WorldWideScience

Sample records for efficient yeast chip-seq

  1. iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

    Science.gov (United States)

    Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

    2016-08-12

    Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the

  2. Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

    NARCIS (Netherlands)

    Johannes, Frank; Wardenaar, Rene; Colomé Tatché, Maria; Mousson, Florence; de Graaf, Petra; Mokry, Michal; Guryev, Victor; Timmers, H. Th. Marc; Cuppen, Edwin; Jansen, Ritsert C.; Bateman, Alex

    2010-01-01

    Motivation: ChIP-chip and ChIP-seq technologies provide genomewide measurements of various types of chromatin marks at an unprecedented resolution. With ChIP samples collected from different tissue types and/ or individuals, we can now begin to characterize stochastic or systematic changes in

  3. Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

    NARCIS (Netherlands)

    Johannes, F.; Wardenaar, R.; Colome-Tatche, M.; Mousson, F.; de Graaf, P.; Mokry, M.; Guryev, V.; Timmers, H.T.; Cuppen, E.; Jansen, R.

    2010-01-01

    MOTIVATION: ChIP-chip and ChIP-seq technologies provide genome-wide measurements of various types of chromatin marks at an unprecedented resolution. With ChIP samples collected from different tissue types and/or individuals, we can now begin to characterize stochastic or systematic changes in

  4. Efficient protein production by yeast requires global tuning of metabolism

    DEFF Research Database (Denmark)

    Huang, Mingtao; Bao, Jichen; Hallstrom, Bjorn M.

    2017-01-01

    The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous...... intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular...... that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion....

  5. Experiment list: SRX186172 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 1=YY1 || chip antibody manufacturer 1=Abcam || chip antibody 2=YY1 || chip antibody manufacturer 2=Santa Cru...ip-Seq; Mus musculus; ChIP-Seq source_name=Rag1 -/- pro-B cells || chip antibody

  6. SeqAn An efficient, generic C++ library for sequence analysis

    Directory of Open Access Journals (Sweden)

    Rausch Tobias

    2008-01-01

    Full Text Available Abstract Background The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome 1 would not have been possible without advanced assembly algorithms. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there is a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use. Results To remedy this trend we propose the use of SeqAn, a library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development. In this paper we describe the design and content of SeqAn and demonstrate its use by giving two examples. In the first example we show an application of SeqAn as an experimental platform by comparing different exact string matching algorithms. The second example is a simple version of the well-known MUMmer tool rewritten in SeqAn. Results indicate that our implementation is very efficient and versatile to use. Conclusion We anticipate that SeqAn greatly simplifies the rapid development of new bioinformatics tools by providing a collection of readily usable, well-designed algorithmic components which are fundamental for the field of sequence analysis. This leverages not only the implementation of new algorithms, but also enables a sound analysis and comparison of existing algorithms.

  7. Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

    Science.gov (United States)

    Guertin, Michael J; Cullen, Amy E; Markowetz, Florian; Holding, Andrew N

    2018-04-17

    A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.

  8. Experiment list: SRX150661 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Adenocarcinoma 59396606,71.7,11.1,1200 GSM935582: Harvard ChipSeq HeLa-S3 BRF1 std source_name=HeLa-S3 ||... biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq

  9. Experiment list: SRX150495 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Adenocarcinoma 62508352,67.6,8.4,1556 GSM935416: Harvard ChipSeq HeLa-S3 ZZZ3 std source_name=HeLa-S3 || ...biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq

  10. Experiment list: SRX150565 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available =Adenocarcinoma 54953593,74.3,12.2,1703 GSM935486: Harvard ChipSeq HeLa-S3 BDP1 std source_name=HeLa-S3 || b...iomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq |

  11. Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses.

    Science.gov (United States)

    Cubillos, Francisco A; Brice, Claire; Molinet, Jennifer; Tisné, Sebastién; Abarca, Valentina; Tapia, Sebastián M; Oporto, Christian; García, Verónica; Liti, Gianni; Martínez, Claudio

    2017-06-07

    Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1 , PDC1 , CPS1 , ASI2 , LYP1 , and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics. Copyright © 2017 Cubillos et al.

  12. Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

    Directory of Open Access Journals (Sweden)

    Francisco A. Cubillos

    2017-06-01

    Full Text Available Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics.

  13. Experiment list: SRX150586 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -Barr Virus 33195472,90.4,25.9,15633 GSM935507: Harvard ChipSeq GM12878 NF-YB IgG-mus source_name=GM12878 ||...?PgId=165&q=GM12878 || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq || dat

  14. Experiment list: SRX150496 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ein-Barr Virus 63040797,85.0,19.7,1435 GSM935417: Harvard ChipSeq GM12878 SPT20 std source_name=GM12878 || b...gId=165&q=GM12878 || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq || datat

  15. Experiment list: SRX150585 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -Barr Virus 32926476,94.0,12.0,2668 GSM935506: Harvard ChipSeq GM12878 NF-YA IgG-mus source_name=GM12878 || ...PgId=165&q=GM12878 || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipSeq || data

  16. 5'-end sequences of budding yeast full-length cDNA clones and quality scores - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available east_seq_qual.zip File URL: ftp://ftp.biosciencedbc.jp/archive/yeast_cdna/LATEST/...yeast_seq_qual.zip File size: 59.9MB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/budding_yeast_cdna

  17. A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(® for methylome profiling.

    Directory of Open Access Journals (Sweden)

    Christine Clark

    Full Text Available DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip® and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68 on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070, which may result in a more comprehensive study of the methylome.

  18. Experiment list: SRX107410 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Adenocarcinoma 37378122,96.3,56.7,376 GSM838388: h3k36me3 si23 ChIP-Seq; Homo sapiens; ChIP-Seq source_name=Hela cells knock...down Med23 || chip antibody=H3K36me3 || treatment=knockdown Med23 || cell line=HeLa || chip

  19. Experiment list: SRX085443 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX085443 mm9 Input control Input control Neural Cerebellum MeSH Description=The pa...ntain balance, and learn motor skills. 38330550,73.2,10.7,866 GSM769020: lab ChipSeq Cerebellum Input source_name=Cerebellum... Cancer Research || datatype=ChipSeq || datatype description=ChIP-Seq || cell=Cerebellum... || cell organism=mouse || cell description=Cerebellum || cell sex=M || antibody=Input || antibody de...on=Standard input signal for most experiments. || controlid=Cerebellum/Input/std || labversion=05/27/09 Lane

  20. Experiment list: SRX150629 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sue Diagnosis=Fibrocystic Disease 27949151,89.1,5.9,589 GSM935550: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pc...t 12hr Input std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harva...rd University || datatype=ChipSeq || datatype descriptio

  1. Experiment list: SRX150494 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available n-Barr Virus 44912180,85.6,7.7,1806 GSM935415: Harvard ChipSeq GM12878 GCN5 std source_name=GM12878 || bioma...ard || lab description=Struhl - Harvard University || datatype=ChipSeq || datatype ...terial_provider=Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878 || lab=Harv

  2. Experiment list: SRX150667 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available t|Tissue Diagnosis=Fibrocystic Disease 69172664,86.5,35.3,28780 GSM935588: Harvard ChipSeq MCF10A-Er-Src EtO...H 0.01pct Pol2 std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Har...vard University || datatype=ChipSeq || datatype descript

  3. Experiment list: SRX150535 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available t|Tissue Diagnosis=Fibrocystic Disease 69171580,86.8,43.7,20874 GSM935456: Harvard ChipSeq MCF10A-Er-Src 4OH...TAM 1uM 36hr Pol2 std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || ...lab description=Struhl - Harvard University || datatype=ChipSeq || datatype descr

  4. Experiment list: SRX150562 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -Barr Virus 57294082,73.4,6.6,1909 GSM935483: Harvard ChipSeq GM12878 ZZZ3 std source_name=GM12878 || biomat...rd || lab description=Struhl - Harvard University || datatype=ChipSeq || datatype d...erial_provider=Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878 || lab=Harva

  5. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads.

    Science.gov (United States)

    Song, Li; Florea, Liliana

    2015-01-01

    Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing. We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read. Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.

  6. Experiment list: SRX085450 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX085450 mm9 Histone H3K4me3 Neural Cerebellum MeSH Description=The part of brain ...e, and learn motor skills. 40109154,65.1,24.9,36907 GSM769027: lab ChipSeq Cerebellum H3K4me3 source_name=Cerebellum...Research || datatype=ChipSeq || datatype description=ChIP-Seq || cell=Cerebellum ...|| cell organism=mouse || cell description=Cerebellum || cell sex=M || antibody=H3K4me3 || antibody antibody...Standard input signal for most experiments. || controlid=Cerebellum/Input/std || labversion=5/26/09 Lane 6 |

  7. Experiment list: SRX085441 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX085441 mm9 Histone H3K4me1 Neural Cerebellum MeSH Description=The part of brain ...e, and learn motor skills. 34909537,81.0,5.9,29316 GSM769018: lab ChipSeq Cerebellum H3K4me1 source_name=Cerebellum...esearch || datatype=ChipSeq || datatype description=ChIP-Seq || cell=Cerebellum |...| cell organism=mouse || cell description=Cerebellum || cell sex=M || antibody=H3K4me1 || antibody antibodyd...iption=Standard input signal for most experiments. || controlid=Cerebellum/Input/std || labversion=12/09/09

  8. Impact of artefact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.

    Directory of Open Access Journals (Sweden)

    Thomas Samuel Carroll

    2014-04-01

    Full Text Available With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium’s large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency.

  9. An Energy-Efficient Reconfigurable Circuit Switched Network-on-Chip

    NARCIS (Netherlands)

    Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Rauwerda, G.K.; Smit, L.T.

    Network-on-Chip (NoC) is an energy-efficient on-chip communication architecture for multi-tile System-on-Chip (SoC) architectures. The SoC architecture, including its run-time software, can replace inflexible ASICs for future ambient systems. These ambient systems have to be flexible as well as

  10. Experiment list: SRX758028 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available agnosis=Carcinoma 82846335,87.8,5.7,22076 GSM1543791: LNCaP TOP1 ChIP-seq 30min vehicle; Homo sapiens; ChIP-...Seq source_name=ChIP-seq with BLRP-tagged TOP1, 30min treatment with vehicle || cell line=LNCaP || chip anti

  11. Experiment list: SRX148878 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available nosis=Carcinoma 71832151,98.1,33.1,1626 GSM934593: H2B ChIP-Seq USP49 knockdown; Homo sapiens; ChIP-Seq sour...ce_name=H2B ChIP-Seq USP49 knockdown || cell line=HCT116 || cell type=colorectal carcinoma || chip antibody=

  12. Experiment list: SRX148876 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available agnosis=Carcinoma 62096923,98.1,90.9,255 GSM934591: uH2b ChIP-Seq USP49 knockdown; Homo sapiens; ChIP-Seq so...urce_name=uH2b ChIP-Seq USP49 knockdown || cell line=HCT116 || cell type=colorectal carcinoma || chip antibo

  13. Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data

    NARCIS (Netherlands)

    Bao, Yanchun; Vinciotti, Veronica; Wit, Ernst; 't Hoen, Peter A C

    2013-01-01

    Background: ImmunoPrecipitation (IP) efficiencies may vary largely between different antibodies and between repeated experiments with the same antibody. These differences have a large impact on the quality of ChIP-seq data: a more efficient experiment will necessarily lead to a higher signal to

  14. Rapid, portable and cost-effective yeast cell viability and concentration analysis using lensfree on-chip microscopy and machine learning

    KAUST Repository

    Feizi, Alborz; Zhang, Yibo; Greenbaum, Alon; Guziak, Alex; Luong, Michelle; Chan, Raymond Yan Lok; Berg, Brandon; Ozkan, Haydar; Luo, Wei; Wu, Michael; Wu, Yichen; Ozcan, Aydogan

    2016-01-01

    and cost-effective automatic yeast analysis platform (AYAP), which can rapidly measure cell concentration and viability. AYAP is based on digital in-line holography and on-chip microscopy and rapidly images a large field-of-view of 22.5 mm2. This lens

  15. Rapid, portable and cost-effective yeast cell viability and concentration analysis using lensfree on-chip microscopy and machine learning

    KAUST Repository

    Feizi, Alborz

    2016-09-24

    Monitoring yeast cell viability and concentration is important in brewing, baking and biofuel production. However, existing methods of measuring viability and concentration are relatively bulky, tedious and expensive. Here we demonstrate a compact and cost-effective automatic yeast analysis platform (AYAP), which can rapidly measure cell concentration and viability. AYAP is based on digital in-line holography and on-chip microscopy and rapidly images a large field-of-view of 22.5 mm2. This lens-free microscope weighs 70 g and utilizes a partially-coherent illumination source and an opto-electronic image sensor chip. A touch-screen user interface based on a tablet-PC is developed to reconstruct the holographic shadows captured by the image sensor chip and use a support vector machine (SVM) model to automatically classify live and dead cells in a yeast sample stained with methylene blue. In order to quantify its accuracy, we varied the viability and concentration of the cells and compared AYAP\\'s performance with a fluorescence exclusion staining based gold-standard using regression analysis. The results agree very well with this gold-standard method and no significant difference was observed between the two methods within a concentration range of 1.4 × 105 to 1.4 × 106 cells per mL, providing a dynamic range suitable for various applications. This lensfree computational imaging technology that is coupled with machine learning algorithms would be useful for cost-effective and rapid quantification of cell viability and density even in field and resource-poor settings.

  16. Rapid, portable and cost-effective yeast cell viability and concentration analysis using lensfree on-chip microscopy and machine learning.

    Science.gov (United States)

    Feizi, Alborz; Zhang, Yibo; Greenbaum, Alon; Guziak, Alex; Luong, Michelle; Chan, Raymond Yan Lok; Berg, Brandon; Ozkan, Haydar; Luo, Wei; Wu, Michael; Wu, Yichen; Ozcan, Aydogan

    2016-11-01

    Monitoring yeast cell viability and concentration is important in brewing, baking and biofuel production. However, existing methods of measuring viability and concentration are relatively bulky, tedious and expensive. Here we demonstrate a compact and cost-effective automatic yeast analysis platform (AYAP), which can rapidly measure cell concentration and viability. AYAP is based on digital in-line holography and on-chip microscopy and rapidly images a large field-of-view of 22.5 mm 2 . This lens-free microscope weighs 70 g and utilizes a partially-coherent illumination source and an opto-electronic image sensor chip. A touch-screen user interface based on a tablet-PC is developed to reconstruct the holographic shadows captured by the image sensor chip and use a support vector machine (SVM) model to automatically classify live and dead cells in a yeast sample stained with methylene blue. In order to quantify its accuracy, we varied the viability and concentration of the cells and compared AYAP's performance with a fluorescence exclusion staining based gold-standard using regression analysis. The results agree very well with this gold-standard method and no significant difference was observed between the two methods within a concentration range of 1.4 × 10 5 to 1.4 × 10 6 cells per mL, providing a dynamic range suitable for various applications. This lensfree computational imaging technology that is coupled with machine learning algorithms would be useful for cost-effective and rapid quantification of cell viability and density even in field and resource-poor settings.

  17. Experiment list: SRX485203 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 346544: Rhino ChIP from control germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq ...source_name=Rhino ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult ||... Sex=female || tissue=ovary || germline knock-down=control || chip antibody=custo

  18. Experiment list: SRX485202 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 346543: Rhino ChIP from control germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq ...source_name=Rhino ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult ||... Sex=female || tissue=ovary || germline knock-down=control || chip antibody=custo

  19. Experiment list: SRX485210 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 6551: Deadlock ChIP from deadlock germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name...=Deadlock ChIP from deadlock germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=fe...male || tissue=ovary || germline knock-down=deadlock || chip antibody=custom-made

  20. Experiment list: SRX485211 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 346552: Cutoff ChIP from control germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=...Cutoff ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female... || tissue=ovary || germline knock-down=control || chip antibody=custom-made rabb

  1. In Silico Pooling of ChIP-seq Control Experiments

    Science.gov (United States)

    Sun, Guannan; Srinivasan, Rajini; Lopez-Anido, Camila; Hung, Holly A.; Svaren, John; Keleş, Sündüz

    2014-01-01

    As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation. Studying such variation requires individual level ChIP-seq experiments. Standard designs for ChIP-seq experiments employ a paired control per ChIP-seq sample. Genomic coverage for control experiments is often sacrificed to increase the resources for ChIP samples. However, the quality of ChIP-enriched regions identifiable from a ChIP-seq experiment depends on the quality and the coverage of the control experiments. Insufficient coverage leads to loss of power in detecting enrichment. We investigate the effect of in silico pooling of control samples within multiple biological replicates, multiple treatment conditions, and multiple cell lines and tissues across multiple datasets with varying levels of genomic coverage. Our computational studies suggest guidelines for performing in silico pooling of control experiments. Using vast amounts of ENCODE data, we show that pairwise correlations between control samples originating from multiple biological replicates, treatments, and cell lines/tissues can be grouped into two classes representing whether or not in silico pooling leads to power gain in detecting enrichment between the ChIP and the control samples. Our findings have important implications for multiplexing samples. PMID:25380244

  2. Experiment list: SRX185907 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP || cell_line=MCF-...7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=DMSO || chip_

  3. Experiment list: SRX150520 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available osis=Fibrocystic Disease 49296691,89.4,24.9,46885 GSM935441: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pct c-Myc Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harv...|| antibody vendorid=sc-764 || control=Harvard_Control || control description=input library was prepared at Harvard. || control=Harva...rd_Control || control description=input library was prepared at Harvard...ard University || datatype=ChipSeq || datatype descripti

  4. Experiment list: SRX150478 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available osis=Fibrocystic Disease 66690540,98.1,24.9,110111 GSM935398: Harvard ChipSeq MCF10A-Er-Src 4OHTAM 1uM 12hr c-Fos Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || ...lab description=Struhl - Harvard University || datatype=ChipSeq || datatype descr... is a leucine-zipper. || antibody vendorname=Santa Cruz Biotech || antibody vendorid=sc-7202 || control=Harvard..._Control || control description=input library was prepared at Harvard. || control=Harvard

  5. Experiment list: SRX150696 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -1 || cell organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX150696 hg19 Input control Input control Pancreas PANC-1 Tissue=Pancreas/Duct|Dis...ease=Epithelioid Carcinoma 41671673,95.8,10.4,1584 GSM935617: USC ChipSeq PANC-1 Input UCDavis source_name=PANC... || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || cell=PANC...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Cau

  6. Experiment list: SRX199860 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available | cell organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX199860 hg19 Input control Input control Pancreas PANC-1 Tissue=Pancreas/Duct|Dis...ease=Epithelioid Carcinoma 27365308,98.2,3.6,969 GSM1022632: UW ChipSeq PANC-1 InputRep1 source_name=PANC-1 ...datatype=ChipSeq || datatype description=Chromatin IP Sequencing || cell=PANC-1 |...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasi

  7. Experiment list: SRX977433 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ates NA 65512838,98.3,15.4,34790 GSM1648684: RNAPII ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 15days of induction || cell type=reprogramming intermediate || genotype=RNAPII-GF

  8. Experiment list: SRX977429 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ates NA 57685706,97.8,16.7,27894 GSM1648680: RNAPII ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 3days of induction || cell type=reprogramming intermediate || genotype=RNAPII-GFP/

  9. Experiment list: SRX977432 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ates NA 56429535,98.1,16.9,32459 GSM1648683: RNAPII ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 11days of induction || cell type=reprogramming intermediate || genotype=RNAPII-GF

  10. Experiment list: SRX185915 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available mo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP || cell_line=MCF-7 |...| cell_type=ER-positive breast adenocarcinoma cells || treatment=DMSO || chip_tar

  11. Experiment list: SRX185909 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available omo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP || cell_line=MCF-7 ...|| cell_type=ER-positive breast adenocarcinoma cells || treatment=DMSO || chip_ta

  12. Experiment list: SRX185917 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available omo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP || cell_line=MCF-7 ...|| cell_type=ER-positive breast adenocarcinoma cells || treatment=DMSO || chip_ta

  13. Experiment list: SRX485205 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 46546: Rhino ChIP from deadlock germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=R...hino ChIP from deadlock germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female ...|| tissue=ovary || germline knock-down=deadlock || chip antibody=custom-made rabb

  14. Experiment list: SRX485212 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 346553: Cutoff ChIP from cutoff germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=C...utoff ChIP from cutoff germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female |...| tissue=ovary || germline knock-down=cutoff || chip antibody=custom-made rabbit

  15. Experiment list: SRX485206 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 346547: Rhino ChIP from cutoff germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=Rh...ino ChIP from cutoff germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female || ...tissue=ovary || germline knock-down=cutoff || chip antibody=custom-made rabbit po

  16. Experiment list: SRX485209 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 346550: Deadlock ChIP from control germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_nam...e=Deadlock ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=fe...male || tissue=ovary || germline knock-down=control || chip antibody=custom-made

  17. An engineered yeast efficiently secreting penicillin.

    Directory of Open Access Journals (Sweden)

    Loknath Gidijala

    Full Text Available This study aimed at developing an alternative host for the production of penicillin (PEN. As yet, the industrial production of this beta-lactam antibiotic is confined to the filamentous fungus Penicillium chrysogenum. As such, the yeast Hansenula polymorpha, a recognized producer of pharmaceuticals, represents an attractive alternative. Introduction of the P. chrysogenum gene encoding the non-ribosomal peptide synthetase (NRPS delta-(L-alpha-aminoadipyl-L-cysteinyl-D-valine synthetase (ACVS in H. polymorpha, resulted in the production of active ACVS enzyme, when co-expressed with the Bacillus subtilis sfp gene encoding a phosphopantetheinyl transferase that activated ACVS. This represents the first example of the functional expression of a non-ribosomal peptide synthetase in yeast. Co-expression with the P. chrysogenum genes encoding the cytosolic enzyme isopenicillin N synthase as well as the two peroxisomal enzymes isopenicillin N acyl transferase (IAT and phenylacetyl CoA ligase (PCL resulted in production of biologically active PEN, which was efficiently secreted. The amount of secreted PEN was similar to that produced by the original P. chrysogenum NRRL1951 strain (approx. 1 mg/L. PEN production was decreased over two-fold in a yeast strain lacking peroxisomes, indicating that the peroxisomal localization of IAT and PCL is important for efficient PEN production. The breakthroughs of this work enable exploration of new yeast-based cell factories for the production of (novel beta-lactam antibiotics as well as other natural and semi-synthetic peptides (e.g. immunosuppressive and cytostatic agents, whose production involves NRPS's.

  18. Experiment list: SRX485220 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 53 GSM1346561: RNA Polymerase II ChIP from rhino germline knock-down ovaries; Drosophila melanogaster; ChIP-...Seq source_name=RNA Polymerase II ChIP from rhino germline knock-down ovaries || developmental stage=4-6 day...s old adult || Sex=female || tissue=ovary || germline knock-down=rhino || chip an

  19. Experiment list: SRX485204 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 346545: Rhino ChIP from rhino germline knock-down ovaries; Drosophila melanogaster; ChIP-Seq source_name=Rhi...no ChIP from rhino germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female || ti...ssue=ovary || germline knock-down=rhino || chip antibody=custom-made rabbit polyc

  20. Experiment list: SRX485208 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 346549: Rhino ChIP from piwi germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq sou...rce_name=Rhino ChIP from piwi germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=f...emale || tissue=ovary || germline knock-down=piwi || chip antibody=custom-made ra

  1. Experiment list: SRX190029 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available l organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX190029 hg19 Input control Input control Pancreas PANC-1 Tissue=Pancreas/Duct|Dis...ease=Epithelioid Carcinoma 27365308,98.2,3.6,980 GSM945246: UW ChipSeq PANC-1 Input source_name=PANC-1 || bi...ype=ChipSeq || datatype description=Chromatin IP Sequencing || cell=PANC-1 || cel...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian in

  2. Experiment list: SRX977378 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 23908,98.7,9.6,43208 GSM1648629: total Oct4 ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming ...intermediate after 11days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26-

  3. Experiment list: SRX977377 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 40719,98.1,13.8,57202 GSM1648628: total Oct4 ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming ...intermediate after 7days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26-M

  4. Experiment list: SRX977366 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available NA 60072229,98.6,9.6,78331 GSM1648617: flag Oct4 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 24hour of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Ros

  5. Experiment list: SRX977375 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 20178,94.6,10.8,52926 GSM1648626: total Oct4 ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming ...intermediate after 3days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26-M

  6. Experiment list: SRX977379 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 93532,97.8,13.3,43901 GSM1648630: total Oct4 ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 15days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26

  7. Experiment list: SRX977368 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available NA 58474287,97.8,9.8,84163 GSM1648619: flag Oct4 ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 5days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa

  8. Experiment list: SRX977369 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available NA 58631406,98.5,10.3,72036 GSM1648620: flag Oct4 ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 7days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Ros

  9. Experiment list: SRX684775 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ng || cell type=intermediate stage of somatic cell reprogramming || chip antibody=M...,29.2,290321 GSM1483904: pre-iPS.H3.MNase-ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogrammi

  10. Experiment list: SRX977371 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available NA 63273752,96.7,14.1,37891 GSM1648622: flag Oct4 ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming... intermediate after 15days of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ R

  11. Experiment list: SRX1090864 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ming || cell type=intermediate stage of somatic cell reprogramming || chip antibody...5,12.8,491 GSM1816301: pre-iPS rep.H3.MNase-ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogram

  12. Experiment list: SRX107407 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available osis=Adenocarcinoma 37670219,66.5,15.7,675 GSM838385: hnrnpl sictrl ChIP-Seq; Homo sapiens; ChIP-Seq source_name=Hela cells knock...down control || chip antibody=hnRNP L || treatment=knockdown control || cell line=HeLa

  13. Experiment list: SRX1122118 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available M1833874: ChIP-seq H3K27Ac DMSO; Homo sapiens; ChIP-Seq source_name=Cultured Leukemic Blasts || chip antibod...y=H3K27ac (ActiveMotif, ab4729) || tissue=Cultured Leukemic Blasts || treatment compound=DMSO http://dbarchi

  14. Experiment list: SRX977374 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 16864,98.6,9.4,51198 GSM1648625: total Oct4 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming i...ntermediate after 24hour of induction || cell type=reprogramming intermediate || genotype=Oct4-GFP/ Rosa26-M

  15. Experiment list: SRX152077 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ll organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX152077 hg19 Histone H3K4me3 Pancreas PANC-1 Tissue=Pancreas/Duct|Disease=Epithel...ioid Carcinoma 53620150,97.5,34.9,29597 GSM945856: USC ChipSeq PANC-1 H3K4me3B UCDavis source_name=PANC-1 ||...type=ChipSeq || datatype description=Chromatin IP Sequencing || cell=PANC-1 || ce...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian i

  16. Experiment list: SRX352046 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SM1232564: CSB M CHIP; Homo sapiens; ChIP-Seq source_name=fibroblast_menadione_CSB-ChIP || cell type=fibroblast || treated with=menad...ione || chip antibody=Mouse monoclonal anti-CSB N Terminus (1B1) http://dbarchive.b

  17. Experiment list: SRX144526 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available stein-Barr Virus transformed 11803840,92.5,91.6,38 GSM922971: NRF2 ChIP vehicle treated rep2; Homo sapiens; ...ChIP-Seq source_name=NRF2 ChIP vehicle treated || biomaterial_provider=Coriell; h

  18. Experiment list: SRX151245 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 0: CTCF ChIPSeq; Homo sapiens; ChIP-Seq source_name=BCBL1 pleural effusion lymphoma, CTCF ChIP || cell line=...BCBL1 || cell type=KSHV-infected pleural effusion lymphoma cells || chip antibody=rabbit anti-CTCF || antibo

  19. Experiment list: SRX485222 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 4me2 ChIP from control germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq source_na...me=H3K4me2 ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=fe...male || tissue=ovary || germline knock-down=control || chip antibody=Anti-dimethy

  20. Experiment list: SRX485221 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available K4me2 ChIP from control germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq source_n...ame=H3K4me2 ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=f...emale || tissue=ovary || germline knock-down=control || chip antibody=Anti-dimeth

  1. Experiment list: SRX684777 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ing || cell type=intermediate stage of somatic cell reprogramming || chip antibody=...,98.5,5.8,239 GSM1483906: pre-iPS.H3K27me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogramm

  2. Experiment list: SRX1122119 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 04 GSM1833875: ChIP-seq H3K27Ac GSI; Homo sapiens; ChIP-Seq source_name=Cultured Leukemic Blasts || chip ant...ibody=H3K27ac (ActiveMotif, ab4729) || tissue=Cultured Leukemic Blasts || treatment compound=GSI BMS-906024

  3. Experiment list: SRX1090865 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available amming || cell type=intermediate stage of somatic cell reprogramming || chip antibo...,95.9,8.5,270 GSM1816302: pre-iPS rep.H3K4me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogr

  4. Experiment list: SRX684776 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ng || cell type=intermediate stage of somatic cell reprogramming || chip antibody=a...98.0,10.6,335 GSM1483905: pre-iPS.H3K4me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogrammi

  5. Experiment list: SRX897943 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 153,97.9,13.9,15440 GSM1624628: ChIP seq Renilla Sox2 IP day3; Mus musculus; ChIP-Seq source_name=OKSM reprogramming... intermediates from Mouse Embryonic Fibroblasts || strain=Black6-129X1/SvJ || cell type=OKSM reprogramming

  6. Experiment list: SRX684778 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.0,9.9,325 GSM1483907: pre-iPS.H3K9me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell reprogrammin...g || cell type=intermediate stage of somatic cell reprogramming || chip antibody=an

  7. Experiment list: SRX150568 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Adenocarcinoma 59265240,72.4,16.4,4779 GSM935489: Harvard ChipSeq HeLa-S3 RPC155 std source_name=HeLa-S3 ...|| biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=ChipS

  8. Experiment list: SRX507380 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available + (wildtype) || age of animals=1-5 day old || tissue=Ovaries || chip antibody=anti-HP1 || chip antibody vend...1770: WT anti-HP1- replicate#2; Drosophila melanogaster; ChIP-Seq source_name=WT_WT_anti-HP1 || strain=piwi/

  9. Experiment list: SRX176054 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available nosis=Carcinoma 13338805,91.2,4.9,792 GSM984386: LNCAP AR vehicle; Homo sapiens; ChIP-Seq source_name=prosta...te cancer cells || cell line=LNCaP || chip antibody=AR || chip antibody manufacturer=Abcam || treatment=EtOH vehicle

  10. Experiment list: SRX144525 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available neage=mesoderm|Description=parental cell type to lymphoblastoid cell lines 14487710,85.8,82.8,188 GSM922970: NRF2 ChIP vehicle... treated rep1; Homo sapiens; ChIP-Seq source_name=NRF2 ChIP vehicle treated || biomaterial

  11. Experiment list: SRX144524 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available neage=mesoderm|Description=parental cell type to lymphoblastoid cell lines 4766716,6.2,89.4,0 GSM922969: NRF2 ChIP vehicle... treated pilot; Homo sapiens; ChIP-Seq source_name=NRF2 ChIP vehicle treated || biomaterial_pr

  12. Experiment list: SRX151246 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 11: SMC1 ChIPSeq; Homo sapiens; ChIP-Seq source_name=BCBL1 pleural effusion lymphoma, SMC1 ChIP || cell line...=BCBL1 || cell type=KSHV-infected pleural effusion lymphoma cells || chip antibody=rabbit anti-SMC1 || antib

  13. Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq

    DEFF Research Database (Denmark)

    Jakobsen, Janus S; Bagger, Frederik O; Hasemann, Marie S

    2015-01-01

    BACKGROUND: Chromatin-Immunoprecipitation coupled with deep sequencing (ChIP-seq) is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libraries has impeded ChIP-seq on in vivo tissues of low...... transcription factor (CEBPA) and histone mark (H3K4me3) ChIP. We further demonstrate that genomic profiles are highly resilient to changes in carrier DNA to ChIP DNA ratios. CONCLUSIONS: This represents a significant advance compared to existing technologies, which involve either complex steps of pre...... cell numbers. RESULTS: We describe a robust, simple and scalable methodology for ChIP-seq of low-abundant cell populations, verified down to 10,000 cells. By employing non-mammalian genome mapping bacterial carrier DNA during amplification, we reliably amplify down to 50 pg of ChIP DNA from...

