movement and color must be important for visual communication, even while producing sound. Through the current knowledge on visual signaling in Neotropical torrent frogs (i.e. hylodids), we discuss and highlight the behavioral diversity in the family Hylodidae. Our findings indicate that communication in species of Hylodes is undoubtedly more sophisticated than we expected and that visual communication in anurans is more widespread than previously thought. This is especially true in tropical regions, most likely due to the higher number of species and phylogenetic groups and/or to ecological factors, such as higher microhabitat diversity. PMID:26760304
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Alton, Eric W F W; Armstrong, David K; Ashby, Deborah; Bayfield, Katie J; Bilton, Diana; Bloomfield, Emily V; Boyd, A Christopher; Brand, June; Buchan, Ruaridh; Calcedo, Roberto; Carvelli, Paula; Chan, Mario; Cheng, Seng H; Collie, D David S; Cunningham, Steve; Davidson, Heather E; Davies, Gwyneth; Davies, Jane C; Davies, Lee A; Dewar, Maria H; Doherty, Ann; Donovan, Jackie; Dwyer, Natalie S; Elgmati, Hala I; Featherstone, Rosanna F; Gavino, Jemyr; Gea-Sorli, Sabrina; Geddes, Duncan M; Gibson, James S R; Gill, Deborah R; Greening, Andrew P; Griesenbach, Uta; Hansell, David M; Harman, Katharine; Higgins, Tracy E; Hodges, Samantha L; Hyde, Stephen C; Hyndman, Laura; Innes, J Alastair; Jacob, Joseph; Jones, Nancy; Keogh, Brian F; Limberis, Maria P; Lloyd-Evans, Paul; Maclean, Alan W; Manvell, Michelle C; McCormick, Dominique; McGovern, Michael; McLachlan, Gerry; Meng, Cuixiang; Montero, M Angeles; Milligan, Hazel; Moyce, Laura J; Murray, Gordon D; Nicholson, Andrew G; Osadolor, Tina; Parra-Leiton, Javier; Porteous, David J; Pringle, Ian A; Punch, Emma K; Pytel, Kamila M; Quittner, Alexandra L; Rivellini, Gina; Saunders, Clare J; Scheule, Ronald K; Sheard, Sarah; Simmonds, Nicholas J; Smith, Keith; Smith, Stephen N; Soussi, Najwa; Soussi, Samia; Spearing, Emma J; Stevenson, Barbara J; Sumner-Jones, Stephanie G; Turkkila, Minna; Ureta, Rosa P; Waller, Michael D; Wasowicz, Marguerite Y; Wilson, James M; Wolstenholme-Hogg, Paul
2015-01-01
Summary Background Lung delivery of plasmid DNA encoding the CFTR gene complexed with a cationic liposome is a potential treatment option for patients with cystic fibrosis. We aimed to assess the efficacy of non-viral CFTR gene therapy in patients with cystic fibrosis. Methods We did this randomised, double-blind, placebo-controlled, phase 2b trial in two cystic fibrosis centres with patients recruited from 18 sites in the UK. Patients (aged ≥12 years) with a forced expiratory volume in 1 s (FEV1) of 50–90% predicted and any combination of CFTR mutations, were randomly assigned, via a computer-based randomisation system, to receive 5 mL of either nebulised pGM169/GL67A gene–liposome complex or 0·9% saline (placebo) every 28 days (plus or minus 5 days) for 1 year. Randomisation was stratified by % predicted FEV1 (<70 vs ≥70%), age (<18 vs ≥18 years), inclusion in the mechanistic substudy, and dosing site (London or Edinburgh). Participants and investigators were masked to treatment allocation. The primary endpoint was the relative change in % predicted FEV1. The primary analysis was per protocol. This trial is registered with ClinicalTrials.gov, number NCT01621867. Findings Between June 12, 2012, and June 24, 2013, we randomly assigned 140 patients to receive placebo (n=62) or pGM169/GL67A (n=78), of whom 116 (83%) patients comprised the per-protocol population. We noted a significant, albeit modest, treatment effect in the pGM169/GL67A group versus placebo at 12 months' follow-up (3·7%, 95% CI 0·1–7·3; p=0·046). This outcome was associated with a stabilisation of lung function in the pGM169/GL67A group compared with a decline in the placebo group. We recorded no significant difference in treatment-attributable adverse events between groups. Interpretation Monthly application of the pGM169/GL67A gene therapy formulation was associated with a significant, albeit modest, benefit in FEV1 compared with placebo at 1 year, indicating a stabilisation of lung function in the treatment group. Further improvements in efficacy and consistency of response to the current formulation are needed before gene therapy is suitable for clinical care; however, our findings should also encourage the rapid introduction of more potent gene transfer vectors into early phase trials. Funding Medical Research Council/National Institute for Health Research Efficacy and Mechanism Evaluation Programme. PMID:26149841
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Alton, Eric W F W; Armstrong, David K; Ashby, Deborah; Bayfield, Katie J; Bilton, Diana; Bloomfield, Emily V; Boyd, A Christopher; Brand, June; Buchan, Ruaridh; Calcedo, Roberto; Carvelli, Paula; Chan, Mario; Cheng, Seng H; Collie, D David S; Cunningham, Steve; Davidson, Heather E; Davies, Gwyneth; Davies, Jane C; Davies, Lee A; Dewar, Maria H; Doherty, Ann; Donovan, Jackie; Dwyer, Natalie S; Elgmati, Hala I; Featherstone, Rosanna F; Gavino, Jemyr; Gea-Sorli, Sabrina; Geddes, Duncan M; Gibson, James S R; Gill, Deborah R; Greening, Andrew P; Griesenbach, Uta; Hansell, David M; Harman, Katharine; Higgins, Tracy E; Hodges, Samantha L; Hyde, Stephen C; Hyndman, Laura; Innes, J Alastair; Jacob, Joseph; Jones, Nancy; Keogh, Brian F; Limberis, Maria P; Lloyd-Evans, Paul; Maclean, Alan W; Manvell, Michelle C; McCormick, Dominique; McGovern, Michael; McLachlan, Gerry; Meng, Cuixiang; Montero, M Angeles; Milligan, Hazel; Moyce, Laura J; Murray, Gordon D; Nicholson, Andrew G; Osadolor, Tina; Parra-Leiton, Javier; Porteous, David J; Pringle, Ian A; Punch, Emma K; Pytel, Kamila M; Quittner, Alexandra L; Rivellini, Gina; Saunders, Clare J; Scheule, Ronald K; Sheard, Sarah; Simmonds, Nicholas J; Smith, Keith; Smith, Stephen N; Soussi, Najwa; Soussi, Samia; Spearing, Emma J; Stevenson, Barbara J; Sumner-Jones, Stephanie G; Turkkila, Minna; Ureta, Rosa P; Waller, Michael D; Wasowicz, Marguerite Y; Wilson, James M; Wolstenholme-Hogg, Paul
2015-09-01
Lung delivery of plasmid DNA encoding the CFTR gene complexed with a cationic liposome is a potential treatment option for patients with cystic fibrosis. We aimed to assess the efficacy of non-viral CFTR gene therapy in patients with cystic fibrosis. We did this randomised, double-blind, placebo-controlled, phase 2b trial in two cystic fibrosis centres with patients recruited from 18 sites in the UK. Patients (aged ≥12 years) with a forced expiratory volume in 1 s (FEV1) of 50-90% predicted and any combination of CFTR mutations, were randomly assigned, via a computer-based randomisation system, to receive 5 mL of either nebulised pGM169/GL67A gene-liposome complex or 0.9% saline (placebo) every 28 days (plus or minus 5 days) for 1 year. Randomisation was stratified by % predicted FEV1 (<70 vs ≥70%), age (<18 vs ≥18 years), inclusion in the mechanistic substudy, and dosing site (London or Edinburgh). Participants and investigators were masked to treatment allocation. The primary endpoint was the relative change in % predicted FEV1. The primary analysis was per protocol. This trial is registered with ClinicalTrials.gov, number NCT01621867. Between June 12, 2012, and June 24, 2013, we randomly assigned 140 patients to receive placebo (n=62) or pGM169/GL67A (n=78), of whom 116 (83%) patients comprised the per-protocol population. We noted a significant, albeit modest, treatment effect in the pGM169/GL67A group versus placebo at 12 months' follow-up (3.7%, 95% CI 0.1-7.3; p=0.046). This outcome was associated with a stabilisation of lung function in the pGM169/GL67A group compared with a decline in the placebo group. We recorded no significant difference in treatment-attributable adverse events between groups. Monthly application of the pGM169/GL67A gene therapy formulation was associated with a significant, albeit modest, benefit in FEV1 compared with placebo at 1 year, indicating a stabilisation of lung function in the treatment group. Further improvements in efficacy and consistency of response to the current formulation are needed before gene therapy is suitable for clinical care; however, our findings should also encourage the rapid introduction of more potent gene transfer vectors into early phase trials. Medical Research Council/National Institute for Health Research Efficacy and Mechanism Evaluation Programme. Copyright © 2015 Alton et al. Open Access article distributed under the terms of CC BY. Published by Elsevier Ltd.. All rights reserved.
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NASA Astrophysics Data System (ADS)
Toyota, Masatsugu; Tasaka, Masao; Morita, Miyo T.; Gilroy, Simon
2012-07-01
The starch-statolith hypothesis is the most widely accepted model for plant gravity sensing and proposes that the sedimentation of high-density starch-filled plastids (amyloplasts) in shoot endodermal cells and root columella cells is important for gravity sensing of each organ. However, starch-deficient phosphoglucomutase (pgm-1) mutants sense gravity and show gravitropism in inflorescence stems, even though most starchless amyloplasts in this mutant fail to sediment toward the gravity vector. These results raise the questions about the role of starch in gravity sensing and the features of statolith/statocyte essential for shoot gravity sensing. To address these questions, we developed a new centrifuge microscope and analyzed two gravitropic mutants, i.e., pgm-1 and endodermal-amyloplast less 1 (eal1). All optical devices (e.g., objective lens, light source and CCD camera) and specimens were rotated on a direct-drive motor, and acquired images were wirelessly transmitted during centrifugation. Live-cell imaging during centrifugation revealed that the starchless amyloplasts sedimented to the hypergravity vector (10 and 30 g) in endodermal cells of pgm-1 stems, indicating that the density of the starchless amyloplasts is higher than that of cytoplasm. Electron micrographs of shoot endodermal cells in pgm-1 mutants suggested that the starchless amyloplast contains an organized thylakoid membrane but not starch granules, which morphologically resembles chloroplasts in the adjacent cortical cells. Therefore, the shoot amyloplasts without starch are possibly as dense as chloroplasts. We examined eal1 mutants, an allele of shoot gravitropism (sgr) 7/short-root (shr), which also have starchless amyloplasts due to abnormal differentiation of amyloplasts and show no gravitropic response at 1 g. Hypergravity up to 30 g induced little gravitropism in eal1 stems and the starchless amyloplasts failed to sediment under 30 g conditions. However, the eal1 mutants treated with latrunculin B, an actin disrupting drug, showed gravitropism under 30 g conditions, during which amyloplasts were artificially sedimented by hypergravity. These results suggest that shoot amyloplasts are intrinsically dense enough to trigger gravity sensing without starch and, rather, intracellular environments that render amyloplasts sedimentable/mobile, such as actin organization, are essential for gravity sensing in Arabidopsis inflorescence stems.
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Tang, Dianping; Lin, Youxiu; Zhou, Qian; Lin, Yuping; Li, Peiwu; Niessner, Reinhard; Knopp, Dietmar
2014-11-18
Aflatoxins are highly toxic secondary metabolites produced by a number of different fungi and present in a wide range of food and feed commodities. Herein, we designed a simple and low-cost immunosensing platform for highly sensitive detection of mycotoxins (aflatoxin B1, AFB1, used as a model) on polyethylenimine (PEI)-coated mesoporous silica nanocontainers (PEI-MSN). The assay was carried out by using a portable personal glucometer (PGM) as the readout based on a competitive displacement reaction mode between target AFB1 and its pseudo-hapten (PEI-MSN) for monoclonal anti-AFB1 antibody (mAb). To construct such an assay protocol, two nanostructures including mAb-labeled gold nanoparticle (mAb-AuNP) and PEI-MSN were initially synthesized, and then numerous glucose molecules were gated into the pores based on the interaction between negatively charged mAb-AuNP and positively charged PEI-MSN. In the presence of target AFB1, a competitive-type displacement reaction was implemented between mAb-AuNP and PEI-MSN by target AFB1 through the specific antigen-antibody reaction. Accompanying the reaction, target AFB1 could displace the mAb-AuNP from the surface of PEI-MSN, resulting in the release of the loading glucose from the pores due to the gate opened. The released glucose molecules could be quantitatively determined by using a portable PGM. Under optimal conditions, the PGM signal increased with the increment of AFB1 concentration in the range from 0.01 to 15 μg/kg (ppb) with a detection limit (LOD) of 5 ng/kg (5 ppt) at the 3sblank criterion. The selectivity and precision were acceptable. Importantly, the methodology was further validated for assaying naturally contaminated or spiked blank peanut samples, and consistent results between the PGM-based immunoassay and the referenced enzyme-linked immunosorbent assay (ELISA) were obtained. Therefore, the developed immunoassay provides a promising approach for rapid screening of organic pollutants because it is simple, low-cost, sensitive, specific, and without the need of multiple separation and washing steps.
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Larno, V; Laroche, J; Launey, S; Flammarion, P; Devaux, A
2001-06-01
Indicators of effects at the population level (genetic variation using allozymes) and early indicators of pollution (EROD activity and DNA strand break formation) were analysed in chub (Leuciscus cephalus) living in weakly and heavily contaminated stations of the Rhône River watershed. The genetic erosion was mainly detected in a fish population living in a contaminated small river system, through modifications in allelic and genotypic frequencies for PGM-2 locus and could be linked to a genetic bottleneck and to the reduced gene flow from upstream unable to maintain or restore the genetic diversity. In a contaminated large river system, the genetic diversity for PGM-2 and other loci was maintained and was probably the consequence of a high gene flow from upstream, linked to a sustained drift of larvae and juveniles in the system. A convergent increase of the frequency of the 90 allele at PGM-2 was observed in two contaminated stations compared with the reference station, this trend being confirmed on a more extensive geographic scale over the Rhône River basin. A high level of EROD activity was detected in both contaminated sites but only the fish in the large river system showed a significant DNA damage level compared to the reference population. The low DNA damage level and high hepato-somatic ratio characterized the impacted population of the small river system and could be associated to a chronic high-level exposure of fish to pollutants which selected individuals exhibiting a high level of DNA damage repair. In the two contaminated systems, some genotypes at the PGM-2 and EST-2 loci showed a low level of DNA damage and/or a high EROD activity and may be considered as being tolerant to pollutants. A higher tolerance of the most heterozygous fish was also detected in the contaminated large system and confirmed that a high level of heterozygosity may be necessary for survival in such a system.
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Hsu, Ching-Lin; Ding, Wang-Hsien
2009-12-15
A rapid and environmental-friendly injection-port derivatization with gas chromatography-mass spectrometry (GC-MS) method was developed to determine selected low-molecular weight (LMW) dicarboxylic acids (from C2 to C10) in atmospheric aerosol samples. The parameters related to the derivatization process (i.e., type of ion-pair reagent, injection-port temperature and concentration of ion-pair reagent) were optimized. Tetrabutylammonium hydroxide (TBA-OH) 20 mM in methanol gave excellent yield for di-butyl ester dicarboxylate derivatives at injection-port temperature at 300 degrees C. Solid-phase extraction (SPE) method instead of rotary evaporation was used to concentrate analytes from filter extracts. The recovery from filter extracts ranged from 78 to 95% with relative standard deviation (RSD) less than 12%. Limits of quantitation (LOQs) ranged from 25 to 250 pg/m(3). The concentrations of di-carboxylated C2-C5 and total C6-C10 in particles of atmospheric aerosols ranged from 91.9 to 240, 11.3 to 56.7, 9.2 to 49.2, 8.7 to 35.3 and n.d. to 37.8 ng/m(3), respectively. Oxalic acid (C2) was the dominant LMW-dicarboxylic acids detected in aerosol samples. The quantitative results were comparable to the results obtained by the off-line derivatization.
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Ma, Yuning; Venier, Marta; Hites, Ronald A
2012-01-03
Two relatively new flame retardants, 2-ethylhexyl-2,3,4,5-tetrabromobenzoate (TBB) and bis(2-ethylhexyl)-tetrabromophthalate (TBPH), were identified and quantitated in gas and particle-phase air samples collected from six sites near the shores of the Great Lakes. TBB and TBPH were detected in more than half of the samples collected from 2008 to 2010. Urban areas, such as Chicago and Cleveland, showed the highest concentrations (0.36-290 pg/m(3)), while remote areas, such as Eagle Harbor and Sleeping Bear Dunes, exhibited the lowest levels (0.050-32 pg/m(3)). The atmospheric concentrations of TBB and TBPH increased rapidly and significantly over this time period, perhaps indicating that these compounds are replacing the polybrominated diphenyl ethers (PBDEs), which have been removed or soon will be removed from the marketplace.
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Er, Ayse; Yazar, Enver
2012-12-01
The aim of this study was to determine the anti-inflammatory effects of macrolides through kinetic parameters in bronchoalveolar lavage fluid (BALF) of lipopolysaccharide-induced lung injury. Rats were divided into four groups: lipopolysaccharide (LPS), LPS + tylosin, LPS + tilmicosin and LPS + tulathromycin. BALF samples were collected at sampling times. TNF, IL-1β, IL-6, IL-10 and 13,14-dihydro-15-keto-prostaglandin F2α (PGM) and C-reactive protein (CRP) were analysed. Area under the curve (AUC) and maximum plasma concentration (Cmax) values of inflammatory mediators were determined by a pharmacokinetic computer programme. When inflammatory mediator concentrations were compared between the LPS group and other groups for each sampling time, the three macrolides had no pronounced depressor effect on cytokine levels, but they depressed PGM and CRP levels. In addition, tylosin and tilmicosin decreased the AUC0-24 level of TNF, while tilmicosin decreased the AUC0-24 level of IL-10. Tylosin and tulathromycin decreased the AUC0-24 of PGM, and all three macrolides decreased the AUC0-24 of CRP. Especially tylosin and tulathromycin may have more expressed anti-inflammatory effects than tilmicosin, via depressing the production of inflammatory mediators in the lung. The AUC may be used for determining the effects of drugs on inflammation. In this study, the antiinflammatory effects of these antibiotics were evaluated with kinetic parameters as a new and different approach.
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A survey of the determination of the platinum group elements.
Kallmann, S
1987-08-01
The platinum-group metals (PGMs), Ru, Rh, Pd, Os, Ir and Pt, are widely used as catalysts in petroleum and chemical processes. They find wide applications in automotive exhaust-gas control converters and are of immense importance to the electronics industry. They are found in many items of jewellery and serve to an increasing extent as a form of investment. The PGMs are extracted in minute quantities from a limited number of ores, found mainly in S. Africa and the USSR. They are concentrated and separated from each other by elaborate chemical processes. Because of their great intrinsic value (Pt $650 per oz; Rh $1400 per oz), the recycling of the PGMs from literally hundreds of different forms of scrap is an essential factor in the overall management of the PGM economy. In this survey emphasis is placed on the need to tailor the analytical method according to (a) the environment in which the PGMs occur, (b) the individual PGM concentrations, and (c) the desired sensitivity and precision. The factors which determine the choice of chemical, physicochemical and/or instrumental approaches are discussed. They are further commented on in extensive presentations of dissolution and separation techniques and methods for the final measurement of individual PGMs. Appendices are provided which present the compositions and sources of the products most frequently encountered in PGM analysis, along with information on methods of decomposition, separations required, type of separation, and final determination.
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A Role for the TOC Complex in Arabidopsis Root Gravitropism1[W][OA
Stanga, John P.; Boonsirichai, Kanokporn; Sedbrook, John C.; Otegui, Marisa S.; Masson, Patrick H.
2009-01-01
Arabidopsis (Arabidopsis thaliana) roots perceive gravity and reorient their growth accordingly. Starch-dense amyloplasts within the columella cells of the root cap are important for gravitropism, and starchless mutants such as pgm1 display an attenuated response to gravistimulation. The altered response to gravity1 (arg1) mutant is known to be involved with the early phases of gravity signal transduction. arg1 responds slowly to gravistimulation and is in a genetically distinct pathway from pgm1, as pgm1 mutants enhance the gravitropic defect of arg1. arg1 seeds were mutagenized with ethylmethane sulfonate to identify new mutants that enhance the gravitropic defect of arg1. Two modifier of arg1 mutants (mar1 and mar2) grow in random directions only when arg1 is present, do not affect phototropism, and respond like the wild type to application of phytohormones. Both have mutations affecting different components of the Translocon of Outer Membrane of Chloroplasts (TOC) complex. mar1 possesses a mutation in the TOC75-III gene; mar2 possesses a mutation in the TOC132 gene. Overexpression of TOC132 rescues the random growth phenotype of mar2 arg1 roots. Root cap amyloplasts in mar2 arg1 appear ultrastructurally normal. They saltate like the wild type and sediment at wild-type rates upon gravistimulation. These data point to a role for the plastidic TOC complex in gravity signal transduction within the statocytes. PMID:19211693
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A role for the TOC complex in Arabidopsis root gravitropism.
Stanga, John P; Boonsirichai, Kanokporn; Sedbrook, John C; Otegui, Marisa S; Masson, Patrick H
2009-04-01
Arabidopsis (Arabidopsis thaliana) roots perceive gravity and reorient their growth accordingly. Starch-dense amyloplasts within the columella cells of the root cap are important for gravitropism, and starchless mutants such as pgm1 display an attenuated response to gravistimulation. The altered response to gravity1 (arg1) mutant is known to be involved with the early phases of gravity signal transduction. arg1 responds slowly to gravistimulation and is in a genetically distinct pathway from pgm1, as pgm1 mutants enhance the gravitropic defect of arg1. arg1 seeds were mutagenized with ethylmethane sulfonate to identify new mutants that enhance the gravitropic defect of arg1. Two modifier of arg1 mutants (mar1 and mar2) grow in random directions only when arg1 is present, do not affect phototropism, and respond like the wild type to application of phytohormones. Both have mutations affecting different components of the Translocon of Outer Membrane of Chloroplasts (TOC) complex. mar1 possesses a mutation in the TOC75-III gene; mar2 possesses a mutation in the TOC132 gene. Overexpression of TOC132 rescues the random growth phenotype of mar2 arg1 roots. Root cap amyloplasts in mar2 arg1 appear ultrastructurally normal. They saltate like the wild type and sediment at wild-type rates upon gravistimulation. These data point to a role for the plastidic TOC complex in gravity signal transduction within the statocytes.
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NASA Astrophysics Data System (ADS)
Aiglsperger, Thomas; Proenza, Joaquín A.; Font-Bardia, Mercè; Baurier-Aymat, Sandra; Galí, Salvador; Lewis, John F.; Longo, Francisco
2017-10-01
Ni-laterites from the Dominican Republic host rare but extremely platinum-group element (PGE)-rich chromitites (up to 17.5 ppm) without economic significance. These chromitites occur either included in saprolite (beneath the Mg discontinuity) or as `floating chromitites' within limonite (above the Mg discontinuity). Both chromitite types have similar iridium-group PGE (IPGE)-enriched chondrite normalized patterns; however, chromitites included in limonite show a pronounced positive Pt anomaly. Investigation of heavy mineral concentrates, obtained via hydroseparation techniques, led to the discovery of multistage PGE grains: (i) Os-Ru-Fe-(Ir) grains of porous appearance are overgrown by (ii) Ni-Fe-Ir and Ir-Fe-Ni-(Pt) phases which are overgrown by (iii) Pt-Ir-Fe-Ni mineral phases. Whereas Ir-dominated overgrowths prevail in chromitites from the saprolite, Pt-dominated overgrowths are observed within floating chromitites. The following formation model for multistage PGE grains is discussed: (i) hypogene platinum-group minerals (PGM) (e.g. laurite) are transformed to secondary PGM by desulphurization during serpentinization; (ii) at the stages of serpentinization and/or at the early stages of lateritization, Ir is mobilized and recrystallizes on porous surfaces of secondary PGM (serving as a natural catalyst) and (iii) at the late stages of lateritization, biogenic mediated neoformation (and accumulation) of Pt-Ir-Fe-Ni nanoparticles occurs. The evidence presented in this work demonstrates that in situ growth of Pt-Ir-Fe-Ni alloy nuggets of isometric symmetry is possible within Ni-laterites from the Dominican Republic.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Qiao, Zhi; Zhang, Hanguang; Karakalos, Stavros
Current platinum group metal (PGM)-free carbon nanocomposite catalysts for the oxygen reduction reaction (ORR) in acidic electrolyte often suffer from rapid degradation associated with carbon corrosion due to the use of large amount of amorphoous carbon black supports. Here, we developed a new concept of using freestanding 3D hydrogel to design support-free Fe-N-C catalysts. A 3D polyaniline (PANI)-based hydrogel was used for preparing a new type of single atomic iron site-rich catalyst, which has exhibited exceptionally enhanced activity and stability compared to conventional Fe-N-C catalysts supported on amorphous carbon blacks. The achieved performance metric on the hydrogel PANI-Fe catalysts ismore » one of the best ever reported PGM-free catalysts, reaching a half-wave potential up to 0.83 V vs. RHE and only leaving 30 mV gap with Pt/C catalysts (60 μgPt/cm2) in challenging acidic media. Remarkable ORR stability was accomplished as well on the same catalyst evidenced by using harsh potential cycling tests. The well dispersion of atomic iron into partially graphitized carbon, featured with dominance of micropores and porous network structures, is capable of accommodating increased number of active sites, strengthening local bonding among iron, nitrogen and carbon, and facilitating mass transfer. The 3D polymer hydrogel approach would be a new pathway to advance PGM-free catalysts.« less
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Simulation and optimization of the SIRIUS IPE soft x-ray beamline
NASA Astrophysics Data System (ADS)
Meyer, Bernd C.; Rocha, Tulio C. R.; Luiz, Sergio A. L.; C. Pinto, Artur; Westfahl, Harry
2017-08-01
The soft X-ray beamline IPE is one of the first phase SIRIUS beamlines at the LNLS, Brazil. Divided into two branches, IPE is designed to perform ambient pressure X-ray photo-electron spectroscopy (AP-XPS) and high resolution resonant inelastic X-ray scattering (RIXS) for samples in operando/environmental conditions inside cells and liquid jets. The aim is to maximize the photon flux in the energy range 200-1400 eV generated by an elliptically polarizing undulator source (EPU) and focus it to a 1 μm vertical spot size at the RIXS station and 10 μm at the AP-XPS station. In order to achieve the required resolving power (40.000 at 930 eV) for RIXS both the dispersion properties of the plane grating monochromator (PGM) and the thermal deformation of the optical elements need special attention. The grating parameters were optimized with the REFLEC code to maximize the efficiency at the required resolution. Thermal deformation of the PGM plane mirror limits the possible range of cff parameters depending of the photon energy used. Hence, resolution of the PGM and thermal deformation effects define the boundary conditions of the optical concept and the simulations of the IPE beamline. We compare simulations performed by geometrical ray-tracing (SHADOW) and wave front propagation (SRW) and show that wave front diffraction effects (apertures, optical surface error profiles) has a small effect on the beam spot size and shape.