  14. Experiment list: SRX897941 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 081,98.0,12.4,11292 GSM1624626: ChIP seq Chaf1a.166 Sox2 IP day3; Mus musculus; ChIP-Seq source_name=OKSM reprogramming... intermediates from Mouse Embryonic Fibroblasts || strain=Black6-129X1/SvJ || cell type=OKSM reprogramming

  15. Experiment list: SRX1090866 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available gramming || cell type=intermediate stage of somatic cell reprogramming || chip anti...1,96.8,4.5,197 GSM1816303: pre-iPS rep.H3K27me3.ChIP-Seq; Mus musculus; ChIP-Seq source_name=intermediate stage of somatic cell repro

  16. Experiment list: SRX107409 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Adenocarcinoma 38890980,97.0,45.8,396 GSM838387: h3k36me3 sictrl ChIP-Seq; Homo sapiens; ChIP-Seq source_name=Hela cells knock...down control || chip antibody=H3K36me3 || treatment=knockdown control || cell line=HeLa ||

  17. Experiment list: SRX485218 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available K9me3 ChIP from piwi germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq source_name...=H3K9me3 ChIP from piwi germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female ...|| tissue=ovary || germline knock-down=piwi || chip antibody=Histone H3K9me3 anti

  18. Experiment list: SRX485213 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available K9me3 ChIP from control germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq source_n...ame=H3K9me3 ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=f...emale || tissue=ovary || germline knock-down=control || chip antibody=Histone H3K

  19. Experiment list: SRX485214 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available K9me3 ChIP from control germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq source_n...ame=H3K9me3 ChIP from control germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=f...emale || tissue=ovary || germline knock-down=control || chip antibody=Histone H3K

  20. Experiment list: SRX153146 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -Seq source_name=Human breast adenocarcinoma cell-line MCF7 || cell-line=MCF7 || passage=5 || chip antibody=...n=Pleura|Tissue Diagnosis=Adenocarcinoma 60170246,98.4,5.7,16756 GSM946850: MCF7 H3K27ac; Homo sapiens; ChIP

  1. Experiment list: SRX176063 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available =Carcinoma 11279321,95.5,3.6,13985 GSM984395: LNCAP ACH3 vehicle; Homo sapiens; ChIP-Seq source_name=prostat...e cancer cells || cell line=LNCaP || chip antibody=AcH3 || chip antibody manufacturer=Millipore || treatment=EtOH vehicle

  2. Experiment list: SRX176057 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available nosis=Carcinoma 21582823,90.1,7.3,1074 GSM984389: 22RV1 AR vehicle; Homo sapiens; ChIP-Seq source_name=prost...ate cancer cells || cell line=22RV1 || chip antibody=AR || chip antibody manufacturer=Abcam || treatment=EtOH vehicle

  3. Experiment list: SRX144527 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available neage=mesoderm|Description=parental cell type to lymphoblastoid cell lines 8704444,92.1,92.5,9 GSM922972: NRF2 ChIP vehicle... treated rep3; Homo sapiens; ChIP-Seq source_name=NRF2 ChIP vehicle treated || biomaterial_pr

  4. Experiment list: SRX160914 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available M970829: IgG for KSHV LANA; Homo sapiens; ChIP-Seq source_name=BCBL1 pleural effusion lymphoma, IgG ChIP || ...cell line=BCBL1 || cell type=KSHV-infected pleural effusion lymphoma cells || chip antibody=Rabbit IgG [Sant

  5. Experiment list: SRX160915 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available M970828: IgG for CTCF SMC1; Homo sapiens; ChIP-Seq source_name=BCBL1 pleural effusion lymphoma, IgG ChIP || ...cell line=BCBL1 || cell type=KSHV-infected pleural effusion lymphoma cells || chip antibody=Mouse IgG [Santa

  6. Experiment list: SRX977401 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.9,13.8,95651 GSM1648652: H3K27ac ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 24hour of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA

  7. Experiment list: SRX977402 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.8,11.6,43739 GSM1648653: H3K27ac ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 3days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA

  8. Experiment list: SRX977406 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.9,8.3,18501 GSM1648657: H3K27ac ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 15days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA

  9. Experiment list: SRX218536 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available strain=C57Bl/6 || age/gender=2-3 month old males || chip antibody=Santa Cruz Tech. rIgG (sc-2027) http://db....7,16.5,1194 GSM1067409: Rabbit IgG mouse liver ChIP-seq; Mus musculus; ChIP-Seq GEO Accession=GSM1067409 ||

  10. Experiment list: SRX977405 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.9,7.4,10239 GSM1648656: H3K27ac ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 11days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA

  11. Experiment list: SRX153147 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -Seq source_name=Human breast adenocarcinoma cell-line MCF7 || cell-line=MCF7 || passage=5 || chip antibody=...on=Pleura|Tissue Diagnosis=Adenocarcinoma 64054379,98.7,5.2,764 GSM946851: MCF7 H3K27me3; Homo sapiens; ChIP

  12. Experiment list: SRX153148 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -Seq source_name=Human breast adenocarcinoma cell-line MCF7 || cell-line=MCF7 || passage=5 || chip antibody=...n=Pleura|Tissue Diagnosis=Adenocarcinoma 57306360,95.7,15.1,2666 GSM946852: MCF7 H3K9me3; Homo sapiens; ChIP

  13. Experiment list: SRX485216 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 3K9me3 ChIP from rhino germline knock-down ovaries, replicate 2; Drosophila melanogaster; ChIP-Seq source_na...me=H3K9me3 ChIP from rhino germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=fema...le || tissue=ovary || germline knock-down=rhino || chip antibody=Histone H3K9me3

  14. Experiment list: SRX485215 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available K9me3 ChIP from rhino germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq source_nam...e=H3K9me3 ChIP from rhino germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=femal...e || tissue=ovary || germline knock-down=rhino || chip antibody=Histone H3K9me3 a

  15. Experiment list: SRX485217 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 3K9me3 ChIP from piwi germline knock-down ovaries, replicate 1; Drosophila melanogaster; ChIP-Seq source_nam...e=H3K9me3 ChIP from piwi germline knock-down ovaries || developmental stage=4-6 days old adult || Sex=female... || tissue=ovary || germline knock-down=piwi || chip antibody=Histone H3K9me3 ant

  16. Experiment list: SRX977412 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 99.3,28.8,54450 GSM1648663: H3K4me3 ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 5days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtTA

  17. Experiment list: SRX977420 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ,98.5,9.4,5405 GSM1648671: H3K27me3 ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 3days of induction || cell type=reprogramming intermediate || genotype=H3K27me3-GFP/ Rosa26-M2rtTA

  18. Experiment list: SRX977415 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 97.4,25.7,24253 GSM1648666: H3K4me3 ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming intermed...iate after 15days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtT

  19. Experiment list: SRX977394 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 99.1,7.7,102329 GSM1648645: H3K4me1 ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 5days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA

  20. Experiment list: SRX977423 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ,99.0,6.9,4818 GSM1648674: H3K27me3 ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming intermed...iate after 11days of induction || cell type=reprogramming intermediate || genotype=H3K27me3-GFP/ Rosa26-M2rt

  1. Experiment list: SRX977392 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.9,6.9,91916 GSM1648643: H3K4me1 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 24hour of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA

  2. Experiment list: SRX977411 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 99.2,25.6,52503 GSM1648662: H3K4me3 ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 3days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtTA

  3. Experiment list: SRX977410 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 99.3,25.0,46365 GSM1648661: H3K4me3 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 24hour of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtTA

  4. Experiment list: SRX977421 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ,98.5,10.5,6589 GSM1648672: H3K27me3 ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming intermed...iate after 5days of induction || cell type=reprogramming intermediate || genotype=H3K27me3-GFP/ Rosa26-M2rtT

  5. Experiment list: SRX977396 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 99.3,8.4,86055 GSM1648647: H3K4me1 ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 11days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA

  6. Experiment list: SRX977413 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 97.5,28.8,20673 GSM1648664: H3K4me3 ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 7days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtTA

  7. Experiment list: SRX977419 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ,99.0,7.8,3913 GSM1648670: H3K27me3 ChipSeq day1; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 24hour of induction || cell type=reprogramming intermediate || genotype=H3K27me3-GFP/ Rosa26-M2rtT

  8. Experiment list: SRX977404 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 99.1,5.7,17625 GSM1648655: H3K27ac ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 7days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA t

  9. Experiment list: SRX977414 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.5,25.1,26501 GSM1648665: H3K4me3 ChipSeq day11; Mus musculus; ChIP-Seq source_name=reprogramming intermed...iate after 11days of induction || cell type=reprogramming intermediate || genotype=H3K4me3-GFP/ Rosa26-M2rtT

  10. Experiment list: SRX977397 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.9,8.9,45421 GSM1648648: H3K4me1 ChipSeq day15; Mus musculus; ChIP-Seq source_name=reprogramming intermedi...ate after 15days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA

  11. Experiment list: SRX977403 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.9,9.4,35286 GSM1648654: H3K27ac ChipSeq day5; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 5days of induction || cell type=reprogramming intermediate || genotype=H3K27ac-GFP/ Rosa26-M2rtTA t

  12. Experiment list: SRX119679 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 8,18360 GSM874985: ES.H3K27me3; Homo sapiens; ChIP-Seq source_name=H1 human Embryonic stem cells || cell line=H1 || treatment=diagnos...tic sample (pre-treatment) || chip antibody=H3K27me3 || chip antibody manufacturer=

  13. Experiment list: SRX119684 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 2,13603 GSM874990: ES.H3K79me2; Homo sapiens; ChIP-Seq source_name=H1 human Embryonic stem cell || cell line=H1 || treatment=diagnost...ic sample (pre-treatment) || chip antibody=H3K79me2 || chip antibody manufacturer=A

  14. Experiment list: SRX977393 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.8,8.9,31577 GSM1648644: H3K4me1 ChipSeq day3; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 3days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA t

  15. Experiment list: SRX977395 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 98.7,7.3,62664 GSM1648646: H3K4me1 ChipSeq day7; Mus musculus; ChIP-Seq source_name=reprogramming intermedia...te after 7days of induction || cell type=reprogramming intermediate || genotype=H3K4me1-GFP/ Rosa26-M2rtTA t

  16. Experiment list: SRX507384 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available + (wildtype) || age of animals=1-5 day old || tissue=Ovaries || chip antibody=Anti-H3K4me2 || chip antibody ... Anti-H3K4me2- replicate#2; Drosophila melanogaster; ChIP-Seq source_name=WT_WT_Anti-H3K4me2 || strain=piwi/

  17. Experiment list: SRX507382 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available + (wildtype) || age of animals=1-5 day old || tissue=Ovaries || chip antibody=Anti-H3K9me3 || chip antibody ... Anti-H3K9me3- replicate#2; Drosophila melanogaster; ChIP-Seq source_name=WT_WT_Anti-H3K9me3 || strain=piwi/

  18. CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis.

    Directory of Open Access Journals (Sweden)

    Iman Rezaeian

    Full Text Available Genome-wide profiling of DNA-binding proteins using ChIP-Seq has emerged as an alternative to ChIP-chip methods. ChIP-Seq technology offers many advantages over ChIP-chip arrays, including but not limited to less noise, higher resolution, and more coverage. Several algorithms have been developed to take advantage of these abilities and find enriched regions by analyzing ChIP-Seq data. However, the complexity of analyzing various patterns of ChIP-Seq signals still needs the development of new algorithms. Most current algorithms use various heuristics to detect regions accurately. However, despite how many formulations are available, it is still difficult to accurately determine individual peaks corresponding to each binding event. We developed Constrained Multi-level Thresholding (CMT, an algorithm used to detect enriched regions on ChIP-Seq data. CMT employs a constraint-based module that can target regions within a specific range. We show that CMT has higher accuracy in detecting enriched regions (peaks by objectively assessing its performance relative to other previously proposed peak finders. This is shown by testing three algorithms on the well-known FoxA1 Data set, four transcription factors (with a total of six antibodies for Drosophila melanogaster and the H3K4ac antibody dataset.

  19. Experiment list: SRX176067 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sis=Carcinoma 6619400,91.7,7.2,13648 GSM984399: LNCAP H3K4ME3 vehicle; Homo sapiens; ChIP-Seq source_name=pr...ostate cancer cells || cell line=LNCaP || chip antibody=H3K4Me3 || chip antibody manufacturer=Millipore || treatment=EtOH vehicle

  20. Experiment list: SRX485219 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 56 GSM1346560: RNA Polymerase II ChIP from control germline knock-down ovaries; Drosophila melanogaster; ChI...P-Seq source_name=RNA Polymerase II ChIP from control germline knock-down ovaries || developmental stage=4-6... days old adult || Sex=female || tissue=ovary || germline knock-down=control || c

  1. Limitations and possibilities of low cell number ChIP-seq

    Directory of Open Access Journals (Sweden)

    Gilfillan Gregor D

    2012-11-01

    Full Text Available Abstract Background Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP, we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers. Results We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells. Conclusions The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells, and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance.

  2. Ethanol fermentation from lignocellulosic hydrolysate by a recombinant xylose- and cellooligosaccharide-assimilating yeast strain

    Energy Technology Data Exchange (ETDEWEB)

    Katahira, Satoshi; Fukuda, Hideki [Kobe Univ. (Japan). Div. of Molecular Science; Mizuike, Atsuko; Kondo, Akihiko [Kobe Univ. (Japan). Dept. of Chemical Science and Engineering

    2006-10-15

    The sulfuric acid hydrolysate of lignocellulosic biomass, such as wood chips, from the forest industry is an important material for fuel bioethanol production. In this study, we constructed a recombinant yeast strain that can ferment xylose and cellooligosaccharides by integrating genes for the intercellular expressions of xylose reductase and xylitol dehydrogenase from Pichia stipitis, and xylulokinase from Saccharomyces cerevisiae and a gene for displaying ss-glucosidase from Aspergillus acleatus on the cell surface. In the fermentation of the sulfuric acid hydrolysate of wood chips, xylose and cellooligosaccharides were completely fermented after 36 h by the recombinant strain, and then about 30 g/l ethanol was produced from 73 g/l total sugar added at the beginning. In this case, the ethanol yield of this recombinant yeast was much higher than that of the control yeast. These results demonstrate that the fermentation of the lignocellulose hydrolysate is performed efficiently by the recombinant Saccharomyces strain with abilities for xylose assimilation and cellooligosaccharide degradation. (orig.)

  3. Experiment list: SRX688848 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available d prostate cancer cell line || treatment=vehicle || chip antibody=rabbit anti-ASH... prostate cancer cells, vehicle, ASH2 ChIP || cell line=VCaP || cell type=vertebral metastatic lesion-derive...agnosis=Carcinoma 25750434,89.3,6.2,7152 GSM1489926: vcap ash2l veh; Homo sapiens; ChIP-Seq source_name=VCaP

  4. Optimal use of tandem biotin and V5 tags in ChIP assays

    NARCIS (Netherlands)

    K.E. Kolodziej (Katarzyna); F. Pourfarzad, F. (Farzin); E. de Boer (Ernie); S. Krpic (Sanja); F.G. Grosveld (Frank); J. Strouboulis (John)

    2009-01-01

    textabstractBackground: Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays (Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the

  5. Single-Cell mRNA-Seq Using the Fluidigm C1 System and Integrated Fluidics Circuits.

    Science.gov (United States)

    Gong, Haibiao; Do, Devin; Ramakrishnan, Ramesh

    2018-01-01

    Single-cell mRNA-seq is a valuable tool to dissect expression profiles and to understand the regulatory network of genes. Microfluidics is well suited for single-cell analysis owing both to the small volume of the reaction chambers and easiness of automation. Here we describe the workflow of single-cell mRNA-seq using C1 IFC, which can isolate and process up to 96 cells. Both on-chip procedure (lysis, reverse transcription, and preamplification PCR) and off-chip sequencing library preparation protocols are described. The workflow generates full-length mRNA information, which is more valuable compared to 3' end counting method for many applications.

  6. Experiment list: SRX142526 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available source_name=C2C12 || biomaterial_provider=Barbara Wold lab || lab=Caltech-m || lab description=Wold - Califonia Institute of Technolo...gy || datatype=ChipSeq || datatype description=Chromatin

  7. ‘Chip-olate’ and dry-film resists for efficient fabrication, singulation and sealing of microfluidic chips

    Science.gov (United States)

    Temiz, Yuksel; Delamarche, Emmanuel

    2014-09-01

    This paper describes a technique for high-throughput fabrication and efficient singulation of chips having closed microfluidic structures and takes advantage of dry-film resists (DFRs) for efficient sealing of capillary systems. The technique is illustrated using 4-inch Si/SiO2 wafers. Wafers carrying open microfluidic structures are partially diced to about half of their thickness. Treatments such as surface cleaning are done at wafer-level, then the structures are sealed using low-temperature (45 °C) lamination of a DFR that is pre-patterned using a craft cutter, and ready-to-use chips are finally separated manually like a chocolate bar by applying a small force (≤ 4 N). We further show that some DFRs have low auto-fluorescence at wavelengths typically used for common fluorescent dyes and that mechanical properties of some DFRs allow for the lamination of 200 μm wide microfluidic structures with negligible sagging (~1 μm). The hydrophilicity (advancing contact angle of ~60°) of the DFR supports autonomous capillary-driven flow without the need for additional surface treatment of the microfluidic chips. Flow rates from 1 to 5 µL min-1 are generated using different geometries of channels and capillary pumps. In addition, the ‘chip-olate’ technique is compatible with the patterning of capture antibodies on DFR for use in immunoassays. We believe this technique to be applicable to the fabrication of a wide range of microfluidic and lab-on-a-chip devices and to offer a viable alternative to many labor-intensive processes that are currently based on wafer bonding techniques or on the molding of poly(dimethylsiloxane) (PDMS) layers.

  8. Experiment list: SRX620297 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available body=Pol II (Santa Cruz Biotechnology, N20, sc-899) http://dbarchive.biosciencedb...IP-Seq source_name=NIH3T3 fibroblasts || culture condition=continuous culture || chemicals=DMSO || chip anti

  9. Experiment list: SRX142520 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Califonia Institute of Technology || datatype=ChipSeq || datatype description=Ch...t 24hr source_name=C2C12 || biomaterial_provider=Barbara Wold lab || lab=Caltech-m || lab description=Wold -

  10. Experiment list: SRX143619 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Califonia Institute of Technology || datatype=ChipSeq || datatype description=Ch...t 24hr source_name=C2C12 || biomaterial_provider=Barbara Wold lab || lab=Caltech-m || lab description=Wold -

  11. Experiment list: SRX142522 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Califonia Institute of Technology || datatype=ChipSeq || datatype description=Ch...t 60hr source_name=C2C12 || biomaterial_provider=Barbara Wold lab || lab=Caltech-m || lab description=Wold -

  12. SignalSpider: Probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles

    KAUST Repository

    Wong, Kachun; Li, Yue; Peng, Chengbin; Zhang, Zhaolei

    2014-01-01

    Motivation: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in vivo. Different combinations of DNA-binding protein occupancies may result in a gene

  13. Hard rock tunnel boring machine penetration test as an indicator of chipping process efficiency

    Directory of Open Access Journals (Sweden)

    M.C. Villeneuve

    2017-08-01

    Full Text Available The transition from grinding to chipping can be observed in tunnel boring machine (TBM penetration test data by plotting the penetration rate (distance/revolution against the net cutter thrust (force per cutter over the full range of penetration rates in the test. Correlating penetration test data to the geological and geomechanical characteristics of rock masses through which a penetration test is conducted provides the ability to reveal the efficiency of the chipping process in response to changing geological conditions. Penetration test data can also be used to identify stress-induced tunnel face instability. This research shows that the strength of the rock is an important parameter for controlling how much net cutter thrust is required to transition from grinding to chipping. It also shows that the geological characteristics of a rock will determine how efficient chipping occurs once it has begun. In particular, geological characteristics that lead to efficient fracture propagation, such as fabric and mica contents, will lead to efficient chipping. These findings will enable a better correlation between TBM performance and geological conditions for use in TBM design, as a basis for contractual payments where penetration rate dominates the excavation cycle and in further academic investigations into the TBM excavation process.

  14. Experiment list: SRX655691 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ; Mus musculus; ChIP-Seq source_name=MEFs cells knockout MED23 || cell type=mouse embryonic fibroblast || ge...notype/variation=MED23 knockout || chip antibody=H2Bub http://dbarchive.bioscienc

  15. Experiment list: SRX191071 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Mus musculus; ChIP-Seq source_name=Kdm2b knockdown mouse ES cells || chip antibody=Flag || antibody manufact... || cell type=embryonbic stem cells || genotype=Kdm2b knockdown http://dbarchive.

  16. ‘Chip-olate’ and dry-film resists for efficient fabrication, singulation and sealing of microfluidic chips

    International Nuclear Information System (INIS)

    Temiz, Yuksel; Delamarche, Emmanuel

    2014-01-01

    This paper describes a technique for high-throughput fabrication and efficient singulation of chips having closed microfluidic structures and takes advantage of dry-film resists (DFRs) for efficient sealing of capillary systems. The technique is illustrated using 4-inch Si/SiO 2 wafers. Wafers carrying open microfluidic structures are partially diced to about half of their thickness. Treatments such as surface cleaning are done at wafer-level, then the structures are sealed using low-temperature (45 °C) lamination of a DFR that is pre-patterned using a craft cutter, and ready-to-use chips are finally separated manually like a chocolate bar by applying a small force (≤ 4 N). We further show that some DFRs have low auto-fluorescence at wavelengths typically used for common fluorescent dyes and that mechanical properties of some DFRs allow for the lamination of 200 μm wide microfluidic structures with negligible sagging (∼1 μm). The hydrophilicity (advancing contact angle of ∼60°) of the DFR supports autonomous capillary-driven flow without the need for additional surface treatment of the microfluidic chips. Flow rates from 1 to 5 µL min -1 are generated using different geometries of channels and capillary pumps. In addition, the ‘chip-olate’ technique is compatible with the patterning of capture antibodies on DFR for use in immunoassays. We believe this technique to be applicable to the fabrication of a wide range of microfluidic and lab-on-a-chip devices and to offer a viable alternative to many labor-intensive processes that are currently based on wafer bonding techniques or on the molding of poly(dimethylsiloxane) (PDMS) layers. (technical note)

  17. Experiment list: SRX620294 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available body=Pol II (Santa Cruz Biotechnology, N20, sc-899) http://dbarchive.biosciencedb...s; ChIP-Seq source_name=NIH3T3 fibroblasts || culture condition=serum starved || chemicals=DMSO || chip anti

  18. Experiment list: SRX891837 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available denocarcinoma || chip antibody=none (input) http://dbarc...ut, treated, replicate 2; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 || cell line=MDA-MB-231 || cell type=triple negative breast a

  19. Experiment list: SRX185908 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available epton 1; Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP || c...ell_line=MCF-7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=

  20. Experiment list: SRX185916 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available on 4; Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP || cell..._line=MCF-7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=thi

  1. Experiment list: SRX745835 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available d Pol II; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || treatment=untreated || sample type=Pleural effu...sion || passages=14-17 || chip antibody=Homemade Anti-Po

  2. Experiment list: SRX143851 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available lance, and learn motor skills. 57796523,71.5,23.1,31516 GSM918759: LICR ChipSeq Cerebellum CTCF adult-8wks s...cerebellar nuclei. Its function is to coordinate voluntary movements, maintain ba

  3. Experiment list: SRX185910 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ton 2; Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP || cel...l_line=MCF-7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=th

  4. Experiment list: SRX185918 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ton 7; Homo sapiens; ChIP-Seq source_name=MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP || cel...l_line=MCF-7 || cell_type=ER-positive breast adenocarcinoma cells || treatment=th

  5. Experiment list: SRX286394 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 3: AR Cast1 [kidney, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=AR_Cast1 || strain=wild type ICR... || tissue=kidney || age=8-12 weeks old || treatment=castrated+vehicle || chip an

  6. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

    Science.gov (United States)

    Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

    2016-11-18

    ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

  7. Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data

    Directory of Open Access Journals (Sweden)

    Minucci Saverio

    2011-10-01

    Full Text Available Abstract Background High-throughput sequencing is generating massive amounts of data at a pace that largely exceeds the throughput of data analysis routines. Here we introduce Fish the ChIPs (FC, a computational pipeline aimed at a broad public of users and designed to perform complete ChIP-Seq data analysis of an unlimited number of samples, thus increasing throughput, reproducibility and saving time. Results Starting from short read sequences, FC performs the following steps: 1 quality controls, 2 alignment to a reference genome, 3 peak calling, 4 genomic annotation, 5 generation of raw signal tracks for visualization on the UCSC and IGV genome browsers. FC exploits some of the fastest and most effective tools today available. Installation on a Mac platform requires very basic computational skills while configuration and usage are supported by a user-friendly graphic user interface. Alternatively, FC can be compiled from the source code on any Unix machine and then run with the possibility of customizing each single parameter through a simple configuration text file that can be generated using a dedicated user-friendly web-form. Considering the execution time, FC can be run on a desktop machine, even though the use of a computer cluster is recommended for analyses of large batches of data. FC is perfectly suited to work with data coming from Illumina Solexa Genome Analyzers or ABI SOLiD and its usage can potentially be extended to any sequencing platform. Conclusions Compared to existing tools, FC has two main advantages that make it suitable for a broad range of users. First of all, it can be installed and run by wet biologists on a Mac machine. Besides it can handle an unlimited number of samples, being convenient for large analyses. In this context, computational biologists can increase reproducibility of their ChIP-Seq data analyses while saving time for downstream analyses. Reviewers This article was reviewed by Gavin Huttley, George

  8. Experiment list: SRX1165098 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available tibody=CREB1 Santa Cruz Biotechnology, sc-240 http://dbarchive.biosciencedbc.jp/k...apiens; ChIP-Seq source_name=HepG2 cells || cell line=HepG2 || cell type=Hepatocellular Carcinoma || chip an

  9. Experiment list: SRX115969 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ; ChIP-Seq source_name=Breast cancer cells || cell lines=MCF-7 || agent=E2 || time=24 hr || chip antibody=ERα, Santa Cruz Biotechnolo...gy, sc-8005 X http://dbarchive.biosciencedbc.jp/kyushu-u

  10. Experiment list: SRX1427025 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available pring produced at one birth by a viviparous animal. 32763382,74.3,19.7,747 GSM1937508: SHP ChIP-seq with vehicle...week || genotype=wildtype || treatment=vehicle || chip antibody=SHP (sc-30169) ht

  11. Experiment list: SRX655689 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 8698: pol2 KO ChIPSeq; Mus musculus; ChIP-Seq source_name=MEFs cells knockout MED23 || cell type=mouse embry...onic fibroblast || genotype/variation=MED23 knockout || chip antibody=Pol II http

  12. Experiment list: SRX190193 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available rce_name=HL-60 || biomaterial_provider=ATCC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody... (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=This gene encod...es the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes || antibody... vendorname=abcam || antibody vendorid=ab5408 || controlid=SL

  13. Experiment list: SRX100504 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available .1 source_name=U87 || biomaterial_provider=ATCC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antib...odydescription=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody... (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=This gene e...ncodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes || antibody... vendorname=abcam || antibody vendorid=ab5408 || controli

  14. Experiment list: SRX100529 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available aterial_provider=WiCell Research Institute || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody... (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=This gene encode...s the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes || antibody... vendorname=abcam || antibody vendorid=ab5408 || controlid=SL9

  15. Experiment list: SRX150451 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Leukemia Chronic Myelogenous 39880346,54.9,7.2,2209 GSM935371: Harvard ChipSeq K562 SIRT6 std source_name...=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype

  16. Experiment list: SRX150472 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Leukemia Chronic Myelogenous 38544300,59.2,11.1,1031 GSM935392: Harvard ChipSeq K562 NELFe std source_nam...e=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatyp

  17. Experiment list: SRX191067 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available us; ChIP-Seq source_name=Kdm2b knockdown mouse ES cells || chip antibody=Ezh2 || antibody manufacturer=Cell ...ine=E14 || cell type=embryonbic stem cells || genotype=Kdm2b knockdown http://dba

  18. Experiment list: SRX1121725 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ChIPSeq; Mus musculus; ChIP-Seq source_name=MEFs cells knockout MED23 || cell type=mouse embryonic fibroblas...t || genotype/variation=MED23 knockout || chip antibody=H3K4me3 http://dbarchive.

  19. Experiment list: SRX248443 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available n PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=40 min || cell type=Pleural effus...ion || passages=14-17 || chip antibody=Homemade Anti-Pol

  20. Experiment list: SRX248446 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available usion || passages=14-17 || chip antibody=Homemade Anti-P...in PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=320 min || cell type=Pleural eff

  1. Experiment list: SRX248445 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available usion || passages=14-17 || chip antibody=Homemade Anti-P...in PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=160 min || cell type=Pleural eff

  2. Experiment list: SRX248442 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available n PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=20 min || cell type=Pleural effus...ion || passages=14-17 || chip antibody=Homemade Anti-Pol

  3. Experiment list: SRX248444 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available n PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=80 min || cell type=Pleural effus...ion || passages=14-17 || chip antibody=Homemade Anti-Pol

  4. Experiment list: SRX248441 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available n PolII rep; Homo sapiens; ChIP-Seq source_name=Breast cancer cells || cell line=MCF7 || time point=10 min || cell type=Pleural effus...ion || passages=14-17 || chip antibody=Homemade Anti-Pol

  5. Experiment list: SRX150623 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Leukemia Chronic Myelogenous 34396876,78.6,11.1,16076 GSM935544: Harvard ChipSeq K562 HMGN3 std source_na...me=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || dataty

  6. Experiment list: SRX150471 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available s=Leukemia Chronic Myelogenous 34337514,69.2,8.6,1665 GSM935391: Harvard ChipSeq K562 ATF3 std source_name=K...562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=C

  7. Experiment list: SRX150423 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sis=Leukemia Chronic Myelogenous 19694334,54.9,12.8,4256 GSM935343: Harvard ChipSeq K562 TFIIIC-110 std sour...ce_name=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || d

  8. Experiment list: SRX150474 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Leukemia Chronic Myelogenous 16833014,69.7,4.8,2339 GSM935394: Harvard ChipSeq K562 GTF2B std source_name...=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype

  9. Experiment list: SRX150452 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available s=Leukemia Chronic Myelogenous 17157530,93.1,18.0,2344 GSM935372: Harvard ChipSeq K562 RPC155 std source_nam...e=K562 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatyp

  10. Experiment list: SRX185912 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available MB-231 foxm1 Thiostrepton 1; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 breast adenocarcinoma cells, thio...strepton, FOXM1 ChIP || cell_line=MDA-MB-231 || cell_type=ER-negative breast adenocarcinoma

  11. Experiment list: SRX185911 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available B-231 foxm1 DMSO 1; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 breast adenocarcinoma cells, control, FOXM...1 ChIP || cell_line=MDA-MB-231 || cell_type=ER-negative breast adenocarcinoma cel

  12. Experiment list: SRX185914 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available B-231 foxm1 Thiostrepton 2; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 breast adenocarcinoma cells, thios...trepton, FOXM1 ChIP || cell_line=MDA-MB-231 || cell_type=ER-negative breast adenocarcinoma

  13. Experiment list: SRX172567 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available P-Seq source_name=Embryonic Stem Cell || background mouse strain=129SvJae/C57BL/6 || chip antibody=streptavidin beads... || antibody vendor/catalog=Invitrogen 656-01 Dynabeads® MyOne? Streptavidin T1 || genotype/variati

  14. Experiment list: SRX191073 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ulus; ChIP-Seq source_name=Kdm2b knockdown mouse ES cells || chip antibody=Ring1b || antibody manufacturer=C...ll line=E14 || cell type=embryonbic stem cells || genotype=Kdm2b knockdown http:/

  15. Experiment list: SRX998277 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ial decompensation with sepsis || postmortem delay=4.2 hrs || experiment type=ChIP-Seq || chip antibody=H3K2...n female occipital pole tissue || tissue=Occipital pole || gender=female || age=68 || Cause of death=Myocard

  16. Experiment list: SRX150674 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available s=Leukemia Chronic Myelogenous 18469470,89.4,7.1,725 GSM935595: Harvard ChipSeq K562 BRF1 std source_name=K5...62 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=Ch

  17. Experiment list: SRX150569 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available s=Leukemia Chronic Myelogenous 51487836,63.2,7.7,861 GSM935490: Harvard ChipSeq K562 BRF2 std source_name=K5...62 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=Ch

  18. Experiment list: SRX891827 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available d, replicate 2; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 || cell line=MDA-MB-231 || cell type=triple negative breast adenocarcin...oma || chip antibody=H3K9ac, Millipore #07-352, Lot 2388

  19. Experiment list: SRX185913 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available MB-231 foxm1 DMSO 2; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 breast adenocarcinoma cells, control, FOX...M1 ChIP || cell_line=MDA-MB-231 || cell_type=ER-negative breast adenocarcinoma ce

  20. Experiment list: SRX891826 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ed, replicate 1; Homo sapiens; ChIP-Seq source_name=MDA-MB-231 || cell line=MDA-MB-231 || cell type=triple negative breast adenocarci...noma || chip antibody=H3K9ac, Millipore #07-352, Lot 238

  1. Experiment list: SRX810435 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available idity in Shneider S2 Drosophila medium(Gibco) supplement...ster; ChIP-Seq source_name=Cell culture || cell line=S2 || chip antibody=none || growth protocol=S2 cells were grown in 24°C, 95% hum

  2. Experiment list: SRX810433 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available er; ChIP-Seq source_name=Cell culture || cell line=S2 || chip antibody=none || growth protocol=S2 cells were grown in 24°C, 95% humid...ity in Shneider S2 Drosophila medium(Gibco) supplemented

  3. Experiment list: SRX810434 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available idity in Shneider S2 Drosophila medium(Gibco) supplement...ster; ChIP-Seq source_name=Cell culture || cell line=S2 || chip antibody=none || growth protocol=S2 cells were grown in 24°C, 95% hum

  4. Experiment list: SRX172568 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available us; ChIP-Seq source_name=Embryonic Stem Cell || background mouse strain=129SvJae/C57BL/6 || chip antibody=streptavidin beads... || antibody vendor/catalog=Invitrogen 656-01 Dynabeads® MyOne? Streptavidin T1 || genotype/

  5. Experiment list: SRX643466 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available itory cortex) || chip antibody=input || tissue=Female Brain: medial superior temporal gyrus (secondary audit...,725 GSM1423167: Area 13 Brain1 input; Homo sapiens; ChIP-Seq source_name=Female Brain: medial superior temporal gyrus (secondary aud

  6. Experiment list: SRX1427026 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available of offspring produced at one birth by a viviparous animal. 22029930,97.6,9.8,279 GSM1937509: Input for SHP ChIP-seq with vehicle...ver || age=8-12 week || genotype=wildtype || treatment=vehicle || chip antibody=n

  7. Experiment list: SRX190244 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 1610.1 source_name=PANC-1 || biomaterial_provider=ATCC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibod...y antibodydescription=Mouse monoclonal to RNA polymerase... II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=This...r RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab5408 || c...ontrolid=SL2340 || labexpid=SL2343,SL5609 || softwareversion=MACS || cell sex=M || antibody=Pol2-4H8 || antibody antibody

  8. Low-Cost Energy-Efficient 3-D Nano-Spikes-Based Electric Cell Lysis Chips

    KAUST Repository

    Riaz, Kashif

    2017-05-04

    Electric cell lysis (ECL) is a promising technique to be integrated with portable lab-on-a-chip without lysing agent due to its simplicity and fast processing. ECL is usually limited by the requirements of high power/voltage and costly fabrication. In this paper, we present low-cost 3-D nano-spikes-based ECL (NSP-ECL) chips for efficient cell lysis at low power consumption. Highly ordered High-Aspect-Ratio (HAR). NSP arrays with controllable dimensions were fabricated on commercial aluminum foils through scalable and electrochemical anodization and etching. The optimized multiple pulse protocols with minimized undesirable electrochemical reactions (gas and bubble generation), common on micro parallel-plate ECL chips. Due to the scalability of fabrication process, 3-D NSPs were fabricated on small chips as well as on 4-in wafers. Phase diagram was constructed by defining critical electric field to induce cell lysis and for cell lysis saturation Esat to define non-ECL and ECL regions for different pulse parameters. NSP-ECL chips have achieved excellent cell lysis efficiencies ηlysis (ca 100%) at low applied voltages (2 V), 2~3 orders of magnitude lower than that of conventional systems. The energy consumption of NSP-ECL chips was 0.5-2 mJ/mL, 3~9 orders of magnitude lower as compared with the other methods (5J/mL-540kJ/mL). [2016-0305

  9. Experiment list: SRX150720 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sue Diagnosis=Fibrocystic Disease 71490650,87.2,15.5,1356 GSM935641: Harvard ChipSeq MCF10A-Er-Src Input std... source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvard

  10. Experiment list: SRX150587 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Adenocarcinoma 32859626,93.1,16.6,6448 GSM935508: Harvard ChipSeq HeLa-S3 NF-YA IgG-rab source_name=HeLa-...S3 || biomaterial_provider=ATCC || lab=Harvard || lab description=Struhl - Harvard University || datatype=Ch

  11. Experiment list: SRX100563 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available s=Leukemia Chronic Myelogenous 39078535,86.0,20.8,1302 GSM803518: HudsonAlpha ChipSeq K562 BCL3 PCR1x source..._name=K562 || biomaterial_provider=ATCC || lab=HudsonAlpha || lab description=Myers - Hudson Alpha Institute

  12. Experiment list: SRX100430 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available s=Leukemia Chronic Myelogenous 47818475,79.5,9.7,26072 GSM803385: HudsonAlpha ChipSeq K562 HEY1 PCR1x source..._name=K562 || biomaterial_provider=ATCC || lab=HudsonAlpha || lab description=Myers - Hudson Alpha Institute

  13. Experiment list: SRX286381 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 7,533 GSM1146460: AR Cast1b [prostate, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=AR_Cast1b || s...train=wild type ICR || tissue=prostate || age=8-12 weeks old || treatment=castrated+vehicle || chip antibody

  14. Experiment list: SRX286380 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 2,497 GSM1146459: AR Cast1a [prostate, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=AR_Cast1a || s...train=wild type ICR || tissue=prostate || age=8-12 weeks old || treatment=castrated+vehicle || chip antibody

  15. Experiment list: SRX286386 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 60.2,17474 GSM1146465: FoxA1 Cast [prostate, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=FoxA1_Ca...st || strain=wild type ICR || tissue=prostate || age=8-12 weeks old || treatment=castrated+vehicle || chip a

  16. CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

    Directory of Open Access Journals (Sweden)

    Tamar Hashimshony

    2012-09-01

    Full Text Available High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method for overcoming this limitation by barcoding and pooling samples before linearly amplifying mRNA with the use of one round of in vitro transcription. We show that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method. We demonstrate the power of this method by studying early C. elegans embryonic development at single-cell resolution. Differential distribution of transcripts between sister cells is seen as early as the two-cell stage embryo, and zygotic expression in the somatic cell lineages is enriched for transcription factors. The robust transcriptome quantifications enabled by CEL-Seq will be useful for transcriptomic analyses of complex tissues containing populations of diverse cell types.

  17. Very High Throughput Electrical Cell Lysis and Extraction of Intracellular Compounds Using 3D Carbon Electrodes in Lab-on-a-Chip Devices

    Directory of Open Access Journals (Sweden)

    Philippe Renaud

    2012-08-01

    Full Text Available Here we present an electrical lysis throughput of 600 microliters per minute at high cell density (108 yeast cells per ml with 90% efficiency, thus improving the current common throughput of one microliter per minute. We also demonstrate the extraction of intracellular luciferase from mammalian cells with efficiency comparable to off-chip bulk chemical lysis. The goal of this work is to develop a sample preparation module that can act as a stand-alone device or be integrated to other functions already demonstrated in miniaturized devices, including sorting and analysis, towards a true lab-on-a-chip.

  18. Experiment list: SRX471838 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available : ChIPseq GS WT Bmi1; Mus musculus; ChIP-Seq source_name=Cultured germline stem cells || genotype/variation=...Wild-type || strain=CD1 x C57BL/6 || cell type=Cultured germline stem cells || chip antibody=Mouse anti-Bmi1

  19. Experiment list: SRX471836 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 0: ChIPseq GS WT Scml2; Mus musculus; ChIP-Seq source_name=Cultured germline stem cells || genotype/variatio...n=Wild-type || strain=CD1 x C57BL/6 || cell type=Cultured germline stem cells || chip antibody=Rabbit anti-S

  20. Experiment list: SRX100493 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available is=Carcinoma Hepatocellular 67635839,78.1,18.6,34708 GSM803448: HudsonAlpha ChipSeq HepG2 HEY1 v041610.1 sou...rce_name=HepG2 || biomaterial_provider=ATCC || lab=HudsonAlpha || lab description=Myers - Hudson Alpha Insti

  1. Experiment list: SRX1084162 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 0 GSM1811344: P2 HA ChIPSeq; Drosophila melanogaster; ChIP-Seq source_name=Female whole animal_paraquat || tissue=whole animal || gen...der=female || age=1-3 days || genotype=k6801/k6801;gHA-KDM5 || chip antibody=HA htt

  2. Experiment list: SRX212457 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available apiens; ChIP-Seq source_name=CD4+CD25+CD45RA- expanded memory regulatory T cells || donor=C || cell type=CD4...+CD25+CD45RA- expanded memory regulatory T cells || chip antibody=H3K27ac (abcam

  3. Experiment list: SRX212463 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sapiens; ChIP-Seq source_name=CD4+CD25-CD45RA- expanded memory conventional T cells || donor=C || cell type...=CD4+CD25-CD45RA- expanded memory conventional T cells || chip antibody=H3K4me1 (

  4. Experiment list: SRX203399 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available r lymph. (Rosen et al., Dictionary of Immunology, 1989, p169 & Abbas et al., Cellular and Molecular Immuno...logy, 2d ed, p20) 30508063,94.1,4.3,15496 GSM1033764: MM.1S RNAPII JQ1 JL ChipSeq;

  5. Experiment list: SRX1084161 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available tissue=whole animal || gender=female || age=1-3 days || genotype=k6801/k6801;gHA-KDM5 || chip antibody=HA ht...,0 GSM1811343: P1 HA ChIPSeq; Drosophila melanogaster; ChIP-Seq source_name=Female whole animal_paraquat ||

  6. Experiment list: SRX837357 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ource_name=ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MD(ND2bHLH) chimera || cell l...ine=P19 || transduction=MD(ND2bHLH) chimera || chip antibody=MyoD antibody 6975 h

  7. Experiment list: SRX837356 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ource_name=ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MD(ND2bHLH) chimera || cell l...ine=P19 || transduction=MD(ND2bHLH) chimera || chip antibody=MyoD antibody 6196 h

  8. Experiment list: SRX192254 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available f offspring produced at one birth by a viviparous animal. 84324878,97.5,12.5,559 GSM1016423: A INPUT vehicle... donor1024; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle

  9. Experiment list: SRX192258 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available f offspring produced at one birth by a viviparous animal. 20609955,77.1,6.7,117 GSM1016427: B INPUT vehicle ...donor1; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle

  10. Experiment list: SRX192259 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available f offspring produced at one birth by a viviparous animal. 15402183,74.5,5.4,117 GSM1016428: B INPUT vehicle ...donor7; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle

  11. Experiment list: SRX192267 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available f offspring produced at one birth by a viviparous animal. 28874920,80.3,4.9,183 GSM1016436: C INPUT vehicle ...donor10; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle

  12. Experiment list: SRX192266 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available f offspring produced at one birth by a viviparous animal. 25871870,71.5,4.2,143 GSM1016435: C INPUT vehicle ...donor5; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle

  13. Experiment list: SRX192253 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available f offspring produced at one birth by a viviparous animal. 106959657,97.4,12.9,578 GSM1016422: A INPUT vehicle... donor1021; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=INPUT || treament=vehicle

  14. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

    NARCIS (Netherlands)

    Teytelman, L.; Thurtle, D.M.; Rine, J.; van Oudenaarden, A.

    2013-01-01

    Chromatin immunoprecipitation (ChIP) is the gold-standard technique for localizing nuclear proteins in the genome. We used ChIP, in combination with deep sequencing (Seq), to study the genome-wide distribution of the Silent information regulator (Sir) complex in Saccharomyces cerevisiae. We analyzed

  15. Experiment list: SRX212459 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available o sapiens; ChIP-Seq source_name=CD4+CD25-CD45RA- expanded memory conventional T cells || donor=C || cell typ...e=CD4+CD25-CD45RA- expanded memory conventional T cells || chip antibody=H3K27ac

  16. Experiment list: SRX212458 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sapiens; ChIP-Seq source_name=CD4+CD25+CD45RA- expanded memory regulatory T cells || donor=D || cell type=C...D4+CD25+CD45RA- expanded memory regulatory T cells || chip antibody=H3K27ac (abca

  17. Experiment list: SRX212464 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available o sapiens; ChIP-Seq source_name=CD4+CD25-CD45RA- expanded memory conventional T cells || donor=D || cell typ...e=CD4+CD25-CD45RA- expanded memory conventional T cells || chip antibody=H3K4me1

  18. Experiment list: SRX212460 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available o sapiens; ChIP-Seq source_name=CD4+CD25-CD45RA- expanded memory conventional T cells || donor=D || cell typ...e=CD4+CD25-CD45RA- expanded memory conventional T cells || chip antibody=H3K27ac

  19. Experiment list: SRX212462 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sapiens; ChIP-Seq source_name=CD4+CD25+CD45RA- expanded memory regulatory T cells || donor=D || cell type=C...D4+CD25+CD45RA- expanded memory regulatory T cells || chip antibody=H3K4me1 (abca

  20. Experiment list: SRX286391 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available 7,47.9,41.3,666 GSM1146470: rIgG1a [prostate, castrated+vehicle]; Mus musculus; ChIP-Seq source_name=rIgG1a ...|| strain=wild type ICR || tissue=prostate || age=8-12 weeks old || treatment=castrated+vehicle || chip anti

  1. Experiment list: SRX590292 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -rep1; Mus musculus; ChIP-Seq source_name=R-Ctrl-Flag ChIP || strain background=C57BL/6 || genotype/variation=Foxd3 conditional knock...out || cell type=embryonic stem cells (ESCs; R cells) || cell line of origin=Foxd3 conditional knock

  2. Experiment list: SRX542620 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sculus; ChIP-Seq source_name=Embryonic Stem Cells || time point=NA || treatment=no treatment || strain=129 X C57bl/6 || cell type=Par...ental mouse ES(KH2) cells || chip antibody=MacroH2A2 antibody, Abcam ab4173 http://

  3. Optimal use of tandem biotin and V5 tags in ChIP assays

    Directory of Open Access Journals (Sweden)

    Krpic Sanja

    2009-02-01

    Full Text Available Abstract Background Chromatin immunoprecipitation (ChIP assays coupled to genome arrays (Chip-on-chip or massive parallel sequencing (ChIP-seq lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies. Results Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking. Conclusion The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes.

  4. Optimal use of tandem biotin and V5 tags in ChIP assays

    Science.gov (United States)

    Kolodziej, Katarzyna E; Pourfarzad, Farzin; de Boer, Ernie; Krpic, Sanja; Grosveld, Frank; Strouboulis, John

    2009-01-01

    Background Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays (Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies. Results Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking. Conclusion The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes. PMID:19196479

  5. Experiment list: SRX150670 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available gnosis=Fibrocystic Disease 53773968,83.9,44.3,13035 GSM935591: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pct ST...AT3 std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvard

  6. Experiment list: SRX150630 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available gnosis=Fibrocystic Disease 42446970,82.6,25.1,47688 GSM935551: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pct 12...hr STAT3 std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvard

  7. Experiment list: SRX100511 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ,37.1,107266 GSM803466: HudsonAlpha ChipSeq H1-hESC Rad21 v041610.2 source_name=H1-hESC || biomaterial_provi...SRX100511 hg19 TFs and others RAD21 Pluripotent stem cell hESC H1 NA 109287919,77.2

  8. Experiment list: SRX153145 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ast adenocarcinoma cell-line MCF7 || cell-line=MCF7 || passage=5 || chip antibody=H...n=Pleura|Tissue Diagnosis=Adenocarcinoma 93237597,98.2,8.2,1358 GSM946849: MCF7 H3K4me1; Homo sapiens; ChIP-Seq source_name=Human bre

  9. Experiment list: SRX212461 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available iens; ChIP-Seq source_name=CD4+CD25+CD45RA- expanded memory regulatory T cells || donor=C || cell type=CD4+CD25+CD45RA- expanded memo...ry regulatory T cells || chip antibody=H3K4me1 (abcam ab

  10. Experiment list: SRX713898 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -D567 || agent=Ethanol (vehicle control) || chip antibody=AR -N20 (Santa Cruz, SC-816 lot B1012) || biologic...5527: R1D567 Eth ARv567es rep2; Homo sapiens; ChIP-Seq source_name=prostate cancer cell line || cell type=R1

  11. Experiment list: SRX713899 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available D567 || agent=Ethanol (vehicle control) || chip antibody=AR -N20 (Santa Cruz, SC-816 lot B1012) || biologica...528: R1D567 Eth ARv567es rep3; Homo sapiens; ChIP-Seq source_name=prostate cancer cell line || cell type=R1-

  12. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

    Directory of Open Access Journals (Sweden)

    Maher Christopher A

    2010-07-01

    Full Text Available Abstract Background Protein-DNA interaction constitutes a basic mechanism for the genetic regulation of target gene expression. Deciphering this mechanism has been a daunting task due to the difficulty in characterizing protein-bound DNA on a large scale. A powerful technique has recently emerged that couples chromatin immunoprecipitation (ChIP with next-generation sequencing, (ChIP-Seq. This technique provides a direct survey of the cistrom of transcription factors and other chromatin-associated proteins. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed to analyze the massive amount of data generated by this method. Results Here we introduce HPeak, a Hidden Markov model (HMM-based Peak-finding algorithm for analyzing ChIP-Seq data to identify protein-interacting genomic regions. In contrast to the majority of available ChIP-Seq analysis software packages, HPeak is a model-based approach allowing for rigorous statistical inference. This approach enables HPeak to accurately infer genomic regions enriched with sequence reads by assuming realistic probability distributions, in conjunction with a novel weighting scheme on the sequencing read coverage. Conclusions Using biologically relevant data collections, we found that HPeak showed a higher prevalence of the expected transcription factor binding motifs in ChIP-enriched sequences relative to the control sequences when compared to other currently available ChIP-Seq analysis approaches. Additionally, in comparison to the ChIP-chip assay, ChIP-Seq provides higher resolution along with improved sensitivity and specificity of binding site detection. Additional file and the HPeak program are freely available at http://www.sph.umich.edu/csg/qin/HPeak.

  13. Experiment list: SRX150497 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sue Diagnosis=Fibrocystic Disease 30305817,89.0,5.1,579 GSM935418: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pc...t 4hr Input std source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvar

  14. Experiment list: SRX100495 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX100495 hg19 TFs and others TAF1 Pluripotent stem cell hESC H1 NA 40640767,80.2,12.3,29488 GSM803450: Huds...onAlpha ChipSeq H1-hESC TAF1 v041610.2 source_name=H1-hESC || biomaterial_provider=

  15. Experiment list: SRX100469 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX100469 hg19 TFs and others GABPA Pluripotent stem cell hESC H1 NA 59698055,78.1,10.0,16884 GSM803424: Hud...sonAlpha ChipSeq H1-hESC GABP PCR1x source_name=H1-hESC || biomaterial_provider=WiC

  16. Experiment list: SRX100587 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX100587 hg19 TFs and others EP300 Pluripotent stem cell hESC H1 NA 46380456,87.7,10.1,18476 GSM803542: Hud...sonAlpha ChipSeq H1-hESC p300 v041610.2 source_name=H1-hESC || biomaterial_provider

  17. Effects of background fluid on the efficiency of inactivating yeast with non-thermal atmospheric pressure plasma.

    Directory of Open Access Journals (Sweden)

    Young-Hyo Ryu

    Full Text Available Non-thermal plasma at atmospheric pressure has been actively applied to sterilization. However, its efficiency for inactivating microorganisms often varies depending on microbial species and environments surrounding the microorganisms. We investigated the influence of environmental factors (surrounding media on the efficiency of microbial inactivation by plasma using an eukaryotic model microbe, Saccharomyces cerevisiae, to elucidate the mechanisms for differential efficiency of sterilization by plasma. Yeast cells treated with plasma in water showed the most severe damage in viability and cell morphology as well as damage to membrane lipids, and genomic DNA. Cells in saline were less damaged compared to those in water, and those in YPD (Yeast extract, Peptone, Dextrose were least impaired. HOG1 mitogen activated protein kinase was activated in cells exposed to plasma in water and saline. Inactivation of yeast cells in water and saline was due to the acidification of the solutions by plasma, but higher survival of yeast cells treated in saline may have resulted from the additional effect related to salt strength. Levels of hydroxyl radical (OH· produced by plasma were the highest in water and the lowest in YPD. This may have resulted in differential inactivation of yeast cells in water, saline, and YPD by plasma. Taken together, our data suggest that the surrounding media (environment can crucially affect the outcomes of yeast cell plasma treatment because plasma modulates vital properties of media, and the toxic nature of plasma can also be altered by the surrounding media.

  18. CRISPR-Cas9-Edited Site Sequencing (CRES-Seq): An Efficient and High-Throughput Method for the Selection of CRISPR-Cas9-Edited Clones.

    Science.gov (United States)

    Veeranagouda, Yaligara; Debono-Lagneaux, Delphine; Fournet, Hamida; Thill, Gilbert; Didier, Michel

    2018-01-16

    The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells). Here we described a next-generation sequencing method called CRISPR-Cas9 Edited Site Sequencing (CRES-Seq) for the efficient and high-throughput screening of CRISPR-Cas9-edited clones. CRES-Seq facilitates the precise genotyping up to 96 CRISPR-Cas9-edited sites (CRES) in a single MiniSeq (Illumina) run with an approximate sequencing cost of $6/clone. CRES-Seq is particularly useful when multiple genes are simultaneously targeted by CRISPR-Cas9, and also for screening of clones generated from multiallelic genes/polyploid cells. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

  19. Experiment list: SRX100473 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX100473 hg19 TFs and others SIN3A Pluripotent stem cell hESC H1 NA 48520029,77.7,11.0,14690 GSM803428: Hud...sonAlpha ChipSeq H1-hESC Sin3Ak-20 PCR1x source_name=H1-hESC || biomaterial_provide

  20. Experiment list: SRX524970 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX524970 hg19 Input control Input control Uterus Endometrial stromal cells NA 3525...5109,88.2,37.7,339 GSM1372862: Input case1 control; Homo sapiens; ChIP-Seq source_name=Human endometrial stromal cells || tissue=Endo...metrial stromal cells || condition=control (without any induction) || chip antibody

  1. Experiment list: SRX524980 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX524980 hg19 Input control Input control Uterus Endometrial stromal cells NA 2708...7271,98.6,31.8,308 GSM1372876: Input case2 control; Homo sapiens; ChIP-Seq source_name=Human endometrial stromal cells || tissue=Endo...metrial stromal cells || condition=control (without any induction) || chip antibody

  2. Experiment list: SRX192270 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available produced at one birth by a viviparous animal. 29213160,79.3,3.6,131 GSM1016439: C H3K27me3 vehicle donor5; ...Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K27me3 || treament=vehicle

  3. Experiment list: SRX192271 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available produced at one birth by a viviparous animal. 29600718,81.2,4.5,188 GSM1016440: C H3K27me3 vehicle donor10;... Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K27me3 || treament=vehicle

  4. Analysis of ChIP-seq Data in R/Bioconductor.

    Science.gov (United States)

    de Santiago, Ines; Carroll, Thomas

    2018-01-01

    The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis techniques are of critical importance to extract the most meaningful results from the data. Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project. Protocols described in this chapter cover basic steps including data alignment, peak calling, quality control and data visualization, as well as more complex methods such as the identification of differentially bound regions and functional analyses to annotate regulatory regions. The steps in the data analysis process were demonstrated on publicly available data sets and will serve as a demonstration of the computational procedures routinely used for the analysis of ChIP-seq data in R/Bioconductor, from which readers can construct their own analysis pipelines.

  5. Experiment list: SRX192263 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available produced at one birth by a viviparous animal. 19707029,78.6,5.0,577 GSM1016432: B H3K4me2 vehicle donor7; Mu...s musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K4me2 || treament=vehicle

  6. Experiment list: SRX192262 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available produced at one birth by a viviparous animal. 13178340,75.6,7.8,715 GSM1016431: B H3K4me2 vehicle donor1; Mu...s musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K4me2 || treament=vehicle

  7. Experiment list: SRX192250 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available produced at one birth by a viviparous animal. 98336587,96.8,24.1,627 GSM1016419: A H3K36me3 vehicle donor10...24; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K36me3 || treament=vehicle

  8. Experiment list: SRX192257 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available produced at one birth by a viviparous animal. 73877067,96.7,23.5,560 GSM1016426: A H3K36me3 vehicle donor10...21; Mus musculus; ChIP-Seq source_name=whole liver extract || age=29-32 days || chip antibody=H3K36me3 || treament=vehicle

  9. Experiment list: SRX190205 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available labexpid=SL7110,SL8075 || softwareversion=MACS || cell sex=M || antibody=NRSF ||...ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) || controlid=SL6021 || labexpid=SL7110,SL8075 || replicate=1,2 || softw...areversion=MACS http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/eachData/bw/SRX1902

  10. New movable plate for efficient millimeter wave vertical on-chip antenna

    KAUST Repository

    Marnat, Loic; Carreno, Armando Arpys Arevalo; Conchouso Gonzalez, David; Galicia Martinez, Miguel Angel; Foulds, Ian G.; Shamim, Atif

    2013-01-01

    A new movable plate concept is presented in this paper to realize mm-wave vertical on-chip antennas through MEMS based post-processing steps in a CMOS compatible process. By virtue of its vertical position, the antenna is isolated from the lossy Si substrate and hence performs with a better efficiency as compared to the horizontal position. In addition, the movable plate concept enables polarization diversity by providing both horizontal and vertical polarizations on the same chip. Through a first iteration fractal bowtie antenna design, dual band (60 and 77 GHz) operation is demonstrated in both horizontal and vertical positions without any change in dimensions or use of switches for two different mediums (Si and air). To support the movable plate concept, the transmission line and antenna are designed on a flexible polyamide, where the former has been optimized to operate in the bent position. The design is highly suitable for compact, low cost and efficient SoC solutions. © 1963-2012 IEEE.

  11. New movable plate for efficient millimeter wave vertical on-chip antenna

    KAUST Repository

    Marnat, Loic

    2013-04-01

    A new movable plate concept is presented in this paper to realize mm-wave vertical on-chip antennas through MEMS based post-processing steps in a CMOS compatible process. By virtue of its vertical position, the antenna is isolated from the lossy Si substrate and hence performs with a better efficiency as compared to the horizontal position. In addition, the movable plate concept enables polarization diversity by providing both horizontal and vertical polarizations on the same chip. Through a first iteration fractal bowtie antenna design, dual band (60 and 77 GHz) operation is demonstrated in both horizontal and vertical positions without any change in dimensions or use of switches for two different mediums (Si and air). To support the movable plate concept, the transmission line and antenna are designed on a flexible polyamide, where the former has been optimized to operate in the bent position. The design is highly suitable for compact, low cost and efficient SoC solutions. © 1963-2012 IEEE.

  12. EVALUATION OF THERMAL EFFICIENCY OF THE TECHNOLOGICAL SCHEME OF APPLE CHIPS AND DRIED FRUITS PRODUCTION

    Directory of Open Access Journals (Sweden)

    G. V. Kalashnikov

    2014-01-01

    Full Text Available The estimation of thermodynamic perfection of separate technological processes is executed at heat-moisture of handling of fruit and a line of manufacture of fruit apple chips and dried fruits. The technological scheme of a line of processing of fruits and manufactures of fruit chips on the basis of convection and the microwave-dryings suggested resource-saving. The technique is made and results of calculation of thermal expenses for various schemes of manufacture of apple chips are resulted. For the offered scheme material, thermal and power streams on the basis of balance parities of technological processes are certain. The comparative thermal production efficiency of apple chips for a base foreign variant and the offered technological scheme with the closed cycle of use of the heat-carrier and the combined convection-microwave-drying is shown. In this paper we define the thermal and energy flows for the processes of convective drying, pre-microwave drying, hydrothermal treatment and final microwave drying plant material, which are one of the main stages of the production of all kinds of fruit and vegetable concentrates, including fruit apple chips. Resource-saving ways moisture-heat of handling (hydration, blanching, drying, etc. produce raw materials in the production of food concentrates suggested a reduced water flow with a high degree of use of its potential power and microwave sources. To assess the thermal efficiency of the various processes and production schemes used as indicators of thermal efficiency and proposed value of specific heat (kJ / kg given mass productivity per unit of feedstock and translational moisture. The values of the mass fraction of the heat of material flows for the base and the proposed resource-saving production scheme fruit chips, for example, apple, based on a combination of convection-microwave drying each control surface.

  13. Experiment list: SRX1056357 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available || cell type=ES cells || treated with=2.5 µM tamoxifen (Tam) || chip antibody=none http://dbarchive.bioscien...tiate into specialized cells. 35337197,98.9,19.2,224 GSM1708671: input DNA +Tam R...2; Mus musculus; ChIP-Seq source_name=input DNA_+Tam || strain=J1 || genotype/variation=inducible SetDB1 KO

  14. Experiment list: SRX026424 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX026424 mm9 RNA polymerase RNA Polymerase II Neural Cerebellum MeSH Description=T..., maintain balance, and learn motor skills. 15567107,93.1,10.8,650 GSM587797: P5 Cerebellum RNAP-II ChIP-Seq... source_name=PostNatal-Day5_Cerebellum || strain=CD1 || age=postnatal day 5 || tissue=cerebellum || chip-ant

  15. Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling.