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Qiao, Zhi; Zhang, Hanguang; Karakalos, Stavros; ...
2017-08-03
Current platinum group metal (PGM)-free carbon nanocomposite catalysts for the oxygen reduction reaction (ORR) in acidic electrolyte often suffer from rapid degradation associated with carbon corrosion due to the use of large amount of amorphoous carbon black supports. Here, we developed a new concept of using freestanding 3D hydrogel to design support-free Fe-N-C catalysts. A 3D polyaniline (PANI)-based hydrogel was used for preparing a new type of single atomic iron site-rich catalyst, which has exhibited exceptionally enhanced activity and stability compared to conventional Fe-N-C catalysts supported on amorphous carbon blacks. The achieved performance metric on the hydrogel PANI-Fe catalysts ismore » one of the best ever reported PGM-free catalysts, reaching a half-wave potential up to 0.83 V vs. RHE and only leaving 30 mV gap with Pt/C catalysts (60 μgPt/cm2) in challenging acidic media. Remarkable ORR stability was accomplished as well on the same catalyst evidenced by using harsh potential cycling tests. The well dispersion of atomic iron into partially graphitized carbon, featured with dominance of micropores and porous network structures, is capable of accommodating increased number of active sites, strengthening local bonding among iron, nitrogen and carbon, and facilitating mass transfer. The 3D polymer hydrogel approach would be a new pathway to advance PGM-free catalysts.« less
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Iwanowicz, D.D.; Iwanowicz, L.R.; Hitt, N.P.; King, T.L.
2013-01-01
First documented in New York State in 2006, white nose syndrome (WNS) quickly became the leading cause of mortality in hibernating bat species in the United States. WNS is caused by a psychrophilic fungus, Geomyces destructans. Clinical signs of this pathogen are expressed as a dusty white fungus predominately around the nose and on the wings of affected bats. Relatively new biomarkers, such as microRNAs (miRNAs) are being targeted as markers to predict the syndrome prior to the clinical manifestation. The primary objective of this study was to identify miRNAs that could serve as biomarkers and proxies of little brown bat health. Bats were collected from hibernacula that had tested positive and negative for WNS. Genetic sequencing was completed using the Ion Torrent platform. A number of miRNAs were identified from the liver as putative biomarkers of WNS. However, given the small sample size for each treatment, this data set has only coarsely identified miRNAs indicative of WNS, and further validation is required.
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MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data.
Alic, Andy S; Blanquer, Ignacio
2016-09-01
Usually, the information known a priori about a newly sequenced organism is limited. Even resequencing the same organism can generate unpredictable output. We introduce MuffinInfo, a FastQ/Fasta/SAM information extractor implemented in HTML5 capable of offering insights into next-generation sequencing (NGS) data. Our new tool can run on any software or hardware environment, in command line or graphically, and in browser or standalone. It presents information such as average length, base distribution, quality scores distribution, k-mer histogram, and homopolymers analysis. MuffinInfo improves upon the existing extractors by adding the ability to save and then reload the results obtained after a run as a navigable file (also supporting saving pictures of the charts), by supporting custom statistics implemented by the user, and by offering user-adjustable parameters involved in the processing, all in one software. At the moment, the extractor works with all base space technologies such as Illumina, Roche, Ion Torrent, Pacific Biosciences, and Oxford Nanopore. Owing to HTML5, our software demonstrates the readiness of web technologies for mild intensive tasks encountered in bioinformatics.
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Behere, G T; Firake, D M; Tay, W T; Azad Thakur, N S; Ngachan, S V
2016-01-01
Ladybird beetles are generally considered as agriculturally beneficial insects, but the ladybird beetles in the coleopteran subfamily Epilachninae are phytophagous and major plant feeding pest species which causes severe economic losses to cucurbitaceous and solanaceous crops. Henosepilachna pusillanima (Mulsant) is one of the important pest species of ladybird beetle. In this report, we sequenced and characterized the complete mitochondrial genome of H. pusillanima. For sequencing of the complete mitochondrial genome, we used the Ion Torrent sequencing platform. The complete circular mitochondrial genome of the H. pusillanima was determined to be 16,216 bp long. There were totally 13 protein coding genes, 22 transfer RNA, 2 ribosomal RNA and a control (A + T-rich) region estimated to be 1690 bp. The gene arrangement and orientations of assembled mitogenome were identical to the reported predatory ladybird beetle Coccinella septempunctata L. This is the first completely sequenced coleopteran mitochondrial genome from the beetle subfamily Epilachninae from India. Data generated in this study will benefit future comparative genomics studies for understanding the evolutionary relationships between predatory and phytophagous coccinellid beetles.
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Napp, Amanda P; Pereira, José Evandro S; Oliveira, Jorge S; Silva-Portela, Rita C B; Agnez-Lima, Lucymara F; Peralba, Maria C R; Bento, Fátima M; Passaglia, Luciane M P; Thompson, Claudia E; Vainstein, Marilene H
2018-06-11
The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds. Copyright © 2018 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Lopez Saez, J.; Corona, C.; Stoffel, M.; Gotteland, A.; Berger, F.; Liébault, F.
2011-05-01
Hydrogeomorphic processes are a major threat in many parts of the Alps, where they periodically damage infrastructure, disrupt transportation corridors or even cause loss of life. Nonetheless, past torrential activity and the analysis of areas affected during particular events remain often imprecise. It was therefore the purpose of this study to reconstruct spatio-temporal patterns of past debris-flow activity in abandoned channels on the forested cone of the Manival torrent (Massif de la Chartreuse, French Prealps). A Light Detecting and Ranging (LiDAR) generated Digital Elevation Model (DEM) was used to identify five abandoned channels and related depositional forms (lobes, lateral levees) in the proximal alluvial fan of the torrent. A total of 156 Scots pine trees (Pinus sylvestris L.) with clear signs of debris flow events was analyzed and growth disturbances (GD) assessed, such as callus tissue, the onset of compression wood or abrupt growth suppression. In total, 375 GD were identified in the tree-ring samples, pointing to 13 debris-flow events for the period 1931-2008. While debris flows appear to be very common at Manival, they have only rarely propagated outside the main channel over the past 80 years. Furthermore, analysis of the spatial distribution of disturbed trees contributed to the identification of four patterns of debris-flow routing and led to the determination of three preferential breakout locations. Finally, the results of this study demonstrate that the temporal distribution of debris flows did not exhibit significant variations since the beginning of the 20th century.
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Citadini, J M; Brandt, R; Williams, C R; Gomes, F R
2018-03-01
The relationships between morphology, performance, behavior and ecology provide evidence for multiple and complex phenotypic adaptations. The anuran body plan, for example, is evolutionarily conserved and shows clear specializations to jumping performance back at least to the early Jurassic. However, there are instances of more recent adaptation to habit diversity in the post-cranial skeleton, including relative limb length. The present study tested adaptive models of morphological evolution in anurans associated with the diversity of microhabitat use (semi-aquatic arboreal, fossorial, torrent, and terrestrial) in species of anuran amphibians from Brazil and Australia. We use phylogenetic comparative methods to determine which evolutionary models, including Brownian motion (BM) and Ornstein-Uhlenbeck (OU) are consistent with morphological variation observed across anuran species. Furthermore, this study investigated the relationship of maximum distance jumped as a function of components of morphological variables and microhabitat use. We found there are multiple optima of limb lengths associated to different microhabitats with a trend of increasing hindlimbs in torrent, arboreal, semi-aquatic whereas fossorial and terrestrial species evolve toward optima with shorter hindlimbs. Moreover, arboreal, semi-aquatic and torrent anurans have higher jumping performance and longer hindlimbs, when compared to terrestrial and fossorial species. We corroborate the hypothesis that evolutionary modifications of overall limb morphology have been important in the diversification of locomotor performance along the anuran phylogeny. Such evolutionary changes converged in different phylogenetic groups adapted to similar microhabitat use in two different zoogeographical regions. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.
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Platinum and lead markers as indicators of transportation impact.
DOT National Transportation Integrated Search
2009-08-20
The intent of this study was to provide information necessary to characterize the present concentrations of an emerging transportation related contaminant, the platinum group metals (PGM), and to provide background information necessary to explore th...
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Preparation and evaluation of advanced electrocatalysts for phosphoric acid fuel cells
NASA Technical Reports Server (NTRS)
Stonehart, P.; Baris, J.; Pagliaro, P.
1980-01-01
Results are presented for hydrogen oxidation and hydrogen oxidation poisoned by carbon monoxide at levels between 0 and 30%. Due to the high activities that are now being observed for our platinum based electrocatalysts, the hydrogen concentrations were reduced to 10% levels in the gas supplies. Perturbation techniques were used to determine that a mechanism for the efficient operation of our porous gas diffusion electrodes is diffusion of the carbon monoxide out of the electrode structure through the electrolyte film on the electro-catalyst. A survey of the literature on platinum group materials (PGM) was carried out so that an identification of successful electrocatalysts could be made. Two PGM electrocatalysts were prepared and performance data for hydrogen oxidation in hot phosphoric acid in the presence of high carbon monoxide concentrations showed that they matched the best platinum on carbon electrocatalysts but with an electrocatalyst cost that was half of the platinum catalyst cost.
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TEM-induced gene mutations at enzyme loci in the mouse.
Soares, E R
1979-01-01
Strain DBA/2J male mice were treated with triethylenemelamine (TEM) and subsequently mated to strain C57BL/6J females. Tissues from F1 progeny produced in these crosses were then examined using starch gel electrophoresis for the presence of presumed induced mutations at a series of 11 specific enzyme loci. In the course of this study, four heritable mutations were identified at the following loci: Es-1, Ldh-1, Pgm-1, and Gpi-1. Of these four, the first two were apparently segregating in parental males and were not TEM-induced. Both of these are viable and fertile in the heterozygous and homozygous condition, and neither confers any readily apparent deleterious effect to the animal. The latter mutations (Pgm-1 and Gpi-1) are presumably induced. Although viable and fertile in the heterozygous state, we have not recovered any offsping homozygous for either of these two mutations.
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Influence of mannosylation on immunostimulating activity of adamant-1-yl tripeptide.
Ribić, Rosana; Habjanec, Lidija; Frkanec, Ruža; Vranešić, Branka; Tomić, Srđanka
2012-07-01
The mannosylated derivative of adamant-1-yl tripeptide (D-(Ad-1-yl)Gly-L-Ala-D-isoGln) was prepared to study the effects of mannosylation on adjuvant (immunostimulating) activity. Mannosylated adamant-1-yl tripeptide (Man-OCH(2) CH(Me)CO-D-(Ad-1-yl)Gly-L-Ala-D-isoGln) is a non-pyrogenic, H(2) O-soluble, and non-toxic compound. Adjuvant activity of mannosylated adamantyl tripeptide was tested in the mouse model with ovalbumin as an antigen and in comparison to the parent tripeptide and peptidoglycan monomer (PGM, β-D-GlcNAc-(1→4)-D-MurNAc-L-Ala-D-isoGln-mesoDAP(εNH(2) )-D-Ala-D-Ala), a well-known effective adjuvant. The mannosylation of adamantyl tripeptide caused the amplification of its immunostimulating activity in such a way that it was comparable to that of PGM. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.
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ERIC Educational Resources Information Center
Balch, Stephen H.
2012-01-01
One thing history's torrent appears to be sweeping away is, ironically, the study of its most productive wellspring, Western civilization. "The Vanishing West", a report the National Association of Scholars released in May 2011, documents the extent of this vanishing. The traditional Western civilization survey requirement, commonplace only…
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Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering.
Hong, Kuk-Ki; Nielsen, Jens
2012-11-01
In a previous study, system level analysis of adaptively evolved yeast mutants showing improved galactose utilization revealed relevant mutations. The governing mutations were suggested to be in the Ras/PKA signaling pathway and ergosterol metabolism. Here, site-directed mutants having one of the mutations RAS2(Lys77), RAS2(Tyr112), and ERG5(Pro370) were constructed and evaluated. The mutants were also combined with overexpression of PGM2, earlier proved as a beneficial target for galactose utilization. The constructed strains were analyzed for their gross phenotype, transcriptome and targeted metabolites, and the results were compared to those obtained from reference strains and the evolved strains. The RAS2(Lys77) mutation resulted in the highest specific galactose uptake rate among all of the strains with an increased maximum specific growth rate on galactose. The RAS2(Tyr112) mutation also improved the specific galactose uptake rate and also resulted in many transcriptional changes, including ergosterol metabolism. The ERG5(Pro370) mutation only showed a small improvement, but when it was combined with PGM2 overexpression, the phenotype was almost the same as that of the evolved mutants. Combination of the RAS2 mutations with PGM2 overexpression also led to a complete recovery of the adaptive phenotype in galactose utilization. Recovery of the gross phenotype by the reconstructed mutants was achieved with much fewer changes in the genome and transcriptome than for the evolved mutants. Our study demonstrates how the identification of specific mutations by systems biology can direct new metabolic engineering strategies for improving galactose utilization by yeast.
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Novembre, Francis J.; De Rosayro, Juliette; O’Neil, Shawn P.; Anderson, Daniel C.; Klumpp, Sherry A.; McClure, Harold M.
1998-01-01
Transfusion of blood from a simian immunodeficiency virus (SIV)- and simian T-cell lymphotropic virus-infected sooty mangabey (designated FGb) to rhesus and pig-tailed macaques resulted in the development of neurologic disease in addition to AIDS. To investigate the role of SIV in neurologic disease, virus was isolated from a lymph node of a pig-tailed macaque (designated PGm) and the cerebrospinal fluid of a rhesus macaque (designated ROn2) and passaged to additional macaques. SIV-related neuropathogenic effects were observed in 100% of the pig-tailed macaques inoculated with either virus. Lesions in these animals included extensive formation of SIV RNA-positive giant cells in the brain parenchyma and meninges. Based upon morphology, the majority of infected cells in both lymphoid and brain tissue appeared to be of macrophage lineage. The virus isolates replicated very well in pig-tailed and rhesus macaque peripheral blood mononuclear cells (PBMC) with rapid kinetics. Differential replicative abilities were observed in both PBMC and macrophage populations, with viruses growing to higher titers in pig-tailed macaque cells than in rhesus macaque cells. An infectious molecular clone of virus derived from the isolate from macaque PGm (PGm5.3) was generated and was shown to have in vitro replication characteristics similar to those of the uncloned virus stock. While molecular analyses of this virus revealed its similarity to SIV isolates from sooty mangabeys, significant amino acid differences in Env and Nef were observed. This virus should provide an excellent system for investigating the mechanism of lentivirus-induced neurologic disease. PMID:9765429
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Zhang, Wenmin; Lin, Mingxia; Wang, Meili; Tong, Ping; Lu, Qiaomei; Zhang, Lan
2017-06-23
Microcystins (MCs) are cyclic heptapeptide toxins and tumor promoters produced by cyanobacteria, which threaten the health of humans. In this study, magnetic porous β-cyclodextrin polymer (Fe 3 O 4 @SiO 2 @P-CDP) was synthesized and characterized by transmission electron microscopy, scanning electron microscopy, energy dispersive X-ray spectrometry, Fourier transform infrared spectrometry, X-ray diffraction, nitrogen adsorption porosimetry and vibrating sample magnetometer. The synthesized Fe 3 O 4 @SiO 2 @P-CDP particles were then used for magnetic solid-phase extraction (MSPE) of MCs from environmental water samples, and exhibited excellent extraction performance, especially for MC-RR. Coupled with high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS), a simple, efficient and sensitive method for determination of trace levels of MCs was established. After the optimization of conditions, wide linear ranges (2.0-1000pgmL -1 ), good linearity (r 2 ≥0.9996) and acceptable repeatability (RSD≤9.4%, n=5) were obtained. The limits of detection (LODs, S/N=3) and limits of quantification (LOQs, S/N=10) for three MCs (MC-LR, MC-RR and MC-YR) were in the range of 1.0-2.0pgmL -1 and 2.0-5.0pgmL -1 , respectively. Typical water samples were analyzed by the developed method, and trace levels of MC-LR and MC-RR were detected. The results demonstrate that the developed method has great potential for the determination of MCs in complicated matrix. Copyright © 2017 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Shoeib, Mahiba; Ahrens, Lutz; Jantunen, Liisa; Harner, Tom
2014-12-01
Concentrations of organobromine (BFRs), organochlorine (CFRs) and organophosphate esters flame retardants and plasticizers (PFRs) in air were monitored for over one year at an urban site in Toronto, Canada during 2010-2011. The mean value for polybrominated diphenyl ethers (BDEs) (gas + particle phase) was 38 pg/m3 with BDE-47 and BDE-99 as the dominant congeners. The mean concentrations in air for ∑non-BDE (BFRs and CFRs), was 9.6 pg/m3 - about four times lower than the BDEs. The brominated FRs: TBP-AE, BTBPE, EH-TBB, BEH-TEBP and the chlorinated syn- and anti-DP were detected frequently, ranging from 87% to 96%. Highest concentrations in air among all flame retardant classes were observed for the Σ-PFRs. The yearly mean concentration in air for ΣPFRs was 2643 pg/m3 with detection frequency higher than 80%. Except for TBP-AE and b- DBE-DBCH, non-BDEs (BFRs, CFRs and PFRs) were mainly associated with the particle phase. BDE concentrations in air were positively correlated with temperature indicating that volatilization from local sources was an important factor controlling levels in air. This correlation did not hold for most BFRs, CFRs and PFRs which were mainly on particles. For these compounds, air concentrations in Toronto are likely related to emissions from point sources and advective inputs. This study highlights the importance of urban air monitoring for FRs. Urban air can be considered a sentinel for detecting changes in the use and application of FRs in commercial products.
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DNA accumulation on ventilation system filters in university buildings in Singapore
Luhung, Irvan; Wu, Yan; Xu, Siyu; Yamamoto, Naomichi; Nazaroff, William W.
2017-01-01
Introduction Biological particles deposit on air handling system filters as they process air. This study reports and interprets abundance and diversity information regarding biomass accumulation on ordinarily used filters acquired from several locations in a university environment. Methods DNA-based analysis was applied both to quantify (via DNA fluorometry and qPCR) and to characterize (via high-throughput sequencing) the microbial material on filters, which mainly processed recirculated indoor air. Results were interpreted in relation to building occupancy and ventilation system operational parameters. Results Based on accumulated biomass, average DNA concentrations per AHU filter surface area across nine indoor locations after twelve weeks of filter use were in the respective ranges 1.1 to 41 ng per cm2 for total DNA, 0.02 to 3.3 ng per cm2 for bacterial DNA and 0.2 to 2.0 ng DNA per cm2 for fungal DNA. The most abundant genera detected on the AHU filter samples were Clostridium, Streptophyta, Bacillus, Acinetobacter and Ktedonobacter for bacteria and Aspergillus, Cladosporium, Nigrospora, Rigidoporus and Lentinus for fungi. Conditional indoor airborne DNA concentrations (median (range)) were estimated to be 13 (2.6–107) pg/m3 for total DNA, 0.4 (0.05–8.4) pg/m3 for bacterial DNA and 2.3 (1.0–5.1) pg/m3 for fungal DNA. Conclusion Conditional airborne concentrations and the relative abundances of selected groups of genera correlate well with occupancy level. Bacterial DNA was found to be more responsive than fungal DNA to differences in occupancy level and indoor environmental conditions. PMID:29023520
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Barbosa, V L; Tandlich, R; Burgess, J E
2007-07-01
Platinum group metal (PGM) refining processes produce large quantities of wastewater, which is contaminated with the compounds that make up the solvents/extractants mixtures used in the process. These compounds often include solvesso, beta-hydroxyxime, amines, amides and methyl isobutyl ketone. A process to clean up PGM refinery wastewaters so that they could be re-used in the refining process would greatly contribute to continual water storage problems and to cost reduction for the industry. Based on the concept that organic compounds that are produced biologically can be destroyed biologically, the use of biological processes for the treatment of organic compounds in other types of waste stream has been favoured in recent years, owing to their low cost and environmental acceptability. This review examines the available biotechnologies and their effectiveness for treating compounds likely to be contained in precious metal extraction process wastewaters. The processes examined include: biofilters, fluidized bed reactors, trickle-bed bioreactors, bioscrubbers, two-phase partitioning bioreactors, membrane bioreactors and activated sludge. Although all processes examined showed adequate to excellent removal of organic compounds from various gaseous and fewer liquid waste streams, there was a variation in their effectiveness. Variations in performance of laboratory-scale biological processes are probably due to the inherent change in the microbial population composition due to selection pressure, environmental conditions and the time allowed for adaptation to the organic compounds. However, if these factors are disregarded, it can be established that activated sludge and membrane bioreactors are the most promising processes for use in the treatment of PGM refinery wastewaters.
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Performance of TenCate Paving interlayers in asphalt concrete pavements.
DOT National Transportation Integrated Search
2017-08-01
As a continued effort of a previously completed project entitled Performance of TenCate Mirafi PGM-G4 Interlayer-Reinforced Asphalt Pavements in Alaska, this project evaluated two newly modified paving interlayers (TruPave and Mirapave) through...
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What are check dams made for? An historical perspective from the French experience
NASA Astrophysics Data System (ADS)
Piton, Guillaume; Carladous, Simon; Recking, Alain
2015-04-01
The mitigation of torrent related hazards is an important issue in mountainous regions. Structural mitigation measures have been implemented on hill slopes and in streambeds for more than 150 years in all Europe. Check dams play a key role in these mitigation plans and can have highly variable functions (horizontal and vertical stabilization of streambeds, consolidation of hillslopes' toe, retention of sediments, modulations of high solid discharges, lowering of streambed slope, etc.). Thousands of structures had been built more than a century ago. Since their construction, land uses evolved, torrent control works, associated with reforestation, curtailed a part of the sediment production. According to field experience, defining the initial and current functions of some old structures can remain challenging in some cases. To better understand for which purposes thousands of these structures were built during the 19th and 20th centuries , we analyzed old books to determine: what was the history of the comprehension of the processes involved in torrent related hazards? and; how the use of check dams evolved to take into account this improving comprehension? i.e. how the human actions on watercourses co-evolved with scientific knowledge from the early 19th centuries to nowadays? The presentation does not aim to determine who, the first, addressed any scientific question: equivalent history and scientific works took place in all regions of the world at different time and the French were not the first to build check dams and to undertook watershed scale mitigation plans. But the French example is interesting because the torrent control works were planned in mountainous regions at the country scale (the Alps, the Pyrenees and the Massif Central). Initial plans were to reforest mountains, relying on civil engineering works if needed. Their implementation , through the French Mountain Lands' reforestation and grass seeding laws of 1860 and 1864, proved to be difficult for technical and sociological reasons. The Mountain lands' conservation and restoration law of 1882 aimed to better fit local issues. The idea of the presentation is thus to highlight how evolved the historical comprehension of torrential hazards and of the usefulness of check dams in mitigation plans in a changing environment on the technical as well as on the sociological and regulatory points of view. Pioneering scientific and technical works on torrential hydraulics and check dams will be presented. Describing the global context that leads to French laws of 1860,1864 and 1882 will allow us to explain the extensive development of the works in more than a thousand of torrents and a hundred of big landslides. We then will discuss the evolution of technics during the beginning of the 20th century and the changes induced after WWII by the arrival of reinforced-concrete technics. We will conclude the presentation with a synthesis table aiming to highlight the different functions of check dams based on a description of their situations in the watershed, compare to other structures' situations and on shape criteria. This historical perspective will hopefully help people to better understand for which purposes some structures have been built in the past centuries and what lessons can be learnt from this assessment.