    Science.gov (United States)

    Marty, Amber J; Wüthrich, Marcel; Carmen, John C; Sullivan, Thomas D; Klein, Bruce S; Cuomo, Christina A; Gauthier, Gregory M

    2013-07-01

    Blastomyces dermatitidis belongs to a group of thermally dimorphic fungi that grow as sporulating mold in the soil and convert to pathogenic yeast in the lung following inhalation of spores. Knowledge about the molecular events important for fungal adaptation and survival in the host remains limited. The development of high-throughput analytic tools such as RNA sequencing (RNA-Seq) has potential to provide novel insight on fungal pathogenesis especially if applied in vivo during infection. However, in vivo transcriptional profiling is hindered by the low abundance of fungal cells relative to mammalian tissue and difficulty in isolating fungal cells from the tissues they infect. For the purpose of obtaining B. dermatitidis RNA for in vivo transcriptional analysis by RNA-Seq, we developed a simple technique for isolating yeast from murine lung tissue. Using a two-step approach of filtration and centrifugation following lysis of murine lung cells, 91% of yeast cells causing infection were isolated from lung tissue. B. dermatitidis recovered from the lung yielded high-quality RNA with minimal murine contamination and was suitable for RNA-Seq. Approximately 87% of the sequencing reads obtained from the recovered yeast aligned with the B. dermatitidis genome. This was similar to 93% alignment for yeast grown in vitro. The use of near-freezing temperature along with short ex vivo time minimized transcriptional changes that would have otherwise occurred with higher temperature or longer processing time. In conclusion, we have developed a technique that recovers the majority of yeast causing pulmonary infection and yields high-quality fungal RNA with minimal contamination by mammalian RNA. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Efficiency of a yeast-based formulation for the biocontrol of postharvest anthracnose of papayas

    Directory of Open Access Journals (Sweden)

    Jaqueline Rabelo de Lima

    2014-09-01

    Full Text Available To identify formulations of biological agents that enable survival, stability and a good surface distribution of the antagonistic agent, studies that test different application vehicles are necessary. The efficiency of two killer yeasts, Wickerhamomyces anomalus (strain 422 and Meyerozyma guilliermondii (strain 443, associated with five different application vehicles, was assessed for the protection of postharvest papayas. In this study, after 90 days of incubation at 4ºC, W. anomalus (strain 422 and M. guilliermondii (strain 443 were viable with all application vehicles tested. Fruits treated with different formulations (yeasts + application vehicles had a decreased severity of disease (by at least 30% compared with untreated fruits. The treatment with W. anomalus (strain 422 + 2% starch lowered disease occurrence by 48.3%. The most efficient treatments using M. guilliermondii (strain 443 were those with 2% gelatin or 2% liquid carnauba wax, both of which reduced anthracnose by 50% in postharvest papayas. Electron micrographs of the surface tissues of the treated fruits showed that all application vehicles provided excellent adhesion of the yeast to the surface. Formulations based on starch (2%, gelatin (2% and carnauba wax (2% were the most efficient at controlling fungal diseases in postharvest papayas.

  17. Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

    Science.gov (United States)

    Chabbert, Christophe D; Adjalley, Sophie H; Steinmetz, Lars M; Pelechano, Vicent

    2018-01-01

    Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.

  18. Sporulation genes associated with sporulation efficiency in natural isolates of yeast.

    Science.gov (United States)

    Tomar, Parul; Bhatia, Aatish; Ramdas, Shweta; Diao, Liyang; Bhanot, Gyan; Sinha, Himanshu

    2013-01-01

    Yeast sporulation efficiency is a quantitative trait and is known to vary among experimental populations and natural isolates. Some studies have uncovered the genetic basis of this variation and have identified the role of sporulation genes (IME1, RME1) and sporulation-associated genes (FKH2, PMS1, RAS2, RSF1, SWS2), as well as non-sporulation pathway genes (MKT1, TAO3) in maintaining this variation. However, these studies have been done mostly in experimental populations. Sporulation is a response to nutrient deprivation. Unlike laboratory strains, natural isolates have likely undergone multiple selections for quick adaptation to varying nutrient conditions. As a result, sporulation efficiency in natural isolates may have different genetic factors contributing to phenotypic variation. Using Saccharomyces cerevisiae strains in the genetically and environmentally diverse SGRP collection, we have identified genetic loci associated with sporulation efficiency variation in a set of sporulation and sporulation-associated genes. Using two independent methods for association mapping and correcting for population structure biases, our analysis identified two linked clusters containing 4 non-synonymous mutations in genes - HOS4, MCK1, SET3, and SPO74. Five regulatory polymorphisms in five genes such as MLS1 and CDC10 were also identified as putative candidates. Our results provide candidate genes contributing to phenotypic variation in the sporulation efficiency of natural isolates of yeast.

  19. Yeast cell surface display: An efficient strategy for improvement of bioethanol fermentation performance.

    Science.gov (United States)

    Chen, Xianzhong

    2017-03-04

    The cell surface serves as a functional interface between the inside and the outside of the cell. Within the past 20 y the ability of yeast (Saccharomyces cerevisiae) to display heterologous proteins on the cell surface has been demonstrated. Furthermore, S. cerevisiae has been both developed and applied in expression of various proteins on the cell surface. Using this novel and useful strategy, proteins and peptides of various kinds can be displayed on the yeast cell surface by fusing the protein of interest with the glycosylphosphatidylinositol (GPI)-anchoring system. Consolidated bioprocessing (CBP) using S. cerevisiae represents a promising technology for bioethanol production. However, further work is needed to improve the fermentation performance. There is some excellent previous research regarding construction of yeast biocatalyst using the surface display system to decrease cost, increase efficiency of ethanol production and directly utilize starch or biomass for fuel production. In this commentary, we reviewed the yeast surface display system and highlighted recent work. Additionally, the strategy for decrease of phytate phosphate content in dried distillers grains with solubles (DDGS) by display of phytase on the yeast cell surface is discussed.

  20. Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data.

    Science.gov (United States)

    Zhu, Mingzhu; Dahmen, Jeremy L; Stacey, Gary; Cheng, Jianlin

    2013-09-22

    High-throughput RNA sequencing (RNA-Seq) is a revolutionary technique to study the transcriptome of a cell under various conditions at a systems level. Despite the wide application of RNA-Seq techniques to generate experimental data in the last few years, few computational methods are available to analyze this huge amount of transcription data. The computational methods for constructing gene regulatory networks from RNA-Seq expression data of hundreds or even thousands of genes are particularly lacking and urgently needed. We developed an automated bioinformatics method to predict gene regulatory networks from the quantitative expression values of differentially expressed genes based on RNA-Seq transcriptome data of a cell in different stages and conditions, integrating transcriptional, genomic and gene function data. We applied the method to the RNA-Seq transcriptome data generated for soybean root hair cells in three different development stages of nodulation after rhizobium infection. The method predicted a soybean nodulation-related gene regulatory network consisting of 10 regulatory modules common for all three stages, and 24, 49 and 70 modules separately for the first, second and third stage, each containing both a group of co-expressed genes and several transcription factors collaboratively controlling their expression under different conditions. 8 of 10 common regulatory modules were validated by at least two kinds of validations, such as independent DNA binding motif analysis, gene function enrichment test, and previous experimental data in the literature. We developed a computational method to reliably reconstruct gene regulatory networks from RNA-Seq transcriptome data. The method can generate valuable hypotheses for interpreting biological data and designing biological experiments such as ChIP-Seq, RNA interference, and yeast two hybrid experiments.

  1. Efficient On-chip Optical Microresonator for Optical Comb Generation: Design and Fabrication

    Science.gov (United States)

    Han, Kyunghun

    An optical frequency comb is a series of equally spaced frequency components. It has gained much attention since Nobel physics prize was awarded John L. Hall and Theodor W. Hansch for their contribution to the optical frequency comb technique in 2005. The optical frequency comb has been extensively studied because of its precision as a tool for spectroscopy, and is now widely used in bio- and chemical sensors, optical clocks, mode-locked dark pulse generation, soliton generation, and optical communication. Recently, thanks to the developments in nanotechnology, the optical frequency comb generation is made possible at a chip-scale level with microresonators. However, because the threshold power of the optical frequency comb generation is beyond the capability of the on-chip laser source, efficient microresonator is required. Here, we demonstrate an ultra-compact and highly efficient strip-slot direct mode coupler, aiming to achieve slotted silicon microresonator cladded with nonlinear polymer Poly-DDMEBT in SOI platform. As an application of the strip-slot direct mode coupling, a double slot fiber-to-chip edge coupler is demonstrated showing 2 dB insertion loss reduction compared to the conventional single tip edge coupler. For silicon nitride platform, we investigated evanescent wave coupling of microresonator, focusing on bus waveguide geometry optimization. The optimized waveguide width offers an efficient excitation of a fundamental mode in the resonator waveguide. This investigation can benefit low threshold comb generation by enhancing the extinction ratio. We experimentally demonstrated the high Q-factor micro-ring resonator with intrinsic Q of 12.6 million as well as the single FSR comb generation with 63 mW.

  2. Sentence‐Chain Based Seq2seq Model for Corpus Expansion

    Directory of Open Access Journals (Sweden)

    Euisok Chung

    2017-08-01

    Full Text Available This study focuses on a method for sequential data augmentation in order to alleviate data sparseness problems. Specifically, we present corpus expansion techniques for enhancing the coverage of a language model. Recent recurrent neural network studies show that a seq2seq model can be applied for addressing language generation issues; it has the ability to generate new sentences from given input sentences. We present a method of corpus expansion using a sentence‐chain based seq2seq model. For training the seq2seq model, sentence chains are used as triples. The first two sentences in a triple are used for the encoder of the seq2seq model, while the last sentence becomes a target sequence for the decoder. Using only internal resources, evaluation results show an improvement of approximately 7.6% relative perplexity over a baseline language model of Korean text. Additionally, from a comparison with a previous study, the sentence chain approach reduces the size of the training data by 38.4% while generating 1.4‐times the number of n‐grams with superior performance for English text.

  3. Preservation of forest wood chips

    Energy Technology Data Exchange (ETDEWEB)

    Kofman, P.D.; Thomsen, I.M.; Ohlsson, C.; Leer, E.; Ravn Schmidt, E.; Soerensen, M.; Knudsen, P.

    1999-01-01

    As part of the Danish Energy Research Programme on biomass utilisation for energy production (EFP), this project concerns problems connected to the handling and storing of wood chips. In this project, the possibility of preserving wood chips of the Norway Spruce (Picea Abies) is addressed, and the potential improvements by anaerobic storage are tested. Preservation of wood chips aims at reducing dry matter losses from extensive heating during storage and to reduce production of fungal spores. Fungal spores pose a health hazards to workers handling the chips. Further the producers of wood chips are interested in such a method since it would enable them to give a guarantee for the delivery of homogeneous wood chips also during the winter period. Three different types of wood chips were stored airtight and further one of these was stored in accordance with normal practise and use as reference. The results showed that airtight storage had a beneficial impact on the quality of the chips: no redistribution of moisture, low dry matter losses, unfavourable conditions for microbial activity of most fungi, and the promotion of yeasts instead of fungi with airborne spores. Likewise the firing tests showed that no combustion problems, and no increased risk to the environment or to the health of staff is caused by anaerobic storage of wood chips. In all, the tests of the anaerobic storage method of forest wood chips were a success and a large-scale test of the method will be carried out in 1999. (au)

  4. Chipping operations and efficiency in different operational environments

    Energy Technology Data Exchange (ETDEWEB)

    Roeser, D.; Mola-Yudego, B.; Prinz, R.; Emer, B.; Sikanen, L., e-mail: dominik.roser@metla.fi

    2012-11-01

    This research analyses the productivity of energy wood chipping operations at several sites in Austria and Finland. The aim of the work is to examine the differences in productivity and the effects of the operational environment for the chipping of bioenergy at the roadside. Furthermore, the study quantifies the effects of different variables such as forest energy assortments, tree species, sieve size and machines on the overall productivity of chipping. The results revealed that there are significant differences in the chipping productivity in Austria and Finland which are largely based on the use of different sieve sizes. Furthermore, the different operational environments in both countries, as well as the characteristics of the raw material also seem to have an effect on productivity. In order to improve the chipping productivity, particularly in Central European conditions, all relevant stakeholders need to work jointly to find solutions that will allow a greater variation of chip size. Furthermore, in the future more consideration has to be given to the close interlinkage between the chipper, crane and grapple. As a result, investments costs can be optimized and operational costs and stress on the machines reduced. (orig.)

  5. The operational efficiency of waterway transport of forest chips on Finland's Lake Saimaa

    Energy Technology Data Exchange (ETDEWEB)

    Karttunen, K.; Ranta, T. [Lappeenranta Univ. of Technology, LUT Savo Sustainable Technologies, Mikkeli (Finland); Vaatainen, K.; Asikainen, A. [The Finnish Forest Research Inst., Joensuu (Finland)], E-mail: kalle.karttunen@lut.fi

    2012-11-01

    New and cost-efficient methods for use in supply chains for energy wood should be found, to reach the targets of the renewable energy utilisation set by the European Union. The long-distance waterway transportation of forest fuels should be thoroughly investigated, especially in areas where the transport distance is long and waterways could provide a feasible method of conveying forest fuel. In comparison to transport of forest chips by truck, barge-based waterway transport shows a competitive advantage due to the larger loads and higher bulk density of chips it allows. The cost-efficiency of waterway transportation operations related to forest chips in Finland's Lake Saimaa region was studied using practical demonstrations and discrete-event simulation. The varying demand for fuel wood in three separate bio-power plants on the Saimaa lakeside (near the cities of Varkaus, Mikkeli, and Savonlinna) was addressed in several barge transportation scenarios. Finally, the economy of barge transportation was compared to the economy of truck transportation as a function of transportation distance and in terms of the annual performance of the transportation methods examined. The waterway supply chain of forest chips was cost-competitive to road transport by truck after 100-150 km. According to the simulation study, the most economical waterway transport options were based on fixed barge system and shift-independent harbor logistics where loading and unloading of barges were carried-out with a wheeled loader and a belt conveyor. Total supply chain costs including the best waterway logistics from road side storage to power plant ranged from 10.75 euros to 11.64 euros/MWh in distances of 100-150 km by waterways. The energy-density of forest chips in the barge load was found to be, on average, 25% higher than that in truck hauling, because of the better compaction of chips. Waterway transport is a viable option for long-distance transportation of forest chips in Eastern

  6. Experiment list: SRX150684 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available sue Diagnosis=Fibrocystic Disease 174026370,97.9,12.7,1654 GSM935605: Harvard ChipSeq MCF10A-Er-Src Input Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harvard...before peaks are called. || control=Harvard_Control || control description=input library was prepared at Harvard. || control=Harvard..._Control || control description=input library was prepared at Harvard. || controlid=

  7. Experiment list: SRX143825 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX143825 mm9 Input control Input control Neural Cerebellum MeSH Description=The pa...ntain balance, and learn motor skills. 38330550,73.2,10.7,868 GSM918733: LICR ChipSeq Cerebellum Input adult-8wks source_name=Cerebel...ption=Chromatin IP Sequencing || cell=Cerebellum || cell organism=mouse || cell description=Cerebellum || ce...lum || biomaterial_provider=1)LICR lab; 2)CSHL lab || lab=LICR-m || lab description

  8. Cassava chip (Manihot esculenta Crantz as an energy source for ruminant feeding

    Directory of Open Access Journals (Sweden)

    Metha Wanapat

    2015-12-01

    Full Text Available Cassava (Manihot esculenta Crantz is widely grown in sub-tropical and tropical areas, producing roots as an energy source while the top biomass including leaves and immature stems can be sun-dried and used as cassava hay. Cassava roots can be processed as dried chip or pellet. It is rich in soluble carbohydrate (75 to 85% but low in crude protein (2 to 3%. Its energy value is comparable to corn meal but has a relatively higher rate of rumen degradation. Higher levels of non-protein nitrogen especially urea (1 to 4% can be successfully incorporated in concentrates containing cassava chip as an energy source. Cassava chip can also be processed with urea and other ingredients (tallow, sulfur, raw banana meal, cassava hay, and soybean meal to make products such as cassarea, cassa-ban, and cassaya. Various studies have been conducted in ruminants using cassava chip to replace corn meal in the concentrate mixtures and have revealed satisfactory results in rumen fermentation efficiency and the subsequent production of meat and milk. In addition, it was advantageous when used in combination with rice bran in the concentrate supplement. Practical home-made-concentrate using cassava chip can be easily prepared for use on farms. A recent development has involved enriching protein in cassava chips, yielding yeast fermented cassava chip protein (YEFECAP of up to 47.5% crude protein, which can be used to replace soybean meal. It is therefore, recommended to use cassava chip as an alternative source of energy to corn meal when the price is economical and it is locally available.

  9. Experiment list: SRX1056356 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available O || cell type=ES cells || treated with=2.5 µM tamoxifen (Tam) || chip antibody=H3K27me3 (Millipore: 07-449)...specialized cells. 43433717,97.9,45.2,1333 GSM1708670: H3K27me3 ChIPSeq+Tam R2; M...us musculus; ChIP-Seq source_name=H3K27me3_ChIPSeq+Tam || strain=J1 || genotype/variation=inducible SetDB1 K

  10. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

    NARCIS (Netherlands)

    Kaufmann, K.; Muiño, J.M.; Østerås, M.; Farinelli, L.; Krajewski, P.; Angenent, G.C.

    2010-01-01

    Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences

  11. Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

    Directory of Open Access Journals (Sweden)

    David A. Orlando

    2014-11-01

    Full Text Available Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.

  12. Characterizing and annotating the genome using RNA-seq data.

    Science.gov (United States)

    Chen, Geng; Shi, Tieliu; Shi, Leming

    2017-02-01

    Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts (especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome- guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.

  13. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

    Science.gov (United States)

    Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

    2011-07-01

    Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

  14. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

    Directory of Open Access Journals (Sweden)

    Dongjun Chung

    2011-07-01

    Full Text Available Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads. This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads. Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

  15. Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.

    Science.gov (United States)

    Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M

    2018-05-01

    This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and subnuclear position. Moreover, RT is regulated during development and is altered in diseases. Here, we describe E/L Repli-seq, an extension of our Repli-chip protocol. E/L Repli-seq is a rapid, robust and relatively inexpensive protocol for analyzing RT by next-generation sequencing (NGS), allowing genome-wide assessment of how cellular processes are linked to RT. Briefly, cells are pulse-labeled with BrdU, and early and late S-phase fractions are sorted by flow cytometry. Labeled nascent DNA is immunoprecipitated from both fractions and sequenced. Data processing leads to a single bedGraph file containing the ratio of nascent DNA from early versus late S-phase fractions. The results are comparable to those of Repli-chip, with the additional benefits of genome-wide sequence information and an increased dynamic range. We also provide computational pipelines for downstream analyses, for parsing phased genomes using single-nucleotide polymorphisms (SNPs) to analyze RT allelic asynchrony, and for direct comparison to Repli-chip data. This protocol can be performed in up to 3 d before sequencing, and requires basic cellular and molecular biology skills, as well as a basic understanding of Unix and R.

  16. An Efficient Radio Access Control Mechanism for Wireless Network-On-Chip Architectures

    Directory of Open Access Journals (Sweden)

    Maurizio Palesi

    2015-03-01

    Full Text Available Modern systems-on-chip (SoCs today contain hundreds of cores, and this number is predicted to reach the thousands by the year 2020. As the number of communicating elements increases, there is a need for an efficient, scalable and reliable communication infrastructure. As technology geometries shrink to the deep submicron regime, however, the communication delay and power consumption of global interconnections become the major bottleneck. The network-on-chip (NoC design paradigm, based on a modular packet-switched mechanism, can address many of the on-chip communication issues, such as the performance limitations of long interconnects and integration of large number of cores on a chip. Recently, new communication technologies based on the NoC concept have emerged with the aim of improving the scalability limitations of conventional NoC-based architectures. Among them, wireless NoCs (WiNoCs use the radio medium for reducing the performance and energy penalties of long-range and multi-hop communications. As the radio medium can be accessed by a single transmitter at a time, a radio access control mechanism (RACM is needed. In this paper, we present a novel RACM, which allows one to improve both the performance and energy figures of the WiNoC. Experiments, carried out on both synthetic and real traffic scenarios, have shown the effectiveness of the proposed RACM. On average, a 30% reduction in communication delay and a 25% energy savings have been observed when the proposed RACM is applied to a known WiNoC architecture.

  17. Experiment list: SRX186751 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available | biomaterial_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide containi...ng K79 di-methylation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the tra...nscriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). || antibody... vendorname=Active Motif || antibody vendorid=39143 || co

  18. Experiment list: SRX186750 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available l_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydes...cription=Rabbit polyclonal antibody raised against a peptide containing K79 di-me...thylation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the transcriptional... transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). || antibody... vendorname=Active Motif || antibody vendorid=39143 || controlid=wgEn

  19. Experiment list: SRX186672 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available RC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of... H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH00...3132 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=F || antibody=H2A.Z || antibody antibody

  20. Continuous High-resolution Microscopic Observation of Replicative Aging in Budding Yeast

    OpenAIRE

    Huberts, Daphne H. E. W.; Janssens, Georges E.; Lee, Sung Sik; Vizcarra, Ima Avalos; Heinemann, Matthias

    2013-01-01

    We demonstrate the use of a simple microfluidic setup, in which single budding yeast cells can be tracked throughout their entire lifespan. The microfluidic chip exploits the size difference between mother and daughter cells using an array of micropads. Upon loading, cells are trapped underneath these micropads, because the distance between the micropad and cover glass is similar to the diameter of a yeast cell (3-4 μm). After the loading procedure, culture medium is continuously flushed thro...

  1. The economic efficiency of forest energy wood chip production in regional use – A case study

    Directory of Open Access Journals (Sweden)

    Dalibor Šafařík

    2013-01-01

    Full Text Available This regional project case study deals with the limiting factors of economic efficiency in the production of forest energy wood chips. The evaluation of production efficiency made use of data obtained from the Lesy města Brna, a.s. (Forest of the City of Brno, Corp., which were subjected to two static methods of investment evaluation: an analysis of the tipping point and determination of the limit of variable costs and a dynamic modified tipping point analysis using cash flow (i.e. cash break even analysis. The results have confirmed an established hypothesis, namely that the decisive factor in the profitability of the production of forest energy wood chips hinges on the costs incurred in the gathering of raw material and the distribution of the produced chips. The results include a further limiting factor: transportation costs to the final consumption location. The output of the study is a recommendation that the concentration of residual forest materials not exceed a distance of 250 m from the place of production to the point of disintegration and that the transport distance of energy chips not exceed 50 km from the place of disintegration to the final consumption point. These limiting values help quantify the full internal costs per cost unit, full internal cost profitability, total revenue profitability and annual profitability expressed in terms of fixed assets depreciation without factoring in financial aid.

  2. Lab-on a-Chip

    Science.gov (United States)

    1999-01-01

    Labs on chips are manufactured in many shapes and sizes and can be used for numerous applications, from medical tests to water quality monitoring to detecting the signatures of life on other planets. The eight holes on this chip are actually ports that can be filled with fluids or chemicals. Tiny valves control the chemical processes by mixing fluids that move in the tiny channels that look like lines, connecting the ports. Scientists at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama designed this chip to grow biological crystals on the International Space Station (ISS). Through this research, they discovered that this technology is ideally suited for solving the challenges of the Vision for Space Exploration. For example, thousands of chips the size of dimes could be loaded on a Martian rover looking for biosignatures of past or present life. Other types of chips could be placed in handheld devices used to monitor microbes in water or to quickly conduct medical tests on astronauts. The portable, handheld Lab-on-a Chip Application Development Portable Test System (LOCAD-PTS) made its debut flight aboard Discovery during the STS-116 mission launched December 9, 2006. The system allowed crew members to monitor their environment for problematic contaminants such as yeast, mold, and even E.coli, and salmonella. Once LOCAD-PTS reached the ISS, the Marshall team continued to manage the experiment, monitoring the study from a console in the Payload Operations Center at MSFC. The results of these studies will help NASA researchers refine the technology for future Moon and Mars missions. (NASA/MSFC/D.Stoffer)

  3. A fast one-chip event-preprocessor and sequencer for the Simbol-X Low Energy Detector

    Science.gov (United States)

    Schanz, T.; Tenzer, C.; Maier, D.; Kendziorra, E.; Santangelo, A.

    2010-12-01

    We present an FPGA-based digital camera electronics consisting of an Event-Preprocessor (EPP) for on-board data preprocessing and a related Sequencer (SEQ) to generate the necessary signals to control the readout of the detector. The device has been originally designed for the Simbol-X low energy detector (LED). The EPP operates on 64×64 pixel images and has a real-time processing capability of more than 8000 frames per second. The already working releases of the EPP and the SEQ are now combined into one Digital-Camera-Controller-Chip (D3C).

  4. A fast one-chip event-preprocessor and sequencer for the Simbol-X Low Energy Detector

    Energy Technology Data Exchange (ETDEWEB)

    Schanz, T., E-mail: schanz@astro.uni-tuebingen.d [Kepler Center for Astro- and Particlephysics, Institut fuer Astronomie und Astrophysik Tuebingen, Sand 1, 72076 Tuebingen (Germany); Tenzer, C., E-mail: tenzer@astro.uni-tuebingen.d [Kepler Center for Astro- and Particlephysics, Institut fuer Astronomie und Astrophysik Tuebingen, Sand 1, 72076 Tuebingen (Germany); Maier, D.; Kendziorra, E.; Santangelo, A. [Kepler Center for Astro- and Particlephysics, Institut fuer Astronomie und Astrophysik Tuebingen, Sand 1, 72076 Tuebingen (Germany)

    2010-12-11

    We present an FPGA-based digital camera electronics consisting of an Event-Preprocessor (EPP) for on-board data preprocessing and a related Sequencer (SEQ) to generate the necessary signals to control the readout of the detector. The device has been originally designed for the Simbol-X low energy detector (LED). The EPP operates on 64x64 pixel images and has a real-time processing capability of more than 8000 frames per second. The already working releases of the EPP and the SEQ are now combined into one Digital-Camera-Controller-Chip (D3C).

  5. A fast one-chip event-preprocessor and sequencer for the Simbol-X Low Energy Detector

    International Nuclear Information System (INIS)

    Schanz, T.; Tenzer, C.; Maier, D.; Kendziorra, E.; Santangelo, A.

    2010-01-01

    We present an FPGA-based digital camera electronics consisting of an Event-Preprocessor (EPP) for on-board data preprocessing and a related Sequencer (SEQ) to generate the necessary signals to control the readout of the detector. The device has been originally designed for the Simbol-X low energy detector (LED). The EPP operates on 64x64 pixel images and has a real-time processing capability of more than 8000 frames per second. The already working releases of the EPP and the SEQ are now combined into one Digital-Camera-Controller-Chip (D3C).

  6. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation.

    Directory of Open Access Journals (Sweden)

    Wei Shen

    Full Text Available FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This paper describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OSX, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. SeqKit is open source and available on Github at https://github.com/shenwei356/seqkit.

  7. RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

    Directory of Open Access Journals (Sweden)

    Severin Andrew J

    2010-08-01

    Full Text Available Abstract Background Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation. Results The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome. Conclusions This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq.

  8. Experiment list: SRX144529 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ChIP-Seq source_name=IgG ChIP vehicle treated || biomaterial_provider=Coriell; ht...tp://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06993 || biomaterial_provider=Coriell; http://...ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM07000 || biomaterial_provider=Coriell; http://ccr.c...oriell.org/Sections/Search/Search.aspx?PgId=165&q=GM11882 || biomaterial_provider...=Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM11992 || biomaterial_provider=Cori

  9. Experiment list: SRX144528 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -Seq source_name=IgG ChIP SFN treated || biomaterial_provider=Coriell; http://ccr....coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06993 || biomaterial_provider=Coriell; http://ccr.cori...ell.org/Sections/Search/Search.aspx?PgId=165&q=GM07000 || biomaterial_provider=Coriell; http://ccr.coriell.o...rg/Sections/Search/Search.aspx?PgId=165&q=GM11882 || biomaterial_provider=Coriell...; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM11992 || biomaterial_provider=Coriell; htt

  10. Experiment list: SRX150477 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available osis=Fibrocystic Disease 70636654,97.7,24.3,106225 GSM935397: Harvard ChipSeq MCF10A-Er-Src 4OHTAM 1uM 4hr c-Fos Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || l... a leucine-zipper. || antibody vendorname=Santa Cruz Biotech || antibody vendorid=sc-7202 || control=Harvard..._Control || control description=input library was prepared at Harvard. || control=Harvard..._Control || control description=input library was prepared at Harvard. || controlid=wgEncodeEH002871

  11. Experiment list: SRX150476 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available osis=Fibrocystic Disease 60050220,94.5,18.5,85444 GSM935396: Harvard ChipSeq MCF10A-Er-Src 4OHTAM 1uM 36hr c-Fos Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || l...is a leucine-zipper. || antibody vendorname=Santa Cruz Biotech || antibody vendorid=sc-7202 || control=Harvard..._Control || control description=input library was prepared at Harvard. || control=Harvard..._Control || control description=input library was prepared at Harvard. || controlid=wgEncodeEH0028

  12. Experiment list: SRX186742 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available l_provider=ATCC || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydesc...ription=Rabbit polyclonal antibody raised against a peptide corresponding to the ...C-terminus of H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH003076 || replic...ate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=M || antibody=H2A.Z || antibody antibody

  13. Experiment list: SRX186752 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available aterial_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding ...to the C-terminus of H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibod...y vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH000060 ||... replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H2A.Z || antibody antibody

  14. Experiment list: SRX186726 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available rovider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescri...terminus of H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH000105 || replicat...e=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H2A.Z || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminu

  15. Experiment list: SRX186723 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available K || biomaterial_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide conta...ining K79 di-methylation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the ...dy vendorname=Active Motif || antibody vendorid=39143 ||... controlid=wgEncodeEH000072 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=M || antibody=H3K79me2 || antibody anti

  16. Experiment list: SRX190252 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available -1 || cell organism=human || cell description=pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a panc...SRX190252 hg19 Input control Input control Pancreas PANC-1 Tissue=Pancreas/Duct|Dis...ease=Epithelioid Carcinoma 117194289,90.9,30.1,1440 GSM1010796: HudsonAlpha ChipSeq PANC-1 RevXlinkChromatin...atin IP Sequencing || controlid=SL3776,SL2340 || labexpid=SL3776,SL2340 || cell=PANC...reatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old

  17. GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.

    Science.gov (United States)

    Stricker, Georg; Engelhardt, Alexander; Schulz, Daniel; Schmid, Matthias; Tresch, Achim; Gagneur, Julien

    2017-08-01

    Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein-DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-Seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective. Here, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays. Software is available from Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/GenoGAM.html . gagneur@in.tum.de. Supplementary information is available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  18. DANoC: An Efficient Algorithm and Hardware Codesign of Deep Neural Networks on Chip.

    Science.gov (United States)

    Zhou, Xichuan; Li, Shengli; Tang, Fang; Hu, Shengdong; Lin, Zhi; Zhang, Lei

    2017-07-18

    Deep neural networks (NNs) are the state-of-the-art models for understanding the content of images and videos. However, implementing deep NNs in embedded systems is a challenging task, e.g., a typical deep belief network could exhaust gigabytes of memory and result in bandwidth and computational bottlenecks. To address this challenge, this paper presents an algorithm and hardware codesign for efficient deep neural computation. A hardware-oriented deep learning algorithm, named the deep adaptive network, is proposed to explore the sparsity of neural connections. By adaptively removing the majority of neural connections and robustly representing the reserved connections using binary integers, the proposed algorithm could save up to 99.9% memory utility and computational resources without undermining classification accuracy. An efficient sparse-mapping-memory-based hardware architecture is proposed to fully take advantage of the algorithmic optimization. Different from traditional Von Neumann architecture, the deep-adaptive network on chip (DANoC) brings communication and computation in close proximity to avoid power-hungry parameter transfers between on-board memory and on-chip computational units. Experiments over different image classification benchmarks show that the DANoC system achieves competitively high accuracy and efficiency comparing with the state-of-the-art approaches.

  19. Fish and chips: implementation of a neural network model into computer chips to maximize swimming efficiency in autonomous underwater vehicles.

    Science.gov (United States)

    Blake, R W; Ng, H; Chan, K H S; Li, J

    2008-09-01

    Recent developments in the design and propulsion of biomimetic autonomous underwater vehicles (AUVs) have focused on boxfish as models (e.g. Deng and Avadhanula 2005 Biomimetic micro underwater vehicle with oscillating fin propulsion: system design and force measurement Proc. 2005 IEEE Int. Conf. Robot. Auto. (Barcelona, Spain) pp 3312-7). Whilst such vehicles have many potential advantages in operating in complex environments (e.g. high manoeuvrability and stability), limited battery life and payload capacity are likely functional disadvantages. Boxfish employ undulatory median and paired fins during routine swimming which are characterized by high hydromechanical Froude efficiencies (approximately 0.9) at low forward speeds. Current boxfish-inspired vehicles are propelled by a low aspect ratio, 'plate-like' caudal fin (ostraciiform tail) which can be shown to operate at a relatively low maximum Froude efficiency (approximately 0.5) and is mainly employed as a rudder for steering and in rapid swimming bouts (e.g. escape responses). Given this and the fact that bioinspired engineering designs are not obligated to wholly duplicate a biological model, computer chips were developed using a multilayer perception neural network model of undulatory fin propulsion in the knifefish Xenomystus nigri that would potentially allow an AUV to achieve high optimum values of propulsive efficiency at any given forward velocity, giving a minimum energy drain on the battery. We envisage that externally monitored information on flow velocity (sensory system) would be conveyed to the chips residing in the vehicle's control unit, which in turn would signal the locomotor unit to adopt kinematics (e.g. fin frequency, amplitude) associated with optimal propulsion efficiency. Power savings could protract vehicle operational life and/or provide more power to other functions (e.g. communications).

  20. Dominant Epistasis Between Two Quantitative Trait Loci Governing Sporulation Efficiency in Yeast Saccharomyces cerevisiae

    Science.gov (United States)

    Bergman, Juraj; Mitrikeski, Petar T.

    2015-01-01

    Summary Sporulation efficiency in the yeast Saccharomyces cerevisiae is a well-established model for studying quantitative traits. A variety of genes and nucleotides causing different sporulation efficiencies in laboratory, as well as in wild strains, has already been extensively characterised (mainly by reciprocal hemizygosity analysis and nucleotide exchange methods). We applied a different strategy in order to analyze the variation in sporulation efficiency of laboratory yeast strains. Coupling classical quantitative genetic analysis with simulations of phenotypic distributions (a method we call phenotype modelling) enabled us to obtain a detailed picture of the quantitative trait loci (QTLs) relationships underlying the phenotypic variation of this trait. Using this approach, we were able to uncover a dominant epistatic inheritance of loci governing the phenotype. Moreover, a molecular analysis of known causative quantitative trait genes and nucleotides allowed for the detection of novel alleles, potentially responsible for the observed phenotypic variation. Based on the molecular data, we hypothesise that the observed dominant epistatic relationship could be caused by the interaction of multiple quantitative trait nucleotides distributed across a 60--kb QTL region located on chromosome XIV and the RME1 locus on chromosome VII. Furthermore, we propose a model of molecular pathways which possibly underlie the phenotypic variation of this trait. PMID:27904371

  1. On-chip concentration of bacteria using a 3D dielectrophoretic chip and subsequent laser-based DNA extraction in the same chip

    International Nuclear Information System (INIS)

    Cho, Yoon-Kyoung; Kim, Tae-hyeong; Lee, Jeong-Gun

    2010-01-01

    We report the on-chip concentration of bacteria using a dielectrophoretic (DEP) chip with 3D electrodes and subsequent laser-based DNA extraction in the same chip. The DEP chip has a set of interdigitated Au post electrodes with 50 µm height to generate a network of non-uniform electric fields for the efficient trapping by DEP. The metal post array was fabricated by photolithography and subsequent Ni and Au electroplating. Three model bacteria samples (Escherichia coli, Staphylococcus epidermidis, Streptococcus mutans) were tested and over 80-fold concentrations were achieved within 2 min. Subsequently, on-chip DNA extraction from the concentrated bacteria in the 3D DEP chip was performed by laser irradiation using the laser-irradiated magnetic bead system (LIMBS) in the same chip. The extracted DNA was analyzed with silicon chip-based real-time polymerase chain reaction (PCR). The total process of on-chip bacteria concentration and the subsequent DNA extraction can be completed within 10 min including the manual operation time.

  2. Efficient on-chip hotspot removal combined solution of thermoelectric cooler and mini-channel heat sink

    International Nuclear Information System (INIS)

    Hao, Xiaohong; Peng, Bei; Xie, Gongnan; Chen, Yi

    2016-01-01

    Highlights: • A combined solution of thermoelectric cooler (TEC) and mini-channel heat sink to remove the hotspot of the chip has been proposed. • The TEC's mathematical model is established to assess its work performance. • A comparative study on the proposed efficient On-Chip Hotspot Removal Combined Solution. - Abstract: Hotspot will significantly degrade the reliability and performance of the electronic equipment. The efficient removal of hotspot can make the temperature distribution uniform, and ensure the reliable operation of the electronic equipment. This study proposes a combined solution of thermoelectric cooler (TEC) and mini-channel heat sink to remove the hotspot of the chip in the electronic equipment. Firstly, The TEC's mathematical model is established to assess its work performance under different boundary conditions. Then, the hotspot removal capability of the TEC is discussed for different cooling conditions, which has shown that the combined equipment has better hotspot removal capability compared with others. Finally, A TEC is employed to investigate the hotspot removal capacity of the combined solution, and the results have indicated that it can effectively remove hotspot in the diameter of 0.5 mm, the power density of 600W/cm 2 when its working current is 3A and heat transfer thermal resistance is 0 K/W.

  3. Is this the right normalization? A diagnostic tool for ChIP-seq normalization.

    Science.gov (United States)

    Angelini, Claudia; Heller, Ruth; Volkinshtein, Rita; Yekutieli, Daniel

    2015-05-09

    Chip-seq experiments are becoming a standard approach for genome-wide profiling protein-DNA interactions, such as detecting transcription factor binding sites, histone modification marks and RNA Polymerase II occupancy. However, when comparing a ChIP sample versus a control sample, such as Input DNA, normalization procedures have to be applied in order to remove experimental source of biases. Despite the substantial impact that the choice of the normalization method can have on the results of a ChIP-seq data analysis, their assessment is not fully explored in the literature. In particular, there are no diagnostic tools that show whether the applied normalization is indeed appropriate for the data being analyzed. In this work we propose a novel diagnostic tool to examine the appropriateness of the estimated normalization procedure. By plotting the empirical densities of log relative risks in bins of equal read count, along with the estimated normalization constant, after logarithmic transformation, the researcher is able to assess the appropriateness of the estimated normalization constant. We use the diagnostic plot to evaluate the appropriateness of the estimates obtained by CisGenome, NCIS and CCAT on several real data examples. Moreover, we show the impact that the choice of the normalization constant can have on standard tools for peak calling such as MACS or SICER. Finally, we propose a novel procedure for controlling the FDR using sample swapping. This procedure makes use of the estimated normalization constant in order to gain power over the naive choice of constant (used in MACS and SICER), which is the ratio of the total number of reads in the ChIP and Input samples. Linear normalization approaches aim to estimate a scale factor, r, to adjust for different sequencing depths when comparing ChIP versus Input samples. The estimated scaling factor can easily be incorporated in many peak caller algorithms to improve the accuracy of the peak identification. The

  4. SNP discovery in the bovine milk transcriptome using RNA-Seq technology.

    Science.gov (United States)

    Cánovas, Angela; Rincon, Gonzalo; Islas-Trejo, Alma; Wickramasinghe, Saumya; Medrano, Juan F

    2010-12-01

    High-throughput sequencing of RNA (RNA-Seq) was developed primarily to analyze global gene expression in different tissues. However, it also is an efficient way to discover coding SNPs. The objective of this study was to perform a SNP discovery analysis in the milk transcriptome using RNA-Seq. Seven milk samples from Holstein cows were analyzed by sequencing cDNAs using the Illumina Genome Analyzer system. We detected 19,175 genes expressed in milk samples corresponding to approximately 70% of the total number of genes analyzed. The SNP detection analysis revealed 100,734 SNPs in Holstein samples, and a large number of those corresponded to differences between the Holstein breed and the Hereford bovine genome assembly Btau4.0. The number of polymorphic SNPs within Holstein cows was 33,045. The accuracy of RNA-Seq SNP discovery was tested by comparing SNPs detected in a set of 42 candidate genes expressed in milk that had been resequenced earlier using Sanger sequencing technology. Seventy of 86 SNPs were detected using both RNA-Seq and Sanger sequencing technologies. The KASPar Genotyping System was used to validate unique SNPs found by RNA-Seq but not observed by Sanger technology. Our results confirm that analyzing the transcriptome using RNA-Seq technology is an efficient and cost-effective method to identify SNPs in transcribed regions. This study creates guidelines to maximize the accuracy of SNP discovery and prevention of false-positive SNP detection, and provides more than 33,000 SNPs located in coding regions of genes expressed during lactation that can be used to develop genotyping platforms to perform marker-trait association studies in Holstein cattle.

  5. FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota

    Directory of Open Access Journals (Sweden)

    Sophie Comtet-Marre

    2018-02-01

    Full Text Available Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6 were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen.

  6. FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota.

    Science.gov (United States)

    Comtet-Marre, Sophie; Chaucheyras-Durand, Frédérique; Bouzid, Ourdia; Mosoni, Pascale; Bayat, Ali R; Peyret, Pierre; Forano, Evelyne

    2018-01-01

    Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme) families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6) were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi) represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen.

  7. Chips 2020

    CERN Document Server

    2016-01-01

    The release of this second volume of CHIPS 2020 coincides with the 50th anniversary of Moore’s Law, a critical year marked by the end of the nanometer roadmap and by a significantly reduced annual rise in chip performance. At the same time, we are witnessing a data explosion in the Internet, which is consuming 40% more electrical power every year, leading to fears of a major blackout of the Internet by 2020. The messages of the first CHIPS 2020, published in 2012, concerned the realization of quantum steps for improving the energy efficiency of all chip functions. With this second volume, we review these messages and amplify upon the most promising directions: ultra-low-voltage electronics, nanoscale monolithic 3D integration, relevant-data, brain- and human-vision-inspired processing, and energy harvesting for chip autonomy. The team of authors, enlarged by more world leaders in low-power, monolithic 3D, video, and Silicon brains, presents new vistas in nanoelectronics, promising  Moore-like exponential g...

  8. Continuous High-resolution Microscopic Observation of Replicative Aging in Budding Yeast

    NARCIS (Netherlands)

    Huberts, Daphne H. E. W.; Janssens, Georges E.; Lee, Sung Sik; Vizcarra, Ima Avalos; Heinemann, Matthias

    We demonstrate the use of a simple microfluidic setup, in which single budding yeast cells can be tracked throughout their entire lifespan. The microfluidic chip exploits the size difference between mother and daughter cells using an array of micropads. Upon loading, cells are trapped underneath

  9. Experiment list: SRX150517 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available osis=Fibrocystic Disease 50667127,93.3,23.9,80828 GSM935438: Harvard ChipSeq MCF10A-Er-Src EtOH 0.01pct c-Fos Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || lab description=Struhl - Harv...me=Santa Cruz Biotech || antibody vendorid=sc-7202 || control=Harvard_Control || control description=input l...ibrary was prepared at Harvard. || control=Harvard_Control || control description...=input library was prepared at Harvard. || controlid=wgEncodeEH002871 || replicate=1 http://dbarchive.biosci

  10. Experiment list: SRX150570 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available osis=Fibrocystic Disease 64692659,93.8,19.3,37417 GSM935491: Harvard ChipSeq MCF10A-Er-Src 4OHTAM 1uM 4hr c-Myc Harvard... Control source_name=MCF10A-Er-Src || biomaterial_provider=Struhl laboratory || lab=Harvard || la...ntibody vendorname=Santa Cruz Biotech || antibody vendorid=sc-764 || control=Harvard_Control || control desc...ription=input library was prepared at Harvard. || control=Harvard_Control || cont...rol description=input library was prepared at Harvard. || controlid=wgEncodeEH002871 || replicate=1 http://d

  11. Experiment list: SRX186686 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available me=NH-A || biomaterial_provider=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide... containing K79 di-methylation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark o...ation marks (K36me3). || antibody vendorname=Active Motif || antibody vendorid=39...143 || controlid=wgEncodeEH001027 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H3K79me2 || antibod

  12. Experiment list: SRX186696 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available nza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescription=Rabbit polyclonal antibody...f H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH000093 || replicate=1,2 || s...oftwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H2A.Z || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ.

  13. Experiment list: SRX186665 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available rovider=DSMZ || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescrip...ation. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the transcriptional tra...nsition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). || antibody... vendorname=Active Motif || antibody vendorid=39143 || controlid=wgEncode...EH002434 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=M || antibody=H3K79me2 || antibody antibody

  14. Experiment list: SRX186661 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available r=DSMZ || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescription=Rabbit polyclonal antibody...s of H2AZ. Antibody Target: H2AZ || antibody targetdescription=H2A.Z is a sequence variant of Histone H2A. || antibody... vendorname=Millipore || antibody vendorid=07-594 || controlid=wgEncodeEH002434 || replicate=1,2 |...| softwareversion=ScriptureVPaperR3 || cell sex=M || antibody=H2A.Z || antibody antibody...description=Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2

  15. CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

    Directory of Open Access Journals (Sweden)

    Alawi Malik

    2011-06-01

    Full Text Available The mapping of DNA-protein interactions is crucial for a full understanding of transcriptional regulation. Chromatin-immunoprecipitation followed bymassively parallel sequencing (ChIP-seq has become the standard technique for analyzing these interactions on a genome-wide scale. We have developed a software system called CASSys (ChIP-seq data Analysis Software System spanning all steps of ChIP-seq data analysis. It supersedes the laborious application of several single command line tools. CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping and the detection of enriched regions (peakdetection to various follow-up analyses. The latter are accessible via a state-of-the-art web interface and can be performed interactively by the user. The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative binding motifs, the identification of over-represented Gene Ontology-terms, pathway analysis and the visualization of interaction networks. The system is client-server based, accessible via a web browser and does not require any software installation on the client side. To demonstrate CASSys’s functionality we used the system for the complete data analysis of a publicly available Chip-seq study that investigated the role of the transcription factor estrogen receptor-α in breast cancer cells.

  16. HMCan: A method for detecting chromatin modifications in cancer samples using ChIP-seq data

    KAUST Repository

    Ashoor, Haitham; Hé rault, Auré lie; Kamoun, Auré lie; Radvanyi, Franç ois; Bajic, Vladimir B.; Barillot, Emmanuel; Boeva, Valentina

    2013-01-01

    genes. Though several tools have been created to enable detection of histone marks in ChIP-seq data from normal samples, it is unclear whether these tools can be efficiently applied to ChIP-seq data generated from cancer samples. Indeed, cancer genomes

  17. SignalSpider: Probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles

    KAUST Repository

    Wong, Kachun

    2014-09-05

    Motivation: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in vivo. Different combinations of DNA-binding protein occupancies may result in a gene being expressed in different tissues or at different developmental stages. To fully understand the functions of genes, it is essential to develop probabilistic models on multiple ChIP-Seq profiles to decipher the combinatorial regulatory mechanisms by multiple transcription factors. Results: In this work, we describe a probabilistic model (SignalSpider) to decipher the combinatorial binding events of multiple transcription factors. Comparing with similar existing methods, we found SignalSpider performs better in clustering promoter and enhancer regions. Notably, SignalSpider can learn higher-order combinatorial patterns from multiple ChIP-Seq profiles. We have applied SignalSpider on the normalized ChIP-Seq profiles from the ENCODE consortium and learned model instances. We observed different higher-order enrichment and depletion patterns across sets of proteins. Those clustering patterns are supported by Gene Ontology (GO) enrichment, evolutionary conservation and chromatin interaction enrichment, offering biological insights for further focused studies. We also proposed a specific enrichment map visualization method to reveal the genome-wide transcription factor combinatorial patterns from the models built, which extend our existing fine-scale knowledge on gene regulation to a genome-wide level. Availability and implementation: The matrix-algebra-optimized executables and source codes are available at the authors\\' websites: http://www.cs.toronto.edu/∼wkc/SignalSpider. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.

  18. High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq).

    Science.gov (United States)

    Jiao, Yang; Li, Ran; Wu, Chao; Ding, Yibin; Liu, Yanning; Jia, Danmei; Wang, Lifeng; Xu, Xiang; Zhu, Jing; Zheng, Min; Jia, Junling

    2018-01-15

    Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine. Here, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing. STC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine.

  19. Isolation and characterization of yeasts capable of efficient utilization of hemicellulosic hydrolyzate as the carbon source.

    Science.gov (United States)

    Cassa-Barbosa, L A; Procópio, R E L; Matos, I T S R; Filho, S A

    2015-09-28

    Few yeasts have shown the potential to efficiently utilize hemicellulosic hydrolyzate as the carbon source. In this study, microorganisms isolated from the Manaus region in Amazonas, Brazil, were characterized based on their utilization of the pentoses, xylose, and arabinose. The yeasts that showed a potential to assimilate these sugars were selected for the better utilization of lignocellulosic biomass. Two hundred and thirty seven colonies of unicellular microorganisms grown on hemicellulosic hydrolyzate, xylose, arabinose, and yeast nitrogen base selective medium were analyzed. Of these, 231 colonies were subjected to sugar assimilation tests. One hundred and twenty five of these were shown to utilize hydrolyzed hemicellulose, xylose, or arabinose as the carbon source for growth. The colonies that showed the best growth (N = 57) were selected, and their internal transcribed spacer-5.8S rDNA was sequenced. The sequenced strains formed four distinct groups in the phylogenetic tree, and showed a high percentage of similarity with Meyerozyma caribbica, Meyerozyma guilliermondii, Trichosporon mycotoxinivorans, Trichosporon loubieri, Pichia kudriavzevii, Candida lignohabitans, and Candida ethanolica. The discovery of these xylose-fermenting yeasts could attract widespread interest, as these can be used in the cost-effective production of liquid fuel from lignocellulosic materials.

  20. Cardinality enhancement utilizing Sequential Algorithm (SeQ code in OCDMA system

    Directory of Open Access Journals (Sweden)

    Fazlina C. A. S.

    2017-01-01

    Full Text Available Optical Code Division Multiple Access (OCDMA has been important with increasing demand for high capacity and speed for communication in optical networks because of OCDMA technique high efficiency that can be achieved, hence fibre bandwidth is fully used. In this paper we will focus on Sequential Algorithm (SeQ code with AND detection technique using Optisystem design tool. The result revealed SeQ code capable to eliminate Multiple Access Interference (MAI and improve Bit Error Rate (BER, Phase Induced Intensity Noise (PIIN and orthogonally between users in the system. From the results, SeQ shows good performance of BER and capable to accommodate 190 numbers of simultaneous users contrast with existing code. Thus, SeQ code have enhanced the system about 36% and 111% of FCC and DCS code. In addition, SeQ have good BER performance 10-25 at 155 Mbps in comparison with 622 Mbps, 1 Gbps and 2 Gbps bit rate. From the plot graph, 155 Mbps bit rate is suitable enough speed for FTTH and LAN networks. Resolution can be made based on the superior performance of SeQ code. Thus, these codes will give an opportunity in OCDMA system for better quality of service in an optical access network for future generation's usage

  1. Cardinality enhancement utilizing Sequential Algorithm (SeQ) code in OCDMA system

    Science.gov (United States)

    Fazlina, C. A. S.; Rashidi, C. B. M.; Rahman, A. K.; Aljunid, S. A.

    2017-11-01

    Optical Code Division Multiple Access (OCDMA) has been important with increasing demand for high capacity and speed for communication in optical networks because of OCDMA technique high efficiency that can be achieved, hence fibre bandwidth is fully used. In this paper we will focus on Sequential Algorithm (SeQ) code with AND detection technique using Optisystem design tool. The result revealed SeQ code capable to eliminate Multiple Access Interference (MAI) and improve Bit Error Rate (BER), Phase Induced Intensity Noise (PIIN) and orthogonally between users in the system. From the results, SeQ shows good performance of BER and capable to accommodate 190 numbers of simultaneous users contrast with existing code. Thus, SeQ code have enhanced the system about 36% and 111% of FCC and DCS code. In addition, SeQ have good BER performance 10-25 at 155 Mbps in comparison with 622 Mbps, 1 Gbps and 2 Gbps bit rate. From the plot graph, 155 Mbps bit rate is suitable enough speed for FTTH and LAN networks. Resolution can be made based on the superior performance of SeQ code. Thus, these codes will give an opportunity in OCDMA system for better quality of service in an optical access network for future generation's usage

  2. Modeling ChIP sequencing in silico with applications.

    Directory of Open Access Journals (Sweden)

    Zhengdong D Zhang

    2008-08-01

    Full Text Available ChIP sequencing (ChIP-seq is a new method for genomewide mapping of protein binding sites on DNA. It has generated much excitement in functional genomics. To score data and determine adequate sequencing depth, both the genomic background and the binding sites must be properly modeled. To develop a computational foundation to tackle these issues, we first performed a study to characterize the observed statistical nature of this new type of high-throughput data. By linking sequence tags into clusters, we show that there are two components to the distribution of tag counts observed in a number of recent experiments: an initial power-law distribution and a subsequent long right tail. Then we develop in silico ChIP-seq, a computational method to simulate the experimental outcome by placing tags onto the genome according to particular assumed distributions for the actual binding sites and for the background genomic sequence. In contrast to current assumptions, our results show that both the background and the binding sites need to have a markedly nonuniform distribution in order to correctly model the observed ChIP-seq data, with, for instance, the background tag counts modeled by a gamma distribution. On the basis of these results, we extend an existing scoring approach by using a more realistic genomic-background model. This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion.

  3. Synergistic effect of sodium and yeast in improving the efficiency of DSSC sensitized with extract from petals of Kigelia Africana

    Science.gov (United States)

    Shalini, S.; Balasundaraprabhu, R.; Satish Kumar, T.; Sivakumaran, K.; Kannan, M. D.

    2018-05-01

    TiO2 nanostructures with two different dopants, sodium and yeast have been successfully synthesized by hydrothermal method. Doping sodium is found to extend the absorbance of TiO2 into the visible region as well as it acts as mordant in fixing and improving the absorption of dye. Yeast, as a dopant, can help in absorption of more anthocyanins from the natural dye extract by TiO2 and also aids in retaining the colour of the dye and increases the stability of the dye at varying pH. Anthocyanins are the major class of pigment present in the newly addressed maroon, velvety and trumpet shaped flower "Kigelia Africana". X-ray diffraction analysis revealed the formation of rutile phase for all the samples. Field Emission Scanning Electron microscopy images revealed the formation of nanorods and nanoflowers with change in dopant as well as their concentration. The photoelectric conversion efficiency of DSSC with undoped TiO2 photoelectrode is 0.87% and DSSC with 6% Na doped TiO2 photoelectrode is 1.56%. The efficiency of DSSC with 6% Na+6% yeast doped TiO2 photoelectrode is found to increase from 2.09% (DSSC with 6% Na+4% yeast doped TiO2 photoelectrode) to 2.31% on varying the dopant concentration. Doping is also found to increase the dye absorption and superior charge transport efficiency which in turn helps to improve the performance of DSSC.

  4. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

    Directory of Open Access Journals (Sweden)

    Courdy Samir J

    2008-12-01

    Full Text Available Abstract Background High throughput signature sequencing holds many promises, one of which is the ready identification of in vivo transcription factor binding sites, histone modifications, changes in chromatin structure and patterns of DNA methylation across entire genomes. In these experiments, chromatin immunoprecipitation is used to enrich for particular DNA sequences of interest and signature sequencing is used to map the regions to the genome (ChIP-Seq. Elucidation of these sites of DNA-protein binding/modification are proving instrumental in reconstructing networks of gene regulation and chromatin remodelling that direct development, response to cellular perturbation, and neoplastic transformation. Results Here we present a package of algorithms and software that makes use of control input data to reduce false positives and estimate confidence in ChIP-Seq peaks. Several different methods were compared using two simulated spike-in datasets. Use of control input data and a normalized difference score were found to more than double the recovery of ChIP-Seq peaks at a 5% false discovery rate (FDR. Moreover, both a binomial p-value/q-value and an empirical FDR were found to predict the true FDR within 2–3 fold and are more reliable estimators of confidence than a global Poisson p-value. These methods were then used to reanalyze Johnson et al.'s neuron-restrictive silencer factor (NRSF ChIP-Seq data without relying on extensive qPCR validated NRSF sites and the presence of NRSF binding motifs for setting thresholds. Conclusion The methods developed and tested here show considerable promise for reducing false positives and estimating confidence in ChIP-Seq data without any prior knowledge of the chIP target. They are part of a larger open source package freely available from http://useq.sourceforge.net/.

  5. A fast template matching method for LED chip Localization

    Directory of Open Access Journals (Sweden)

    Zhong Fuqiang

    2015-01-01

    Full Text Available Efficiency determines the profits of the semiconductor producers. So the producers spare no effort to enhance the efficiency of every procedure. The purpose of the paper is to present a method to shorten the time to locate the LED chips on wafer. The method consists of 3 steps. Firstly, image segmentation and blob analyzation are used to predict the positions of potential chips. Then predict the orientations of potential chips based on their dominant orientations. Finally, according to the positions and orientations predicted above, locate the chips precisely based on gradient orientation features. Experiments show that the algorithm is faster than the traditional method we choose to locate the LED chips. Besides, even the orientations of the chips on wafer are of big deviation to the orientation of the template, the efficiency of this method won't be affected.

  6. Effect of different levels of mangosteen peel powder supplement on the performance of dairy cows fed concentrate containing yeast fermented cassava chip protein.

    Science.gov (United States)

    Polyorach, Sineenart; Wanapat, Metha; Phesatcha, Kampanat; Kang, Sungchhang

    2015-12-01

    This study aimed to investigate the effect of mangosteen (Garcinia mangostana) peel powder (MSP) supplementation on feed intake, nutrient digestibility, ruminal fermentation, and milk production in lactating dairy cows fed a concentrate containing yeast fermented cassava chip protein (YEFECAP). Four crossbred dairy cows (50 % Holstein-Friesian and 50 % Thai native breed) in mid-lactation, 404 ± 50.0 kg of body weight and 90 ± 5 day in milk with daily milk production of 9 ± 2.0 kg/day, were randomly assigned according to a 4 × 4 Latin square design to receive 4 dietary treatments. The treatments were different levels of MSP supplementation at 0, 100, 200, and 300 g/head/day. Rice straw was used as a roughage source and fed ad libitum to all cows, and concentrate containing YEFECAP at 200 g/kg concentrate was offered corresponding to concentrate to milk yield ratio at 1:2. Results revealed that feed intake, apparent nutrient digestibility, ruminal pH and temperature, and total volatile fatty acid were not significantly affected by MSP supplementation (P > 0.05). However, increasing levels of MSP supplementation increased molar proportion of propionate while ammonia-nitrogen, acetate, and acetate to propionate ratio were decreased (P fermentation efficiency, milk production and protein content, and economical return of lactating dairy cows fed on rice straw.

  7. Efficient generation of single and entangled photons on a silicon photonic integrated chip

    International Nuclear Information System (INIS)

    Mower, Jacob; Englund, Dirk

    2011-01-01

    We present a protocol for generating on-demand, indistinguishable single photons on a silicon photonic integrated chip. The source is a time-multiplexed spontaneous parametric down-conversion element that allows optimization of single-photon versus multiphoton emission while realizing high output rate and indistinguishability. We minimize both the scaling of active elements and the scaling of active element loss with multiplexing. We then discuss detection strategies and data processing to further optimize the procedure. We simulate an improvement in single-photon-generation efficiency over previous time-multiplexing protocols, assuming existing fabrication capabilities. We then apply this system to generate heralded Bell states. The generation efficiency of both nonclassical states could be increased substantially with improved fabrication procedures.

  8. Experiment list: SRX186753 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available der=Lonza || datatype=ChipSeq || datatype description=Chromatin IP Sequencing || antibody antibodydescription=Rabbit polyclonal antib...on. Antibody Target: H3K79me2 || antibody targetdescription=H3K79me2 is a mark of the transcriptional transi...tion region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). || antibody... vendorname=Active Motif || antibody vendorid=39143 || controlid=wgEncodeEH0...00093 || replicate=1,2 || softwareversion=ScriptureVPaperR3 || cell sex=U || antibody=H3K79me2 || antibody antibody

  9. Research to Improve the Efficiency of Double Stereo PCR Microfluidic Chip by Passivating the Inner Surface of Steel Capillary with NOA61.

    Science.gov (United States)

    Wu, Jian; Guo, Wei; Wang, Chunyan; Yu, Kuanxin; Ma, Ying; Chen, Tao; Li, Yinghui

    2015-06-01

    In this paper, we report the improvement of PCR microfluidic chip efficiency achieved by coating the inner surface of steel capillary microchannel with a 22-µm film of the ultraviolet-solidified NOA61 using a device invented by us. Our results indicate that with this treatment, the roughness of the inside wall of steel capillary was improved from Ra = 0.921 to Ra = 0.254. The contact angle was decreased from about 95° to 56°, and the surface hydrophobicity was also increased. The flow pressure for performing the real-time PCR in the microfluidic chip with modified surface was reduced by twofold (2.11/1) and that resulted in a substantially increased efficiency of PCR. A modification of the microchannel interior surface improved the quality of the on-chip integrated PCR procedure.

  10. Chip-based generation of carbon nanodots via electrochemical oxidation of screen printed carbon electrodes and the applications for efficient cell imaging and electrochemiluminescence enhancement.

    Science.gov (United States)

    Xu, Yuanhong; Liu, Jingquan; Zhang, Jizhen; Zong, Xidan; Jia, Xiaofang; Li, Dan; Wang, Erkang

    2015-06-07

    A portable lab-on-a-chip methodology to generate ionic liquid-functionalized carbon nanodots (CNDs) was developed via electrochemical oxidation of screen printed carbon electrodes. The CNDs can be successfully applied for efficient cell imaging and solid-state electrochemiluminescence sensor fabrication on the paper-based chips.