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An In Vitro Enzyme System for the Production of myo-Inositol from Starch
Fujisawa, Tomoko; Fujinaga, Shohei
2017-01-01
ABSTRACT We developed an in vitro enzyme system to produce myo-inositol from starch. Four enzymes were used, maltodextrin phosphorylase (MalP), phosphoglucomutase (PGM), myo-inositol-3-phosphate synthase (MIPS), and inositol monophosphatase (IMPase). The enzymes were thermostable: MalP and PGM from the hyperthermophilic archaeon Thermococcus kodakarensis, MIPS from the hyperthermophilic archaeon Archaeoglobus fulgidus, and IMPase from the hyperthermophilic bacterium Thermotoga maritima. The enzymes were individually produced in Escherichia coli and partially purified by subjecting cell extracts to heat treatment and removing denatured proteins. The four enzyme samples were incubated at 90°C with amylose, phosphate, and NAD+, resulting in the production of myo-inositol with a yield of over 90% at 2 h. The effects of varying the concentrations of reaction components were examined. When the system volume was increased and NAD+ was added every 2 h, we observed the production of 2.9 g myo-inositol from 2.9 g amylose after 7 h, achieving gram-scale production with a molar conversion of approximately 96%. We further integrated the pullulanase from T. maritima into the system and observed myo-inositol production from soluble starch and raw potato with yields of 73% and 57 to 61%, respectively. IMPORTANCE myo-Inositol is an important nutrient for human health and provides a wide variety of benefits as a dietary supplement. This study demonstrates an alternative method to produce myo-inositol from starch with an in vitro enzyme system using thermostable maltodextrin phosphorylase (MalP), phosphoglucomutase (PGM), myo-inositol-3-phosphate synthase, and myo-inositol monophosphatase. By utilizing MalP and PGM to generate glucose 6-phosphate, we can avoid the addition of phosphate donors such as ATP, the use of which would not be practical for scaled-up production of myo-inositol. myo-Inositol was produced from amylose on the gram scale with yields exceeding 90%. Conversion rates were also high, producing over 2 g of myo-inositol within 4 h in a 200-ml reaction mixture. By adding a thermostable pullulanase, we produced myo-inositol from raw potato with yields of 57 to 61% (wt/wt). The system developed here should provide an attractive alternative to conventional methods that rely on extraction or microbial production of myo-inositol. PMID:28600316
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NASA Astrophysics Data System (ADS)
Kumaresan, Deepak; Munoz-Rojas, Miriam; Moreira-Grez, Benjamin; Kariman, Khalil; Whiteley, Andrew
2017-04-01
Mine operations generate substantial volumes of waste substrates, which are crushed and/or chemically treated waste rock from which ores are extracted. Establishment of rehabilitated landforms using post-mining substrates (i.e. waste rocks, tailings) that typically exhibit extreme conditions (such as high pH, nutrient deficiency, excessive salinity and metal toxicity) can be a major environmental problem and a critical issue during mine closure operations. More importantly, mine sites are located predominantly in arid or semi-arid lands where our understanding of basic ecosystem processes and microbial interactions with native plants (e.g. Eucalyptus spp., Acacia spp., Grevillea spp. in Western Australia) are limited. Despite the wide acknowledgement on the impact of microbial functional diversity on overall soil and plant health, no detailed attention has been paid to understand the role of belowground microbial functional diversity in the context of mine rehabilitation strategies. In this research, we investigated the role of nitrogen-based and microbial consortia amendments on improving the microbial ecology parameters of "topsoil inoculum" and subsequently its cascading effect on seedling establishment and plant morphology of Acacia ancistrocarpa, a legume native to the Pilbara and other regions of Western Australia and commonly used in arid zone restoration. The study was conducted under controlled environmental conditions in potted plants using topsoil retrieved from previously stockpiled material as growth media. A morphological assessment was undertaken to measure shoot length, shoot weight, root length, root area and root weight. Soil chemical properties, e.g. carbon, nitrogen and trace metals concentrations were determined Microbial activity was measured with the 1-day CO2 test, which determines soil microbial respiration rate based on the measurement of the CO2 burst produced after moistening dry soil (Muñoz-Rojas et al., 2016). Bacterial and archaeal community composition was assessed using high-throughput sequencing of the 16S rRNA marker gene analysis (Whiteley et al., 2012). Our results showed significant (P <0.05) larger rates of microbial activity and shoot:root ratio in those pots amended with both N and microbial consortia. Both amendments significantly influenced the chemical and bacterial-archaeal community composition in the topsoil inoculum. Topsoil amended with inorganic nitrogen revealed higher relative abundance of 16S rRNA gene sequences related to phylum Nitrospira, Planctomycetes, Gemmatimonadetes and Cyanobacteria/Chloroplast in comparison to "water-only" (control) and "microbial consortia" treatment. Addition of microbial consortia to topsoil significantly increased the concentrations of soil potassium, iron, copper and manganese. Interestingly, a large proportion of sequences that can only be assigned at the domain level (either Bacteria or Archaea) were detected in the control samples suggesting the presence of novel taxa/lineages in the native soil and their relative abundances are significantly influenced by the addition of amendments. Our data indicates that whilst amendments results significant improvement of plant growth and establishment at early stages it also results in considerable phylogenetic divergence within soil bacterial/archaeal communities, in particular loss of indigenous taxa/lineages that could have above-below ground feedback with native plants. Muñoz-Rojas M, Erickson TE, Martini D, Dixon KW, Merritt DJ. 2016. Soil physicochemical and microbiological indicators of short, medium and long term post-fire recovery in semi-arid ecosystems. Ecological indicators 63, 14-22.DOI: 10.1016/j.ecolind.2015.11.038 Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O'Donnell AG. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 91, 80-88, doi:10.1016/j.mimet.2012.07.008 (2012).
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Advancing Future Network Science through Content Understanding
2014-05-01
BitTorrent, PostgreSQL, MySQL , and GRSecurity) and emerging technologies (HadoopDFS, Tokutera, Sector/Sphere, HBase, and other BigTable-like...result. • Multi-Source Network Pulse Analyzer and Correlator provides course of action planning by enhancing the understanding of the complex dynamics
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Antonio, Carla; Larson, Tony; Gilday, Alison; Graham, Ian; Bergström, Ed; Thomas-Oates, Jane
2007-11-23
This work reports the development and optimisation of a negative ion mode on-line LC-ESI-MS/MS method for the sensitive targeted analysis of the key glycolytic intermediates, sugars and sugar phosphates from plants, using a porous graphitic carbon (PGC) stationary phase and an MS compatible mobile phase. Using this newly developed method, separation and detection of a solution of standard compounds is achieved in less than 20min. Target metabolite compounds were identified in plant extracts from their characteristic retention times, and product ion spectra. This on-line PGC-ESI-MS/MS method shows good linearity over the concentration range 0-100microM, selectivity, short analysis time, and limits of detection of 0.1microM for disaccharides trehalose (Tre), sucrose (Suc), and maltose, and 1.5microM for hexose phosphates fructose-6-phosphate (Fru6P), glucose-1-phosphate (Glc1P), and glucose-6-phosphate (Glc6P), and phosphoenolpyruvate (PEP). This paper describes details of our method and its application to the simultaneous quantitative analysis of soluble sugars and sugar phosphates from Arabidopsis thaliana tissues. We have demonstrated the utility of our method for the analysis of biological samples by applying it to the simultaneous quantitation of changes in soluble sugars and sugar phosphates in A. thaliana Columbia-0 (Col-0) and its starchless phosphoglucomutase (pgm) mutant over a 12-h light/12-h dark growth cycle.
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Hazard connected to tunnel construction in Mt Stena karstic area (Rosandra Valley, Classical Karst)
NASA Astrophysics Data System (ADS)
Cucchi, F.; Boschin, W.; Visintin, L.; Zini, L.
2009-04-01
Rosandra Valley -a unique geomorphological environment- is located in the western side of the Classical Karst plateau. This deep limestone gorge is crossed by a stream that is fed by a large basin located in Slovenia. Rosandra Valley is the only example of Classical Karst river valley with surface hydrography; the torrent digs a deep gully into the rock, rich in rapids, swirl holes, small waterfalls, enclosed meanders and basins; here, the first seepage phenomena occur, and part of the water feeds the underground aquifer. Rosandra Valley is theatre to complex structural situation; the NE slope culminates in the structure of Mt Stena, a limestone tectonic scale located between two faults and firmly rooted in the karst platform. Tectonics is quite important for the development of deep karst in this area; Mt Stena, in particular, hosts a comprehensive net of articulated and diversely shaped caves, basically organised on several levels, which stretches over a total of 9,000 metres, bearing testimony to ancient geological and hydrogeological origins. The deepest areas of the system reach a suspended aquifer that is probably sustained by an overthrust and placed about 100 meters above Rosandra torrent underground aquifer. During feasibility studies about Trieste-Divača high velocity railway link, interaction between project and karst features was examined; in fact the proximity of proposal project and Mt Stena karst system suggest to improve the knowledge related to karst and hydrogeological aspects of the massif. Compatibly with the project requirements, risk of voids intersection and water contamination were analyzed. In fact the Mt Stena suspended aquifer partially feeds Rosandra torrent which flows in a protected natural area. Karst features were represented in a 3D model in order to better understand the spatial relationship between railway project and karst system.
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Rainfall control of debris-flow triggering in the Réal Torrent, Southern French Prealps
NASA Astrophysics Data System (ADS)
Bel, Coraline; Liébault, Frédéric; Navratil, Oldrich; Eckert, Nicolas; Bellot, Hervé; Fontaine, Firmin; Laigle, Dominique
2017-08-01
This paper investigates the occurrence of debris flow due to rainfall forcing in the Réal Torrent, a very active debris flow-prone catchment in the Southern French Prealps. The study is supported by a 4-year record of flow responses and rainfall events, from three high-frequency monitoring stations equipped with geophones, flow stage sensors, digital cameras, and rain gauges measuring rainfall at 5-min intervals. The classic method of rainfall intensity-duration (ID) threshold was used, and a specific emphasis was placed on the objective identification of rainfall events, as well as on the discrimination of flow responses observed above the ID threshold. The results show that parameters used to identify rainfall events significantly affect the ID threshold and are likely to explain part of the threshold variability reported in the literature. This is especially the case regarding the minimum duration of rain interruption (MDRI) between two distinct rainfall events. In the Réal Torrent, a 3-h MDRI appears to be representative of the local rainfall regime. A systematic increase in the ID threshold with drainage area was also observed from the comparison of the three stations, as well as from the compilation of data from experimental debris-flow catchments. A logistic regression used to separate flow responses above the ID threshold, revealed that the best predictors are the 5-min maximum rainfall intensity, the 48-h antecedent rainfall, the rainfall amount and the number of days elapsed since the end of winter (used as a proxy of sediment supply). This emphasizes the critical role played by short intense rainfall sequences that are only detectable using high time-resolution rainfall records. It also highlights the significant influence of antecedent conditions and the seasonal fluctuations of sediment supply.
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Bissias, George; Levine, Brian; Liberatore, Marc; Lynn, Brian; Moore, Juston; Wallach, Hanna; Wolak, Janis
2016-02-01
We provide detailed measurement of the illegal trade in child exploitation material (CEM, also known as child pornography) from mid-2011 through 2014 on five popular peer-to-peer (P2P) file sharing networks. We characterize several observations: counts of peers trafficking in CEM; the proportion of arrested traffickers that were identified during the investigation as committing contact sexual offenses against children; trends in the trafficking of sexual images of sadistic acts and infants or toddlers; the relationship between such content and contact offenders; and survival rates of CEM. In the 5 P2P networks we examined, we estimate there were recently about 840,000 unique installations per month of P2P programs sharing CEM worldwide. We estimate that about 3 in 10,000 Internet users worldwide were sharing CEM in a given month; rates vary per country. We found an overall month-to-month decline in trafficking of CEM during our study. By surveying law enforcement we determined that 9.5% of persons arrested for P2P-based CEM trafficking on the studied networks were identified during the investigation as having sexually offended against children offline. Rates per network varied, ranging from 8% of arrests for CEM trafficking on Gnutella to 21% on BitTorrent. Within BitTorrent, where law enforcement applied their own measure of content severity, the rate of contact offenses among peers sharing the most-severe CEM (29%) was higher than those sharing the least-severe CEM (15%). Although the persistence of CEM on the networks varied, it generally survived for long periods of time; e.g., BitTorrent CEM had a survival rate near 100%. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Senevirathne, Gayani; Thomas, Ashish; Kerney, Ryan; Hanken, James; Biju, S. D.; Meegaskumbura, Madhava
2016-01-01
The Indian Purple frog, Nasikabatrachus sahyadrensis, occupies a basal phylogenetic position among neobatrachian anurans and has a very unusual life history. Tadpoles have a large ventral oral sucker, which they use to cling to rocks in torrents, whereas metamorphs possess adaptations for life underground. The developmental changes that underlie these shifts in habits and habitats, and especially the internal remodeling of the cranial and postcranial skeleton, are unknown. Using a nearly complete metamorphic series from free-living larva to metamorph, we describe the postembryonic skeletal ontogeny of this ancient and unique monotypic lineage. The torrent-dwelling larva possesses a dorsoventrally flattened body and a head with tiny dorsal eyes, robust lower and upper jaw cartilages, well-developed trabecular horns, and a definable gap between the trabecular horns and the tip of the snout. Unlike tadpoles of many other frogs, those of Nasikabatrachus retain larval mouthparts into late metamorphic stages. This unusual feature enables the larvae to maintain their clinging habit until near the end of metamorphosis. The subsequent ontogenetic shift from clinging to digging is correlated with rapid morphological changes and behavioral modifications. Metamorphs are equipped with a shortened tibiafibula and ossified prehallical elements, which likely facilitate initial digging using the hind limbs. Subsequently, the frogs may shift to headfirst burrowing by using the wedge-shaped skull, anteriorly positioned pectoral girdle, well-developed humeral crests and spatula-shaped forelimbs. The transition from an aquatic life in torrents to a terrestrial life underground entails dramatic changes in skeletal morphology and function that represent an extreme in metamorphic remodeling. Our analysis enhances the scope for detailed comparative studies across anurans, a group renowned for the diversity of its life history strategies. PMID:27028113
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Storms in Ancient Egypt: the Examples of Historical Natural Disasters Impacts on the Society
NASA Astrophysics Data System (ADS)
Petrova, Anastasia
2013-04-01
Though rain storms are infrequent in Egypt, which is normally a rainless country, some Ancient Egyptian texts give accounts of violent storms and rains. Actually, even small amounts of rain in that area could cause huge impact, as none of the water was absorbed by soil, and, running off, it could create dangerous torrents. The Tempest stele, circa 1550 BC, recounts a highly destructive storm happened during the reign of Ahmose I, the king of Egypt's 18 dynasty. The catastrophy is described in details, including the specific noise, overall darkness, torrent so that no torch could be lit. Many houses were washed into the river, temples, tombs and pyramids damaged and collapsed. The stele commemorates the restoration works made by the king who was able to cope with this great disaster and "re-establish the Two Lands". Some egyptologists believe that this event is related to the Minoan eruption of Thera, but this is unlikely given the description in the stele.
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Isozyme variation in wild and cultivated pineapple
USDA-ARS?s Scientific Manuscript database
Isozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs . Considerable variation exists within and between species of Ananas. Sixt...
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ERIC Educational Resources Information Center
Asheim, Lester
1982-01-01
Reexamines Ortega y Gasset's proposition that the professional role of the librarian is to act as a selective "filter between man and the torrent of books." Responsibilities of the librarian in light of the increasing volume of information, increases in speed of access to information, and information overload, are discussed. (Author/JL)
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NASA Astrophysics Data System (ADS)
Kubota, T.; Silva, I. C.; Hasnawir, H.
2009-12-01
The research including observation of rain, soil moisture content and sediment discharge is conducted on a torrent in northern Kyushu whose geology consists of Paleozoic metamorphic rocks (mainly schist) and whose vegetation consists of mainly Japanese cypress and cedar. Soil depth is approximately 50cm in average and permeability k is 0.1~0.01 order. With data obtained by the observation for more than 4 years, standard rainfalls of warning and evacuation against the sudden sediment runoffs are analyzed. Then, the result was compared with the ones in Nuevo Leon Mexico (geology of schist, slate, k=0.01~0.001 order) and in southern Sulawesi Island Indonesia (volcanic geology, k=0.001~0.0001 order). Hitherto, various methods were proposed to analyze the warning critical standard for landslide disaster or large sediment discharge. In this study, we employed Hirano's element slope runoff theory, the Self Organized Criticality Assumption (SOC), and the Elementary Catastrophe Theory (ETC) to analyze the data, although the soil moisture fluctuation, meteorological condition such as upper air wind and dew point depression, the rainfall-soil moisture index provided by Japan Meteorological Agency was considered. The last one is a cutting edge technology based on the tank model calculation of soil moisture content combined with short term rainfall prediction which is a product of numerical simulation using radar image advection analysis compensated with surface rain data and with orographic rain effect. In Hirano's theory, we can describe the critical rain Rc and rain intensity Ric as following equation. Q/A/M/ cosθ = Ri ∫(r*cosθ)dt = Ri*R (1) ∴ Ric*Rc = C (2) Here, Q: sediment runoff or debris flow discharge, A: watershed area, M: function concerning with sediment deposit features on the upstream torrents or slopes (porosity, torrent bed slope gradient, sediment accumulation length and depth, cohesion), t: time, θ: torrent bed or hillside slope gradient, r: instant precipitation. C: constant, given as 8000 in Fukuoka (Kyushu, Japan), as 3750 in Sierra Madere Oriental (Nuevo Leon, Mexico), as 9000 in southern Sulawesi(Indonesia). Consequently, the forecast-warning system which has enough accuracy of 80% against sediment runoffs or debris flows for both wide range region with meteorological conditions and narrow region with the critical rain standard are established. However, in the region with lower soil permeability we may revise the standard rain by the compensation with the soil moisture content response such as increasing rate.
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NASA Astrophysics Data System (ADS)
Lucchetti, Gabriella; Cutroneo, Laura; Carbone, Cristina; Consani, Sirio; Vagge, Greta; Canepa, Giuseppe; Capello, Marco
2017-04-01
Ports are complex environments due to their complicated geometry (quays, channels, and piers), the presence of human activities (vessel traffic, yards, industries, and discharges), and natural factors (stream and torrent inputs, sea action, and currents). Due to the many activities that take place in a port, sediments and waters are often contaminated by different kinds of chemicals, such as hydrocarbons, dioxins, pesticides, nutrients, and metals. The contamination rate of a port basin is site specific and depends on the sources of contamination in the nearby urban system as well as the port system itself, such as city discharges and sewers, river intake, vessel traffic, factories (Taylor and Owens, 2009). Moreover, two important sources and vehicles of contaminants are: a) anthropogenic road deposited sediments derived from the runoff of the port and city area, and natural road deposited sediments derived from rivers and torrents, and b) airborne particulate matter and sediments (Taylor and Owens, 2009). The Port of Genoa is situated at the apex of the Ligurian Sea in the north western Mediterranean Sea and is characterised by the presence of several commercial activities that have contributed, over the years, and still contribute today, to the contaminant accumulation in both the water column and the bottom sediments. This port basin includes the mouth of several streams and the mouth of the Bisagno and the Polcevera Torrents, along the banks of which can be found several small towns, quarries, factories, and the suburbs of the city of Genoa, a ferry terminal, different container terminals, marinas, dry docks, the coal power plant of Genoa, and different wastewater treatment plant discharges. Starting from these considerations, we have examined the marine environment of a port from the point of view of the water mass circulation, hydrological characteristics, distribution of the sediment grain size, mineralogical characteristics, and metal concentrations of the bottom sediments. Our results show that, in the case of the Port of Genoa (north western Italy), both the impact of the human activities (such as coal power plant, oil depots, yards, dredging of the bottom sediments, etc.) and the natural processes (such as currents, fresh water and sediment inputs from the torrents), together with the morphology of the basin, are important factors in sediment, water and metal distributions and give rise to a complex environment. Taylor, K.G., Owens, P.N., 2009. Sediments in urban river basins: a review of sediment contaminant dynamics in an environmental system conditioned by human activities. Journal of Soils and Sediments 9: 281-303.
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Golding, Jean; Northstone, Kate; Gregory, Steven; Miller, Laura L; Pembrey, Marcus
2014-01-01
Objectives Previously, in the Avon Longitudinal Study of Parents and Children (ALSPAC), we have shown different sex-specific birth anthropometric measurements contingent upon whether or not prenatal smoking was undertaken by paternal grandmother (PGM±), maternal grandmother (MGM±), and the study mother (M±). The findings raised the question as to whether there were long-term associations on the growth of the study children over time. Methods Measures of weight, height, body mass index, waist circumference, lean mass, and fat mass of children in the ALSPAC study from 7 to 17 years of age were used. We compared growth in four categories at each age: PGM+M− with PGM−M−; MGM+M− with MGM−M−; PGM+M+ with PGM−M+; MGM+M+ with MGM−M+; and adjusted for housing tenure, maternal education, parity, and paternal smoking at the start of the study pregnancy. Results We found that if the PGM had, but the study mother had not, smoked in pregnancy, the girls were taller and both genders had greater bone and lean mass. However, if the MGM had smoked prenatally but the mother had not (MGM+M−), the boys became heavier than expected with increasing age—an association that was particularly due to lean rather than fat mass, reflected in increased strength and fitness. When both the maternal grandmother and the mother had smoked (MGM+M+) girls had reduced height, weight, and fat/lean/bone mass when compared with girls born to smoking mothers whose own mothers had not smoked (MGM−M+). Conclusions This study indicates that smoking in humans can have sex-specific transgenerational effects. Am. J. Hum. Biol. 26:731–739, 2014. © 2014 The Authors American Journal of Human Biology Published by Wiley Periodicals, Inc. PMID:25130101
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Observations of reactive gaseous mercury in the free troposphere at the Mount Bachelor Observatory
NASA Astrophysics Data System (ADS)
Swartzendruber, P. C.; Jaffe, D. A.; Prestbo, E. M.; Weiss-Penzias, P.; Selin, N. E.; Park, R.; Jacob, D. J.; Strode, S.; Jaeglé, L.
2006-12-01
We measured gaseous elemental mercury (GEM), particulate mercury (PHg), and reactive gaseous mercury (RGM), along with CO, ozone, and aerosol scatter at the Mount Bachelor Observatory (2.7 km above sea level), Oregon, from May to August 2005. The mean mercury concentrations (at standard conditions) were 1.54 ng/m3 (GEM), 5.2 pg/m3 (PHg), and 43 pg/m3 (RGM). RGM enhancements, up to 600 pg/m3, occurred at night and were linked to a diurnal pattern of upslope and downslope flows that mixed in boundary layer air during the day and free tropospheric air at night. During the night, RGM was inversely correlated (P < 0.0001) with CO (r = -0.36), GEM (r = -0.73), and H2O (r = -0.44), was positively correlated with ozone (r = 0.38), and could not be linked to recent anthropogenic emissions from local sources or long-range transport. Principal component analysis and a composite of change in RGM versus change in GEM during RGM enhancements indicate that a nearly quantitative shift in speciation is associated with increases in ozone and decreases in water vapor and CO. This argues that high concentrations of RGM are present in the free troposphere because of in situ oxidation of GEM to RGM. A global chemical transport model reproduces the RGM mean and diurnal pattern but underestimates the magnitude of the largest observed enhancements. Since the only modeled, in situ RGM production mechanisms are oxidation of GEM by ozone and OH, this implies that there are faster reaction rates or additional RGM production mechanisms in the free troposphere.
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Sebastian, David; Serov, Alexey; Matanovic, Ivana; ...
2017-02-21
Direct alcohol fuel cells (DAFCs) represent the best alternative to batteries for portable and auxiliary power units application due to the high energy density of short chain alcohols. Currently, the utilization of the best platinum group metal (PGM) cathode catalysts is limited, not only by a high cost and scarce resources, but also by the inefficient oxygen reduction reaction (ORR) when permeated alcohols adsorb on the catalytic active sites. In this work, a highly active Fe-N-C catalyst derived from the pyrolysis of nicarbazin (a nitrogen charge transfer organic salt) and an iron precursor has been investigated to get insights onmore » the extraordinary tolerance to the presence of alcohols (methanol and ethanol) of such a PGM-free catalyst. Density functional theory (DFT) calculations demonstrate for the first time that Fe-N 4 and Fe-N 2C 2 active sites preferentially adsorb oxygen with much higher energy than methanol, ethanol and products of partial ethanol oxidation (0.73–1.16 eV stronger adsorption), while nitrogen-carbon related sites (pyridinic and graphitic nitrogen) are much less selective towards ORR. Half-cell electrochemical characterization showed that the Fe-N-C catalyst overcomes Pt ORR activity in acidic medium with methanol or ethanol concentrations as low as 0.01 M. The feasibility of DAFCs operation based on high methanol (up to 17 M) and ethanol (up to 5 M) concentration thanks to the utilization of Fe-N-C cathode catalyst is demonstrated. Lastly, a new strategy is proposed for DAFCs where using Pt only at the anode and Fe-N-C at the cathode allows extending the device energy density compared to PGM-based catalysts at both electrodes.« less
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Superior model for fault tolerance computation in designing nano-sized circuit systems
DOE Office of Scientific and Technical Information (OSTI.GOV)
Singh, N. S. S., E-mail: narinderjit@petronas.com.my; Muthuvalu, M. S., E-mail: msmuthuvalu@gmail.com; Asirvadam, V. S., E-mail: vijanth-sagayan@petronas.com.my
2014-10-24
As CMOS technology scales nano-metrically, reliability turns out to be a decisive subject in the design methodology of nano-sized circuit systems. As a result, several computational approaches have been developed to compute and evaluate reliability of desired nano-electronic circuits. The process of computing reliability becomes very troublesome and time consuming as the computational complexity build ups with the desired circuit size. Therefore, being able to measure reliability instantly and superiorly is fast becoming necessary in designing modern logic integrated circuits. For this purpose, the paper firstly looks into the development of an automated reliability evaluation tool based on the generalizationmore » of Probabilistic Gate Model (PGM) and Boolean Difference-based Error Calculator (BDEC) models. The Matlab-based tool allows users to significantly speed-up the task of reliability analysis for very large number of nano-electronic circuits. Secondly, by using the developed automated tool, the paper explores into a comparative study involving reliability computation and evaluation by PGM and, BDEC models for different implementations of same functionality circuits. Based on the reliability analysis, BDEC gives exact and transparent reliability measures, but as the complexity of the same functionality circuits with respect to gate error increases, reliability measure by BDEC tends to be lower than the reliability measure by PGM. The lesser reliability measure by BDEC is well explained in this paper using distribution of different signal input patterns overtime for same functionality circuits. Simulation results conclude that the reliability measure by BDEC depends not only on faulty gates but it also depends on circuit topology, probability of input signals being one or zero and also probability of error on signal lines.« less
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Carbon Limitation Induces ςS-Dependent Gene Expression in Pseudomonas fluorescens in Soil
Koch, Birgit; Worm, Jakob; Jensen, Linda E.; Højberg, Ole; Nybroe, Ole
2001-01-01
Recent studies employing reporter gene technology indicate that the availabilities of the major nutrients nitrogen, phosphate, and iron to Pseudomonas are not severely limited in bulk soil. Indirect evidence has pointed to carbon limitation as a severe nutritional stress in this environment. We show that a plasmid (pGM115)-borne transcriptional fusion between the ςS-dependent Escherichia coli promoter Pfic and lacZ functions as a reliable reporter for carbon availability in Pseudomonas fluorescens. When P. fluorescens strain DF57(pGM115) was introduced into bulk soil, carbon-limiting conditions were indicated by citrate-repressible induction of β-galactosidase activity. To address carbon availability at the single-cell level, we developed an immunofluorescence double-staining procedure for individual DF57 cells expressing β-galactosidase from Pfic. Changes in cell size and expression of β-galactosidase were analyzed by flow cytometry. Cells extracted from soil microcosms reduced their size less than carbon-starved cells in pure culture and showed an increased tendency to aggregate. The single-cell analysis revealed that for cells residing in soil, the expression of β-galactosidase became heterogeneous and only a DF57 subpopulation appeared to be carbon limited. In soil amended with barley straw, limited nitrogen availability has been determined by use of the bioluminescent reporter strain P. fluorescens DF57-N3. We used strain DF57-N3(pGM115) as a double reporter for carbon and nitrogen limitation that allowed us to study the dynamics of carbon and nitrogen availabilities in more detail. In straw-amended soil β-galactosidase activity remained low, while nitrogen limitation-dependent bioluminescence appeared after a few days. Hence, nitrogen became limited under conditions where carbon resources were not completely exhausted. PMID:11472905
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Zhong, Guangcai; Xie, Zhiyong; Cai, Minghong; Möller, Axel; Sturm, Renate; Tang, Jianhui; Zhang, Gan; He, Jianfeng; Ebinghaus, Ralf
2012-01-03
Surface seawater and marine boundary layer air samples were collected on the ice-breaker R/V Xuelong (Snow Dragon) from the East China Sea to the high Arctic (33.23-84.5° N) in July to September 2010 and have been analyzed for six current-use pesticides (CUPs): trifluralin, endosulfan, chlorothalonil, chlorpyrifos, dacthal, and dicofol. In all oceanic air samples, the six CUPs were detected, showing highest level (>100 pg/m(3)) in the Sea of Japan. Gaseous CUPs basically decreased from East Asia (between 36.6 and 45.1° N) toward Bering and Chukchi Seas. The dissolved CUPs in ocean water ranged widely from
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sebastian, David; Serov, Alexey; Matanovic, Ivana
Direct alcohol fuel cells (DAFCs) represent the best alternative to batteries for portable and auxiliary power units application due to the high energy density of short chain alcohols. Currently, the utilization of the best platinum group metal (PGM) cathode catalysts is limited, not only by a high cost and scarce resources, but also by the inefficient oxygen reduction reaction (ORR) when permeated alcohols adsorb on the catalytic active sites. In this work, a highly active Fe-N-C catalyst derived from the pyrolysis of nicarbazin (a nitrogen charge transfer organic salt) and an iron precursor has been investigated to get insights onmore » the extraordinary tolerance to the presence of alcohols (methanol and ethanol) of such a PGM-free catalyst. Density functional theory (DFT) calculations demonstrate for the first time that Fe-N 4 and Fe-N 2C 2 active sites preferentially adsorb oxygen with much higher energy than methanol, ethanol and products of partial ethanol oxidation (0.73–1.16 eV stronger adsorption), while nitrogen-carbon related sites (pyridinic and graphitic nitrogen) are much less selective towards ORR. Half-cell electrochemical characterization showed that the Fe-N-C catalyst overcomes Pt ORR activity in acidic medium with methanol or ethanol concentrations as low as 0.01 M. The feasibility of DAFCs operation based on high methanol (up to 17 M) and ethanol (up to 5 M) concentration thanks to the utilization of Fe-N-C cathode catalyst is demonstrated. Lastly, a new strategy is proposed for DAFCs where using Pt only at the anode and Fe-N-C at the cathode allows extending the device energy density compared to PGM-based catalysts at both electrodes.« less
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Wu, Yunqing; Zeng, Lifeng; Xiong, Ying; Leng, Yuankui; Wang, Hui; Xiong, Yonghua
2018-05-01
Herein, we present a novel sandwich fluorescence enzyme linked immunosorbent assay (ELISA) for highly sensitive detection of Hepatitis B virus surface antigen (HBsAg) based on glucose oxidase (GOx)-induced fluorescence quenching of mercaptopropionic acid-modified CdTe quantum dots (MPA-QDs). In this system, hydrogen peroxide (H 2 O 2 ) sensitive MPA-QDs was used as a signal output, and glucose oxidase (GOx) was used as label which can generate H 2 O 2 via catalytic oxidation of glucose. The proposed method showed dynamic linear detection of HBsAg both in the range of 47pgmL -1 ~ 380pgmL -1 and 0.75ngmL -1 ~ 12.12ngmL -1 . The detection limit of the proposed fluorescence ELISA was 1.16pgmL -1 , which was approximately 430-fold lower than that of horseradish peroxidase (HRP)-based conventional ELISA. The average recoveries for HBsAg-spiked serum samples ranged from 98.0% to 126.8% with the relative standard derivation below 10%, thus indicating acceptable precision and high reproducibility of the proposed fluorescence ELISA for HBsAg detection. Additionally, the developed method showed no false positive results analyzing 35 real HBsAg-negative serum samples, and exhibited excellent agreement (R 2 =0.9907) with a commercial time-resolved fluorescence immunoassay (TRFIA) kit for detecting 31 HBsAg-positive serum samples. In summary, the proposed method based on fluorescence quenching of H 2 O 2 sensitive QDs is considerably to be an excellent biodetection platform with ultrahigh sensitivity, good accuracy and excellent reliability. Copyright © 2018 Elsevier B.V. All rights reserved.
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Dong, Tao; Pires, Nuno Miguel Matos
2017-08-15
This work reports a novel optical microfluidic biosensor with highly sensitive organic photodetectors (OPDs) for absorbance-based detection of salivary protein biomarkers at the point of care. The compact and miniaturized biosensor has comprised OPDs made of polythiophene-C 70 bulk heterojunction for the photoactive layer; whilst a calcium-free cathode interfacial layer, made of linear polyethylenimine, was incorporated to the photodetectors to enhance the low cost. The OPDs realized onto a glass chip were aligned to antibody-functionalized chambers of a poly(methyl methacrylate) microfluidic chip, in where immunogold-silver assays were conducted. The biosensor has detected IL-8, IL-1β and MMP-8 protein in spiked saliva with high detection specificity and short analysis time exhibiting detection limits between 80pgmL -1 and 120pgmL -1 . The result for IL-8 was below the clinical established cut-off of 600pgmL -1 , which revealed the potential of the biosensor to early detection of oral cancer. The detection limit was also comparable to other previously reported immunosensors performed with bulky instrumentation or using inorganic photodetectors. The optical detection sensitivity of the polythiophene-C 70 OPD was enhanced by optimizing the thickness of the photoactive layer and anode interfacial layer prior to the saliva immunoassays. Further, the biosensor was tested with unspiked human saliva samples, and the results of measuring IL-8 and IL-1β were in statistical agreement with those provided by two commercial assays of ELISA. The optical microfluidic biosensor reported hereby offers an attractive and cost-effective tool to diagnostics or screening purposes at the point of care. Copyright © 2017 Elsevier B.V. All rights reserved.
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Inactivation of human norovirus using chemical sanitizers.
Kingsley, David H; Vincent, Emily M; Meade, Gloria K; Watson, Clytrice L; Fan, Xuetong
2014-02-03
The porcine gastric mucin binding magnetic bead (PGM-MB) assay was used to evaluate the ability of chlorine, chlorine dioxide, peroxyacetic acid, hydrogen peroxide, and trisodium phosphate to inactivate human norovirus within 10% stool filtrate. One-minute free chlorine treatments at concentrations of 33 and 189 ppm reduced virus binding in the PGM-MB assay by 1.48 and 4.14 log₁₀, respectively, suggesting that chlorine is an efficient sanitizer for inactivation of human norovirus (HuNoV). Five minute treatments with 5% trisodium phosphate (pH~12) reduced HuNoV binding by 1.6 log₁₀, suggesting that TSP, or some other high pH buffer, could be used to treat food and food contact surfaces to reduce HuNoV. One minute treatments with 350 ppm chlorine dioxide dissolved in water did not reduce PGM-MB binding, suggesting that the sanitizer may not be suitable for HuNoV inactivation in liquid form. However a 60-min treatment with 350 ppm chlorine dioxide did reduce human norovirus by 2.8 log₁₀, indicating that chlorine dioxide had some, albeit limited, activity against HuNoV. Results also suggest that peroxyacetic acid has limited effectiveness against human norovirus, since 1-min treatments with up to 195 ppm reduced human norovirus binding by <1 log₁₀. Hydrogen peroxide (4%) treatment of up to 60 min resulted in minimal binding reduction (~0.1 log₁₀) suggesting that H₂O₂ is not a good liquid sanitizer for HuNoV. Overall this study suggests that HuNoV is remarkably resistant to several commonly used disinfectants and advocates for the use of chlorine (sodium hypochlorite) as a HuNoV disinfectant wherever possible. Copyright © 2013. Published by Elsevier B.V.
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Watanabe, Daisuke; Zhou, Yan; Hirata, Aiko; Sugimoto, Yukiko; Takagi, Kenichi; Akao, Takeshi; Ohya, Yoshikazu; Takagi, Hiroshi
2015-01-01
The high fermentation rate of Saccharomyces cerevisiae sake yeast strains is attributable to a loss-of-function mutation in the RIM15 gene, which encodes a Greatwall-family protein kinase that is conserved among eukaryotes. In the present study, we performed intracellular metabolic profiling analysis and revealed that deletion of the RIM15 gene in a laboratory strain impaired glucose-anabolic pathways through the synthesis of UDP-glucose (UDPG). Although Rim15p is required for the synthesis of trehalose and glycogen from UDPG upon entry of cells into the quiescent state, we found that Rim15p is also essential for the accumulation of cell wall β-glucans, which are also anabolic products of UDPG. Furthermore, the impairment of UDPG or 1,3-β-glucan synthesis contributed to an increase in the fermentation rate. Transcriptional induction of PGM2 (phosphoglucomutase) and UGP1 (UDPG pyrophosphorylase) was impaired in Rim15p-deficient cells in the early stage of fermentation. These findings demonstrate that the decreased anabolism of glucose into UDPG and 1,3-β-glucan triggered by a defect in the Rim15p-mediated upregulation of PGM2 and UGP1 redirects the glucose flux into glycolysis. Consistent with this, sake yeast strains with defective Rim15p exhibited impaired expression of PGM2 and UGP1 and decreased levels of β-glucans, trehalose, and glycogen during sake fermentation. We also identified a sake yeast-specific mutation in the glycogen synthesis-associated glycogenin gene GLG2, supporting the conclusion that the glucose-anabolic pathway is impaired in sake yeast. These findings demonstrate that downregulation of the UDPG synthesis pathway is a key mechanism accelerating alcoholic fermentation in industrially utilized S. cerevisiae sake strains. PMID:26497456
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Pure gravity mediation and spontaneous B–L breaking from strong dynamics
Babu, Kaladi S.; Schmitz, Kai; Yanagida, Tsutomu T.
2016-04-01
In pure gravity mediation (PGM), the most minimal scheme for the mediation of supersymmetry (SUSY) breaking to the visible sector, soft masses for the standard model gauginos are generated at one loop rather than via direct couplings to the SUSY-breaking field. In any concrete implementation of PGM, the SUSY-breaking field is therefore required to carry nonzero charge under some global or local symmetry. As we point out in this note, a prime candidate for such a symmetry might be B–L, the Abelian gauge symmetry associated with the difference between baryon number Band lepton number L. The F-term of the SUSY-breakingmore » field then not only breaks SUSY, but also B–L, which relates the respective spontaneous breaking of SUSY and B–Lat a fundamental level. As a particularly interesting consequence, we find that the heavy Majorana neutrino mass scale ends up being tied to the gravitino mass, Λ N~m 3/2. Furthermore, assuming nonthermal leptogenesis to be responsible for the generation of the baryon asymmetry of the universe, this connection may then explain why SUSY necessarily needs to be broken at a rather high energy scale, so that m 3/2≳1000 TeV in accord with the concept of PGM. We illustrate our idea by means of a minimal model of dynamical SUSY breaking, in which B–Lis identified as a weakly gauged flavor symmetry. We also discuss the effect of the B–L gauge dynamics on the superparticle mass spectrum as well as the resulting constraints on the parameter space of our model. In particular, we comment on the role of the B–LD-term.« less
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Allozyme variation in spineless Pejibaye (Bactris gasipaes Kunth)
USDA-ARS?s Scientific Manuscript database
Isozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs . Considerable variation exists within and between species of Ananas. Sixt...
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Kurtuluş-Ulküer, M; Ulküer, U; Kesici, T; Menevşe, S
2002-09-01
In this study, the phenotype and allele frequencies of five enzyme systems were determined in a total of 611 unrelated Turkish individuals and analyzed by using the exact and the chi 2 test. The following five red cell enzymes were identified by cellulose acetate electrophoresis: phosphoglucomutase (PGM), adenosine deaminase (ADA), phosphoglucose isomerase (PGI), adenylate kinase (AK), and 6-phosphogluconate dehydrogenase (6-PGD). The ADA, PGM and AK enzymes were found to be polymorphic in the Turkish population. The results of the statistical analysis showed, that the phenotype frequencies of the five enzyme under study are in Hardy-Weinberg equilibrium. Statistical analysis was performed in order to examine whether there are significant differences in the phenotype frequencies between the Turkish population and four American population groups. This analysis showed, that there are some statistically significant differences between the Turkish and the other groups. Moreover, the observed phenotype and allele frequencies were compared with those obtained in other population groups of Turkey.
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Ji, Sen-Lin; Liu, Rui; Ren, Meng-Fei; Li, Huan-Jun; Xu, Jun-Wei
2015-01-01
This study aimed to improve polysaccharide production by engineering the biosynthetic pathway in Ganoderma lucidum through the overexpression of the homologous UDP glucose pyrophosphorylase (UGP) gene. The effects of UGP gene overexpression on intracellular polysaccharide (IPS) content, extracellular polysaccharide (EPS) production, and transcription levels of 3 genes encoding the enzymes involved in polysaccharide biosynthesis, including phosphoglucomutase (PGM), UGP, and α-1,3-glucan synthase (GLS), were investigated. The maximum IPS content and EPS production in G. lucidum overexpressing the UGP gene were 24.32 mg/100 mg dry weight and 1.66 g/L, respectively, which were higher by 42% and 36% than those of the wild-type strain. The transcription levels of PGM, UGP, and GLS were up-regulated by 1.6, 2.6, and 2.4-fold, respectively, in the engineered strain, suggesting that increased polysaccharide biosynthesis may result from a higher expression of those genes.
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Jongsma, A P; Burgerhout, W G
1977-01-01
Regional localization studies of genes coding for human PGD, PPH1, PGM1, UGPP, GuK1, Pep-C, and FH, which have been assigned to chromosome 1, were performed with man-Chinese hamster somatic cell hybrids, Informative hybrids that retained fragments of the human chromosome 1 were produced by fusion of hamster cells with human cells carrying reciprocal translocations involving chromosome 1. Analysis of the hybrids that retained one of the translocation chromosomes or de novo rearrangements involving the human 1 revealed the following gene positions: PGD and PPH1 in 1pter leads to 1p32, PGM1 in 1p32 leads to 1p22, UGPP and GuK1 in 1q21 leads to 1q42, FH in 1qter leads to 1q42, and Pep-C probably in 1q42.
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Bubbling and foaming assisted clearing of mucin plugs in microfluidic Y-junctions.
Abdula, Daner; Lerud, Ryan; Rananavare, Shankar
2017-11-07
Microfluidic Y-junctions were used to study mechanical mechanisms involved in pig gastric mucin (PGM) plug removal from within one of two bifurcation branches with 2-phase air and liquid flow. Water control experiments showed moderate plug removal due to shear from vortex formation in the blockage branch and suggest a PGM yield stress of 35Pa, as determined by computational fluid dynamics. Addition of hexadecyltrimethylammonium bromide (CTAB) surfactant improved clearing effectiveness due to bubbling in 1mm diameter channels and foaming in 500μm diameter channels. Plug removal mechanisms have been identified as vortex shear, bubble scouring, and then foam scouring as air flow rate is increased with constant liquid flow. The onset of bubbling and foaming is attributed to a flow regime transition from slug to slug-annular. Flow rates explored for 1mm channels are typically experienced by bronchioles in generations 8 and 9 of lungs. Results have implications on treatment of cystic fibrosis and other lung diseases. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Enhanced Performance of non-PGM Catalysts in Air Operated PEM-Fuel Cells
Barkholtz, Heather M.; Chong, Lina; Kaiser, Zachary Brian; ...
2016-10-13
Here a non-platinum group metal (non-PGM) oxygen reduction catalyst was prepared from “support-free” zeolitic imidazolate framework (ZIF) precursor and tested in the proton exchange membrane fuel cell with air as the cathode feed. The iron nitrogen and carbon composite (FeeNeC) based catalyst has high specific surface area decorated uniformly with active sites, which redefines the triple phase boundary (TPB) and requires re-optimization of the cathodic membrane electrode fabrication to ensure efficient mass and charge transports to the catalyst surface. This study reports an effort in optimizing catalytic ink formulation for the membrane electrode preparation and its impact to the fuelmore » cell performance under air. Through optimization, the fuel cell areal current density as high as 115.2 mA/cm 2 at 0.8 V or 147.6 mA/cm 2 at 0.8 V iR-free has been achieved under one bar air. We also investigated impacts on fuel cell internal impedance and the water formation.« less
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Design of a multilayer-based collimated plane-grating monochromator for tender X-ray range.
Yang, Xiaowei; Wang, Hongchang; Hand, Matthew; Sawhney, Kawal; Kaulich, Burkhard; Kozhevnikov, Igor V; Huang, Qiushi; Wang, Zhanshan
2017-01-01
Collimated plane-grating monochromators (cPGMs), consisting of a plane mirror and plane diffraction grating, are essential optics in synchrotron radiation sources for their remarkable flexibility and good optical characteristics in the soft X-ray region. However, the poor energy transport efficiency of a conventional cPGM (single-layer-coated) degrades the source intensity and leaves reduced flux at the sample, especially for the tender X-ray range (1-4 keV) that covers a large number of K- and L-edges of medium-Z elements, and M-edges of high-Z elements. To overcome this limitation, the use of a multilayer-based cPGM is proposed, combining a multilayer-coated plane mirror with blazed multilayer gratings. With this combination, the effective efficiency of cPGMs can be increased by an order of magnitude compared with the conventional single-layer cPGMs. In addition, higher resolving power can be achieved with improved efficiency by increasing the blaze angle and working at higher diffraction order.
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Design of a multilayer-based collimated plane-grating monochromator for tender X-ray range
Yang, Xiaowei; Wang, Hongchang; Hand, Matthew; Sawhney, Kawal; Kaulich, Burkhard; Kozhevnikov, Igor V.; Huang, Qiushi; Wang, Zhanshan
2017-01-01
Collimated plane-grating monochromators (cPGMs), consisting of a plane mirror and plane diffraction grating, are essential optics in synchrotron radiation sources for their remarkable flexibility and good optical characteristics in the soft X-ray region. However, the poor energy transport efficiency of a conventional cPGM (single-layer-coated) degrades the source intensity and leaves reduced flux at the sample, especially for the tender X-ray range (1–4 keV) that covers a large number of K- and L-edges of medium-Z elements, and M-edges of high-Z elements. To overcome this limitation, the use of a multilayer-based cPGM is proposed, combining a multilayer-coated plane mirror with blazed multilayer gratings. With this combination, the effective efficiency of cPGMs can be increased by an order of magnitude compared with the conventional single-layer cPGMs. In addition, higher resolving power can be achieved with improved efficiency by increasing the blaze angle and working at higher diffraction order. PMID:28009556
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Xu, Xue-tao; Liang, Kai-yi; Zeng, Jia-ying
2015-02-15
A portable and sensitive quantitative DNA detection method based on personal glucose meters and isothermal circular strand-displacement polymerization reaction was developed. The target DNA triggered target recycling process, which opened capture DNA. The released target then found another capture DNA to trigger another polymerization cycle, which was repeated for many rounds, resulting in the multiplication of the DNA-invertase conjugation on the surface of Streptavidin-MNBs. The DNA-invertase was used to catalyze the hydrolysis of sucrose into glucose for PGM readout. There was a liner relationship between the signal of PGM and the concentration of target DNA in the range of 5.0 to 1000 fM, which is lower than some DNA detection method. In addition, the method exhibited excellent sequence selectivity and there was almost no effect of biological complex to the detection performance, which suggested our method can be successfully applied to DNA detection in real biological samples. Copyright © 2014 Elsevier B.V. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Visweswara Sathanur, Arun; Choudhury, Sutanay; Joslyn, Cliff A.
Property graphs can be used to represent heterogeneous networks with attributed vertices and edges. Given one property graph, simulating another graph with same or greater size with identical statistical properties with respect to the attributes and connectivity is critical for privacy preservation and benchmarking purposes. In this work we tackle the problem of capturing the statistical dependence of the edge connectivity on the vertex labels and using the same distribution to regenerate property graphs of the same or expanded size in a scalable manner. However, accurate simulation becomes a challenge when the attributes do not completely explain the network structure.more » We propose the Property Graph Model (PGM) approach that uses an attribute (or label) augmentation strategy to mitigate the problem and preserve the graph connectivity as measured via degree distribution, vertex label distributions and edge connectivity. Our proposed algorithm is scalable with a linear complexity in the number of edges in the target graph. We illustrate the efficacy of the PGM approach in regenerating and expanding the datasets by leveraging two distinct illustrations.« less
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Wang, Dong; Wang, Jian; Chen, Guojun
2013-12-01
To investigate the association of serum levels of decoy receptor 3(DcR3) protein and the clinicopathologic features of bladder transitional cell carcinoma. Enzyme-linked immunosorbent assay was used to examine the serum levels of DcR3 in patients with bladder transitional cell carcinoma for analysis of its association with the patients' age, gender, clinical stages and pathological classification. The patients with bladder transitional cell carcinoma showed a significantly elevated serum level of DcR3 (183.43 ∓78.45 pg/m1) compared with the normal level (116.65∓97.43 pg/m1, P<0.05). The serum level of DcR3 in the patients showed close correlations with the TNM stage and pathological classification of the tumor (P<0.05) but not with the patients' age or gender (P>0.05). In patients with bladder transitional cell carcinoma, a high serum level of DcR3 suggests a higher malignancy of the tumor.
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Bargar, K.E.; Fournier, R.O.