  11. MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies

    Directory of Open Access Journals (Sweden)

    Pankaj Kumar

    2015-01-01

    Full Text Available The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments. Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA, Biosample, Bioprojects, and Gene Expression Omnibus (GEO. Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study. Here we describe “MetaRNA-Seq,” a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.

  12. Fisetin yeast-based bio-capsules via osmoporation: effects of process variables on the encapsulation efficiency and internalized fisetin content.

    Science.gov (United States)

    de Câmara, Antonio Anchieta; Dupont, Sébastien; Beney, Laurent; Gervais, Patrick; Rosenthal, Amauri; Correia, Roberta Targino Pinto; Pedrini, Márcia Regina da Silva

    2016-06-01

    Osmoporation is an innovative method that can be used with food-grade yeast cells of Saccharomyces cerevisiae as natural encapsulating matrices. This technique overcomes barriers that difficult encapsulation and enables the internalization of fragile bioactive molecules such as fisetin into yeasts. In the present study, we assessed the effects of concentration, osmotic pressure, and temperature on the encapsulation efficiency (EE) and internalized fisetin content (IF). Two different quantification strategies were investigated: direct extraction (DE) without cell washing or freeze-drying steps and indirect extraction (IE) performed after washings with ethanol and freeze-drying. Our results showed that osmoporation improved EE (33 %) and IF (1.199 mg). The best experimental conditions were found by using DE. High-resolution images showed that the yeast cell envelope was preserved during osmoporation at 30 MPa and 84 % of yeast cells remained viable after treatment. Washing cells with organic solvent led to decreased EE (0.65 %) and IF (0.023 mg). This was probably due to either damages caused to yeast cell envelope or fisetin dragged out of cell. Overall, the results demonstrated the adequacy and relevant biotechnological potential of yeasts as encapsulating matrices for hydrophobic compounds. This fresh biotechnological approach has proven to be a promising tool for the production of bioactive-rich food products.

  13. Computational Methods for ChIP-seq Data Analysis and Applications

    KAUST Repository

    Ashoor, Haitham

    2017-04-25

    The development of Chromatin immunoprecipitation followed by sequencing (ChIP-seq) technology has enabled the construction of genome-wide maps of protein-DNA interaction. Such maps provide information about transcriptional regulation at the epigenetic level (histone modifications and histone variants) and at the level of transcription factor (TF) activity. This dissertation presents novel computational methods for ChIP-seq data analysis and applications. The work of this dissertation addresses four main challenges. First, I address the problem of detecting histone modifications from ChIP-seq cancer samples. The presence of copy number variations (CNVs) in cancer samples results in statistical biases that lead to inaccurate predictions when standard methods are used. To overcome this issue I developed HMCan, a specially designed algorithm to handle ChIP-seq cancer data by accounting for the presence of CNVs. When using ChIP-seq data from cancer cells, HMCan demonstrates unbiased and accurate predictions compared to the standard state of the art methods. Second, I address the problem of identifying changes in histone modifications between two ChIP-seq samples with different genetic backgrounds (for example cancer vs. normal). In addition to CNVs, different antibody efficiency between samples and presence of samples replicates are challenges for this problem. To overcome these issues, I developed the HMCan-diff algorithm as an extension to HMCan. HMCan-diff implements robust normalization methods to address the challenges listed above. HMCan-diff significantly outperforms another state of the art methods on data containing cancer samples. Third, I investigate and analyze predictions of different methods for enhancer prediction based on ChIP-seq data. The analysis shows that predictions generated by different methods are poorly overlapping. To overcome this issue, I developed DENdb, a database that integrates enhancer predictions from different methods. DENdb also

  14. Chip compacting press; Jido kirikuzu asshukuki

    Energy Technology Data Exchange (ETDEWEB)

    Oura, K. [Yuken Kogyo Co. Ltd., Kanagawa (Japan)

    1998-08-15

    The chips exhausted from various machine tools are massy, occupy much space and make working environment worse by staying added cutting oil to lower part. The chips are exhausted as a result of machining and have not constant quality. Even if used material is same the chips have various shapes and properties by kinds and machining methods of used machine tools, and are troublesome materials from a standpoint of their treatment. Pressing and solidification of the chips have frequently been tried. A chip compacting press introduced in this paper, a relatively cheap chip compacting press aimed for relatively small scale chip treatment, and has such characteristics and effects as follows. Chips are pressed and solidified by each raw material, so fractional management can be easily conducted. As casting metal chips and curled chips of iron and aluminum can be pressed to about 1/3 to 1/5 and about 1/40, respectively, space saving can be conducted. Chip compacting pressing upgrades its transporting efficiency to make possible to reduce its transporting cost. As chip solidification controls its oxidation and most cutting oil are removed, chips are easy to recycle. 2 figs., 1 tab.

  15. rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data.

    Science.gov (United States)

    Shi, Yang; Chinnaiyan, Arul M; Jiang, Hui

    2015-07-01

    High-throughput sequencing of transcriptomes (RNA-Seq) has become a powerful tool to study gene expression. Here we present an R package, rSeqNP, which implements a non-parametric approach to test for differential expression and splicing from RNA-Seq data. rSeqNP uses permutation tests to access statistical significance and can be applied to a variety of experimental designs. By combining information across isoforms, rSeqNP is able to detect more differentially expressed or spliced genes from RNA-Seq data. The R package with its source code and documentation are freely available at http://www-personal.umich.edu/∼jianghui/rseqnp/. jianghui@umich.edu 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.

  16. An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data

    Directory of Open Access Journals (Sweden)

    Wilson Zoe A

    2010-02-01

    Full Text Available Abstract Background ChIP-Seq, which combines chromatin immunoprecipitation (ChIP with high-throughput massively parallel sequencing, is increasingly being used for identification of protein-DNA interactions in vivo in the genome. However, to maximize the effectiveness of data analysis of such sequences requires the development of new algorithms that are able to accurately predict DNA-protein binding sites. Results Here, we present SIPeS (Site Identification from Paired-end Sequencing, a novel algorithm for precise identification of binding sites from short reads generated by paired-end solexa ChIP-Seq technology. In this paper we used ChIP-Seq data from the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS, which is expressed within the anther during pollen development, the results show that SIPeS has better resolution for binding site identification compared to two existing ChIP-Seq peak detection algorithms, Cisgenome and MACS. Conclusions When compared to Cisgenome and MACS, SIPeS shows better resolution for binding site discovery. Moreover, SIPeS is designed to calculate the mappable genome length accurately with the fragment length based on the paired-end reads. Dynamic baselines are also employed to effectively discriminate closely adjacent binding sites, for effective binding sites discovery, which is of particular value when working with high-density genomes.

  17. Full on-chip and area-efficient CMOS LDO with zero to maximum load stability using adaptive frequency compensation

    International Nuclear Information System (INIS)

    Ma Haifeng; Zhou Feng

    2010-01-01

    A full on-chip and area-efficient low-dropout linear regulator (LDO) is presented. By using the proposed adaptive frequency compensation (AFC) technique, full on-chip integration is achieved without compromising the LDO's stability in the full output current range. Meanwhile, the use of a compact pass transistor (the compact pass transistor serves as the gain fast roll-off output stage in the AFC technique) has enabled the LDO to be very area-efficient. The proposed LDO is implemented in standard 0.35 μm CMOS technology and occupies an active area as small as 220 x 320 μm 2 , which is a reduction to 58% compared to state-of-the-art designs using technologies with the same feature size. Measurement results show that the LDO can deliver 0-60 mA output current with 54 μA quiescent current consumption and the regulated output voltage is 1.8 V with an input voltage range from 2 to 3.3 V. (semiconductor integrated circuits)

  18. Solving wood chip transport problems with computer simulation.

    Science.gov (United States)

    Dennis P. Bradley; Sharon A. Winsauer

    1976-01-01

    Efficient chip transport operations are difficult to achieve due to frequent and often unpredictable changes in distance to market, chipping rate, time spent at the mill, and equipment costs. This paper describes a computer simulation model that allows a logger to design an efficient transport system in response to these changing factors.

  19. Construction of gateway-compatible yeast two-hybrid vectors for ...

    African Journals Online (AJOL)

    Yeast two-hybrid system combined with the gateway technology will greatly facilitate the cloning of interested DNA fragment into yeast two-hybrid vectors and therefore increase the efficiency of yeast two-hybrid analysis. In this study, we constructed a pair of Gateway-compatible yeast two-hybrid vectors pBTM116GW and ...

  20. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey; Bruno, Vincent M.; Fang, Zhide; Meng, Xiandong; Blow, Matthew; Zhang, Tao; Sherlock, Gavin; Snyder, Michael; Wang, Zhong

    2010-11-19

    Background: Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. While high throughput mRNA sequencing (RNA-Seq) has emerged as a powerful tool for addressing these problems, its success is dependent upon the availability and quality of reference genome sequences, thus limiting the organisms to which it can be applied. Results: Here, we describe Rnnotator, an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome. We have applied the Rnnotator assembly pipeline to two yeast transcriptomes and compared the results to the reference gene catalogs of these organisms. The contigs produced by Rnnotator are highly accurate (95percent) and reconstruct full-length genes for the majority of the existing gene models (54.3percent). Furthermore, our analyses revealed many novel transcribed regions that are absent from well annotated genomes, suggesting Rnnotator serves as a complementary approach to analysis based on a reference genome for comprehensive transcriptomics. Conclusions: These results demonstrate that the Rnnotator pipeline is able to reconstruct full-length transcripts in the absence of a complete reference genome.

  1. PMAA-stabilized ferrofluid/chitosan/yeast composite for bioapplications

    International Nuclear Information System (INIS)

    Baldikova, Eva; Prochazkova, Jitka; Stepanek, Miroslav; Hajduova, Jana; Pospiskova, Kristyna; Safarikova, Mirka; Safarik, Ivo

    2017-01-01

    A simple, one-pot process for the preparation of magnetically responsive yeast-based biocatalysts was developed. Saccharomyces cerevisiae, Candida utilis and Kluyveromyces lactis cells were successfully incorporated into chitosan gel magnetically modified with poly(methacrylic acid)-stabilized magnetic fluid (PMAA-FF) during its formation. Magnetic PMAA-FF/chitosan/yeast composites were efficiently employed for invert sugar production. The dependence of invertase activity on used yeast, amount of magnetic biocatalyst, agitation time and after reuse was studied in detail. The tested magnetic biocatalysts retained at least 69% of their initial activity after 8 reuse cycles. - Highlights: • New types of magnetically responsive yeast biocomposites were prepared. • Recently developed PMAA-stabilized magnetic fluid was used. • Three yeast species were entrapped into magnetic chitosan gel during its formation. • All biocatalysts were efficiently employed for invert sugar formation.

  2. PMAA-stabilized ferrofluid/chitosan/yeast composite for bioapplications

    Energy Technology Data Exchange (ETDEWEB)

    Baldikova, Eva, E-mail: baldie@email.cz [Global Change Research Institute, CAS, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic); Department of Applied Chemistry, Faculty of Agriculture, University of South Bohemia, Branisovska 1457, 370 05 Ceske Budejovice (Czech Republic); Prochazkova, Jitka [Global Change Research Institute, CAS, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic); Stepanek, Miroslav; Hajduova, Jana [Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 2030, 128 40 Prague 2 (Czech Republic); Pospiskova, Kristyna [Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 27, 783 71 Olomouc (Czech Republic); Safarikova, Mirka [Global Change Research Institute, CAS, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic); Department of Nanobiotechnology, Biology Centre, CAS, ISB, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic); Safarik, Ivo [Global Change Research Institute, CAS, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic); Regional Centre of Advanced Technologies and Materials, Palacky University, Slechtitelu 27, 783 71 Olomouc (Czech Republic); Department of Nanobiotechnology, Biology Centre, CAS, ISB, Na Sadkach 7, 370 05 Ceske Budejovice (Czech Republic)

    2017-04-01

    A simple, one-pot process for the preparation of magnetically responsive yeast-based biocatalysts was developed. Saccharomyces cerevisiae, Candida utilis and Kluyveromyces lactis cells were successfully incorporated into chitosan gel magnetically modified with poly(methacrylic acid)-stabilized magnetic fluid (PMAA-FF) during its formation. Magnetic PMAA-FF/chitosan/yeast composites were efficiently employed for invert sugar production. The dependence of invertase activity on used yeast, amount of magnetic biocatalyst, agitation time and after reuse was studied in detail. The tested magnetic biocatalysts retained at least 69% of their initial activity after 8 reuse cycles. - Highlights: • New types of magnetically responsive yeast biocomposites were prepared. • Recently developed PMAA-stabilized magnetic fluid was used. • Three yeast species were entrapped into magnetic chitosan gel during its formation. • All biocatalysts were efficiently employed for invert sugar formation.

  3. Dr. Monaco Examines Lab-on a-Chip

    Science.gov (United States)

    2003-01-01

    Dr. Lisa Monaco, Marshall Space Flight Center's (MSFC's) project scientist for the Lab-on-a-Chip Applications Development (LOCAD) program, examines a lab on a chip. The small dots are actually ports where fluids and chemicals can be mixed or samples can be collected for testing. Tiny channels, only clearly visible under a microscope, form pathways between the ports. Many chemical and biological processes, previously conducted on large pieces of laboratory equipment, can now be performed on these small glass or plastic plates. Monaco and other researchers at MSFC in Huntsville, Alabama, are customizing the chips to be used for many space applications, such as monitoring microbes inside spacecraft and detecting life on other planets. The portable, handheld Lab-on-a Chip Application Development Portable Test System (LOCAD-PTS) made its debut flight aboard Discovery during the STS-116 mission launched December 9, 2006. The system allowed crew members to monitor their environment for problematic contaminants such as yeast, mold, and even E.coli, and salmonella. Once LOCAD-PTS reached the International Space Station (ISS), the Marshall team continued to manage the experiment, monitoring the study from a console in the Payload Operations Center at MSFC. The results of these studies will help NASA researchers refine the technology for future Moon and Mars missions. (NASA/MSFC/D.Stoffer)

  4. Variation Tolerant On-Chip Interconnects

    CERN Document Server

    Nigussie, Ethiopia Enideg

    2012-01-01

    This book presents design techniques, analysis and implementation of high performance and power efficient, variation tolerant on-chip interconnects.  Given the design paradigm shift to multi-core, interconnect-centric designs and the increase in sources of variability and their impact in sub-100nm technologies, this book will be an invaluable reference for anyone concerned with the design of next generation, high-performance electronics systems. Provides comprehensive, circuit-level explanation of high-performance, energy-efficient, variation-tolerant on-chip interconnect; Describes design techniques to mitigate problems caused by variation; Includes techniques for design and implementation of self-timed on-chip interconnect, delay variation insensitive communication protocols, high speed signaling techniques and circuits, bit-width independent completion detection and process, voltage and temperature variation tolerance.                          

  5. ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data.

    Directory of Open Access Journals (Sweden)

    Yuttachon Promworn

    Full Text Available Biochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not be suitable for Cappable-seq data. The more efficient enrichment method employed in Cappable-seq compared with dRNA-seq could affect data distribution and thus algorithm performance.We present Transformation of Nucleotide Enrichment Ratios (ToNER, a tool for statistical modeling of enrichment from RNA-seq data obtained from enriched and unenriched libraries. The tool calculates nucleotide enrichment scores and determines the global transformation for fitting to the normal distribution using the Box-Cox procedure. From the transformed distribution, sites of significant enrichment are identified. To increase power of detection, meta-analysis across experimental replicates is offered. We tested the tool on Cappable-seq and dRNA-seq data for identifying Escherichia coli transcript 5' ends and compared the results with those from the TSSAR tool, which is designed for analyzing dRNA-seq data. When combining results across Cappable-seq replicates, ToNER detects more known transcript 5' ends than TSSAR. In general, the transcript 5' ends detected by ToNER but not TSSAR occur in regions which cannot be locally modeled by TSSAR.ToNER uses a simple yet robust statistical modeling approach, which can be used for detecting RNA 5'ends from Cappable-seq data, in particular when combining information from experimental replicates. The ToNER tool could potentially be applied for analyzing other RNA-seq datasets in which enrichment for other structural features of RNA is employed. The program is freely available for download at ToNER webpage (http://www4a

  6. ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data.

    Science.gov (United States)

    Promworn, Yuttachon; Kaewprommal, Pavita; Shaw, Philip J; Intarapanich, Apichart; Tongsima, Sissades; Piriyapongsa, Jittima

    2017-01-01

    Biochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq) and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not be suitable for Cappable-seq data. The more efficient enrichment method employed in Cappable-seq compared with dRNA-seq could affect data distribution and thus algorithm performance. We present Transformation of Nucleotide Enrichment Ratios (ToNER), a tool for statistical modeling of enrichment from RNA-seq data obtained from enriched and unenriched libraries. The tool calculates nucleotide enrichment scores and determines the global transformation for fitting to the normal distribution using the Box-Cox procedure. From the transformed distribution, sites of significant enrichment are identified. To increase power of detection, meta-analysis across experimental replicates is offered. We tested the tool on Cappable-seq and dRNA-seq data for identifying Escherichia coli transcript 5' ends and compared the results with those from the TSSAR tool, which is designed for analyzing dRNA-seq data. When combining results across Cappable-seq replicates, ToNER detects more known transcript 5' ends than TSSAR. In general, the transcript 5' ends detected by ToNER but not TSSAR occur in regions which cannot be locally modeled by TSSAR. ToNER uses a simple yet robust statistical modeling approach, which can be used for detecting RNA 5'ends from Cappable-seq data, in particular when combining information from experimental replicates. The ToNER tool could potentially be applied for analyzing other RNA-seq datasets in which enrichment for other structural features of RNA is employed. The program is freely available for download at ToNER webpage (http://www4a.biotec.or.th/GI/tools/toner) and Git

  7. Mechanisms of yeast stress tolerance and its manipulation for efficient fuel ethanol production.

    Science.gov (United States)

    Zhao, X Q; Bai, F W

    2009-10-12

    Yeast strains of Saccharomyces cerevisiae have been extensively studied in recent years for fuel ethanol production, in which yeast cells are exposed to various stresses such as high temperature, ethanol inhibition, and osmotic pressure from product and substrate sugars as well as the inhibitory substances released from the pretreatment of lignocellulosic biomass. An in-depth understanding of the mechanism of yeast stress tolerance contributes to breeding more robust strains for ethanol production, especially under very high gravity conditions. Taking advantage of the "omics" technology, the stress response and defense mechanism of yeast cells during ethanol fermentation were further explored, and the newly emerged tools such as genome shuffling and global transcription machinery engineering have been applied to breed stress resistant yeast strains for ethanol production. In this review, the latest development of stress tolerance mechanisms was focused, and improvement of yeast stress tolerance by both random and rational tools was presented.

  8. Simulation and experimental validation of a SU-8 based PCR thermocycler chip with integrated heaters and temperature sensor

    DEFF Research Database (Denmark)

    El-Ali, Jamil; Perch-Nielsen, Ivan R.; Poulsen, Claus Riber

    2004-01-01

    We present a SU-8 based polymerase chain reaction (PCR) chip with integrated platinum thin film heaters and temperature sensor. The device is fabricated in SU-8 on a glass substrate. The use of SU-8 provides a simple microfabrication process for the PCR chamber, controllable surface properties......C/s, respectively, the performance of the chip is comparable with the best silicon micromachined PCR chips presented in the literature. The SU-8 chamber surface was found to be PCR compatible by amplification of yeast gene ribosomal protein S3 and Campylobacter gene cadF. The PCR compatibility of the chamber...

  9. Alternative mapping of probes to genes for Affymetrix chips

    DEFF Research Database (Denmark)

    Gautier, Laurent; Møller, M.; Friis-Hansen, L.

    2004-01-01

    transcripts: the NCBI RefSeq database. We also built mappings and used them in place of the original probe to genes associations provided by the manufacturer of the arrays. Results: In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes...... by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data. Conclusions: While the probes on Affymetrix arrays remain the same for several years, the biological knowledge concerning the genomic sequences evolves rapidly. Using up...

  10. Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.

    Science.gov (United States)

    Hocking, Toby Dylan; Goerner-Potvin, Patricia; Morin, Andreanne; Shao, Xiaojian; Pastinen, Tomi; Bourque, Guillaume

    2017-02-15

    Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily labeled by visual inspection of aligned read counts in a genome browser. We propose a supervised machine learning approach for ChIP-seq data analysis, using labels that encode qualitative judgments about which genomic regions contain or do not contain peaks. The main idea is to manually label a small subset of the genome, and then learn a model that makes consistent peak predictions on the rest of the genome. We created 7 new histone mark datasets with 12 826 visually determined labels, and analyzed 3 existing transcription factor datasets. We observed that default peak detection parameters yield high false positive rates, which can be reduced by learning parameters using a relatively small training set of labeled data from the same experiment type. We also observed that labels from different people are highly consistent. Overall, these data indicate that our supervised labeling method is useful for quantitatively training and testing peak detection algorithms. Labeled histone mark data http://cbio.ensmp.fr/~thocking/chip-seq-chunk-db/ , R package to compute the label error of predicted peaks https://github.com/tdhock/PeakError. toby.hocking@mail.mcgill.ca or guil.bourque@mcgill.ca. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  11. A novel non-dairy beverage from durian pulp fermented with selected probiotics and yeast.

    Science.gov (United States)

    Lu, Yuyun; Putra, Satya Dwi; Liu, Shao-Quan

    2018-01-16

    This study investigated the effects of sequential inoculation (Seq-I) of Bifidobacterium animalis subsp. lactis or Lactobacillus casei with yeast Williopsis saturnus on durian pulp fermentation. Seq-I of W. saturnus following B. animalis subsp. lactis did not bring about any significant differences compared to the B. animalis subsp. lactis monoculture due to the sharp early death of W. saturnus soon after inoculation. However, Seq-I of W. saturnus significantly enhanced the survival of L. casei and improved the utilization of fructose and glucose compared to L. casei monoculture. In addition, there were significant differences in the metabolism of organic acids especially for lactic acid and succinic acid. Furthermore, Seq-I produced significantly higher levels of volatile compounds including alcohols (ethanol and 2-phenylethyl alcohol) and acetate esters (2-phenylethyl acetate, isoamyl acetate and ethyl acetate), which would positively contribute to the flavour notes. Although the initial volatile sulphur compounds were reduced to trace levels after fermentation, but the durian odour still remained. This study suggests that the use of probiotics and W. saturnus to ferment durian pulp could act as a potential avenue to develop a novel non-dairy durian-based functional beverage to deliver probiotics. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. New yeasts-new brews: modern approaches to brewing yeast design and development.

    Science.gov (United States)

    Gibson, B; Geertman, J-M A; Hittinger, C T; Krogerus, K; Libkind, D; Louis, E J; Magalhães, F; Sampaio, J P

    2017-06-01

    The brewing industry is experiencing a period of change and experimentation largely driven by customer demand for product diversity. This has coincided with a greater appreciation of the role of yeast in determining the character of beer and the widespread availability of powerful tools for yeast research. Genome analysis in particular has helped clarify the processes leading to domestication of brewing yeast and has identified domestication signatures that may be exploited for further yeast development. The functional properties of non-conventional yeast (both Saccharomyces and non-Saccharomyces) are being assessed with a view to creating beers with new flavours as well as producing flavoursome non-alcoholic beers. The discovery of the psychrotolerant S. eubayanus has stimulated research on de novo S. cerevisiae × S. eubayanus hybrids for low-temperature lager brewing and has led to renewed interest in the functional importance of hybrid organisms and the mechanisms that determine hybrid genome function and stability. The greater diversity of yeast that can be applied in brewing, along with an improved understanding of yeasts' evolutionary history and biology, is expected to have a significant and direct impact on the brewing industry, with potential for improved brewing efficiency, product diversity and, above all, customer satisfaction. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

    Directory of Open Access Journals (Sweden)

    Kevin Weitemier

    2014-08-01

    Full Text Available Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. Methods and Results: Genome and transcriptome assemblies for milkweed (Asclepias syriaca were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. Conclusions: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics.

  14. Energy Model of Networks-on-Chip and a Bus

    NARCIS (Netherlands)

    Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Kavaldjiev, N.K.; Becker, Jens E.; Becker, Jürgen; Nurmi, J.; Takala, J.; Hamalainen, T.D.

    2005-01-01

    A Network-on-Chip (NoC) is an energy-efficient onchip communication architecture for Multi-Processor Systemon-Chip (MPSoC) architectures. In earlier papers we proposed two Network-on-Chip architectures based on packet-switching and circuit-switching. In this paper we derive an energy model for both

  15. Full on-chip and area-efficient CMOS LDO with zero to maximum load stability using adaptive frequency compensation

    Energy Technology Data Exchange (ETDEWEB)

    Ma Haifeng; Zhou Feng, E-mail: fengzhou@fudan.edu.c [State Key Laboratory of ASIC and System, Fudan University, Shanghai 201203 (China)

    2010-01-15

    A full on-chip and area-efficient low-dropout linear regulator (LDO) is presented. By using the proposed adaptive frequency compensation (AFC) technique, full on-chip integration is achieved without compromising the LDO's stability in the full output current range. Meanwhile, the use of a compact pass transistor (the compact pass transistor serves as the gain fast roll-off output stage in the AFC technique) has enabled the LDO to be very area-efficient. The proposed LDO is implemented in standard 0.35 {mu}m CMOS technology and occupies an active area as small as 220 x 320 {mu}m{sup 2}, which is a reduction to 58% compared to state-of-the-art designs using technologies with the same feature size. Measurement results show that the LDO can deliver 0-60 mA output current with 54 {mu}A quiescent current consumption and the regulated output voltage is 1.8 V with an input voltage range from 2 to 3.3 V. (semiconductor integrated circuits)

  16. Chromosome VIII disomy influences the nonsense suppression efficiency and transition metal tolerance of the yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Zadorsky, S P; Sopova, Y V; Andreichuk, D Y; Startsev, V A; Medvedeva, V P; Inge-Vechtomov, S G

    2015-06-01

    The SUP35 gene of the yeast Saccharomyces cerevisiae encodes the translation termination factor eRF3. Mutations in this gene lead to the suppression of nonsense mutations and a number of other pleiotropic phenotypes, one of which is impaired chromosome segregation during cell division. Similar effects result from replacing the S. cerevisiae SUP35 gene with its orthologues. A number of genetic and epigenetic changes that occur in the sup35 background result in partial compensation for this suppressor effect. In this study we showed that in S. cerevisiae strains in which the SUP35 orthologue from the yeast Pichia methanolica replaces the S. cerevisiae SUP35 gene, chromosome VIII disomy results in decreased efficiency of nonsense suppression. This antisuppressor effect is not associated with decreased stop codon read-through. We identified SBP1, a gene that localizes to chromosome VIII, as a dosage-dependent antisuppressor that strongly contributes to the overall antisuppressor effect of chromosome VIII disomy. Disomy of chromosome VIII also leads to a change in the yeast strains' tolerance of a number of transition metal salts. Copyright © 2015 John Wiley & Sons, Ltd.

  17. SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.

    Science.gov (United States)

    Ryan, Michael C; Cleland, James; Kim, RyangGuk; Wong, Wing Chung; Weinstein, John N

    2012-09-15

    SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats. SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie. mryan@insilico.us.com Supplementary data are available at Bioinformatics online.

  18. Between science and industry-applied yeast research.

    Science.gov (United States)

    Korhola, Matti

    2018-03-01

    I was fortunate to enter yeast research at the Alko Research Laboratories with a strong tradition in yeast biochemistry and physiology studies. At the same time in the 1980s there was a fundamental or paradigm change in molecular biology research with discoveries in DNA sequencing and other analytical and physical techniques for studying macromolecules and cells. Since that time biotechnological research has expanded the traditional fermentation industries to efficient production of industrial and other enzymes and specialty chemicals. Our efforts were directed towards improving the industrial production organisms: minerals enriched yeasts (Se, Cr, Zn) and high glutathione content yeast, baker´s, distiller´s, sour dough and wine yeasts, and the fungal Trichoderma reesei platform for enzyme production. I am grateful for the trust of my colleagues in several leadership positions at the Alko Research Laboratories, Yeast Industry Platform and at the international yeast community.

  19. The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast.

    Science.gov (United States)

    Hartono, Stella R; Malapert, Amélie; Legros, Pénélope; Bernard, Pascal; Chédin, Frédéric; Vanoosthuyse, Vincent

    2018-02-02

    R-loops, which result from the formation of stable DNA:RNA hybrids, can both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loops in fission yeast, we used the S9.6 antibody-based DRIPc-seq method to sequence the RNA strand of R-loops and obtain strand-specific R-loop maps at near nucleotide resolution. Surprisingly, preliminary DRIPc-seq experiments identified mostly RNase H-resistant but exosome-sensitive RNAs that mapped to both DNA strands and resembled RNA:RNA hybrids (dsRNAs), suggesting that dsRNAs form widely in fission yeast. We confirmed in vitro that S9.6 can immuno-precipitate dsRNAs and provide evidence that dsRNAs can interfere with its binding to R-loops. dsRNA elimination by RNase III treatment prior to DRIPc-seq allowed the genome-wide and strand-specific identification of genuine R-loops that responded in vivo to RNase H levels and displayed classical features associated with R-loop formation. We also found that most transcripts whose levels were altered by in vivo manipulation of RNase H levels did not form detectable R-loops, suggesting that prolonged manipulation of R-loop levels could indirectly alter the transcriptome. We discuss the implications of our work in the design of experimental strategies to probe R-loop functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

    Science.gov (United States)

    Beccuti, Marco; Cordero, Francesca; Arigoni, Maddalena; Panero, Riccardo; Amparore, Elvio G; Donatelli, Susanna; Calogero, Raffaele A

    2018-03-01

    Short reads sequencing technology has been used for more than a decade now. However, the analysis of RNAseq and ChIPseq data is still computational demanding and the simple access to raw data does not guarantee results reproducibility between laboratories. To address these two aspects, we developed SeqBox, a cheap, efficient and reproducible RNAseq/ChIPseq hardware/software solution based on NUC6I7KYK mini-PC (an Intel consumer game computer with a fast processor and a high performance SSD disk), and Docker container platform. In SeqBox the analysis of RNAseq and ChIPseq data is supported by a friendly GUI. This allows access to fast and reproducible analysis also to scientists with/without scripting experience. Docker container images, docker4seq package and the GUI are available at http://www.bioinformatica.unito.it/reproducibile.bioinformatics.html. beccuti@di.unito.it. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  1. Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics1

    Science.gov (United States)

    Weitemier, Kevin; Straub, Shannon C. K.; Cronn, Richard C.; Fishbein, Mark; Schmickl, Roswitha; McDonnell, Angela; Liston, Aaron

    2014-01-01

    • Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. • Methods and Results: Genome and transcriptome assemblies for milkweed (Asclepias syriaca) were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. • Conclusions: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics. PMID:25225629

  2. QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization.

    Science.gov (United States)

    Zhao, Shanrong; Xi, Li; Quan, Jie; Xi, Hualin; Zhang, Ying; von Schack, David; Vincent, Michael; Zhang, Baohong

    2016-01-08

    RNA sequencing (RNA-seq), a next-generation sequencing technique for transcriptome profiling, is being increasingly used, in part driven by the decreasing cost of sequencing. Nevertheless, the analysis of the massive amounts of data generated by large-scale RNA-seq remains a challenge. Multiple algorithms pertinent to basic analyses have been developed, and there is an increasing need to automate the use of these tools so as to obtain results in an efficient and user friendly manner. Increased automation and improved visualization of the results will help make the results and findings of the analyses readily available to experimental scientists. By combing the best open source tools developed for RNA-seq data analyses and the most advanced web 2.0 technologies, we have implemented QuickRNASeq, a pipeline for large-scale RNA-seq data analyses and visualization. The QuickRNASeq workflow consists of three main steps. In Step #1, each individual sample is processed, including mapping RNA-seq reads to a reference genome, counting the numbers of mapped reads, quality control of the aligned reads, and SNP (single nucleotide polymorphism) calling. Step #1 is computationally intensive, and can be processed in parallel. In Step #2, the results from individual samples are merged, and an integrated and interactive project report is generated. All analyses results in the report are accessible via a single HTML entry webpage. Step #3 is the data interpretation and presentation step. The rich visualization features implemented here allow end users to interactively explore the results of RNA-seq data analyses, and to gain more insights into RNA-seq datasets. In addition, we used a real world dataset to demonstrate the simplicity and efficiency of QuickRNASeq in RNA-seq data analyses and interactive visualizations. The seamless integration of automated capabilites with interactive visualizations in QuickRNASeq is not available in other published RNA-seq pipelines. The high degree

  3. EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

    Science.gov (United States)

    Lee, Soohyun; Seo, Chae Hwa; Alver, Burak Han; Lee, Sanghyuk; Park, Peter J

    2015-09-03

    RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity among genes and among isoforms, the source of a given read is often ambiguous. Existing approaches for estimating expression levels from RNA-seq reads tend to compromise between accuracy and computational cost. We introduce a new approach for quantifying transcript abundance from RNA-seq data. EMSAR (Estimation by Mappability-based Segmentation And Reclustering) groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts. The method uses nearly all mapped reads, including those mapped to multiple genes. With an efficient transcriptome indexing based on modified suffix arrays, EMSAR minimizes the use of CPU time and memory while achieving accuracy comparable to the best existing methods. EMSAR is a method for quantifying transcripts from RNA-seq data with high accuracy and low computational cost. EMSAR is available at https://github.com/parklab/emsar.