1988-01-01
Heating and freezing data were obtained for liquid-rich secondary fluid inclusions in magmatic quartz, hydrothermal calcite and hydrothermal quartz crystals from 19 sampled depths in eight production drill holes (PGM-1, 2, 3, 5, 10, 11, 12 and 15) of the Miravalles geothermal field in northwestern Costa Rica. Homogenization temperatures for 386 fluid inclusions range from near the present measured temperatures to as much as 70??C higher than the maximum measured well temperature of about 240??C. Melting-point temperature measurements for 76 fluid inclusions suggest a calculated salinity range of about 0.2-1.9 wt% NaCl equivalent. Calculated salinities as high as 3.1-4.0 wt% NaCl equivalent for 20 fluid inclusions from the lower part of drill hole PGM-15 (the deepest drill hole) indicate that higher salinity water probably was present in the deeper part of the Miravalles geothermal field at the time these fluid inclusions were formed. ?? 1988.
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Fish assemblages in the Oregon-Washington coast range consist primarily of coldwater taxa of salmonids, cottids, dace, and Pacific giant salamander. This region has a dynamic natural disturbance regime, where mass failures, debris torrents, fire, and tree-fall are driven by clim...
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Mapping the kinematics of the Blaubach landslide (Austria) using digital photogrammetry
NASA Astrophysics Data System (ADS)
Kaufmann, V.; Lieb, G. K.
2003-04-01
The Blaubach landslide (12°08'E, 47°12'N, northern margin of the Hohe Tauern range, Austria) is located in the upper part of the catchment area of the Blaubach torrent. The latter follows an important Eastern Alpine fault. The area of interest is built of tectonically fractured rock favoring fluvial erosion, debris flows, and other types of mass movements triggered by widespread deep reaching gravitational slope deformations. The Blaubach landslide is characterized by high surface movement and a front with several secondary slides, which are free of vegetation and provide high quantities of material to the torrent below. This natural hazard has induced the construction of protective measures such as retaining walls in the torrent bed since 1950. However, as of yet no numerical data have been available concerning the surface kinematics of the landslide, such as flow/creep velocity, surface height change, or volumetric change. The Austrian Forest Engineering Service of Torrent and Avalanche Control therefore launched a project related to these questions. One task was to reconstruct the morphodynamics of the landslide area using historical multi-temporal aerial photographs. Aerial photographs at various image scales between 1:9,300 and 1:45,800 of 11 different data acquisition periods between 1953 and 1999 were acquired from the Austrian Federal Office of Surveying and Mapping. The photographs were scanned using the UltraScan 5000 of Vexcel Imaging Austria in order to facilitate digital photogrammetry. A special software package ADVM (Automatic Displacement Vector Measurement), originally developed at the Institute of Geodesy for monitoring debris-covered glaciers and rock glaciers, was used to automatically derive three-dimensional displacement vectors, both area-wide and dense, based on advanced image matching techniques. The digital photogrammetric method applied is based on quasi-orthophotos. This approach supports the fusion of multi-temporal aerial photographs irrespective of the geometrical differences in scale and orientation of the photographs. As a result, high-resolution digital terrain models were obtained for all periods, thus facilitating the computation of the changes in surface height and volume of the landslide in the course of the past 46 years. Maximum changes in surface height due to surface deformation were measured at +10.0 m and -15.0 m. A mean annual sediment load of 12,000 m3/year was estimated as an input to the Blaubach torrent for the 1990s. An average of 39,900 three-dimensional displacement vectors were obtained for all time periods calculated. Numerical and graphical representations of the results obtained show that the landslide was active throughout the observed time span, with maximum creep velocities of up to 1.6-1.8 m/year for the time period 1953-1962. For 1991-1999 a maximum creep velocity of 1.3 m/year was measured. In conclusion, slope deformation and creep velocity of the Blaubach landslide could be measured successfully with high spatial and temporal resolution using digital photogrammetric methods applied to time-series of aerial photographs from a public archive. However, the digital method proposed only works satisfactorily if the available photographs are of good quality and have distinct photo textures and if the landscape observed does not change too much in its surface representation during observation periods.
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Cuervo, Adriana; Hevia, Arancha; López, Patricia; Suárez, Ana; Diaz, Carmen; Sánchez, Borja; Margolles, Abelardo; González, Sonia
2016-01-01
The dietary modulation of gut microbiota, suggested to be involved in allergy processes, has recently attracted much interest. While several studies have addressed the use of fibres to modify intestinal microbial populations, information about other components, such as phenolic compounds, is scarce. The aim of this work was to identify the dietary components able to influence the microbiota in 23 subjects suffering from rhinitis and allergic asthma, and 22 age- and sex-matched controls. The food intake was recorded by means of an annual food frequency questionnaire. Dietary fibre tables were obtained from Marlett et al., and the Phenol-Explorer database was used to assess the phenolic compound intake. The quantification of microbial groups was performed using an Ion Torrent 16S rRNA gene-based analysis. The results showed a direct association between the intake of red wine, a source of stilbenes, and the relative abundance of Bacteroides, and between the intake of coffee, rich in phenolic acids, and the abundance of Clostridium, Lactococcus and Lactobacillus genera. Despite epidemiological analyses not establishing causality, these results support the association between polyphenol-rich beverages and faecal microbiota in allergic patients.
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Pratas, Diogo; Pinho, Armando J; Rodrigues, João M O S
2014-01-16
The emerging next-generation sequencing (NGS) is bringing, besides the natural huge amounts of data, an avalanche of new specialized tools (for analysis, compression, alignment, among others) and large public and private network infrastructures. Therefore, a direct necessity of specific simulation tools for testing and benchmarking is rising, such as a flexible and portable FASTQ read simulator, without the need of a reference sequence, yet correctly prepared for producing approximately the same characteristics as real data. We present XS, a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores). XS provides an efficient and convenient method for fast simulation of FASTQ files, such as those from Ion Torrent (currently uncovered by other simulators), Roche-454, Illumina and ABI-SOLiD sequencing machines. This tool is publicly available at http://bioinformatics.ua.pt/software/xs/.
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Anslan, Sten; Bahram, Mohammad; Hiiesalu, Indrek; Tedersoo, Leho
2017-11-01
High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable. © 2017 John Wiley & Sons Ltd.
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probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016
Greuter, Daniel; Loy, Alexander; Horn, Matthias; Rattei, Thomas
2016-01-01
probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase. PMID:26586809
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ERIC Educational Resources Information Center
Matthews, Frank J.; Matthews, Joan Morgan
2008-01-01
This article features the University of Maryland Eastern Shore (UMES), which becomes the first historically Black university (HBCU) to receive a PGA Professional Golf Management Program. The PGA/PGM[TM] University Program is a four-and-a-half-year structured college curriculum for aspiring PGA professionals. The educational program is accredited…
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Tu, Haijian; Lin, Kun; Lun, Yongzhi; Yu, Liuming
2018-06-01
A digital detection strategy based on a portable personal glucometer (PGM) was developed for the simple, rapid, and sensitive detection of hepatitis C virus (HCV) RNA, involving the release of glucose-loaded nanoliposomes due to coupling-site-specific cleavage by the endonuclease BamHI. The glucose-loaded nanoliposomes were synthesized using a reversed-phase evaporation method and provided an amplified signal at the PGM in the presence of HCV RNA. Initially, a 21-mer oligonucleotide complementary to HCV RNA was covalently conjugated to a magnetic bead through the amino group at the 5' end of the oligonucleotide, and then bound to a glucose-loaded liposome by typical carbodiimide coupling at its 3' end. In the presence of the target HCV RNA, the target hybridized with the oligonucleotide to form double-stranded DNA. The symmetrical duplex sequence 5'-GGATCC-3' between guanines was then catalytically cleaved by BamHI, which detached the glucose-loaded liposome from the magnetic bead. Following magnetic separation of the bead, the detached glucose-loaded liposome was lysed using Triton X-100 to release the glucose molecules within it, which were then detected as an amplified signal at the digital PGM. Under optimal conditions, the PGM signal increased with increasing HCV RNA, and displayed a strongly linear dependence on the level of HCV RNA for concentrations ranging from 10 pM to 1.0 μM. The detection limit (LOD) of the system was 1.9 pM. Good reproducibility and favorable specificity were achieved in the analysis of the target HCV RNA. Human serum samples containing HCV RNA were analyzed using this strategy, and the developed sensing platform was observed to yield satisfactory results based on a comparison with the corresponding results from a Cobas ® Amplicor HCV Test Analyzer. Graphical abstract A digital detection strategy utilizing a personal glucometer was developed for the detection of hepatitis C virus RNA. The strategy involved the use of the endonuclease BamHI along with a 21-mer oligonucleotide conjugated to both a magnetic bead and a glucose-loaded nanoliposome. Hybridization of the nucleotide with the target RNA triggered the coupling-site-specific cleavage of the duplex by BamHI, leading to the release of the glucose-loaded nanoliposome. Following separation of the magnetic bead, the free nanoliposome was dissolved, liberating the glucose molecules within it, which in turn were detected as an amplified signal by the glucometer.
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Juras, Anna; Chyleński, Maciej; Krenz-Niedbała, Marta; Malmström, Helena; Ehler, Edvard; Pospieszny, Łukasz; Łukasik, Sylwia; Bednarczyk, Józef; Piontek, Janusz; Jakobsson, Mattias; Dabert, Miroslawa
2017-01-01
We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq™ Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS 14 C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq™ Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct maternal relationship in ancient individuals. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
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Veldore, Vidya H; Patil, S; Satheesh, C T; Shashidhara, H P; Tejaswi, R; Prabhudesai, Shilpa A; Krishnamoorthy, N; Hazarika, D; Naik, R; Rao, Raghavendra M; Ajai Kumar, B S
2015-01-01
Patients' who are positive for kinase domain activating mutations in epidermal growth factor receptor (EGFR) gene, constitute 30-40% of non-small cell lung cancer (NSCLC), and are suitable candidates for Tyrosine Kinase Inhibitor based targeted/personalized therapy. In EGFR non-mutated subset, 8-10% that show molecular abnormalities such as EML4-ALK, ROS1-ALK, KIP4-ALK, may also derive the benefit of targeted therapy. However, 40% of NSCLC belong to a grey zone of tumours that are negative for the clinically approved biomarkers for personalized therapy. This pilot study aims to identify and classify molecular subtypes of this group to address the un-met need for new drug targets in this category. Here we screened for known/novel oncogenic driver mutations using a 46 gene Ampliseq Panel V1.0 that includes Ser/Thr/Tyr kinases, transcription factors and tumor suppressors. NSCLC with tumor burden of at least 40% on histopathology were screened for 29 somatic mutations in the EGFR kinase domain by real-time polymerase chain reaction methods. 20 cases which were EGFR non-mutated for TK domain mutations were included in this study. DNA Quality was verified from each of the 20 cases by fluorimeter, pooled and subjected to targeted re-sequencing in the Ion Torrent platform. Torrent Suite software was used for next generation sequencing raw data processing and variant calling. The clinical relevance and pathological role of all the mutations/variants that include SNPs and Indels was assessed using polyphen-2/SIFT/PROVEAN/mutation assessor structure function prediction programs. There were 10 pathogenic mutations in six different oncogenes for which annotation was available in the COSMIC database; C420R mutation in PIK3CA, Q472H mutation in vascular endothelial growth factor receptor 2 (VEGFR2) (KDR), C630W and C634R in RET, K367M mutation in fibroblast growth factor receptor 2 (FGFR2), G12C in KRAS and 4 pathogenic mutations in TP53 in the DNA binding domain (E285K, R213L, R175H, V173G). Results suggest, a potential role for PIK3CA, VEGFR2, RET and FGFR2 as therapeutic targets in EGFR non-mutated NSCLC that requires further clinical validation.
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NASA Astrophysics Data System (ADS)
Luguet, Ambre; Behrens, Melanie; Pearson, D. Graham; König, Stephan; Herwartz, Daniel
2015-09-01
The Re-Os isotopic system is the geochronometer of choice to constrain the timing of lithospheric mantle root formation and reconstruct the evolution of Earth's dynamics from the "mantle" perspective. In order to constrain the effects of metasomatic processes on the Re-Os isotopic system, eleven peridotites from the Letlhakane kimberlite pipe were investigated for whole rock major and trace elements, highly siderophile elements (HSE), Se, Te and 187Os/188Os signatures. These spinel peridotites (SP), garnet peridotites (GP), garnet-phlogopite peridotites (GPP) and phlogopite peridotites (PP) experienced cryptic metasomatism and the GP-GPP-PP additionally constitute a sequence of increasing modal metasomatism. The cryptically metasomatised SP appear devoid of base metal sulphides (BMS) and show suprachondritic Se/Te ratios (15-40) and extremely Pd- and Pt-depleted HSE patterns. These features are characteristic of high-degree partial melting residues. Their 187Os/188Os signatures are thus considered to be inherited from the partial melting event. This implies a Neoarchean (2.5-2.8 Ga, TRD eruption) stabilisation of the Letlhakane mantle root and supports the Letlhakane mantle root being a westerly extension of the Zimbabwe cratonic root. The modally metasomatised peridotites contain BMS whose abundance significantly increases from the GPP to the GP and PP. The BMS-poor GPP are only slightly richer in Pt and Pd than the BMS-free SP but have similarly high Se/Te ratios. The BMS-rich GP and PP exhibit significant enrichments in Pt, Pd, Se, Te resulting in HSE-Se-Te signatures similar to that of the Primitive Upper Mantle (PUM). Addition of 0.001-0.05 wt.% metasomatic BMS ± PGM (platinum group minerals, i.e., Pt-tellurides) to highly refractory residues, such as the Letlhakane SP, reproduce well the HSE-Se-Te systematics observed in the BMS-poor and BMS-rich modally metasomatised peridotites. In the GPP, the negligible addition of metasomatic BMS ± PGM did not disturb the 187Os/188Os signatures, indicating TRD eruption ages identical with those of the SP. By contrast, the PP and GP, which suffered significant BMS ± PGM addition, have 187Os/188Os considerably shifted toward more radiogenic values. As a result, unrealistically young TRD eruption ages are obtained that cannot be used to constrain the time frame of the stabilisation of the cratonic roots and the mechanisms of craton formation. The Se-Te and incompatible HSE (i.e., Pt, Pd) are powerful geochemical tools to assess the robustness of the Re-Os isotopic system in mantle peridotites. Specifically, Se/Te and Pd/Ir ratios provide complementary insights into the complex metasomatic history of mantle peridotites. The Se/Te ratio is very sensitive to Os-free PGM metasomatism producing highly variable Se/Te >15 at low, relatively constant Pd/Ir< 0.4 but does not affect the 187Os/188Os systematics. This contrasts with BMS metasomatism, where Pd/Ir becomes more variable (>0.4), at constant but low Se/Te <10 and which is accompanied by modification of the Os isotopic composition of the host peridotite. As they are sensitive indicators of BMS ± PGM metasomatism, HSE, Se and Te should be systematically considered when investigating the timing of stabilisation of lithospheric mantle and its petrogenetic history. This would allow a more robust assessment of the Re-Os ages obtained and provide firmer constraints on the evolution and formation of Archean cratons and early Earth dynamics.
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Dialects, Gender, and the Writing Class
ERIC Educational Resources Information Center
Shafer, Greg
2007-01-01
On the first day of English composition, students unleash a torrent of reasons why writing scared them as they write their opening day personal autobiographies. Most comments focus on reasons that have little to do with the craft or complexities of great writing. Numerous students bemoan their use of "substandard" English, thinking that their ways…
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Scholars, Scholarship, and the Scholarly Enterprise in the Digital Age
ERIC Educational Resources Information Center
Katz, Richard N.
2010-01-01
Information technologies have empowered the individual and are unleashing a torrent of change, one that will reshape nearly all of institutions. To secure the place of the traditional scholarly enterprise, the author argues that leaders must rethink a number of the fundamentals behind the higher education institution. He discusses the impact of…
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A Survey of Meaning Discrimination in Selected English/Spanish Dictionaries.
ERIC Educational Resources Information Center
Powers, Michael D.
1985-01-01
Examines the treatment of sense discrimination in eight Spanish/English English/Spanish bilingual dictionaries and one specialized dictionary. Does this by analyzing 30 words that Torrents des Prats determined have at least nine different sense discriminations from English into Spanish. Larousse was found to be far superior to the others. (SED)
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What Do We Know about Civic Engagement?
ERIC Educational Resources Information Center
Levine, Peter
2011-01-01
A decade ago, research on the civic engagement and learning of young people was still in a "bear market" (Cook 1985). The body of literature was strikingly small, considering that the future of democracy depends on the preparation of young citizens. Today, the situation is dramatically different. There is a torrent of research on youth civic…
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ERIC Educational Resources Information Center
Garofalo, Denise A.
2012-01-01
Branding and the idea that ebooks are still essentially books are important concepts to keep in mind, especially when confronted with all there is to oversee and consider in the arena of electronic resources; it is easy to feel overwhelmed by the torrent of change and the intricacies of the business. The author states that electronic resources…
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On the Web, a Textbook Proliferation of Piracy
ERIC Educational Resources Information Center
Young, Jeffrey R.
2008-01-01
Book publishers are stepping up efforts to stop college students from downloading illegal copies of textbooks online. One Web site, Textbook Torrents, promises more than 5,000 textbooks for download in PDF format, complete with the original books' layouts and full-color illustrations. Users must simply set up a free account and download a free…
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Adventures from Justin's Life: Engaging Your Physics Students
ERIC Educational Resources Information Center
Ridgley, James A., Jr.; Herron, Sherry S.
2018-01-01
Many teachers have had students ask the proverbial question, "When will I ever use this in my life?" In the sciences, especially physics, teachers seem to battle this torrent of indifference continually. Although many areas of our students' lives can distract them from their academic pursuits, we as teachers must be introspective in…
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Physical consequences of large organic debris in Pacific Northwest streams.
Frederick J. Swanson; George W. Lienkaemper
1978-01-01
Large organic debris in streams controls the distribution of aquatic habitats, the routing of sediment through stream systems, and the stability of streambed and banks. Management activities directly alter debris loading by addition or removal of material and indirectly by increasing the probability of debris torrents and removing standing streamside trees. We propose...
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The shots heard 'round the world.
Marshall, E
2000-07-28
The massacre at Columbine High School last year unleashed a torrent of fresh concern over the threat that violence poses to society. It also energized a government research effort to understand and prevent violence. Ironically, this flurry of activity comes at a time when youth violence, as reflected in crime statistics, is in decline.
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Optimizing Data Management in Grid Environments
NASA Astrophysics Data System (ADS)
Zissimos, Antonis; Doka, Katerina; Chazapis, Antony; Tsoumakos, Dimitrios; Koziris, Nectarios
Grids currently serve as platforms for numerous scientific as well as business applications that generate and access vast amounts of data. In this paper, we address the need for efficient, scalable and robust data management in Grid environments. We propose a fully decentralized and adaptive mechanism comprising of two components: A Distributed Replica Location Service (DRLS) and a data transfer mechanism called GridTorrent. They both adopt Peer-to-Peer techniques in order to overcome performance bottlenecks and single points of failure. On one hand, DRLS ensures resilience by relying on a Byzantine-tolerant protocol and is able to handle massive concurrent requests even during node churn. On the other hand, GridTorrent allows for maximum bandwidth utilization through collaborative sharing among the various data providers and consumers. The proposed integrated architecture is completely backwards-compatible with already deployed Grids. To demonstrate these points, experiments have been conducted in LAN as well as WAN environments under various workloads. The evaluation shows that our scheme vastly outperforms the conventional mechanisms in both efficiency (up to 10 times faster) and robustness in case of failures and flash crowd instances.
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Sediment trapping efficiency of adjustable check dam in laboratory and field experiment
NASA Astrophysics Data System (ADS)
Wang, Chiang; Chen, Su-Chin; Lu, Sheng-Jui
2014-05-01
Check dam has been constructed at mountain area to block debris flow, but has been filled after several events and lose its function of trapping. For the reason, the main facilities of our research is the adjustable steel slit check dam, which with the advantages of fast building, easy to remove or adjust it function. When we can remove transverse beams to drain sediments off and keep the channel continuity. We constructed adjustable steel slit check dam on the Landow torrent, Huisun Experiment Forest station as the prototype to compare with model in laboratory. In laboratory experiments, the Froude number similarity was used to design the dam model. The main comparisons focused on types of sediment trapping and removing, sediment discharge, and trapping rate of slit check dam. In different types of removing transverse beam showed different kind of sediment removal and differences on rate of sediment removing, removing rate, and particle size distribution. The sediment discharge in check dam with beams is about 40%~80% of check dam without beams. Furthermore, the spacing of beams is considerable factor to the sediment discharge. In field experiment, this research uses time-lapse photography to record the adjustable steel slit check dam on the Landow torrent. The typhoon Soulik made rainfall amounts of 600 mm in eight hours and induced debris flow in Landow torrent. Image data of time-lapse photography demonstrated that after several sediment transport event the adjustable steel slit check dam was buried by debris flow. The result of lab and field experiments: (1)Adjustable check dam could trap boulders and stop woody debris flow and flush out fine sediment to supply the need of downstream river. (2)The efficiency of sediment trapping in adjustable check dam with transverse beams was significantly improved. (3)The check dam without transverse beams can remove the sediment and keep the ecosystem continuity.
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NASA Astrophysics Data System (ADS)
Valls, Ana; Garcia, Francisco; Ramirez, Manuel; Benlloch, Javier
2015-04-01
Ground penetrating radar is usually employed for non-destructive detection of cavities in karst areas and road maintenance. This paper describes the inspection for cavity detection in a street located in Torrente (Valencia, Spain) where a new sewerage project was planned. Torrente population growth (more than 80,000 inhabitants last year) has caused urban development southwards from its downtown. According to municipality geologic configuration, new urbanized areas are located in mountains composed of limestone with presence of karst systems. During excavation work for a sewerage system installation, a 4 x 2 x 1.5 m shallow cave was found in one planned street. For this reason, digging activities were stopped and a GPR survey was carried out on the street. A 1x1 m grid was collected using a GSSI SIR-3000 equipment. A 400 MHz frequency antenna was used for reaching 2.5 m approx. depth, attending the characteristics of the discovered cave and the excavation project depth. GPR records were calibrated in situ, thanks to the unearthed cavity. The 3D GPR-data interpretation mapped several caves only on one side of the street. The detected cavities coincided with the sewerage system layout. These underground spaces were isolated from each other, as small individual karst caves. The outcomes of this study allowed the modification of the sewerage project. Therefore, the sewerage system layout was moved to the other side of the street where no cavities were detected with the GPR survey. GPR is proved to be an efficient tool to be taken into consideration by civil engineers and architects for designing new infrastructures (e.g. sewerage systems) in urban planning areas. We conclude GPR helps minimising cost, time and inconveniences to neighbourhood during excavation works, especially in cities.
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U. S. Naval Forces Vietnam Monthly Historical Summary for July 1966
1966-09-06
to come out lor inspection they frequently evaded ssarch by running in to the beech where the occupants fled to nearby protective rocks or trees ...results during July. On 21 July, PGM 601 engineering personnel worked throughout the night to replace a main engine camshaft . Timely completion of the
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Personal glucose meters for detection and quantification of a broad range of analytes
Lu, Yi; Xiang, Yu
2015-02-03
A general methodology for the development of highly sensitive and selective sensors that can achieve portable, low-cost and quantitative detection of a broad range of targets using only a personal glucose meter (PGM) is disclosed. The method uses recognition molecules that are specific for a target agent, enzymes that can convert an enzyme substrate into glucose, and PGM. Also provided are sensors, which can include a solid support to which is attached a recognition molecule that permits detection of a target agent, wherein the recognition molecule specifically binds to the target agent in the presence of the target agent but not significantly to other agents as well as an enzyme that can catalyze the conversion of a substance into glucose, wherein the enzyme is attached directly or indirectly to the recognition molecule, and wherein in the presence of the target agent the enzyme can convert the substance into glucose. The disclosed sensors can be part of a lateral flow device. Methods of using such sensors for detecting target agents are also provided.
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Neira, Carmen; Laca, Amanda; Laca, Adriana; Díaz, Mario
2017-12-04
A novel DNA-based technique (PGM) has been employed for first time to analyse commercial eggs with the advantage of allowing an exhaustive identification of the microbiota present. Eggs from two different production systems, i.e. a free range system and a cage system, were analysed. Twenty-one and twenty-two phyla were identified on the surface of cage system and free range system eggs, respectively. In both cases, Firmicutes was the dominant phylum (representing around 50% of total phyla), being found families frequently reported to be present in the intestinal microbiota of chickens or hens, such as Clostridiaceae, Ruminococcaceae and Lachnospiraceae. Additionally, other phyla and families not previously described in association with eggshells could also be identified in this work. Most of the potential pathogenic genera associated with eggs (Salmonella, Clostridium, Helicobacter, Pseudomonas and Staphylococcus) showed higher incidence in eggs coming from cage systems than in eggs coming from free range systems, although the abundance of these genera were very low in both cases (<5% of total bacteria). Copyright © 2017 Elsevier B.V. All rights reserved.