  4. Airtight storage of wood chips for use as a fuel

    Energy Technology Data Exchange (ETDEWEB)

    Lamond, W.J.; Graham, R.; Boyd, J.E.L.; Harling, R.; Lowe, J.F.

    1993-11-01

    This study was carried out to see if airtight storage was a possible alternative to drying as a procedure for the successful storage of chipped wood for fuel. Twelve insulated bins, with a capacity of approximately 0.1 m{sup 3} each, were filled with freshly cut Sitka Spruce wood chips. Ten of these bins were sealed immediately after filling and the remaining two left unsealed for the duration of the experiment (12 months). The programme of sampling for gas, moisture content, mycology and bacteriology is described. The results showed that sealed storage reduced the overall dry matter loss in the bins to around 1% per month compared to 2% for the unsealed bins. This compares favourably with losses of around 3% per month which have been reported for open stacks of chips with much lower initial moisture contents than that used in these experiments. There was a slight reduction in the colorific value of oven dried chips between the initial and after storage samples. The moisture content of the chips in all the bins increased over the storage period. The average energy loss was 2.9% per month for sealed and 2.0% per month for unsealed treatment. A typical ecological succession was shown by the chips, commencing with field fungi and terminating with a dominant yeast population. Potential costs for suitable stores vary from Pounds 1.27 per m{sup 3} per year for a plastic covered outdoor stack to Pounds 11.72 per m{sup 3} per year for a vitreous enamel silo. (UK)

  5. An improved yeast transformation method for the generation of very large human antibody libraries.

    Science.gov (United States)

    Benatuil, Lorenzo; Perez, Jennifer M; Belk, Jonathan; Hsieh, Chung-Ming

    2010-04-01

    Antibody library selection by yeast display technology is an efficient and highly sensitive method to identify binders to target antigens. This powerful selection tool, however, is often hampered by the typically modest size of yeast libraries (approximately 10(7)) due to the limited yeast transformation efficiency, and the full potential of the yeast display technology for antibody discovery and engineering can only be realized if it can be coupled with a mean to generate very large yeast libraries. We describe here a yeast transformation method by electroporation that allows for the efficient generation of large antibody libraries up to 10(10) in size. Multiple components and conditions including CaCl(2), MgCl(2), sucrose, sorbitol, lithium acetate, dithiothreitol, electroporation voltage, DNA input and cell volume have been tested to identify the best combination. By applying this developed protocol, we have constructed a 1.4 x 10(10) human spleen antibody library essentially in 1 day with a transformation efficiency of 1-1.5 x 10(8) transformants/microg vector DNA. Taken together, we have developed a highly efficient yeast transformation method that enables the generation of very large and productive human antibody libraries for antibody discovery, and we are now routinely making 10(9) libraries in a day for antibody engineering purposes.

  6. Biofuels. Altered sterol composition renders yeast thermotolerant

    DEFF Research Database (Denmark)

    Caspeta, Luis; Chen, Yun; Ghiaci, Payam

    2014-01-01

    adaptive laboratory evolution to select yeast strains with improved growth and ethanol production at ≥40°C. Sequencing of the whole genome, genome-wide gene expression, and metabolic-flux analyses revealed a change in sterol composition, from ergosterol to fecosterol, caused by mutations in the C-5 sterol......Ethanol production for use as a biofuel is mainly achieved through simultaneous saccharification and fermentation by yeast. Operating at ≥40°C would be beneficial in terms of increasing efficiency of the process and reducing costs, but yeast does not grow efficiently at those temperatures. We used...... desaturase gene, and increased expression of genes involved in sterol biosynthesis. Additionally, large chromosome III rearrangements and mutations in genes associated with DNA damage and respiration were found, but contributed less to the thermotolerant phenotype....

  7. Chip-Level Electromigration Reliability for Cu Interconnects

    International Nuclear Information System (INIS)

    Gall, M.; Oh, C.; Grinshpon, A.; Zolotov, V.; Panda, R.; Demircan, E.; Mueller, J.; Justison, P.; Ramakrishna, K.; Thrasher, S.; Hernandez, R.; Herrick, M.; Fox, R.; Boeck, B.; Kawasaki, H.; Haznedar, H.; Ku, P.

    2004-01-01

    Even after the successful introduction of Cu-based metallization, the electromigration (EM) failure risk has remained one of the most important reliability concerns for most advanced process technologies. Ever increasing operating current densities and the introduction of low-k materials in the backend process scheme are some of the issues that threaten reliable, long-term operation at elevated temperatures. The traditional method of verifying EM reliability only through current density limit checks is proving to be inadequate in general, or quite expensive at the best. A Statistical EM Budgeting (SEB) methodology has been proposed to assess more realistic chip-level EM reliability from the complex statistical distribution of currents in a chip. To be valuable, this approach requires accurate estimation of currents for all interconnect segments in a chip. However, no efficient technique to manage the complexity of such a task for very large chip designs is known. We present an efficient method to estimate currents exhaustively for all interconnects in a chip. The proposed method uses pre-characterization of cells and macros, and steps to identify and filter out symmetrically bi-directional interconnects. We illustrate the strength of the proposed approach using a high-performance microprocessor design for embedded applications as a case study

  8. Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling

    OpenAIRE

    Marty, Amber J.; Wüthrich, Marcel; Carmen, John C.; Sullivan, Thomas D.; Klein, Bruce S.; Cuomo, Christina A.; Gauthier, Gregory M.

    2013-01-01

    B. dermatitidis belongs to a group of thermally dimorphic fungi that grow as sporulating mold in the soil and convert to pathogenic yeast in the lung following inhalation of spores. Knowledge about the molecular events important for fungal adaptation and survival in the host remains limited. The development of high-throughput analytic tools such as RNA sequencing (RNA-Seq) has potential to provide novel insight on fungal pathogenesis especially if applied in vivo during infection. However, in...

  9. Taming wild yeast: potential of conventional and nonconventional yeasts in industrial fermentations.

    Science.gov (United States)

    Steensels, Jan; Verstrepen, Kevin J

    2014-01-01

    Yeasts are the main driving force behind several industrial food fermentation processes, including the production of beer, wine, sake, bread, and chocolate. Historically, these processes developed from uncontrolled, spontaneous fermentation reactions that rely on a complex mixture of microbes present in the environment. Because such spontaneous processes are generally inconsistent and inefficient and often lead to the formation of off-flavors, most of today's industrial production utilizes defined starter cultures, often consisting of a specific domesticated strain of Saccharomyces cerevisiae, S. bayanus, or S. pastorianus. Although this practice greatly improved process consistency, efficiency, and overall quality, it also limited the sensorial complexity of the end product. In this review, we discuss how Saccharomyces yeasts were domesticated to become the main workhorse of food fermentations, and we investigate the potential and selection of nonconventional yeasts that are often found in spontaneous fermentations, such as Brettanomyces, Hanseniaspora, and Pichia spp.

  10. Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide

    Directory of Open Access Journals (Sweden)

    Hinnebusch Alan G

    2011-01-01

    Full Text Available Abstract Background Eukaryotic translation initiation factor 4G (eIF4G is thought to influence the translational efficiencies of cellular mRNAs by its roles in forming an eIF4F-mRNA-PABP mRNP that is competent for attachment of the 43S preinitiation complex, and in scanning through structured 5' UTR sequences. We have tested this hypothesis by determining the effects of genetically depleting eIF4G from yeast cells on global translational efficiencies (TEs, using gene expression microarrays to measure the abundance of mRNA in polysomes relative to total mRNA for ~5900 genes. Results Although depletion of eIF4G is lethal and reduces protein synthesis by ~75%, it had small effects (less than a factor of 1.5 on the relative TE of most genes. Within these limits, however, depleting eIF4G narrowed the range of translational efficiencies genome-wide, with mRNAs of better than average TE being translated relatively worse, and mRNAs with lower than average TE being translated relatively better. Surprisingly, the fraction of mRNAs most dependent on eIF4G display an average 5' UTR length at or below the mean for all yeast genes. Conclusions This finding suggests that eIF4G is more critical for ribosome attachment to mRNAs than for scanning long, structured 5' UTRs. Our results also indicate that eIF4G, and the closed-loop mRNP it assembles with the m7 G cap- and poly(A-binding factors (eIF4E and PABP, is not essential for translation of most (if not all mRNAs but enhances the differentiation of translational efficiencies genome-wide.

  11. Fab is the most efficient format to express functional antibodies by yeast surface display.

    Science.gov (United States)

    Sivelle, Coline; Sierocki, Raphaël; Ferreira-Pinto, Kelly; Simon, Stéphanie; Maillere, Bernard; Nozach, Hervé

    2018-04-30

    Multiple formats are available for engineering of monoclonal antibodies (mAbs) by yeast surface display, but they do not all lead to efficient expression of functional molecules. We therefore expressed four anti-tumor necrosis factor and two anti-IpaD mAbs as single-chain variable fragment (scFv), antigen-binding fragment (Fab) or single-chain Fabs and compared their expression levels and antigen-binding efficiency. Although the scFv and scFab formats are widely used in the literature, 2 of 6 antibodies were either not or weakly expressed. In contrast, all 6 antibodies expressed as Fab revealed strong binding and high affinity, comparable to that of the soluble form. We also demonstrated that the variations in expression did not affect Fab functionality and were due to variations in light chain display and not to misfolded dimers. Our results suggest that Fab is the most versatile format for the engineering of mAbs.

  12. Chip cleaning and regeneration for electrochemical sensor arrays

    Energy Technology Data Exchange (ETDEWEB)

    Bhalla, Vijayender [Biochemistry Department ' G.Moruzzi' , University of Bologna, Via Irnerio 48, 40126 Bologna (Italy); Carrara, Sandro, E-mail: sandro.carrara@epfl.c [Biochemistry Department ' G.Moruzzi' , University of Bologna, Via Irnerio 48, 40126 Bologna (Italy); Stagni, Claudio [Department DEIS, University of Bologna, viale Risorgimento 2, 40136 Bologna (Italy); Samori, Bruno [Biochemistry Department ' G.Moruzzi' , University of Bologna, Via Irnerio 48, 40126 Bologna (Italy)

    2010-04-02

    Sensing systems based on electrochemical detection have generated great interest because electronic readout may replace conventional optical readout in microarray. Moreover, they offer the possibility to avoid labelling for target molecules. A typical electrochemical array consists of many sensing sites. An ideal micro-fabricated sensor-chip should have the same measured values for all the equivalent sensing sites (or spots). To achieve high reliability in electrochemical measurements, high quality in functionalization of the electrodes surface is essential. Molecular probes are often immobilized by using alkanethiols onto gold electrodes. Applying effective cleaning methods on the chip is a fundamental requirement for the formation of densely-packed and stable self-assembly monolayers. However, the available well-known techniques for chip cleaning may not be so reliable. Furthermore, it could be necessary to recycle the chip for reuse. Also in this case, an effective recycling technique is required to re-obtain well cleaned sensing surfaces on the chip. This paper presents experimental results on the efficacy and efficiency of the available techniques for initial cleaning and further recycling of micro-fabricated chips. Piranha, plasma, reductive and oxidative cleaning methods were applied and the obtained results were critically compared. Some interesting results were attained by using commonly considered cleaning methodologies. This study outlines oxidative electrochemical cleaning and recycling as the more efficient cleaning procedure for electrochemical based sensor arrays.

  13. Identificarion of contaminant bacteria in cachaça yeast by 16s rDNA gene sequencing Identificação de bactérias contaminantes de fermento de cachaça por seqüenciamento do gene 16s rDNA

    Directory of Open Access Journals (Sweden)

    Osmar Vaz de Carvalho-Netto

    2008-01-01

    Full Text Available Cachaça is a typical Brazilian liquor produced from the distillation of fermented sugarcane juice mainly by Saccharomyces cerevisiae. Most of the domestic production is artisanal, and producers usually are not concerned regarding microbiological control of the fermentation. This study aimed to characterize the contaminant bacterial community of the yeast used in the production of cachaça in an artisanal still. Four samples were collected, of which one (NA was used for comparison purposes and was collected one year earlier. The remaining samples were collected at three different periods: at the end of the first day of fermentation (NP, after fifteen days (NS, and thirty days after the same yeast was used (NT. Five hundred and eighty-seven sequences were analyzed from the partial sequencing of the 16S rDNA gene. Sequence analyses revealed the presence of 170 operational taxonomic units (OTUs. Of these, only one was shared among three samples and seventeen were shared between two samples. The remaining 152 OTUs were identified only once in distinct samples indicating that the contaminant bacterial population is highly dynamic along the fermentation process. Statistical analyses revealed differences in bacterial composition among samples. Undescribed species in the literature on yeasts of cachaça were found, such as Weissella cibaria, Leuconostoc citreum, and some species of Lactobacillus, in addition to some unknown bacteria. The community of bacteria in the fermentation process is much more complex than it was previously considered. No previous report is known regarding the use of this technique to determine bacterial contaminants in yeast for the production of cachaça.A cachaça é uma bebida típica brasileira produzida a partir da destilação do caldo de cana-de-açúcar fermentado principalmente por Saccharomyces cerevisiae. Grande parte da produção nacional é artesanal, e não há uma preocupação por parte dos produtores quanto ao

  14. Scalable Motion Estimation Processor Core for Multimedia System-on-Chip Applications

    Science.gov (United States)

    Lai, Yeong-Kang; Hsieh, Tian-En; Chen, Lien-Fei

    2007-04-01

    In this paper, we describe a high-throughput and scalable motion estimation processor architecture for multimedia system-on-chip applications. The number of processing elements (PEs) is scalable according to the variable algorithm parameters and the performance required for different applications. Using the PE rings efficiently and an intelligent memory-interleaving organization, the efficiency of the architecture can be increased. Moreover, using efficient on-chip memories and a data management technique can effectively decrease the power consumption and memory bandwidth. Techniques for reducing the number of interconnections and external memory accesses are also presented. Our results demonstrate that the proposed scalable PE-ringed architecture is a flexible and high-performance processor core in multimedia system-on-chip applications.

  15. PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq.

    Science.gov (United States)

    Gao, Yubang; Wang, Huiyuan; Zhang, Hangxiao; Wang, Yongsheng; Chen, Jinfeng; Gu, Lianfeng

    2018-05-01

    The single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) based on Pacific Bioscience (PacBio) platform has received increasing attention for its ability to explore full-length isoforms. Thus, comprehensive tools for Iso-Seq bioinformatics analysis are extremely useful. Here, we present a one-stop solution for Iso-Seq analysis, called PRAPI to analyze alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) comprehensively. PRAPI is capable of combining Iso-Seq full-length isoforms with short read data, such as RNA-Seq or polyadenylation site sequencing (PAS-seq) for differential expression analysis of NAT, AS, APA and circRNAs. Furthermore, PRAPI can annotate new genes and correct mis-annotated genes when gene annotation is available. Finally, PRAPI generates high-quality vector graphics to visualize and highlight the Iso-Seq results. The Dockerfile of PRAPI is available at http://www.bioinfor.org/tool/PRAPI. lfgu@fafu.edu.cn.

  16. Four linked genes participate in controlling sporulation efficiency in budding yeast.

    Directory of Open Access Journals (Sweden)

    Giora Ben-Ari

    2006-11-01

    Full Text Available Quantitative traits are conditioned by several genetic determinants. Since such genes influence many important complex traits in various organisms, the identification of quantitative trait loci (QTLs is of major interest, but still encounters serious difficulties. We detected four linked genes within one QTL, which participate in controlling sporulation efficiency in Saccharomyces cerevisiae. Following the identification of single nucleotide polymorphisms by comparing the sequences of 145 genes between the parental strains SK1 and S288c, we analyzed the segregating progeny of the cross between them. Through reciprocal hemizygosity analysis, four genes, RAS2, PMS1, SWS2, and FKH2, located in a region of 60 kilobases on Chromosome 14, were found to be associated with sporulation efficiency. Three of the four "high" sporulation alleles are derived from the "low" sporulating strain. Two of these sporulation-related genes were verified through allele replacements. For RAS2, the causative variation was suggested to be a single nucleotide difference in the upstream region of the gene. This quantitative trait nucleotide accounts for sporulation variability among a set of ten closely related winery yeast strains. Our results provide a detailed view of genetic complexity in one "QTL region" that controls a quantitative trait and reports a single nucleotide polymorphism-trait association in wild strains. Moreover, these findings have implications on QTL identification in higher eukaryotes.

  17. A sensitive molecularly imprinted polymer based quartz crystal microbalance nanosensor for selective determination of lovastatin in red yeast rice.

    Science.gov (United States)

    Eren, Tanju; Atar, Necip; Yola, Mehmet Lütfi; Karimi-Maleh, Hassan

    2015-10-15

    Lovastatin (LOV) is a statin, used to lower cholesterol which has been found as a hypolipidemic agent in commercial red yeast rice. In present study, a sensitive molecular imprinted quartz crystal microbalance (QCM) sensor was prepared by fabricating a self-assembling monolayer formation of allylmercaptane on QCM chip surface for selective determination of lovastatin (LOV) in red yeast rice. To prepare molecular imprinted quartz crystal microbalance (QCM) nanosensor, LOV imprinted poly(2-hydroxyethyl methacrylate-methacryloylamidoaspartic acid) [p(HEMA-MAAsp)] nanofilm was attached on the modified gold surface of QCM chip. The non-modified and improved surfaces were characterized by using contact angle, atomic force microscopy (AFM) and Fourier transform infrared (FTIR) spectroscopy. The imprinted QCM sensor was validated according to the ICH guideline (International Conference on Harmonisation). The linearity range was obtained as 0.10-1.25 nM. The detection limit of the prepared material was calculated as 0.030 nM. The developed QCM nanosensor was successfully used to examine red yeast rice. Furthermore, the stability and repeatability of the prepared QCM nanosensor were studied. The spectacular long-term stability and repeatability of the prepared LOV-imprinted QCM nanosensor make them intriguing for use in QCM sensors. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Yeast cell wall chitin reduces wine haze formation.

    Science.gov (United States)

    Ndlovu, Thulile; Divol, Benoit; Bauer, Florian F

    2018-04-27

    Protein haze formation in bottled wines is a significant concern for the global wine industry and wine clarification before bottling is therefore a common but expensive practice. Previous studies have shown that wine yeast strains can reduce haze formation through the secretion of certain mannoproteins, but it has been suggested that other yeast-dependent haze protective mechanisms exist. On the other hand, addition of chitin has been shown to reduce haze formation, likely because grape chitinases have been shown to be the major contributors to haze. In this study, Chardonnay grape must fermented by various yeast strains resulted in wines with different protein haze levels indicating differences in haze protective capacities of the strains. The cell wall chitin levels of these strains were determined, and a strong correlation between cell wall chitin levels and haze protection capability was observed. To further evaluate the mechanism of haze protection, Escherichia coli -produced GFP-tagged grape chitinase was shown to bind efficiently to yeast cell walls in a cell wall chitin concentration-dependent manner, while commercial chitinase was removed from synthetic wine in quantities also correlated with the cell wall chitin levels of the strains. Our findings suggest a new mechanism of reducing wine haze, and propose a strategy for optimizing wine yeast strains to improve wine clarification. Importance In this study, we establish a new mechanism by which wine yeast strains can impact on the protein haze formation of wines, and demonstrate that yeast cell wall chitin binds grape chitinase in a chitin-concentration dependent manner. We also show that yeast can remove this haze-forming protein from wine. Chitin has in the past been shown to efficiently reduce wine haze formation when added to the wine in high concentration as a clarifying agent. Our data suggest that the selection of yeast strains with high levels of cell wall chitin can reduce protein haze. We also

  19. Multiplex PCR, amplicon size and hybridization efficiency on the NanoChip electronic microarray

    DEFF Research Database (Denmark)

    Børsting, Claus; Sanchez, Juan J; Morling, Niels

    2004-01-01

    We tested the SNP typing protocol developed for the NanoChip electronic microarray by analyzing the four Y chromosome loci SRY1532, SRY8299, TAT, and 92R7. Amplicons of different lengths containing the same locus were purified and addressed to the NanoChip array and fluorescently labelled reporte...

  20. Development of a high-throughput Candida albicans biofilm chip.

    Directory of Open Access Journals (Sweden)

    Anand Srinivasan

    2011-04-01

    Full Text Available We have developed a high-density microarray platform consisting of nano-biofilms of Candida albicans. A robotic microarrayer was used to print yeast cells of C. albicans encapsulated in a collagen matrix at a volume as low as 50 nL onto surface-modified microscope slides. Upon incubation, the cells grow into fully formed "nano-biofilms". The morphological and architectural complexity of these biofilms were evaluated by scanning electron and confocal scanning laser microscopy. The extent of biofilm formation was determined using a microarray scanner from changes in fluorescence intensities due to FUN 1 metabolic processing. This staining technique was also adapted for antifungal susceptibility testing, which demonstrated that, similar to regular biofilms, cells within the on-chip biofilms displayed elevated levels of resistance against antifungal agents (fluconazole and amphotericin B. Thus, results from structural analyses and antifungal susceptibility testing indicated that despite miniaturization, these biofilms display the typical phenotypic properties associated with the biofilm mode of growth. In its final format, the C. albicans biofilm chip (CaBChip is composed of 768 equivalent and spatially distinct nano-biofilms on a single slide; multiple chips can be printed and processed simultaneously. Compared to current methods for the formation of microbial biofilms, namely the 96-well microtiter plate model, this fungal biofilm chip has advantages in terms of miniaturization and automation, which combine to cut reagent use and analysis time, minimize labor intensive steps, and dramatically reduce assay costs. Such a chip should accelerate the antifungal drug discovery process by enabling rapid, convenient and inexpensive screening of hundreds-to-thousands of compounds simultaneously.

  1. Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters

    Directory of Open Access Journals (Sweden)

    Mamoru Oshiki

    2018-04-01

    Full Text Available Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI, GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan; genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.

  2. Fully Automated On-Chip Imaging Flow Cytometry System with Disposable Contamination-Free Plastic Re-Cultivation Chip

    Directory of Open Access Journals (Sweden)

    Tomoyuki Kaneko

    2011-06-01

    Full Text Available We have developed a novel imaging cytometry system using a poly(methyl methacrylate (PMMA based microfluidic chip. The system was contamination-free, because sample suspensions contacted only with a flammable PMMA chip and no other component of the system. The transparency and low-fluorescence of PMMA was suitable for microscopic imaging of cells flowing through microchannels on the chip. Sample particles flowing through microchannels on the chip were discriminated by an image-recognition unit with a high-speed camera in real time at the rate of 200 event/s, e.g., microparticles 2.5 μm and 3.0 μm in diameter were differentiated with an error rate of less than 2%. Desired cells were separated automatically from other cells by electrophoretic or dielectrophoretic force one by one with a separation efficiency of 90%. Cells in suspension with fluorescent dye were separated using the same kind of microfluidic chip. Sample of 5 μL with 1 × 106 particle/mL was processed within 40 min. Separated cells could be cultured on the microfluidic chip without contamination. The whole operation of sample handling was automated using 3D micropipetting system. These results showed that the novel imaging flow cytometry system is practically applicable for biological research and clinical diagnostics.

  3. Origami chip-on-sensor design: progress and new developments

    International Nuclear Information System (INIS)

    Irmler, C; Bergauer, T; Frankenberger, A; Friedl, M; Gfall, I; Valentan, M; Ishikawa, A; Kato, E; Negishi, K; Kameswara, R; Mohanty, G; Onuki, Y; Shimizu, N; Tsuboyama, T

    2013-01-01

    The Belle II silicon vertex detector will consist of four layers of double-sided silicon strip detectors, arranged in ladders. Each sensor will be read out individually by utilizing the Origami chip-on-sensor concept, where the APV25 chips are placed on flexible circuits, glued on top of the sensors. Beside a best compromise between low material budget and sufficient SNR, this concept allows efficient CO 2 cooling of the readout chips by a single, thin cooling pipe per ladder. Recently, we assembled a module consisting of two consecutive 6'' double-sided silicon strip detectors, both read out by Origami flexes. Such a compound of Origami modules is required for the ladders of the outer Belle II SVD layers. Consequently, it is intended to verify the scalability of the assembly procedure, the performance of combined Origami flexes as well as the efficiency of the CO 2 cooling system for a higher number of APV25 chips.

  4. A yeast-based model system for cloning secreted and membrane proteins

    Directory of Open Access Journals (Sweden)

    MARCELO J. SURPILI

    2002-12-01

    Full Text Available The targeting of proteins to cell organelles and membranes, or of proteins destined to secretion, is coordinated by signal sequences located at the 5´-end of their respective genes. A signal sequence trap system was envisaged in which a truncated version of the yeast acid phosphatase pho5 gene lacking the start codon and signal sequence could serve as a reporter gene. A fraction enriched in 5´-end fragments obtained by PCR from a potato guard-cell cDNA library was cloned in frame to the acid phosphatase gene and the acid phosphatase activity was assayed directly in yeast colonies grown on selective medium. Putative signal sequences targeting the acid phosphatase to the membrane or to the outside of the cell were used to screen the cDNA bank in order to recover the original full-size sequence which gave rise to the signal sequence. Two unknown sequences displaying marked tissue-specific expression were retrieved, one of them (YE139 with a higher expression level in green buds and stem cells, and the other one (YE290 with a higher expression level in androceum, gyneceum, and roots. The limitations of the system are further analyzed using other sequences as control.O direcionamento de proteínas a organelas e à membrana celular, ou de proteínas a serem secretadas, é coordenado por seqüências sinalizadoras localizadas na extremidade 5´ de seus respectivos genes que codificam peptídeos-sinal. Este trabalho analisa um sistema para seleção de seqüências sinalizadoras utilizando uma fosfatase ácida de levedura, enzima reconhecidamente secretada por estes organismos, desprovida de seu códon de iniciação e de sua seqüência sinalizadora, como gene repórter. Uma fração enriquecida em fragmentos provenientes da região 5´ de uma biblioteca de cDNA de células-guarda de batata foi inserida in frame ao gene truncado da fosfatase ácida em vetores apropriados. Após a transformação em leveduras, a atividade da fosfatase ácida foi

  5. Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation

    Directory of Open Access Journals (Sweden)

    Edward D. Kerr

    2016-08-01

    Full Text Available Vegemite is an iconic Australian food spread made from spent brewers’ yeast extract, which has been reported to be used as an ingredient in illegal home brewing. In this study, we tested the utility of Vegemite and the similar spread Marmite in promoting fermentation. We could not culture microorganisms from either Vegemite or Marmite, consistent with these food-grade spreads being essentially sterile. To test if the addition of Vegemite or Marmite could assist in fermentation when additional viable yeast was also present, solutions containing glucose and a range of concentrations of either Vegemite or Marmite were inoculated with brewers’ yeast. No fermentation occurred in any condition without addition of extra brewer’s yeast. Fermentation did not occur when yeast was inoculated into solutions containing only glucose, but progressed efficiently with when Vegemite or Marmite was also added. Gas Chromatography confirmed that ethanol was present at ∼3% v/v post-fermentation in all samples which contained glucose, Vegemite or Marmite, and brewers’ yeast. Trace amounts of methanol were also detected. Mass spectrometry proteomics identified abundant intracellular yeast proteins and barley proteins in Vegemite and Marmite, and abundant secreted yeast proteins from actively growing yeast in those samples to which extra brewers’ yeast had been added. We estimate that the real-world cost of home brewed “Vegemite Beer” would be very low. Our results show that Vegemite or other yeast extract spreads could provide cheap and readily available sources of nutrient supplementation to increase the efficiency of fermentation in home brewing or other settings.

  6. Design and Analysis of Delayed Chip Slope Modulation in Optical Wireless Communication

    KAUST Repository

    Park, Kihong

    2015-08-23

    In this letter, we propose a novel slope-based binary modulation called delayed chip slope modulation (DCSM) and develop a chip-based hard-decision receiver to demodulate the resulting signal, detect the chip sequence, and decode the input bit sequence. Shorter duration of chips than bit duration are used to represent the change of state in an amplitude level according to consecutive bit information and to exploit the trade-off between bandwidth and power efficiency. We analyze the power spectral density and error rate performance of the proposed DCSM. We show from numerical results that the DCSM scheme can exploit spectrum density more efficiently than the reference schemes while providing an error rate performance comparable to conventional modulation schemes.

  7. Design and Analysis of Delayed Chip Slope Modulation in Optical Wireless Communication

    KAUST Repository

    Park, Kihong; Alouini, Mohamed-Slim

    2015-01-01

    In this letter, we propose a novel slope-based binary modulation called delayed chip slope modulation (DCSM) and develop a chip-based hard-decision receiver to demodulate the resulting signal, detect the chip sequence, and decode the input bit sequence. Shorter duration of chips than bit duration are used to represent the change of state in an amplitude level according to consecutive bit information and to exploit the trade-off between bandwidth and power efficiency. We analyze the power spectral density and error rate performance of the proposed DCSM. We show from numerical results that the DCSM scheme can exploit spectrum density more efficiently than the reference schemes while providing an error rate performance comparable to conventional modulation schemes.

  8. Effect of yeast storage temperature and flour composition on fermentative activities of baker's yeast

    Directory of Open Access Journals (Sweden)

    Pejin Dušanka J.