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Direct atomic-level insight into the active sites of a high-performance PGM-free ORR catalyst
NASA Astrophysics Data System (ADS)
Chung, Hoon T.; Cullen, David A.; Higgins, Drew; Sneed, Brian T.; Holby, Edward F.; More, Karren L.; Zelenay, Piotr
2017-08-01
Platinum group metal-free (PGM-free) metal-nitrogen-carbon catalysts have emerged as a promising alternative to their costly platinum (Pt)-based counterparts in polymer electrolyte fuel cells (PEFCs) but still face some major challenges, including (i) the identification of the most relevant catalytic site for the oxygen reduction reaction (ORR) and (ii) demonstration of competitive PEFC performance under automotive-application conditions in the hydrogen (H2)-air fuel cell. Herein, we demonstrate H2-air performance gains achieved with an iron-nitrogen-carbon catalyst synthesized with two nitrogen precursors that developed hierarchical porosity. Current densities recorded in the kinetic region of cathode operation, at fuel cell voltages greater than ~0.75 V, were the same as those obtained with a Pt cathode at a loading of 0.1 milligram of Pt per centimeter squared. The proposed catalytic active site, carbon-embedded nitrogen-coordinated iron (FeN4), was directly visualized with aberration-corrected scanning transmission electron microscopy, and the contributions of these active sites associated with specific lattice-level carbon structures were explored computationally.
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Five-year trends of selected halogenated flame retardants in the atmosphere of Northeast China.
Li, Wen-Long; Liu, Li-Yan; Song, Wei-Wei; Zhang, Zi-Feng; Qiao, Li-Na; Ma, Wan-Li; Li, Yi-Fan
2016-01-01
This study collected 227 pairs of gas phase and particle phase air samples in a typical urban city of Northeast China from 2008 to 2013. Four alternative halogenated flame retardants for polybrominated diphenyl ethers (PBDEs) were analyzed, namely 2-ethylhexyl 2,3,4,5-tetrabromobenzoate (EHTBB), bis (2-ethylhexyl) tetrabromophthalate (BEHTBP), syn-dechlorane plus (syn-DP) and anti-dechlorane plus (anti-DP). The average concentrations for EHTBB and BEHTBP were 5.2 ± 20 and 30 ± 200 pg/m3, respectively, while for syn-DP and anti-DPwere 1.9±5.1 and 5.8±18 pg/m3, respectively. Generally, they were frequently detected in the particle phase, and the gas/particle partitioning suggested they were the maximum partition chemicals. The fractional abundance of EHTBB (fEHTBB) and syn-DP (fsyn)were comparablewith those in other studies. Strong local sources were identified based on the air parcel backward trajectories and the potential source contribution function. The concentrations of these chemicals were significantly increased during this sampling campaign, possibly suggesting their increasing usages from 2008 to 2013 in China.
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Jha, Neetu; Ramesh, Palanisamy; Bekyarova, Elena; Tian, Xiaojuan; Wang, Feihu; Itkis, Mikhail E.; Haddon, Robert C.
2013-01-01
Chemically modified single-walled carbon nanotubes (SWNTs) with varying degrees of functionalization were utilized for the fabrication of SWNT thin film catalyst support layers (CSLs) in polymer electrolyte membrane fuel cells (PEMFCs), which were suitable for benchmarking against the US DOE 2017 targets. Use of the optimum level of SWNT -COOH functionality allowed the construction of a prototype SWNT-based PEMFC with total Pt loading of 0.06 mgPt/cm2 - well below the value of 0.125 mgPt/cm2 set as the US DOE 2017 technical target for total Pt group metals (PGM) loading. This prototype PEMFC also approaches the technical target for the total Pt content per kW of power (<0.125 gPGM/kW) at cell potential 0.65 V: a value of 0.15 gPt/kW was achieved at 80°C/22 psig testing conditions, which was further reduced to 0.12 gPt/kW at 35 psig back pressure. PMID:23877112
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Jha, Neetu; Ramesh, Palanisamy; Bekyarova, Elena; Tian, Xiaojuan; Wang, Feihu; Itkis, Mikhail E; Haddon, Robert C
2013-01-01
Chemically modified single-walled carbon nanotubes (SWNTs) with varying degrees of functionalization were utilized for the fabrication of SWNT thin film catalyst support layers (CSLs) in polymer electrolyte membrane fuel cells (PEMFCs), which were suitable for benchmarking against the US DOE 2017 targets. Use of the optimum level of SWNT -COOH functionality allowed the construction of a prototype SWNT-based PEMFC with total Pt loading of 0.06 mg(Pt)/cm²--well below the value of 0.125 mg(Pt)/cm² set as the US DOE 2017 technical target for total Pt group metals (PGM) loading. This prototype PEMFC also approaches the technical target for the total Pt content per kW of power (<0.125 g(PGM)/kW) at cell potential 0.65 V: a value of 0.15 g(Pt)/kW was achieved at 80°C/22 psig testing conditions, which was further reduced to 0.12 g(Pt)/kW at 35 psig back pressure.
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HLA antigens and other genetic markers in the Mapuche Indians of Argentina.
Haas, E J; Salzano, F M; Araujo, H A; Grossman, F; Barbetti, A; Weimer, T A; Franco, M H; Verruno, L; Nasif, O; Morales, V H
1985-01-01
A total of 107 Mapuche Indians living in western Argentina were studied with respect to 16 genetic systems. For HLA, there were a few differences in relation to previous studies; and considering the averages observed in 15 other South American tribes, Mapuche Indians showed low values for A2, A9 and C3, but high ones for A28 and B16. This is the first report of the presence (in low frequencies, 1-6%) of alleles C2, C6 and C7, as well as of DR antigens (most frequent alleles DR4 and DR2) in South American Indians. Some peculiar reactions shown by products of locus B suggest the presence of antigens that are characteristic of the Mapuche. As for the other systems, the frequencies of R1 (Rh) and PGM1(1) were lower but those for r (Rh), GLO1 and Hp1 were higher than the averages obtained considering previous studies of this ethnic group. Other salient findings were the variability observed in the PGM2 and C3 systems, and the low prevalence of Bfs.
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Direct atomic-level insight into the active sites of a high-performance PGM-free ORR catalyst
Chung, Hoon T.; Cullen, David A.; Higgins, Drew; ...
2017-08-04
Platinum group metal–free (PGM-free) metal-nitrogen-carbon catalysts have emerged as a promising alternative to their costly platinum (Pt)–based counterparts in polymer electrolyte fuel cells (PEFCs) but still face some major challenges, including (i) the identification of the most relevant catalytic site for the oxygen reduction reaction (ORR) and (ii) demonstration of competitive PEFC performance under automotive-application conditions in the hydrogen (H 2)–air fuel cell. We demonstrate H 2-air performance gains achieved with an iron-nitrogen-carbon catalyst synthesized with two nitrogen precursors that developed hierarchical porosity. In current densities recorded in the kinetic region of cathode operation, at fuel cell voltages greater thanmore » ~0.75 V, were the same as those obtained with a Pt cathode at a loading of 0.1 milligram of Pt per centimeter squared. The catalytic active site we proposed, carbon-embedded nitrogen-coordinated iron (FeN 4), was directly visualized with aberration-corrected scanning transmission electron microscopy, and the contributions of these active sites associated with specific lattice-level carbon structures were explored computationally.« less
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Highly active non-PGM catalysts prepared from metal organic frameworks
Barkholtz, Heather M.; Chong, Lina; Kaiser, Zachary B.; ...
2015-06-11
Finding inexpensive alternatives to platinum group metals (PGMs) is essential for reducing the cost of proton exchange membrane fuel cells (PEMFCs). Numerous materials have been investigated as potential replacements of Pt, of which the transition metal and nitrogen-doped carbon composites (TM/N x/C) prepared from iron doped zeolitic imidazolate frameworks (ZIFs) are among the most active ones in catalyzing the oxygen reduction reaction based on recent studies. In this report, we demonstrate that the catalytic activity of ZIF-based TM/N x/C composites can be substantially improved through optimization of synthesis and post-treatment processing conditions. Ultimately, oxygen reduction reaction (ORR) electrocatalytic activity mustmore » be demonstrated in membrane-electrode assemblies (MEAs) of fuel cells. The process of preparing MEAs using ZIF-based non-PGM electrocatalysts involves many additional factors which may influence the overall catalytic activity at the fuel cell level. Evaluation of parameters such as catalyst loading and perfluorosulfonic acid ionomer to catalyst ratio were optimized. Our overall efforts to optimize both the catalyst and MEA construction process have yielded impressive ORR activity when tested in a fuel cell system.« less
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Li, Yongfeng; Ma, Hua; Wang, Jiafu; Pang, Yongqiang; Zheng, Qiqi; Chen, Hongya; Han, Yajuan; Zhang, Jieqiu; Qu, Shaobo
2017-01-01
A high-efficiency tri-band quasi-continuous phase gradient metamaterial is designed and demonstrated based on spoof surface plasmon polaritons (SSPPs). High-efficiency polarizaiton conversion transmission is firstly achieved via tailoring phase differece between the transmisive SSPP and the space wave in orthogonal directions. As an example, a tri-band circular-to-circular (CTC) polarization conversion metamateiral (PCM) was designed by a nonlinearly dispersive phase difference. Using such PCM unit cell, a tri-band quasi-continuous phase gradient metamaterial (PGM) was then realized by virtue of the Pancharatnam-Berry phase. The distribution of the cross-polarization transmission phase along the x-direction is continuous except for two infinitely small intervals near the phases 0° and 360°, and thus the phase gradient has definition at any point along the x-direction. The simulated normalized polarization conversion transmission spectrums together with the electric field distributions for circularly polarized wave and linearly polarized wave demonstrated the high-efficiency anomalous refraction of the quasi-continuous PGM. The experimental verification for the linearly polarized incidence was also provided. PMID:28079185
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Educating the World: Essential Schools as Agents of Change and Influence
ERIC Educational Resources Information Center
Cohen, Lewis
2008-01-01
Schools face a relentless torrent of demands without receiving the kinds of support they need and deserve. So it is not easy to expect that they would voluntarily add to their ever-growing lists of responsibilities. Essential schools have the responsibility of educating not only their own school communities, but also the larger community about the…
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Open Source Digital Image Management Took Us from Raging Rivers to Quiet Waters
ERIC Educational Resources Information Center
Dunlap, Isaac Hunter
2005-01-01
In this article, the author describes his experience when Kathy Nichols contacted him seeking suggestions, recommendations--really anything he could think of--that might help her seize control of a bewildering and rapidly surging torrent of digital image files. The challenges that Nichols described interested him, and he felt they might be…
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A Torrent of Change: Enhancing Effective Change in Special Education--One School's Journey
ERIC Educational Resources Information Center
Morris, Chris; Katon, Shirley
2006-01-01
This article is the story of a school's journey from a deficit model of special education needs programming to an inclusive model of student learning support. The heart of this journey was the identification and management of tensions and complexities surrounding educational beliefs, school values, and pedagogical practices. This article will…
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Five Trends of School Arts Education Reform in Taiwan
ERIC Educational Resources Information Center
Hwang, Ren-Lai
2006-01-01
In the torrents of globalization and social transition in Taiwan, it is particularly important to reinforce a sense of cultural subjectivity and localization, and promote new trends of arts education that emphasize the development of self and spirit. The fundamental principles of these new trends are: (1) that the purpose of arts education is to…
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Shooting from the Hip in Nevada
ERIC Educational Resources Information Center
Fischer, Karin
2007-01-01
When the Board of Regents of the Nevada System of Higher Education named James E. Rogers, the system's largest benefactor, as state chancellor in May 2004, they were looking for a strong leader who could stanch a torrent of ethics problems, end backbiting among the state's eight public colleges and the board's own members, and repair the system's…
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Neher, Jon O.
2005-01-01
This essay portrays the moment an adult survivor of childhood sexual abuse tells his physician about his traumatic past. Because of denial by both parties, the diagnosis had remained buried for years, and opportunities for appropriate intervention were repeatedly missed. When the patient is finally able to face his past, it unleashes a torrent of potentially lethal anger that challenges everyone involved. PMID:16189064
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ERIC Educational Resources Information Center
Orr, Kevin
2009-01-01
The New Labour government identified the further education (FE) sector as a vehicle to deliver its central policies on social justice and economic competitiveness in England, which has led to a torrent of initiatives that have increased central scrutiny and control over FE. Although the connections between social justice, economic competitiveness…
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Prevent Spam Filters from Blocking Legitimate E-Mail
ERIC Educational Resources Information Center
Goldsborough, Reid
2004-01-01
There's no question about it: Spam is a scourge. This ever-increasing torrent of unsolicited commercial mass e-mail saps productivity and, for some, threatens the very viability of e-mail. The battle against spam, unfortunately, is creating problems of its own, with people sometimes unable to send legitimate e-mail and other times unable to…
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Beyond Keyword Search: Representations and Models for Personalization
ERIC Educational Resources Information Center
El-Arini, Khalid
2013-01-01
We live in an era of information overload. From online news to online shopping to scholarly research, we are inundated with a torrent of information on a daily basis. With our limited time, money and attention, we often struggle to extract actionable knowledge from this deluge of data. A common approach for addressing this challenge is…
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Hong, Lu; Zhou, Fu; Shi, Dongmin; Zhang, Xiaojun; Wang, Guangfeng
2017-09-15
Sensitive and rapid detection of platelet-derived growth factor BB (PDGF-BB), a cancer-related protein, could help early diagnosis, treatment, and prognosis of cancers. Although some methods have been developed to detect PDGF-BB, few can provide quantitative results using an affordable and portable device that is suitable for home use or field application. In this work, we report the first use of a portable kind of personal glucose meter (PGM) combining a catalytic and molecular beacon (CAMB) system with a cation exchange reaction (CX reaction) for ultrasensitive PDGF-BB assay. It realized the amplification of the detection in three ways, including greater aptamer payload on nanoparticles, CX reaction releasing thousands of Zn 2+ and the cycle by the catalyzing cleavage of 8-17 DNAzyme. In the process, with the addition of PDGF-BB into the aptasensor, the specific recognition between aptamer and protein was initiated resulting in the combination of ZnS NNC for further CX reaction to release thousands of Zn 2+ , which could cleave the substrate DNA in the CAMB system realizing multiple cycle. The cleaved DNA fragment was designed with invertase-labeled could convert sucrose into glucose which could be detected and quantified by PGM accompanying with the change of color of the control window from yellow to green. The enhanced signal of the PGM has a relationship with the concentration of PDGF-BB in the range of 3.16×10 -16 M to 3.16×10 -12 M, and the detection limit is 0.11fM. Moreover, the catalytic and cleavage activities of 8-17 DNAzyme can be achieved in solution; thus, no enzyme immobilization is needed for detection. The triply amplified strategy showed high selectivity, stability, and applicability for detecting the desired protein. Copyright © 2017. Published by Elsevier B.V.
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Chao, How-Ran; Lin, Ding-Yan; Chen, Kuang-Yu; Gou, Yan-Yu; Chiou, Tsyr-Huei; Lee, Wen-Jhy; Chen, Shui-Jen; Wang, Lin-Chi
2014-09-01
This study investigates the atmospheric occurrence of persistent organic pollutants (POPs) over the Pacific Ocean near southern Taiwan and the northern Philippines. We determined sixty-six compounds, including polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), dioxin-like polychlorinated biphenyls (DLPCBs), polybrominated diphenyl ethers (PBDEs), as well as polychlorinated diphenyl ethers (PCDEs), polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs), and polybrominated biphenyls (PBBs), in air samples simultaneously collected from the offshore oceanic atmosphere (n=6) and over a rural area (n=2). We calculated the atmospheric World Health Organization 2005 toxic equivalency levels (WHO2005-TEQ), for the total dioxin-like POPs, including PCDD/Fs, DLPCBs, and PBDD/Fs, being 0.00612 pg WHO2005-TEQ/m(3) and 0.0138 pg WHO2005-TEQ/m(3) over the ocean and land, respectively. We found unexpected lower averaged atmospheric PBDE concentrations in the rural area (15.9 pg/m(3)) than over the ocean (31.1 pg/m(3)) due to higher levels of the BDE209 congener, although the difference was not statistically significant. We have compared and reported our field results with previously published datasets over the global oceans, which suggest PCBs and PBDEs are the dominant chemical contaminants in the global oceanic atmosphere among these halogenated POPs (e.g. PCBs and Σdi-hepta PBDEs could be found in the range of 0.09-48.7 and 8.07-94.0 pg/m(3), respectively, including our dataset). However, there are still very few investigations on the global atmospheric levels of PBDD/Fs, PCDEs and PBBs and our data sums to these earlier studies. Finally, we point out that the halogenated POPs originated from Taiwan or the continental East Asia which could easily reach remote ocean sites via atmospheric transport. Copyright © 2014 Elsevier B.V. All rights reserved.
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Watanabe, Daisuke; Zhou, Yan; Hirata, Aiko; Sugimoto, Yukiko; Takagi, Kenichi; Akao, Takeshi; Ohya, Yoshikazu; Takagi, Hiroshi; Shimoi, Hitoshi
2016-01-01
The high fermentation rate of Saccharomyces cerevisiae sake yeast strains is attributable to a loss-of-function mutation in the RIM15 gene, which encodes a Greatwall-family protein kinase that is conserved among eukaryotes. In the present study, we performed intracellular metabolic profiling analysis and revealed that deletion of the RIM15 gene in a laboratory strain impaired glucose-anabolic pathways through the synthesis of UDP-glucose (UDPG). Although Rim15p is required for the synthesis of trehalose and glycogen from UDPG upon entry of cells into the quiescent state, we found that Rim15p is also essential for the accumulation of cell wall β-glucans, which are also anabolic products of UDPG. Furthermore, the impairment of UDPG or 1,3-β-glucan synthesis contributed to an increase in the fermentation rate. Transcriptional induction of PGM2 (phosphoglucomutase) and UGP1 (UDPG pyrophosphorylase) was impaired in Rim15p-deficient cells in the early stage of fermentation. These findings demonstrate that the decreased anabolism of glucose into UDPG and 1,3-β-glucan triggered by a defect in the Rim15p-mediated upregulation of PGM2 and UGP1 redirects the glucose flux into glycolysis. Consistent with this, sake yeast strains with defective Rim15p exhibited impaired expression of PGM2 and UGP1 and decreased levels of β-glucans, trehalose, and glycogen during sake fermentation. We also identified a sake yeast-specific mutation in the glycogen synthesis-associated glycogenin gene GLG2, supporting the conclusion that the glucose-anabolic pathway is impaired in sake yeast. These findings demonstrate that downregulation of the UDPG synthesis pathway is a key mechanism accelerating alcoholic fermentation in industrially utilized S. cerevisiae sake strains. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
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Non-Platinum Group Metal OER/ORR Catalysts for Alkaline Membrane Fuel Cells and Electrolyzers
DOE Office of Scientific and Technical Information (OSTI.GOV)
Danilovic, Nemanja; Ayers, Katherine
Regenerative fuel cells (RFC) are energy storage devices that capture electrical energy in the form of hydrogen, with potential application for backup power and energy storage in remote locations, unmanned missions, and renewable energy capture. A unitized regenerative fuel cell (URFC) combines two separate electrochemical devices (fuel cell and electrolyzer) into one stack. The stack cost is driven by the platinum group metal (PGM) catalysts and the flow field components designed to withstand high potentials in acidic environments. Since the stack is the most expensive subcomponent of both the fuel cell and electrolyzer system, combining the two devices results inmore » substantial reduction in capital cost. However, in the past, combining the two stacks sacrificed device performance (operating cost) largely because the fuel cell had to operate with the thick electrolysis membranes in a URFC configuration, and due to water management issues in switching modes. Recent work in membrane-based electrolysis has resulted in more mechanically robust designs and materials that allow much thinner membranes, and work in flow cell design such as flow batteries has shown improved water transport through channel design and wet-proofing approaches. Therefore, the URFC concept is worth revisiting. At the same time, alkaline exchange membrane (AEM) devices are gathering attention due to the promise of PGM and valve metal elimination from the stack and a resulting strategic and capital cost benefit as compared with proton exchange membrane (PEM) systems. The result is a lower capital cost system that has half the precious metal group (PGM) catalysts, membrane and other stack component materials compared with discrete RFCs, although at the sacrifice of performance (operating cost). Proton has identified innovative AEM based RFC's to fulfill the role of low capital cost energy storage device owing to the use of non-precious metal containing electrodes, that enables certain markets where higher operating costs can be tolerated.« less
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NASA Astrophysics Data System (ADS)
Byers, J. M.; Doctor, K.
2017-12-01
A common application of the satellite and airborne acquired hyperspectral imagery in the visible and NIR spectrum is the assessment of vegetation. Various absorption features of plants related to both water and chlorophyll content can be used to measure the vigor and access to underlying water sources of the vegetation. The typical strategy is to form hand-crafted features from the hyperspectral data cube by selecting two wavelengths to form difference or ratio images in the pixel space. The new image attempts to provide greater contrast for some feature of the vegetation. The Normalized Difference Vegetation Index (NDVI) is a widely used example formed from the ratio of differences and sums at two different wavelengths. There are dozens of these indices that are ostensibly formed using insights about the underlying physics of the spectral absorption with claims to efficacy in representing various properties of vegetation. In the language of machine learning these vegetation indices are features that can be used as a useful data representation within an algorithm. In this work we use a powerful approach from machine learning, probabilistic graphical models (PGM), to balance the competing needs of using existing hydrological classifications of terrain while finding statistically reliable features within hyperspectral data for identifying the generative process of the data. The algorithm in its simplest form is called a Naïve Bayes (NB) classifier and can be constructed in a data-driven estimation procedure of the conditional probability distributions that form the PGM. The Naïve Bayes model assumes that all vegetation indices (VI) are independent of one another given the hydrological class label. We seek to test its validity in a pilot study of detecting subsurface water flow pathways from VI. A more sophisticated PGM will also be explored called a tree-augmented NB that accounts for the probabilistic dependence between VI features. This methodology provides a general approach for classifying hydrological structures from hyperspectral data.
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Targeted mutagenesis in tetraploid switchgrass (Panicum virgatum L.) using CRISPR/Cas9.
Liu, Yang; Merrick, Paul; Zhang, Zhengzhi; Ji, Chonghui; Yang, Bing; Fei, Shui-Zhang
2018-02-01
The CRISPR/Cas9 system has become a powerful tool for targeted mutagenesis. Switchgrass (Panicum virgatum L.) is a high yielding perennial grass species that has been designated as a model biomass crop by the U.S. Department of Energy. The self-infertility and high ploidy level make it difficult to study gene function or improve germplasm. To overcome these constraints, we explored the feasibility of using CRISPR/Cas9 for targeted mutagenesis in a tetraploid cultivar 'Alamo' switchgrass. We first developed a transient assay by which a non-functional green-fluorescent protein gene containing a 1-bp frameshift insertion in its 5' coding region was successfully mutated by a Cas9/sgRNA complex resulting in its restored function. Agrobacterium-mediated stable transformation of embryogenic calli derived from mature caryopses averaged a 3.0% transformation efficiency targeting the genes of teosinte branched 1(tb1)a and b and phosphoglycerate mutase (PGM). With a single construct containing two sgRNAs targeting different regions of tb1a and tb1b genes, primary transformants (T0) containing CRISPR/Cas9-induced mutations were obtained at frequencies of 95.5% (tb1a) and 11% (tb1b), respectively, with T0 mutants exhibiting increased tiller production. Meanwhile, a mutation frequency of 13.7% was obtained for the PGM gene with a CRISPR/Cas9 construct containing a single sgRNA. Among the PGM T0 mutants, six are heterozygous and one is homozygous for a 1-bp deletion in the target region with no apparent phenotypical alterations. We show that CRISPR/Cas9 system can generate targeted mutagenesis effectively and obtain targeted homozygous mutants in T0 generation in switchgrass, circumventing the need of inbreeding. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
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Gas/particle partitioning and particle size distribution of PCDD/Fs and PCBs in urban ambient air.
Barbas, B; de la Torre, A; Sanz, P; Navarro, I; Artíñano, B; Martínez, M A
2018-05-15
Urban ambient air samples, including gas-phase (PUF), total suspended particulates (TSP), PM 10 , PM 2.5 and PM 1 airborne particle fractions were collected to evaluate gas-particle partitioning and size particle distribution of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and polychlorinated biphenyls (PCBs). Clausius-Clapeyron equation, regressions of logKp vs logP L and logK OA, and human respiratory risk assessment were used to evaluate local or long-distance transport sources, gas-particle partitioning sorption mechanisms, and implications for health. Total ambient air levels (gas phase+particulate phase) of TPCBs and TPCDD/Fs, were 437 and 0.07pgm -3 (median), respectively. Levels of PCDD/F in the gas phase (0.004-0.14pgm -3 , range) were significantly (p<0.05) lower than those found in the particulate phase (0.02-0.34pgm -3 ). The concentrations of PCDD/Fs were higher in winter. In contrast, PCBs were mainly associated to the gas phase, and displayed maximum levels in warm seasons, probably due to an increase in evaporation rates, supported by significant and strong positive dependence on temperature observed for several congeners. No significant differences in PCDD/Fs and PCBs concentrations were detected between the different particle size fractions considered (TSP, PM 10 , PM 2.5 and PM 1 ), reflecting that these chemicals are mainly bounded to PM 1 . The toxic content of samples was also evaluated. Total toxicity (PUF+TSP) attributable to dl-PCBs (13.4fg-TEQ 05 m -3 , median) was higher than those reported for PCDD/Fs (6.26fg-TEQ 05 m -3 ). The inhalation risk assessment concluded that the inhalation of PCDD/Fs and dl-PCBs pose a low cancer risk in the studied area. Copyright © 2017 Elsevier B.V. All rights reserved.
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Zabik, John M.; Seiber, James N.
1993-01-01
Atmospheric transport of organophosphate pesticides from California's Central Valley to the Sierra Nevada mountains was assessed by collecting air- and wet-deposition samples during December, January, February, and March, 1990 to 1991. Large-scale spraying of these pesticides occurs during December and January to control insect infestations in valley orchards. Sampling sites were placed at 114- (base of the foothills), 533-, and 1920-m elevations. Samples acquired at these sites contained chlorpyrifos [phosphorothioic acid; 0,0-diethyl 0-(3,5,6-trichloro-2-pyridinyl) ester], parathion [phosphorothioic acid, 0-0-diethylo-(4-nitrophenyl) ester], diazinon {phosphorothioic acid, 0,0-diethyl 0-[6-methyl-2-(1-methylethyl)-4-pyrimidinyl] ester} diazinonoxon {phosphoric acid, 0,0-diethyl 0-[6-methyl-2-(1-methylethyl)-4-pyrimidinyl] ester}, and paraoxon [phosphoric acid, 0,0-diethyl 0-(4-nitrophenyl) ester] in both air and wet deposition samples. Air concentrations of chloropyrifos, diazinon and parathion ranged from 13 to 13 000 pg/m3 at the base of the foothills. At 533-m air concentrations were below the limit of quantification (1.4 pg/m3) to 83 pg/m3 and at 1920 m concentrations were below the limit of quantification. Concentrations in wet deposition varied with distance and elevation from the Central Valley. Rainwater concentrations at the base of the foot hills ranged from 16 to 7600 pg/mL. At 533-m rain and snow water concentrations ranged from below the limit of quantification (1.3 pg/mL) to 140 pg/mL and at 1920 m concentrations ranged from below the limit of quantification to 48 pg/mL. These findings indicate that atmospheric transport of pesticides applied in the valley to the Sierra Nevada mountains is occurring, but the levels decrease as distance and elevation increase from the valley floor.
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NASA Astrophysics Data System (ADS)
Qiao, Zhi
Current platinum group metal (PGM)-free carbon nanocomposite catalysts for the oxygen reduction reaction (ORR) in acidic electrolyte often suffer from rapid degradation associated with carbon corrosion due to the use of large amount of the amorphoous carbon black supports. Here, we developed a new concept of using freestanding 3D hydrogel to design support-free Fe-N-C catalysts. A 3D polyaniline (PANI)-based hydrogel approach was used for preparing a new type of single atomic iron site-rich catalyst, which has exhibited exceptionally enhanced activity and stability compared to conventional Fe-N-C catalysts supported on amorphous carbon blacks. The achieved performance metric on the hydrogel PANI-Fe catalysts is one of the best ever reported PGM-free catalysts, reaching a half-wave potential up to 0.83 V vs. RHE and only leaving 30 mV gap with Pt/C catalysts (60mugPt/cm 2) in challenging acidic media. Remarkable ORR stability was accomplished as well on the same catalyst evidenced by using harsh potential cycling tests. The well dispersion of atomic iron into partially graphitized carbon, featured with dominance of micropores and porous network structures, is capable of accommodating increased number of active sites, strengthening local bonding among iron, nitrogen and carbon, and facilitating mass transfer. On the other hand, in order to decrease the produced Fenton reagent, which will oxidize the proton exchange membrane and ionomer in membrane electrode assembly (MEA), we produce Mn-based catalysts by this novel hydrogel method. This is the first time that Mn-based catalysts can show such outstanding performance in acid media, whose half-wave potential is up to 0.80 V vs. RHE. The work related to the performance improvement is still in processing. We believe the 3D polymer hydrogel approach would be a new pathway to advance PGM-free catalysts.
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Luo, Yiheng; Dou, Wenchao; Zhao, Guangying
2017-07-01
In this article, a facile and sensitive electrochemical method for quantification of Salmonella Pullorum and Salmonella Gallinarum (S. Pullorum and S. Gallinarum) was established by monitoring glucose consumption with a personal glucose meter (PGM). Antibody-functionalized magnetic nanoparticles (IgG-MNPs) were used to capture and enrich S. Pullorum and S. Gallinarum, and IgG-MNPs-S. Pullorum and IgG-MNPs-S. Gallinarum complexes were magnetically separated from a sample using a permanent magnet. The trace tag was prepared by loading polyclonal antibodies and high-content glucose oxidase on amino-functionalized silica nanoparticles (IgG-SiNPs-GOx). With a sandwich-type immunoassay format, IgG-SiNPs-GOx were added into the above mixture solution and conjugated to the complexes, forming sandwich composites IgG-MNPs/S. Pullorum and S. Gallinarum/IgG-SiNPs-GOx. The above sandwich composites were dispersed in glucose solution. Before and after the hydrolysis of glucose, the concentration of glucose was measured using PGM. Under optimal conditions, a linear relationship between the decrease of glucose concentration and the logarithm of S. Pullorum and S. Gallinarum concentration was obtained in the concentration range from 1.27 × 10 2 to 1.27 × 10 5 CFU mL -1 , with a detection limit of 7.2 × 10 1 CFU mL -1 (S/N = 3). This study provides a portable, low-cost, and quantitative analytical method for bacteria detection; thus, it has a great potential in the prevention of disease caused by S. Pullorum and S. Gallinarum in poultry. Graphical abstract A schematic illustration of the fabrication process of IgG-SiNPs-GOD nanomaterials (A) and IgG-MNPs (B) and experimental procedure of detection of S. Pullorum and S. Gallinarum using GOD-functionalized silica nanospheres as trace tags based on PGM (C).
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Watkins, Emily R; Richardson, Alan J
2017-01-01
Fire Service Instructors frequently experience high levels of physiological and perceptual strain during live fire exposures. Instructors are also at risk of cardiovascular illnesses, with cardiac death being the greatest cause of fire fighter death. Current practice for UK instructors is to select undergarment type based on personal preference, between a boiler suit (BOILER) and a wicking base layer (WBL). Research suggests that shorts and t-shirt (SHORTS) may also be a beneficial alternative undergarment choice. The UK South East Fire Service requested an investigation to identify if undergarment selection can lessen the strain experienced by instructors, and reduce the acute inflammatory response to fire exposures. Eight males completed three 45min sessions in a heat chamber (49.5±1.4°C and 16.9±4.3% RH) whilst performing intermittent walking. At the end of heat exposure change in heart rate was not effected by garment type (p=0.061, ηp 2 =0.373). Change in rectal temperature was different between garments (p=0.009, η p 2 =0.271), with trends suggesting that BOILER resulted in a greater change (1.03±0.60°C) than SHORTS (0.76±0.37°C, p=0.589, d=0.21) and WBL (0.72±0.33°C, p=0.545, d=0.25). Interleukin-6 post exposure was greater for BOILER (6.96±0.28pgmL -1 ) than both SHORTS (6.59±0.30pgmL -1 , p=0.043, d=0.42) and WBL (6.45±0.43pgmL -1 , p=0.031, d=0.51). Overall, undergarment type had little impact on physiological or perceptual strain. However, wearing WBL or SHORTS may reduce the inflammatory response, and consequently decrease the risk of cardiovascular events. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.
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Esseili, Malak A.
2012-01-01
Norovirus (NoV) genogroup II genotype 4 (GII.4) strains are the dominant cause of the majority of food-borne outbreaks, including those that involve leafy greens, such as lettuce. Since human NoVs use carbohydrates of histo-blood group antigens as receptors/coreceptors, we examined the role of carbohydrates in the attachment of NoV to lettuce leaves by using virus-like particles (VLPs) of a human NoV/GII.4 strain. Immunofluorescence analysis showed that the VLPs attached to the leaf surface, especially to cut edges, stomata, and along minor veins. Binding was quantified using enzyme-linked immunosorbent assay (ELISA) performed on cell wall materials (CWM) from innermost younger leaves and outermost lamina of older leaves. The binding to CWM of older leaves was significantly (P < 0.05) higher (1.5- to 2-fold) than that to CWM of younger leaves. Disrupting the carbohydrates of CWM or porcine gastric mucin (PGM) (a carbohydrate control) using 100 mM sodium periodate (NaIO4) significantly decreased the binding an average of 17% in younger leaves, 43% in older leaves, and 92% for PGM. In addition, lectins recognizing GalNAc, GlcNAc, and sialic acid at 100 μg/ml significantly decreased the binding an average of 41%, 33%, and 20% on CWM of older leaves but had no effect on younger leaves. Lectins recognizing α-d-Gal, α-d-Man/α-d-Glc, and α-l-Fuc showed significant inhibition on CWM of older leaves as well as that of younger leaves. All lectins, except for the lectin recognizing α-d-Gal, significantly inhibited NoV VLP binding to PGM. Collectively, our results indicate that NoV VLPs bind to lettuce CWM by utilizing multiple carbohydrate moieties. This binding may enhance virus persistence on the leaf surface and prevent effective decontamination. PMID:22138991
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2011-02-25
On September 18, 2009, the Chicago Department of Public Health (CDPH) was notified by a local hospital of a suspected case of fatal laboratory-acquired infection with Yersinia pestis, the causative agent of plague. The patient, a researcher in a university laboratory, had been working along with other members of the laboratory group with a pigmentation-negative (pgm-) attenuated Y. pestis strain (KIM D27). The strain had not been known to have caused laboratory-acquired infections or human fatalities. Other researchers in a separate university laboratory facility in the same building had contact with a virulent Y. pestis strain (CO92) that is considered a select biologic agent; however, the pgm- attenuated KIM D27 is excluded from the National Select Agent Registry. The university, CDPH, the Illinois Department of Public Health (IDPH), and CDC conducted an investigation to ascertain the cause of death. This report summarizes the results of that investigation, which determined that the cause of death likely was an unrecognized occupational exposure (route unknown) to Y. pestis, leading to septic shock. Y. pestis was isolated from premortem blood cultures. Polymerase chain reaction (PCR) identified the clinical isolate as a pgm- strain of Y. pestis. Postmortem examination revealed no evidence of pneumonic plague. A postmortem diagnosis of hereditary hemochromatosis was made on the basis of histopathologic, laboratory, and genetic testing. One possible explanation for the unexpected fatal outcome in this patient is that hemochromatosis-induced iron overload might have provided the infecting KIM D27 strain, which is attenuated as a result of defects in its ability to acquire iron, with sufficient iron to overcome its iron-acquisition defects and become virulent. Researchers should adhere to recommended biosafety practices when handling any live bacterial cultures, even attenuated strains, and institutional biosafety committees should implement and maintain effective surveillance systems to detect and monitor unexpected acute illness in laboratory workers.
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Gwimbi, Patrick
2017-11-16
Persistently high sulphur dioxide (SO 2 ) emissions from platinum group metal (PGM) smelting pose a major threat to communities located around smelters. This paper examined SO 2 emission trends, emission regulations and residents' perceived health risks from exposures to such emissions at Selous Metallurgical Complex (SMC) PGM smelting facility in Zimbabwe. SO 2 data from roof monitoring sites at the smelter furnace were aggregated into annual, quarterly and monthly emission trends from 2008 to 2015. The regulatory regime's ability to protect human health from SO 2 pollution in communities located around the smelter was examined. Questionnaire responses to perceived health risks from SO 2 exposure from 40 purposively sampled residents were assessed. The relationships between SO 2 emission trends and residents' self-reported health risks from exposure to SO 2 emissions were explored using STATA version 11. Descriptive statistics were used to illustrate SO 2 emission trends and residents' self-reported health risks from exposure to SO 2 . Between 2008 and 2015, annual SO 2 emissions increased from 7951 to 2500 tonnes. Emissions exceeded the recommended standard limit of 50 mg/Nm 3 , presenting considerable adverse health risks to local residents. Concerns relating to inefficient environmental impact assessment (EIA) licensing system, poor monitoring and auditing by the environmental management agency, as well as non-deterring SO 2 emission exceedance penalties were identified as major drivers of emission increase. Thirty-two (80%) of the forty respondents perceived exposure to SO 2 emissions as adverse and the cause of their illnesses, with coughing, nasal congestion and shortness of breath the most frequently self-reported symptoms. A set of legally-binding SO 2 emission standards supported by stringent EIA licensing arrangements for smelting industries are suggested for development and enforcement to reduce the SO 2 emission problem. Community participation in SO 2 emissions monitoring is also proposed as a core part of sustainable environmental management in communities located around smelters.
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Beristain-Montiel, E; Villalobos-Pietrini, R; Arias-Loaiza, G E; Gómez-Arroyo, S L; Amador-Muñoz, O
2016-12-16
New clean technologies are needed to determine concentration of organic pollutants without generating more pollution. A method to extract Persistent Organic Pollutants (POPs) from airborne particulate matter was developed using a novel technology recently patented called ultrasound assisted extraction micro-scale cell (UAE-MSC). This technology extracts, filters, collects the sample, and evaporates the solvent, on-line. No sample transfer is needed. The cell minimizes sample manipulation, solvent consumption, waste generation, time, and energy; fulfilling most of the analytical green chemistry protocol. The methodology was optimized applying a centred 2 3 factorial experimental design. Optimum conditions were used to validate and determine concentration of 16 organochlorine pesticides (OCls) and 6 polybrominated diphenyl ethers (PBDEs). The best conditions achieved were 2 extractions with 5mL (each) of dichloromethane over 5min (each) at 60°C and 80% ultrasound potency. POPs were determined by gas chromatography/mass spectrometry in negative chemical ionization (GC/MS-NCI). Analytical method validation was carried out on airborne particles spiked with POPs at seven concentration levels between 0.5 and 26.9pgm -3 . This procedure was done by triplicate (N=21). Recovery, ranged between 65.5±2.3% and 107.5±3.0% for OCls and between 79.1±6.5% and 105.2±3.8% for PBDEs. Linearity (r 2 ) was ≥0.94 for all compounds. Method detection limits, ranged from 0.5 to 2.7pgm -3 , while limits of quantification (LOQ), ranged from 1.7 to 9.0pgm -3 . A Bias from -18.6% to 9% for PBDEs was observed in the Standard Reference Material (SRM) 2787. SRM 2787 did not contain OCls. OCls recoveries were equivalent by UAE-MSC and Soxhlet methods UAE-MSC optimized extraction conditions reduced 30 times less solvent and decreased the extraction time from several hours to ten minutes, respect to Soxhlet. UAE-MSC was applied to 15 samples of particles less than 2.5μm (PM 2.5 ) from three seasons (warm dry, rainy, and cold dry) collected in five sites around Mexico City. OCls (4,4'-DDE and endrin aldehyde) concentrations ranged from
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Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy
2016-01-01
Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.
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Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy
2016-01-01
Background Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. Objectives To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Study Design Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. Results A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. Conclusion While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns. PMID:26918330
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Trujillano, Daniel; Weiss, Maximilian E R; Schneider, Juliane; Köster, Julia; Papachristos, Efstathios B; Saviouk, Viatcheslav; Zakharkina, Tetyana; Nahavandi, Nahid; Kovacevic, Lejla; Rolfs, Arndt
2015-03-01
Genetic testing for hereditary breast and/or ovarian cancer mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the BRCA1 and BRCA2 genes. We explored a more efficient genetic screening strategy based on next-generation sequencing of the BRCA1 and BRCA2 genes in 210 hereditary breast and/or ovarian cancer patients. We first validated this approach in a cohort of 115 samples with previously known BRCA1 and BRCA2 mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq BRCA1 and BRCA2 panel. The DNA Libraries were pooled, barcoded, and sequenced using an Ion Torrent Personal Genome Machine sequencer. The combination of different robust bioinformatics tools allowed detection of all previously known pathogenic mutations and polymorphisms in the 115 samples, without detecting spurious pathogenic calls. We then used the same assay in a discovery cohort of 95 uncharacterized hereditary breast and/or ovarian cancer patients for BRCA1 and BRCA2. In addition, we describe the allelic frequencies across 210 hereditary breast and/or ovarian cancer patients of 74 unique definitely and likely pathogenic and uncertain BRCA1 and BRCA2 variants, some of which have not been previously annotated in the public databases. Targeted next-generation sequencing is ready to substitute classic molecular methods to perform genetic testing on the BRCA1 and BRCA2 genes and provides a greater opportunity for more comprehensive testing of at-risk patients. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
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Prospective identification of parasitic sequences in phage display screens
Matochko, Wadim L.; Cory Li, S.; Tang, Sindy K.Y.; Derda, Ratmir
2014-01-01
Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 109 random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the ‘parasites’), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 ‘parasites’. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ∼106 diverse clones prevents the biased selection of parasitic clones. PMID:24217917
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Alteration of microbial community structure affects diesel biodegradation in an Arctic soil.
Bell, Terrence H; Yergeau, Etienne; F Juck, Dave; G Whyte, Lyle; W Greer, Charles
2013-07-01
A wide range of microbial taxa are active in hydrocarbon-contaminated Arctic soils, and many are capable of hydrocarbon metabolism. The most effective hydrocarbon degraders may not naturally dominate following contamination events, so shifts in microbial abundance could potentially increase hydrocarbon biodegradation. In this study, we contaminated an Arctic soil with diesel and used gentamicin and vancomycin to inhibit distinct portions of the microbial community. We measured diesel loss using gas chromatography, bacterial and fungal abundance with qPCR, and assessed bacterial diversity and community composition through Ion Torrent sequencing of 16S rRNA gene amplicons. The combined addition of both antibiotics increased diesel biodegradation significantly relative to the no-antibiotic treatment, despite reduced bacterial and fungal abundance; however, this effect was not observed when nutrients were also added. All treatments produced unique bacterial communities, and both Xanthomonadaceae and Micrococcineae were dominant in the dual antibiotic treatment. The bacterial communities resulting from dual gentamicin and vancomycin addition were similar both with and without nutrients, although nutrient addition produced a much larger fungal population, which may partly explain the differences in biodegradation between these two treatments. These results suggest that the most efficient hydrocarbon-degrading community may not always be promoted naturally in contaminated soils. © Her Majesty the Queen in Right of Canada 2013.
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Xi, Yanwei; Arbabi, Aryan; McNaughton, Amy J M; Hamilton, Alison; Hull, Danna; Perras, Helene; Chiu, Tillie; Morrison, Shawna; Goldsmith, Claire; Creede, Emilie; Anger, Gregory J; Honeywell, Christina; Cloutier, Mireille; Macchio, Natasha; Kiss, Courtney; Liu, Xudong; Crocker, Susan; Davies, Gregory A; Brudno, Michael; Armour, Christine M
2017-01-01
To develop an alternate noninvasive prenatal testing method for the assessment of trisomy 21 (T21) using a targeted semiconductor sequencing approach. A customized AmpliSeq panel was designed with 1,067 primer pairs targeting specific regions on chromosomes 21, 18, 13, and others. A total of 235 samples, including 30 affected with T21, were sequenced with an Ion Torrent Proton sequencer, and a method was developed for assessing the probability of fetal aneuploidy via derivation of a risk score. Application of the derived risk score yields a bimodal distribution, with the affected samples clustering near 1.0 and the unaffected near 0. For a risk score cutoff of 0.345, above which all would be considered at "high risk," all 30 T21-positive pregnancies were correctly predicted to be affected, and 199 of the 205 non-T21 samples were correctly predicted. The average hands-on time spent on library preparation and sequencing was 19 h in total, and the average number of reads of sequence obtained was 3.75 million per sample. With the described targeted sequencing approach on the semiconductor platform using a custom-designed library and a probabilistic statistical approach, we have demonstrated the feasibility of an alternate method of assessment for fetal T21. © 2017 S. Karger AG, Basel.
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Frank-Fahle, Béatrice A.; Yergeau, Étienne; Greer, Charles W.; Lantuit, Hugues; Wagner, Dirk
2014-01-01
Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic. PMID:24416279
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Elevation of glycosaminoglycans in the amniotic fluid of a fetus with mucopolysaccharidosis VII
Kubaski, Francyne; Brusius-Facchin, Ana Carolina; Mason, Robert W.; Patel, Pravin; Burin, Maira G.; Michelin-Tirelli, Kristiane; Kessler, Rejane Gus; Bender, Fernanda; Leistner-Segal, Sandra; Moreno, Carolina A.; Cavalcanti, Denise P.; Giugliani, Roberto; Tomatsu, Shunji
2017-01-01
Objective The aim of this study was to quantify GAGs in amniotic fluid (AF) from an MPS VII fetus compared with age-matched fetuses obtained from normal pregnancies. Method Disaccharides were measured by liquid chromatography tandem mass spectrometry (LC/MS/MS), compared to age-matched controls. Enzyme assay was performed in AF supernatant or cultured amniocytes. GUSB was analyzed by next generation sequencing using Ion Torrent Personal Genome Machine with a customized panel. Results No activity of β-glucuronidase was detected in fetal cells. The pregnancy was spontaneously terminated in the third trimester. Genetic studies identified a homozygous mutation of p.N379D (c.1135A>G) in the GUSB gene. LC/MS/MS showed that chondroitin sulfate, dermatan sulfate, heparan sulfate, and keratan sulfate levels were markedly increased in the MPS VII AF, compared to those in age-matched control AF (DS, HS, and C6S more than 10 × than age-matched controls; C4S and KS more than 3 times higher). Conclusion This is the first report of specific GAG analysis in AF from an MPS VII fetus, indicating that GAG elevation in AF occurs by 21 weeks of gestation and could be an additional tool for prenatal diagnosis of MPS VII and potentially other MPS types. PMID:28207930
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Water mass dynamics shape Ross Sea protist communities in mesopelagic and bathypelagic layers
NASA Astrophysics Data System (ADS)
Zoccarato, Luca; Pallavicini, Alberto; Cerino, Federica; Fonda Umani, Serena; Celussi, Mauro
2016-12-01
Deep-sea environments host the largest pool of microbes and represent the last largely unexplored and poorly known ecosystems on Earth. The Ross Sea is characterized by unique oceanographic dynamics and harbors several water masses deeply involved in cooling and ventilation of deep oceans. In this study the V9 region of the 18S rDNA was targeted and sequenced with the Ion Torrent high-throughput sequencing technology to unveil differences in protist communities (>2 μm) correlated with biogeochemical properties of the water masses. The analyzed samples were significantly different in terms of environmental parameters and community composition outlining significant structuring effects of temperature and salinity. Overall, Alveolata (especially Dinophyta), Stramenopiles and Excavata groups dominated mesopelagic and bathypelagic layers, and protist communities were shaped according to the biogeochemistry of the water masses (advection effect and mixing events). Newly-formed High Salinity Shelf Water (HSSW) was characterized by high relative abundance of phototrophic organisms that bloom at the surface during the austral summer. Oxygen-depleted Circumpolar Deep Water (CDW) showed higher abundance of Excavata, common bacterivores in deep water masses. At the shelf-break, Antarctic Bottom Water (AABW), formed by the entrainment of shelf waters in CDW, maintained the eukaryotic genetic signature typical of both parental water masses.
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Semenova, Tatiana A; Morgado, Luis N; Welker, Jeffrey M; Walker, Marilyn D; Smets, Erik; Geml, József
2015-01-01
Arctic tundra regions have been responding to global warming with visible changes in plant community composition, including expansion of shrubs and declines in lichens and bryophytes. Even though it is well known that the majority of arctic plants are associated with their symbiotic fungi, how fungal community composition will be different with climate warming remains largely unknown. In this study, we addressed the effects of long-term (18 years) experimental warming on the community composition and taxonomic richness of soil ascomycetes in dry and moist tundra types. Using deep Ion Torrent sequencing, we quantified how OTU assemblage and richness of different orders of Ascomycota changed in response to summer warming. Experimental warming significantly altered ascomycete communities with stronger responses observed in the moist tundra compared with dry tundra. The proportion of several lichenized and moss-associated fungi decreased with warming, while the proportion of several plant and insect pathogens and saprotrophic species was higher in the warming treatment. The observed alterations in both taxonomic and ecological groups of ascomycetes are discussed in relation to previously reported warming-induced shifts in arctic plant communities, including decline in lichens and bryophytes and increase in coverage and biomass of shrubs. © 2014 John Wiley & Sons Ltd.
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Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat
Bernardo, Amy; Wang, Shan; St. Amand, Paul; Bai, Guihua
2015-01-01
With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat ( Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat. PMID:26625271
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Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng
2017-01-01
Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration. PMID:28349918
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Mediterranean diet and faecal microbiota: a transversal study.
Gutiérrez-Díaz, I; Fernández-Navarro, T; Sánchez, B; Margolles, A; González, S
2016-05-18
Despite the existing evidence on the impact of olive oil and red wine on the intestinal microbiota, the effect of the global Mediterranean Diet (MD) has not been sufficiently studied. We explored the association between the adherence to a Mediterranean dietary pattern, and its components, with faecal microbiota in a cohort of adults with non-declared pathology. This transversal study involved 31 adults without a previous diagnosis of cancer, autoimmune or digestive diseases. Based on the data obtained by means of an annual food frequency questionnaire (FFQ), and the information existing in the literature, a Mediterranean Diet Score (MDS) was calculated. Dietary fibre was obtained from Marlett et al. tables and Phenol-Explorer Database was used for phenolic compounds intake. Quantification of microbial groups was performed by Ion Torrent 16S rRNA gene-based analysis and quantification of short-chain fatty acids (SCFAs) was performed using gas chromatography-mass spectrometry (MS). MDS was associated with a higher abundance of Bacteroidetes (p = 0.001), Prevotellacea (p = 0.002) and Prevotella (p = 0.003) and a lower concentration of Firmicutes (p = 0.003) and Lachnospiraceae (p = 0.045). Also, in subjects with MDS ≥ 4, higher concentrations of faecal propionate (p = 0.034) and butyrate (p = 0.018) were detected. These results confirm the complexity of the diet-microbiota interrelationship.
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NASA Astrophysics Data System (ADS)
Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng
2017-03-01
Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration.
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Bridging the Generation Gap: "Growing Golf" through an Action Learning Activity
ERIC Educational Resources Information Center
Elbert, Norb; Cumiskey, Kevin J.
2014-01-01
This paper describes an action learning simulation designed for a Professional Golf Management (PGM) program housed in a College of Business of a public university. The PGA Golf Management University Program, a 4.5- to 5-year college curriculum for aspiring PGA Professionals is offered at 19 PGA accredited universities nationwide. The program…
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USDA-ARS?s Scientific Manuscript database
This study examined the inactivation of human norovirus (HuNoV) GI.1 and GII.4 by chlorine under conditions that mimic sewage treatment. Using a porcine gastric mucin-magnetic bead (PGM-MB) assay, no statistically significant loss in HuNoV binding (inactivation) was observed for secondary effluent ...
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"In the Midst of Strange and Terrible Times": The New York City Draft Riots of 1863
ERIC Educational Resources Information Center
Cruz, Barbara C.; Patterson, Jennifer Marques
2005-01-01
During the New York City Draft Riots the city's own inhabitants unleashed a torrent of violence and destruction that chiefly targeted African Americans. What originated as a protest against the enforcement of the Conscription Act quickly escalated into a riot that erupted at the volatile nineteenth century crossroads of race, class, and economic…
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ERIC Educational Resources Information Center
Becker, Peter
2007-01-01
Adventure is a playful pacemaker for real border crossings from reality to possibility; it can, from a benevolent point of view, be the trigger for individual changes of reality, a provider of impulses for the development of self. Confronted with the unpredictability of the wilderness, the turbulences of torrents, the chaotic state of the oceans,…
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ERIC Educational Resources Information Center
Holley, Debbie; Santos, Patricia; Cook, John; Kerr, Micky
2016-01-01
This paper responds to the Alpine Rendez-Vous "crisis" in technology-enhanced learning. It takes a contested area of policy as well as a rapid change in the National Health Service, and documents the responses to "information overload" by a group of general practitioners practices in the North of England. Located between the…
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Life cycles of dominant mayflies (Ephemeroptera) on a torrent of the high Bolivian Andes
Molina, Carlos I; Puliafico, Kenneth P
2016-03-01
The mayflies of the temperate and cold zones have well-synchronized life cycles, distinct cohorts, short emergence and flight periods. In contrast, aquatic insects from the tropical zones are characterized by multivoltine life cycles, “non-discernible cohorts” and extended flight periods throughout the year. This report is the first observation of life cycle patterns made of two species of mayflies on a torrent in the high elevation Bolivian Andes. The samples were taken from four sites and four periods during a hydrological season. The life cycle of each species was examined using size-class frequency analysis and a monthly modal progression model (von Bertalanffy’s model) to infer the life cycle synchrony type. These first observations showed a moderately synchronized univoltine life cycle for Andesiops peruvianus (Ulmer, 1920), whereas Meridialaris tintinnabula Pescador and Peters (1987), had an unsynchronized multivoltine life cycle. These results showed that the generalization of all aquatic insects as unsynchronized multivoltine species in the Andean region may not be entirely accurate since there is still a need to further clarify the life cycle patterns of the wide variety of aquatic insects living in this high elevation tropical environment.
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Potential implications of the helical heart in congenital heart defects.
Corno, Antonio F; Kocica, Mladen J
2007-01-01
The anatomic and functional observations made by Francisco Torrent-Guasp, in particular his discovery of the helical ventricular myocardial band (HVMB), have challenged what has been taught to cardiologists and cardiac surgeons over centuries. A literature debate is ongoing, with interdependent articles and comments from supporters and critics. Adequate understanding of heart structure and function is obviously indispensable for the decision-making process in congenital heart defects. The HVMB described by Torrent-Guasp and the potential impact on the understanding and treatment of congenital heart defects has been analyzed in the following settings: embryology, ventriculo-arterial discordance (transposition of great arteries), Ebstein's anomaly, pulmonary valve regurgitation after repair of tetralogy of Fallot, Ross operation, and other congenital heart defects. The common structural spiral feature is only one of the elements responsible for the functional interaction of right and left ventricles, and understanding the form/function relationship in congenital heart defects is more difficult than for acquired heart disease because of the variety and complexity of congenital heart defects. Individuals involved in the care of patients with congenital heart defects have to be stimulated to consider further investigations and alternative surgical strategies.
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The helical ventricular myocardial band of Torrent-Guasp.
Kocica, Mladen J; Corno, Antonio F; Lackovic, Vesna; Kanjuh, Vladimir I
2007-01-01
We live in an era of substantial progress in understanding myocardial structure and function at genetic, molecular, and microscopic levels. Yet, ventricular myocardium has proven remarkably resistant to macroscopic analyses of functional anatomy. Pronounced and practically indefinite global and local structural anisotropy of its fibers and other ventricular wall constituents produces electrical and mechanical properties that are nonlinear, anisotropic, time varying, and spatially inhomogeneous. The helical ventricular myocardial band of Torrent-Guasp is a revolutionary new concept in understanding global, 3-dimensional, functional architecture of the ventricular myocardium. This concept defines the principal, cumulative vectors, integrating the tissue architecture (ie, form) and net forces developed (ie, function) within the ventricular mass. The primary purpose of this review is to emphasize the importance of this concept, in the light of collaborative efforts to establish an integrative approach, defining ventricular form and function by linking across multiple scales of biological organization, as explained in the ongoing Physiome project. Because one of the most important scientific missions in this century is integration of basic research with clinical medicine, we believe that this knowledge is not of merely academic importance, but is also the essential prerequisite in clinical evaluation and treatment of different heart diseases.
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NASA Astrophysics Data System (ADS)
Bergamin, Luisa; Capello, Marco; Carbone, Cristina; Magno, Maria Celia; Consani, Sirio; Cutroneo, Laura; Ferraro, Luciana; Pierfranceschi, Giancarlo; Romano, Elena
2016-04-01
Benthic foraminiferal assemblages react in short time to natural and anthropogenic environmental changes and, for this, they are considered as reliable indicators of environmental quality. An interesting application of these indicators is the study of their response to environmental changes in coastal marine areas, affected by dismissed mines and dump areas. The Libiola Fe-Cu sulphide mine was intensively exploited in 19th and 20th centuries, and the activity ended in 1962. The sulphide mineral assemblages consist of pyrite and chalcopyrite, with minor sphalerite and pyrrhotite, in a gangue of quartz and chlorite. The sulphide ore occurs within the Jurassic ophiolites of the Northern Apennines which were subjected to metamorphic and tectonic processes during the subsequent Apennine orogenesis. Waters circulating in the Libiola mine area, and discharging in the adjacent streams and creeks, are strongly polluted due to the diffuse occurrence of Acid Mine Drainage processes. The Gromolo torrent collects these acidic waters enriched of heavy metals which flow into Ligurian Sea. The study area is characterised by a shelf with a gentle slope, mainly constituted by sediment supplied by Entella torrent. The general circulation has trend from East to West and the coastal drift is generally eastwards. A total of 15 marine sediment samples (upper 2 cm) were collected by means of Van Veen grab in the coastal zone close to the Gromolo mouth and analyzed for living (rose Bengal stained) and dead benthic foraminifera, together with grain size, metals and trace elements, and metal fractioning. Quantitative foraminiferal parameters, like as abundance, species diversity, heterogeneity and assemblage composition, were determined and evaluated for environmental purpose. Additionally, possible increase above the natural background level of deformed specimens was considered as indicative of metal contamination. The grain-size analyses highlighted mainly sandy sediments, characterized by a small pelitic fraction, ranging from 0.5% to 28%. Sediments are greyish, usually very fine-grained, with infrequent organogenic fraction. The mineralogical composition is based on dark green grains of serpentine nature, sometimes fibrous, with spread inclusions of magnetite, associated with lithic sandstone, dark gray shales, gabbros, fragments of quartz, feldspar, serpentine and chlorite. Metal concentration shows, in the whole study area, high concentrations of As, Cr, and Ni while, in the samples close to the Gromolo mouth, high values also for Cu, Co, Zn, Pb, Hg, and Cd were recorded. The foraminiferal study highlighted several samples with very low abundance, especially in the coastal belt between Gromolo and Entella torrents. Slightly higher abundance was recorded close to the Gromolo mouth, where sediments are strongly characterized by Ammonia. Both living and dead assemblages displayed low diversity and high dominance with Ammonia beccarii which accounts up to 66% of total abundance. Moreover, percentage of deformed specimens generally exceeded the natural background reaching 5%. All these aspects are clear evidence of an environmental stress.
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Ezquerra-Inchausti, Maitane; Barandika, Olatz; Anasagasti, Ander; Irigoyen, Cristina; López de Munain, Adolfo; Ruiz-Ederra, Javier
2017-01-01
Retinitis pigmentosa is the most frequent group of inherited retinal dystrophies. It is highly heterogeneous, with more than 80 disease-causing genes 27 of which are known to cause autosomal dominant RP (adRP), having been identified. In this study a total of 29 index cases were ascertained based on a family tree compatible with adRP. A custom panel of 31 adRP genes was analysed by targeted next-generation sequencing using the Ion PGM platform in combination with Sanger sequencing. This allowed us to detect putative disease-causing mutations in 14 out of the 29 (48.28%) families analysed. Remarkably, around 38% of all adRP cases analysed showed mutations affecting the splicing process, mainly due to mutations in genes coding for spliceosome factors (SNRNP200 and PRPF8) but also due to splice-site mutations in RHO. Twelve of the 14 mutations found had been reported previously and two were novel mutations found in PRPF8 in two unrelated patients. In conclusion, our results will lead to more accurate genetic counselling and will contribute to a better characterisation of the disease. In addition, they may have a therapeutic impact in the future given the large number of studies currently underway based on targeted RNA splicing for therapeutic purposes. PMID:28045043
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Raman and CT scan mapping of chalcogenide glass diffusion generated gradient index profiles
NASA Astrophysics Data System (ADS)
Lindberg, G. P.; Berg, R. H.; Deegan, J.; Benson, R.; Salvaggio, P. S.; Gross, N.; Weinstein, B. A.; Gibson, D.; Bayya, S.; Sanghera, J.; Nguyen, V.; Kotov, M.
2016-05-01
Metrology of a gradient index (GRIN) material is non-trivial, especially in the realm of infrared and large refractive index. Traditional methods rely on index matching fluids which are not available for indexes as high as those found in the chalcogenide glasses (2.4-3.2). By diffusing chalcogenide glasses of similar composition one can blend the properties in a continuous way. In an effort to measure this we will present data from both x-ray computed tomography scans (CT scans) and Raman mapping scans of the diffusion profiles. Proof of concept measurements on undiffused bonded sheets of chalcogenide glasses were presented previously. The profiles measured will be of axially stacked sheets of chalcogenide glasses diffused to create a linear GRIN profile and nested tubes of chalcogenide glasses diffused to create a radial parabolic GRIN profile. We will show that the x-ray absorption in the CT scan and the intensity of select Raman peaks spatially measured through the material are indicators of the concentration of the diffusion ions and correlate to the spatial change in refractive index. We will also present finite element modeling (FEM) results and compare them to post precision glass molded (PGM) elements that have undergone CT and Raman mapping.
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USDA-ARS?s Scientific Manuscript database
Human histo-blood group antigens (HBGA) have been identified previously as candidate receptors for human norovirus (NOR). Type A, type H1, Lewis HBGAs have been identified major HBGA for NOR binding. We have identified that pig stomach mucin (PGM) contains group A, type H1, and Lewis b type HBGAs...
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NASA Astrophysics Data System (ADS)
Chen, Mengjie; Wang, Lei; Yang, Haipeng; Zhao, Shuai; Xu, Hui; Wu, Gang
2018-01-01
A reversible fuel cell (RFC), which integrates a fuel cell with an electrolyzer, is similar to a rechargeable battery. This technology lies on high-performance bifunctional catalysts for the oxygen reduction reaction (ORR) in the fuel cell mode and the oxygen evolution reaction (OER) in the electrolyzer mode. Current catalysts are platinum group metals (PGM) such as Pt and Ir, which are expensive and scarce. Therefore, it is highly desirable to develop PGM-free catalysts for large-scale application of RFCs. In this mini review, we discussed the most promising nanocarbon/oxide composite catalysts for ORR/OER bifunctional catalysis in alkaline media, which is mainly based on our recent progress. Starting with the effectiveness of selected oxides and nanocarbons in terms of their activity and stability, we outlined synthetic methods and the resulting structures and morphologies of catalysts to provide a correlation between synthesis, structure, and property. A special emphasis is put on understanding of the possible synergistic effect between oxide and nanocarbon for enhanced performance. Finally, a few nanocomposite catalysts are discussed as typical examples to elucidate the rules of designing highly active and durable bifunctional catalysts for RFC applications.
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Pyrometallurgical Recovery of Platinum Group Metals from Spent Catalysts
NASA Astrophysics Data System (ADS)
Peng, Zhiwei; Li, Zhizhong; Lin, Xiaolong; Tang, Huimin; Ye, Lei; Ma, Yutian; Rao, Mingjun; Zhang, Yuanbo; Li, Guanghui; Jiang, Tao
2017-09-01
As an important secondary resource with abundant platinum group metals (PGMs), spent catalysts demand recycling for both economic and environmental benefits. This article reviews the main pyrometallurgical processes for PGM recovery from spent catalysts. Existing processes, including smelting, vaporization, and sintering processes, are discussed based in part on a review of the physiochemical characteristics of PGMs in spent catalysts. The smelting technology, which produces a PGM-containing alloy, is significantly influenced by the addition of various collectors, such as lead, copper, iron, matte, or printed circuit board (PCB), considering their chemical affinities for PGMs. The vaporization process can recover PGMs in vapor form at low temperatures (250-700°C), but it suffers high corrosion and potential environmental and health risks as a result of involvement of the hazardous gases, mainly Cl2 and CO. The sintering process serves as a reforming means for recycling of the spent catalysts by in situ reduction of their oxidized PGMs components. Among these processes, the smelting process seems more promising although its overall performance can be further improved by seeking a suitable target-oriented collector and flux, together with proper pretreatment and process intensification using an external field.
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Lin, Bingqian; Liu, Dan; Yan, Jinmao; Qiao, Zhi; Zhong, Yunxin; Yan, Jiawei; Zhu, Zhi; Ji, Tianhai; Yang, Chaoyong James
2016-03-23
There is considerable demand for sensitive, selective, and portable detection of disease-associated proteins, particularly in clinical practice and diagnostic applications. Portable devices are highly desired for detection of disease biomarkers in daily life due to the advantages of being simple, rapid, user-friendly, and low-cost. Herein we report an enzyme-encapsulated liposome-linked immunosorbent assay for sensitive detection of proteins using personal glucose meters (PGM) for portable quantitative readout. Liposomes encapsulating a large amount of amyloglucosidase or invertase are surface-coated with recognition elements such as aptamers or antibodies for target recognition. By translating molecular recognition signal into a large amount of glucose with the encapsulated enzyme, disease biomarkers such as thrombin or C-reactive protein (CRP) can be quantitatively detected by a PGM with a high detection limit of 1.8 or 0.30 nM, respectively. With the advantages of portability, ease of use, and low-cost, the method reported here has potential for portable and quantitative detection of various targets for different POC testing scenarios, such as rapid diagnosis in clinic offices, health monitoring at the bedside, and chemical/biochemical safety control in the field.
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NASA Astrophysics Data System (ADS)
Fan, Ya; Wang, Jiafu; Li, Yongfeng; Pang, Yongqiang; Zheng, Lin; Xiang, Jiayu; Zhang, Jieqiu; Qu, Shaobo
2018-05-01
Based on the effect of anomalous reflection and refraction caused by the circularly cross-polarized phase gradient metasurface (PGM), an ultra-thin and -broadband composite absorber composed of metasurface and conventional magnetic absorbing film is proposed and demonstrated in this paper. In the case of keeping nearly the same thickness of absorbing layer, the equivalent thickness of magnetic absorbing film is enlarged by the effect of anomalous reflection and refraction, resulting in the expansion and improvement of the absorbing bandwidth and efficiency in low microwave frequency. A biarc metallic sub-cell for circularly crossed polarization is adopted to form a broadband phase gradient, by the means of rotating the Pancharatnam–Berry phases. As indicated in the experimental results, the fabricated 3.6 mm-thick absorber can averagely absorb microwave energy with the specular reflection below ‑10 dB in the frequency interval of 2–12 GHz, which shows a good match with simulated results. Due to ultra-thin thickness and ultra-wide operating bandwidth, the proposed application of PGM in absorbing can provide an alternative way to enhance the absorbing property of current absorbing materials.
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Hou, Li; Cui, Yuling; Xu, Mingdi; Gao, Zhuangqiang; Huang, Jianxin; Tang, Dianping
2013-09-15
A new sandwich-type impedimetric immunosensor based on functionalized graphene oxide nanosheets with a high ratio of horseradish peroxidase (HRP) and detection antibody was developed for the detection of carcinoembryonic antigen (CEA) by coupling with enzymatic biocatalytic precipitation of 4-chloro-1-naphthol (4-CN) on the captured antibody-modified glassy carbon electrode. Two molecular tags (with and without the graphene oxide nanosheets) were investigated for the detection of CEA and improved analytical features were acquired with the graphene-based labeling. With the labeling method, the performance and factors influencing the properties of the impedimetric immunosensors were also studied and evaluated. Under the optimal conditions, the dynamic concentration range of the impedimetric immunosensors spanned from 1.0pgmL(-1) to 80ngmL(-1) CEA with a detection limit (LOD) of 0.64pgmL(-1). Intra- and inter-assay coefficients of variation were less than 7.5% and 11%, respectively. Additionally, the methodology was evaluated for CEA analysis of 10 clinical serum samples and 5 diluted serum samples, receiving in a good accordance with the results obtained by the impedimetric immunoassay and the commercialized electrochemiluminescent method. Copyright © 2013 Elsevier B.V. All rights reserved.
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Investigation of the pH-dependence of dye-doped protein-protein interactions.
Nudelman, Roman; Gloukhikh, Ekaterina; Rekun, Antonina; Richter, Shachar
2016-11-01
Proteins can dramatically change their conformation under environmental conditions such as temperature and pH. In this context, Glycoprotein's conformational determination is challenging. This is due to the variety of domains which contain rich chemical characters existing within this complex. Here we demonstrate a new, straightforward and efficient technique that uses the pH-dependent properties of dyes-doped Pig Gastric Mucin (PGM) for predicting and controlling protein-protein interaction and conformation. We utilize the PGM as natural host matrix which is capable of dynamically changing its conformational shape and adsorbing hydrophobic and hydrophilic dyes under different pH conditions and investigate and control the fluorescent properties of these composites in solution. It is shown at various pH conditions, a large variety of light emission from these complexes such as red, green and white is obtained. This phenomenon is explained by pH-dependent protein folding and protein-protein interactions that induce different emission spectra which are mediated and controlled by means of dye-dye interactions and surrounding environment. This process is used to form the technologically challenging white light-emitting liquid or solid coating for LED devices. © 2016 The Protein Society.
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Fetherston, Jacqueline D; Kirillina, Olga; Bobrov, Alexander G; Paulley, James T; Perry, Robert D
2010-05-01
Iron acquisition from the host is an important step in the pathogenic process. While Yersinia pestis has multiple iron transporters, the yersiniabactin (Ybt) siderophore-dependent system plays a major role in iron acquisition in vitro and in vivo. In this study, we determined that the Ybt system is required for the use of iron bound by transferrin and lactoferrin and examined the importance of the Ybt system for virulence in mouse models of bubonic and pneumonic plague. Y. pestis mutants unable to either transport Ybt or synthesize the siderophore were both essentially avirulent via subcutaneous injection (bubonic plague model). Surprisingly, via intranasal instillation (pneumonic plague model), we saw a difference in the virulence of Ybt biosynthetic and transport mutants. Ybt biosynthetic mutants displayed an approximately 24-fold-higher 50% lethal dose (LD(50)) than transport mutants. In contrast, under iron-restricted conditions in vitro, a Ybt transport mutant had a more severe growth defect than the Ybt biosynthetic mutant. Finally, a Delta pgm mutant had a greater loss of virulence than the Ybt biosynthetic mutant, indicating that the 102-kb pgm locus encodes a virulence factor, in addition to Ybt, that plays a role in the pathogenesis of pneumonic plague.
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Argentina's chemical makers seek government support
DOE Office of Scientific and Technical Information (OSTI.GOV)
Salles, F.
1993-02-10
Argentina's chemical industry association, Camara de la Industria Quimica y Petroquimica (CIQYP; Buenos Aires), has started negotiations with the government aiming to stem industry-wide losses, which reached $236 million during the past 18 months. CIQYP blames the poor performance on worldwide over-supply and falling prices, which have curbed exports, and low tariffs, which have spurred imports. It is calling for higher import tariffs and export incentives. The talks will also focus on a possible bond issue that would support companies willing to restructure and modernize operations. The main factor hindering competitiveness is what CIQYP president Alejandro Achaval calls Argentinean cost,more » including high energy costs, high provincial and federal taxes, and high financing charges. Since 1988, the industry has cut prices by 30%, formed mergers and joint ventures, closed 11 plants and started five new ones, slashed the workforce by 27%, and engaged in the government's privatization program. Meanwhile, plans to privatize 64% of aromatics producer Petroquimica General Mosconi(PGM) were derailed when potential bidders Diamond Shamrock, Shell, and Perez Companc refused for the second time to make offers on February 2. Jorge Olazabal, planning secretary of the Ministry of Defense, says PGM will be put up for sale again by March.« less
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Durability of template-free Fe-N-C foams for electrochemical oxygen reduction in alkaline solution
NASA Astrophysics Data System (ADS)
Mufundirwa, Albert; Harrington, George F.; Smid, Břetislav; Cunning, Benjamin V.; Sasaki, Kazunari; Lyth, Stephen M.
2018-01-01
Due to the high cost and limited availability of platinum, the development of non-platinum-group metals (non-PGM) catalysts is of paramount importance. A promising alternative to Pt are Fe-N-C-based materials. Here we present the synthesis, characterization and electrochemistry of a template-free nitrogen-doped carbon foam, impregnated with iron. This low-cost and gram-scale method results in materials with micron-scale pore size and large surface area (1600 m2g-1). When applied as an oxygen reduction reaction (ORR) electrocatalyst in alkaline solution, the Fe-N-C foams display extremely high initial activity, slightly out-performing commercially available non-PGM catalysts (NCP-2000, Pajarito Powder). The load-cycle durability in alkaline solution is investigated, and the performance steadily degrades over 60,000 potential cycles, whilst the commercial catalyst is remarkably stable. The post-operation catalyst microstructure is elucidated by transmission electron microscopy (TEM), to provide insight into the degradation processes. The resulting images suggest that potential cycling leads to leaching of atomically dispersed Fe-N2/4 sites in all the catalysts, whereas encapsulated iron nanoparticles are protected.
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Immunogenicity of peptides of measles virus origin and influence of adjuvants.
Halassy, Beata; Mateljak, Sanja; Bouche, Fabienne B; Pütz, Mike M; Muller, Claude P; Frkanec, Ruza; Habjanec, Lidija; Tomasić, Jelka
2006-01-12
Epitope-based peptide antigens have been under development for protection against measles virus. The immunogenicity of five peptides composed of the same B cell epitope (BCE) (H236-250 of the measles virus hemagglutinin), and different T cell epitopes of measles virus fusion protein (F421-435, F256-270, F288-302) and nucleoprotein (NP335-345) was studied in mice (subcutaneous immunisation). The adjuvant effects of peptidoglycan monomer (PGM), Montanide ISA 720 and 206 were also investigated. Results showed basic differences in peptide immunogenicity that were consistent with already described structural differences. PGM elevated peptide-specific IgG when applied together with four of five tested peptides. A strong synergistic effect was observed after co-immunisation of mice with a mixture containing all five chimeric peptides in small and equal amounts. Results revealed for the first time that immunisation with several peptides having the common BCE generated significantly higher levels of both anti-peptide and anti-BCE IgG in comparison to those obtained after immunisation with a single peptide in much higher quantity. Further improvement of immune response was obtained after incorporation of such a peptide mixture into oil-based adjuvants.
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Raymond M. Rice
1991-01-01
The proceedings contains 11 the 17 papers presented at the technical session on geometric hazards in managed forests at the XIX World Congress, International Union of Forestry Research Organizations, August 5-11, 1990, Montreal, Canada, plus one paper not presented orally. Two papers report research on torrents, two are about snow, three concern landslides, and five...