    2009-01-01

    Full Text Available Baker's yeast is a set of living cells of Saccharomyces cerevisiae. It contains around 70-72% of water, 42-45% of proteins, around 40% of carbohydrates, around 7.5% of lipids (based on dry matter, and vitamin B-complex. On the basis of yeast cell analysis it can be concluded that yeast is a complex biological system which changes in time. The intensity of the changes depends on temperature. Yeast sample was stored at 4°C i 24°C for 12 days. During storage at 4°C, the content of total carbohydrates decreased from 48.81% to 37.50% (dry matter, whereas carbohydrate loss ranged from 40.81% to 29.28% at 24°C. The content of trehalose was 12.33% in the yeast sample stored at 4°C and 0.24% at 24°C. Loss of fermentative activity was 81.76% in the sample stored at 24°C for 12 days. The composition of five samples of 1st category flour was investigated. It was found that flours containing more reducing sugars and maltose enable higher fermentation activities. The flours with higher ash content (in the range 0.5-0.94% had higher contents of phytic acid. Higher ash and phytic contents in flour increased the yeast fermentative efficiency. In bakery industry, a range of ingredients has been applied to improve the product's quality such as surface active substances (emulsifiers, enzymes, sugars and fats. In the paper, the effect of some ingredients added to dough (margarine, saccharose, sodium chloride and malted barley on the yeast fermentative activity was studied. The mentioned ingredients were added to dough at different doses: 0.5, 1.0, 1.5 and 2.0%, flour basis. It was found that the investigated ingredients affected the fermentative activity of yeast and improved the bread quality.

  9. Co-fermentation of glucose, xylose and/or cellobiose by yeast

    Science.gov (United States)

    Jeffries, Thomas W.; Willis, Laura B.; Long, Tanya M.; Su, Yi-Kai

    2013-09-10

    Provided herein are methods of using yeast cells to produce ethanol by contacting a mixture comprising xylose with a Spathaspora yeast cell under conditions suitable to allow the yeast to ferment at least a portion of the xylose to ethanol. The methods allow for efficient ethanol production from hydrolysates derived from lignocellulosic material and sugar mixtures including at least xylose and glucose or xylose, glucose and cellobiose.

  10. On-chip power delivery and management

    CERN Document Server

    Vaisband, Inna P; Popovich, Mikhail; Mezhiba, Andrey V; Köse, Selçuk; Friedman, Eby G

    2016-01-01

    This book describes methods for distributing power in high speed, high complexity integrated circuits with power levels exceeding many tens of watts and power supplies below a volt. It provides a broad and cohesive treatment of power delivery and management systems and related design problems, including both circuit network models and design techniques for on-chip decoupling capacitors, providing insight and intuition into the behavior and design of on-chip power distribution systems. Organized into subareas to provide a more intuitive flow to the reader, this fourth edition adds more than a hundred pages of new content, including inductance models for interdigitated structures, design strategies for multi-layer power grids, advanced methods for efficient power grid design and analysis, and methodologies for simultaneously placing on-chip multiple power supplies and decoupling capacitors. The emphasis of this additional material is on managing the complexity of on-chip power distribution networks.

  11. How to build VLSI-efficient neural chips

    Energy Technology Data Exchange (ETDEWEB)

    Beiu, V.

    1998-02-01

    This paper presents several upper and lower bounds for the number-of-bits required for solving a classification problem, as well as ways in which these bounds can be used to efficiently build neural network chips. The focus will be on complexity aspects pertaining to neural networks: (1) size complexity and depth (size) tradeoffs, and (2) precision of weights and thresholds as well as limited interconnectivity. They show difficult problems-exponential growth in either space (precision and size) and/or time (learning and depth)-when using neural networks for solving general classes of problems (particular cases may enjoy better performances). The bounds for the number-of-bits required for solving a classification problem represent the first step of a general class of constructive algorithms, by showing how the quantization of the input space could be done in O (m{sup 2}n) steps. Here m is the number of examples, while n is the number of dimensions. The second step of the algorithm finds its roots in the implementation of a class of Boolean functions using threshold gates. It is substantiated by mathematical proofs for the size O (mn/{Delta}), and the depth O [log(mn)/log{Delta}] of the resulting network (here {Delta} is the maximum fan in). Using the fan in as a parameter, a full class of solutions can be designed. The third step of the algorithm represents a reduction of the size and an increase of its generalization capabilities. Extensions by using analogue COMPARISONs, allows for real inputs, and increase the generalization capabilities at the expense of longer training times. Finally, several solutions which can lower the size of the resulting neural network are detailed. The interesting aspect is that they are obtained for limited, or even constant, fan-ins. In support of these claims many simulations have been performed and are called upon.

  12. ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.

    Science.gov (United States)

    Zhu, Lin; Guo, Wei-Li; Deng, Su-Ping; Huang, De-Shuang

    2016-01-01

    In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.

  13. Computer Simulation Elucidates Yeast Flocculation and Sedimentation for Efficient Industrial Fermentation.

    Science.gov (United States)

    Liu, Chen-Guang; Li, Zhi-Yang; Hao, Yue; Xia, Juan; Bai, Feng-Wu; Mehmood, Muhammad Aamer

    2018-05-01

    Flocculation plays an important role in the immobilized fermentation of biofuels and biochemicals. It is essential to understand the flocculation phenomenon at physical and molecular scale; however, flocs cannot be studied directly due to fragile nature. Hence, the present study is focused on the morphological specificities of yeast flocs formation and sedimentation via the computer simulation by a single floc growth model, based on Diffusion-Limited Aggregation (DLA) model. The impact of shear force, adsorption, and cell propagation on porosity and floc size is systematically illustrated. Strong shear force and weak adsorption reduced floc size but have little impact on porosity. Besides, cell propagation concreted the compactness of flocs enabling them to gain a larger size. Later, a multiple flocs growth model is developed to explain sedimentation at various initial floc sizes. Both models exhibited qualitative agreements with available experimental data. By regulating the operation constraints during fermentation, the present study will lead to finding optimal conditions to control the floc size distribution for efficient fermentation and harvesting. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. A molecular imprinted SPR biosensor for sensitive determination of citrinin in red yeast rice.

    Science.gov (United States)

    Atar, Necip; Eren, Tanju; Yola, Mehmet Lütfi

    2015-10-01

    A novel and sensitive molecular imprinted surface plasmon resonance (SPR) biosensor was developed for selective determination of citrinin (CIT) in red yeast rice. Firstly, the gold surface of SPR chip was modified with allyl mercaptane. Then, CIT-imprinted poly(2-hydroxyethyl methacrylate-methacryloylamidoglutamic acid) (p(HEMA-MAGA)) film was generated on the gold surface modified with allyl mercaptane. The unmodified and imprinted surfaces were characterized by Fourier transform infrared (FTIR) spectroscopy, atomic force microscopy (AFM) and contact angle measurements. The linearity range and the detection limit were obtained as 0.005-1.0 ng/mL and 0.0017 ng/mL, respectively. The SPR biosensor was applied to determination of CIT in red yeast rice sample. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Development and utilization of protein enriched feed by yeast (Saccharomyces cerevisiae) fermentation in ruminants

    International Nuclear Information System (INIS)

    Wanapat, M.; Piadang, Nattayana; Boonnop, K.; Polyorach S; Nontaso, N.; Khampa, S.

    2006-09-01

    The two experiments have been carried out to investigate on the development and supplementation of yeast fermented cassava chip (YEFECAP) and yeast-fermented liquid (YEL) with coconut oil (CCO) in concentrate containing soybean meal or cassava hay in rumen ecology, digestibility, nitrogen balance and feed intakes in ruminants. This paper reports on the progress of the on-going work with in vivo digestion trials which are currently evaluating the protein value of the two sources and their effects on the rumen fermentation, microorganisms, fermentation end-products, blood metabolite, nitrogen balance nutrient digest abilities. Based on the preliminary data, the two proteins sources have potential protein and feeding values as protein sources and rumen enhancers for possible rumen fermentation and the subsequent ruminant productivity.

  16. RNA-Seq-Based Transcript Structure Analysis with TrBorderExt.

    Science.gov (United States)

    Wang, Yejun; Sun, Ming-An; White, Aaron P

    2018-01-01

    RNA-Seq has become a routine strategy for genome-wide gene expression comparisons in bacteria. Despite lower resolution in transcript border parsing compared with dRNA-Seq, TSS-EMOTE, Cappable-seq, Term-seq, and others, directional RNA-Seq still illustrates its advantages: low cost, quantification and transcript border analysis with a medium resolution (±10-20 nt). To facilitate mining of directional RNA-Seq datasets especially with respect to transcript structure analysis, we developed a tool, TrBorderExt, which can parse transcript start sites and termination sites accurately in bacteria. A detailed protocol is described in this chapter for how to use the software package step by step to identify bacterial transcript borders from raw RNA-Seq data. The package was developed with Perl and R programming languages, and is accessible freely through the website: http://www.szu-bioinf.org/TrBorderExt .

  17. Yeasts in sustainable bioethanol production: A review.

    Science.gov (United States)

    Mohd Azhar, Siti Hajar; Abdulla, Rahmath; Jambo, Siti Azmah; Marbawi, Hartinie; Gansau, Jualang Azlan; Mohd Faik, Ainol Azifa; Rodrigues, Kenneth Francis

    2017-07-01

    Bioethanol has been identified as the mostly used biofuel worldwide since it significantly contributes to the reduction of crude oil consumption and environmental pollution. It can be produced from various types of feedstocks such as sucrose, starch, lignocellulosic and algal biomass through fermentation process by microorganisms. Compared to other types of microoganisms, yeasts especially Saccharomyces cerevisiae is the common microbes employed in ethanol production due to its high ethanol productivity, high ethanol tolerance and ability of fermenting wide range of sugars. However, there are some challenges in yeast fermentation which inhibit ethanol production such as high temperature, high ethanol concentration and the ability to ferment pentose sugars. Various types of yeast strains have been used in fermentation for ethanol production including hybrid, recombinant and wild-type yeasts. Yeasts can directly ferment simple sugars into ethanol while other type of feedstocks must be converted to fermentable sugars before it can be fermented to ethanol. The common processes involves in ethanol production are pretreatment, hydrolysis and fermentation. Production of bioethanol during fermentation depends on several factors such as temperature, sugar concentration, pH, fermentation time, agitation rate, and inoculum size. The efficiency and productivity of ethanol can be enhanced by immobilizing the yeast cells. This review highlights the different types of yeast strains, fermentation process, factors affecting bioethanol production and immobilization of yeasts for better bioethanol production.

  18. Yeasts in sustainable bioethanol production: A review

    Directory of Open Access Journals (Sweden)

    Siti Hajar Mohd Azhar

    2017-07-01

    Full Text Available Bioethanol has been identified as the mostly used biofuel worldwide since it significantly contributes to the reduction of crude oil consumption and environmental pollution. It can be produced from various types of feedstocks such as sucrose, starch, lignocellulosic and algal biomass through fermentation process by microorganisms. Compared to other types of microoganisms, yeasts especially Saccharomyces cerevisiae is the common microbes employed in ethanol production due to its high ethanol productivity, high ethanol tolerance and ability of fermenting wide range of sugars. However, there are some challenges in yeast fermentation which inhibit ethanol production such as high temperature, high ethanol concentration and the ability to ferment pentose sugars. Various types of yeast strains have been used in fermentation for ethanol production including hybrid, recombinant and wild-type yeasts. Yeasts can directly ferment simple sugars into ethanol while other type of feedstocks must be converted to fermentable sugars before it can be fermented to ethanol. The common processes involves in ethanol production are pretreatment, hydrolysis and fermentation. Production of bioethanol during fermentation depends on several factors such as temperature, sugar concentration, pH, fermentation time, agitation rate, and inoculum size. The efficiency and productivity of ethanol can be enhanced by immobilizing the yeast cells. This review highlights the different types of yeast strains, fermentation process, factors affecting bioethanol production and immobilization of yeasts for better bioethanol production.

  19. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

    Directory of Open Access Journals (Sweden)

    Dewey Colin N

    2011-08-01

    Full Text Available Abstract Background RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. Results We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads. On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene. Conclusions RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient

  20. Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies.

    Science.gov (United States)

    Needhamsen, Maria; Ewing, Ewoud; Lund, Harald; Gomez-Cabrero, David; Harris, Robert Adam; Kular, Lara; Jagodic, Maja

    2017-11-15

    The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for rodent animal samples. We examined the feasibility of using the new Infinium MethylationEPIC BeadChip for studying DNA methylation in mouse. In silico, we identified 19,420 EPIC probes (referred as mEPIC probes), which align with a unique best alignment score to the bisulfite converted reference mouse genome mm10. Further annotation revealed that 85% of mEPIC probes overlapped with mm10.refSeq genes at different genomic features including promoters (TSS1500 and TSS200), 1st exons, 5'UTRs, 3'UTRs, CpG islands, shores, shelves, open seas and FANTOM5 enhancers. Hybridization of mouse samples to Infinium Human MethylationEPIC BeadChips showed successful measurement of mEPIC probes and reproducibility between inter-array biological replicates. Finally, we demonstrated the utility of mEPIC probes for data exploration such as hierarchical clustering. Given the absence of cost and labor convenient genome-wide technologies in the murine system, our findings show that the Infinium MethylationEPIC BeadChip platform is suitable for investigation of the mouse methylome. Furthermore, we provide the "mEPICmanifest" with genomic features, available to users of Infinium Human MethylationEPIC arrays for mouse samples.

  1. RNA-Seq Analysis of Abdominal Fat Reveals Differences between Modern Commercial Broiler Chickens with High and Low Feed Efficiencies.

    Directory of Open Access Journals (Sweden)

    Zhu Zhuo

    Full Text Available For economic and environmental reasons, chickens with superior feed efficiency (FE are preferred in the broiler chicken industry. High FE (HFE chickens typically have reduced abdominal fat, the major adipose tissue in chickens. In addition to its function of energy storage, adipose tissue is a metabolically active organ that also possesses endocrine and immune regulatory functions. It plays a central role in maintaining energy homeostasis. Comprehensive understanding of the gene expression in the adipose tissue and the biological basis of FE are of significance to optimize selection and breeding strategies. Through gene expression profiling of abdominal fat from high and low FE (LFE commercial broiler chickens, the present study aimed to characterize the differences of gene expression between HFE and LFE chickens. mRNA-seq analysis was carried out on the total RNA of abdominal fat from 10 HFE and 12 LFE commercial broiler chickens, and 1.48 billion of 75-base sequence reads were generated in total. On average, 11,565 genes were expressed (>5 reads/gene/sample in the abdominal fat tissue, of which 286 genes were differentially expressed (DE at q (False Discover Rate 1.3 between HFE and LFE chickens. Expression levels from RNA-seq were confirmed with the NanoString nCounter analysis system. Functional analysis showed that the DE genes were significantly (p < 0.01 enriched in lipid metabolism, coagulation, and immune regulation pathways. Specifically, the LFE chickens had higher expression of lipid synthesis genes and lower expression of triglyceride hydrolysis and cholesterol transport genes. In conclusion, our study reveals the overall differences of gene expression in the abdominal fat from HFE and LFE chickens, and the results suggest that the divergent expression of lipid metabolism genes represents the major differences.

  2. The Use Of Local Product Yeast For Substitution Torula Yeast In The Formulation Of Artificial Diet Fruit Fly Larvae Bactrocera Carambolae Drew and Hancock

    International Nuclear Information System (INIS)

    Sikumbang, I.; Nasution, A.I.; Indarwatmi, M.; Kuswandi, A.N.

    2000-01-01

    The use of local product yeast I.e brewer yeast, yeast of tapai (fermented cassava), yeast of tempe (fermented soy beam), and brem(intoxicating beverage made of fermented rice) after cooked and uncooked were used to substitute torula yeast to reduce cost production for mass-rearing of fruit fly had been carried out. Artificial diet formulation consisted of torula yeast, wheat bran, nipagin, sodium benzoate, cane sugar, water and HCI ti make pH of 4. One kilogram of diet was inoculated with 1 ml of fruit fly eggs. Parameters of the experiment were, the number of pupae, weight of pupae, percentage of pupae and the percentage of viable fly. The results showed that the number of pupae were 6356 for brewers yeast with cooked and 0.942 gram/100 pupae for brem. Percentage viable emergence fly were 70%, 18.25% and 15.25% for brewers yeast with cooked and uncooked respectively. Cost production for 1.000.000 using cooked brewer yeast was reduced about Rp.179,200 or cost efficiency were 55.56%

  3. Evaluation of Human Adipose Tissue Stromal Heterogeneity in Metabolic Disease Using Single Cell RNA-Seq

    Science.gov (United States)

    2016-09-01

    human adipose tissue compared to grams of mouse hypothalamic) has required protocol development to make sample preparation more efficient and scalable ...Drop-seq techniques required moving funding from initial proposal of outsourcing library construction and sequencing costs to the Broad Institute to

  4. Addressing On-Chip Power Converstion and Dissipation Issues in Many-Core System-on-a-Chip Based on Conventional Silicon and Emerging Nanotechnologies

    Science.gov (United States)

    Ashenafi, Emeshaw

    Integrated circuits (ICs) are moving towards system-on-a-chip (SOC) designs. SOC allows various small and large electronic systems to be implemented in a single chip. This approach enables the miniaturization of design blocks that leads to high density transistor integration, faster response time, and lower fabrication costs. To reap the benefits of SOC and uphold the miniaturization of transistors, innovative power delivery and power dissipation management schemes are paramount. This dissertation focuses on on-chip integration of power delivery systems and managing power dissipation to increase the lifetime of energy storage elements. We explore this problem from two different angels: On-chip voltage regulators and power gating techniques. On-chip voltage regulators reduce parasitic effects, and allow faster and efficient power delivery for microprocessors. Power gating techniques, on the other hand, reduce the power loss incurred by circuit blocks during standby mode. Power dissipation (Ptotal = Pstatic and Pdynamic) in a complementary metal-oxide semiconductor (CMOS) circuit comes from two sources: static and dynamic. A quadratic dependency on the dynamic switching power and a more than linear dependency on static power as a form of gate leakage (subthreshold current) exist. To reduce dynamic power loss, the supply power should be reduced. A significant reduction in power dissipation occurs when portions of a microprocessor operate at a lower voltage level. This reduction in supply voltage is achieved via voltage regulators or converters. Voltage regulators are used to provide a stable power supply to the microprocessor. The conventional off-chip switching voltage regulator contains a passive floating inductor, which is difficult to be implemented inside the chip due to excessive power dissipation and parasitic effects. Additionally, the inductor takes a very large chip area while hampering the scaling process. These limitations make passive inductor based on-chip

  5. A Single-Chip Solar Energy Harvesting IC Using Integrated Photodiodes for Biomedical Implant Applications.

    Science.gov (United States)

    Chen, Zhiyuan; Law, Man-Kay; Mak, Pui-In; Martins, Rui P

    2017-02-01

    In this paper, an ultra-compact single-chip solar energy harvesting IC using on-chip solar cell for biomedical implant applications is presented. By employing an on-chip charge pump with parallel connected photodiodes, a 3.5 × efficiency improvement can be achieved when compared with the conventional stacked photodiode approach to boost the harvested voltage while preserving a single-chip solution. A photodiode-assisted dual startup circuit (PDSC) is also proposed to improve the area efficiency and increase the startup speed by 77%. By employing an auxiliary charge pump (AQP) using zero threshold voltage (ZVT) devices in parallel with the main charge pump, a low startup voltage of 0.25 V is obtained while minimizing the reversion loss. A 4 V in gate drive voltage is utilized to reduce the conduction loss. Systematic charge pump and solar cell area optimization is also introduced to improve the energy harvesting efficiency. The proposed system is implemented in a standard 0.18- [Formula: see text] CMOS technology and occupies an active area of 1.54 [Formula: see text]. Measurement results show that the on-chip charge pump can achieve a maximum efficiency of 67%. With an incident power of 1.22 [Formula: see text] from a halogen light source, the proposed energy harvesting IC can deliver an output power of 1.65 [Formula: see text] at 64% charge pump efficiency. The chip prototype is also verified using in-vitro experiment.

  6. Yeast metabolic engineering for hemicellulosic ethanol production

    Science.gov (United States)

    Jennifer Van Vleet; Thomas W. Jeffries

    2009-01-01

    Efficient fermentation of hemicellulosic sugars is critical for the bioconversion of lignocellulosics to ethanol. Efficient sugar uptake through the heterologous expression of yeast and fungal xylose/glucose transporters can improve fermentation if other metabolic steps are not rate limiting. Rectification of cofactor imbalances through heterologous expression of...

  7. An innovative container supply chain for forest chips

    Energy Technology Data Exchange (ETDEWEB)

    Karttunen, Kalle; Korpinen, Olli-Jussi; Laettilae, Lauri; Foehr, Jarno; Ranta, Tapio [Lappeenranta Univ. of Technology, Mikkeli (Finland)], e-mail: kalle.karttunen@lut.fi

    2012-11-01

    Most forest chips are transported by trucks with a solid frame. Forest-chip volumes will at least double before 2020, which means longer transport distances from the supply areas to the largest demand sites in Finland. The study concentrates on an innovative container solution based on a channel composite structure, creating a lighter, temperature-isolated, and more durable structure. In addition to the structural benefits, the container includes an innovative supply chain with a beneficial handling operation, interchangeability and maximising of the payload capacity, resulting in an energy- and cost-efficient solution. This innovative-container-based supply chain for forest chips has been studied via cost analysis, GIS analysis, and discrete-event simulation methods. The purpose of the study was to compare a truck of interchangeable containers with solid-frame trucks. The option of interchangeable containers allows combining truck logistics with other modes of transport, such as trains and waterways. The study showed the cost-efficiency potential of container truck logistics, stemming from the cost and payload savings and the supply-chain productivity advantages over solid-frame trucks. The innovative solution for interchangeable-container logistics is an option for large-scale supply of forest chips.

  8. High-throughput particle manipulation by hydrodynamic, electrokinetic, and dielectrophoretic effects in an integrated microfluidic chip

    KAUST Repository

    Li, Shunbo; Li, Ming; Bougot-Robin, Kristelle; Cao, Wenbin; Yeung Yeung Chau, Irene; Li, Weihua; Wen, Weijia

    2013-01-01

    Integrating different steps on a chip for cell manipulations and sample preparation is of foremost importance to fully take advantage of microfluidic possibilities, and therefore make tests faster, cheaper and more accurate. We demonstrated particle manipulation in an integrated microfluidic device by applying hydrodynamic, electroosmotic (EO), electrophoretic (EP), and dielectrophoretic (DEP) forces. The process involves generation of fluid flow by pressure difference, particle trapping by DEP force, and particle redirect by EO and EP forces. Both DC and AC signals were applied, taking advantages of DC EP, EO and AC DEP for on-chip particle manipulation. Since different types of particles respond differently to these signals, variations of DC and AC signals are capable to handle complex and highly variable colloidal and biological samples. The proposed technique can operate in a high-throughput manner with thirteen independent channels in radial directions for enrichment and separation in microfluidic chip. We evaluated our approach by collecting Polystyrene particles, yeast cells, and E. coli bacteria, which respond differently to electric field gradient. Live and dead yeast cells were separated successfully, validating the capability of our device to separate highly similar cells. Our results showed that this technique could achieve fast pre-concentration of colloidal particles and cells and separation of cells depending on their vitality. Hydrodynamic, DC electrophoretic and DC electroosmotic forces were used together instead of syringe pump to achieve sufficient fluid flow and particle mobility for particle trapping and sorting. By eliminating bulky mechanical pumps, this new technique has wide applications for in situ detection and analysis.

  9. High-throughput particle manipulation by hydrodynamic, electrokinetic, and dielectrophoretic effects in an integrated microfluidic chip

    KAUST Repository

    Li, Shunbo

    2013-03-20

    Integrating different steps on a chip for cell manipulations and sample preparation is of foremost importance to fully take advantage of microfluidic possibilities, and therefore make tests faster, cheaper and more accurate. We demonstrated particle manipulation in an integrated microfluidic device by applying hydrodynamic, electroosmotic (EO), electrophoretic (EP), and dielectrophoretic (DEP) forces. The process involves generation of fluid flow by pressure difference, particle trapping by DEP force, and particle redirect by EO and EP forces. Both DC and AC signals were applied, taking advantages of DC EP, EO and AC DEP for on-chip particle manipulation. Since different types of particles respond differently to these signals, variations of DC and AC signals are capable to handle complex and highly variable colloidal and biological samples. The proposed technique can operate in a high-throughput manner with thirteen independent channels in radial directions for enrichment and separation in microfluidic chip. We evaluated our approach by collecting Polystyrene particles, yeast cells, and E. coli bacteria, which respond differently to electric field gradient. Live and dead yeast cells were separated successfully, validating the capability of our device to separate highly similar cells. Our results showed that this technique could achieve fast pre-concentration of colloidal particles and cells and separation of cells depending on their vitality. Hydrodynamic, DC electrophoretic and DC electroosmotic forces were used together instead of syringe pump to achieve sufficient fluid flow and particle mobility for particle trapping and sorting. By eliminating bulky mechanical pumps, this new technique has wide applications for in situ detection and analysis.

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

    Science.gov (United States)

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

    2013-05-30

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

  11. Stiffness-Independent Highly Efficient On-Chip Extraction of Cell-Laden Hydrogel Microcapsules from Oil Emulsion into Aqueous Solution by Dielectrophoresis.

    Science.gov (United States)

    Huang, Haishui; Sun, Mingrui; Heisler-Taylor, Tyler; Kiourti, Asimina; Volakis, John; Lafyatis, Gregory; He, Xiaoming

    2015-10-28

    A dielectrophoresis (DEP)-based method achieves highly efficient on-chip extraction of cell-laden microcapsules of any stiffness from oil into aqueous solution. The hydrogel microcapsules can be extracted into the aqueous solution by DEP and interfacial tension forces with no trapped oil, while the encapsulated cells are free from electrical damage due to the Faraday cage effect. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. COBRA-Seq: Sensitive and Quantitative Methylome Profiling

    Directory of Open Access Journals (Sweden)

    Hilal Varinli

    2015-10-01

    Full Text Available Combined Bisulfite Restriction Analysis (COBRA quantifies DNA methylation at a specific locus. It does so via digestion of PCR amplicons produced from bisulfite-treated DNA, using a restriction enzyme that contains a cytosine within its recognition sequence, such as TaqI. Here, we introduce COBRA-seq, a genome wide reduced methylome method that requires minimal DNA input (0.1–1.0 mg and can either use PCR or linear amplification to amplify the sequencing library. Variants of COBRA-seq can be used to explore CpG-depleted as well as CpG-rich regions in vertebrate DNA. The choice of enzyme influences enrichment for specific genomic features, such as CpG-rich promoters and CpG islands, or enrichment for less CpG dense regions such as enhancers. COBRA-seq coupled with linear amplification has the additional advantage of reduced PCR bias by producing full length fragments at high abundance. Unlike other reduced representative methylome methods, COBRA-seq has great flexibility in the choice of enzyme and can be multiplexed and tuned, to reduce sequencing costs and to interrogate different numbers of sites. Moreover, COBRA-seq is applicable to non-model organisms without the reference genome and compatible with the investigation of non-CpG methylation by using restriction enzymes containing CpA, CpT, and CpC in their recognition site.

  13. Autophagy is required for efficient meiosis progression and proper meiotic chromosome segregation in fission yeast.

    Science.gov (United States)

    Matsuhara, Hirotada; Yamamoto, Ayumu

    2016-01-01

    Autophagy is a conserved intracellular degradation system, which contributes to development and differentiation of various organisms. Yeast cells undergo meiosis under nitrogen-starved conditions and require autophagy for meiosis initiation. However, the precise roles of autophagy in meiosis remain unclear. Here, we show that autophagy is required for efficient meiosis progression and proper meiotic chromosome segregation in fission yeast. Autophagy-defective strains bearing a mutation in the autophagy core factor gene atg1, atg7, or atg14 exhibit deformed nuclear structures during meiosis. These mutant cells require an extracellular nitrogen supply for meiosis progression following their entry into meiosis and show delayed meiosis progression even with a nitrogen supply. In addition, they show frequent chromosome dissociation from the spindle together with spindle overextension, forming extra nuclei. Furthermore, Aurora kinase, which regulates chromosome segregation and spindle elongation, is significantly increased at the centromere and spindle in the mutant cells. Aurora kinase down-regulation eliminated delayed initiation of meiosis I and II, chromosome dissociation, and spindle overextension, indicating that increased Aurora kinase activity may cause these aberrances in the mutant cells. Our findings show a hitherto unrecognized relationship of autophagy with the nuclear structure, regulation of cell cycle progression, and chromosome segregation in meiosis. © 2015 The Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  14. An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.

    Science.gov (United States)

    Cheng, Chia-Yang; Chu, Chia-Han; Hsu, Hung-Wei; Hsu, Fang-Rong; Tang, Chung Yi; Wang, Wen-Ching; Kung, Hsing-Jien; Chang, Pei-Ching

    2014-01-01

    Post-translational modification (PTM) of transcriptional factors and chromatin remodelling proteins is recognized as a major mechanism by which transcriptional regulation occurs. Chromatin immunoprecipitation (ChIP) in combination with high-throughput sequencing (ChIP-seq) is being applied as a gold standard when studying the genome-wide binding sites of transcription factor (TFs). This has greatly improved our understanding of protein-DNA interactions on a genomic-wide scale. However, current ChIP-seq peak calling tools are not sufficiently sensitive and are unable to simultaneously identify post-translational modified TFs based on ChIP-seq analysis; this is largely due to the wide-spread presence of multiple modified TFs. Using SUMO-1 modification as an example; we describe here an improved approach that allows the simultaneous identification of the particular genomic binding regions of all TFs with SUMO-1 modification. Traditional peak calling methods are inadequate when identifying multiple TF binding sites that involve long genomic regions and therefore we designed a ChIP-seq processing pipeline for the detection of peaks via a combinatorial fusion method. Then, we annotate the peaks with known transcription factor binding sites (TFBS) using the Transfac Matrix Database (v7.0), which predicts potential SUMOylated TFs. Next, the peak calling result was further analyzed based on the promoter proximity, TFBS annotation, a literature review, and was validated by ChIP-real-time quantitative PCR (qPCR) and ChIP-reChIP real-time qPCR. The results show clearly that SUMOylated TFs are able to be pinpointed using our pipeline. A methodology is presented that analyzes SUMO-1 ChIP-seq patterns and predicts related TFs. Our analysis uses three peak calling tools. The fusion of these different tools increases the precision of the peak calling results. TFBS annotation method is able to predict potential SUMOylated TFs. Here, we offer a new approach that enhances ChIP-seq

  15. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform.

    Directory of Open Access Journals (Sweden)

    Si Hong Park

    Full Text Available Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer's yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1 C: control (no prebiotic, 2 T1: Biolex® MB40 with 0.2%, and 3 T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40 group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS, microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds.

  16. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform.

    Science.gov (United States)

    Park, Si Hong; Lee, Sang In; Ricke, Steven C

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer's yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds.

  17. Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data.

    Science.gov (United States)

    Li, Peipei; Piao, Yongjun; Shon, Ho Sun; Ryu, Keun Ho

    2015-10-28

    Recently, rapid improvements in technology and decrease in sequencing costs have made RNA-Seq a widely used technique to quantify gene expression levels. Various normalization approaches have been proposed, owing to the importance of normalization in the analysis of RNA-Seq data. A comparison of recently proposed normalization methods is required to generate suitable guidelines for the selection of the most appropriate approach for future experiments. In this paper, we compared eight non-abundance (RC, UQ, Med, TMM, DESeq, Q, RPKM, and ERPKM) and two abundance estimation normalization methods (RSEM and Sailfish). The experiments were based on real Illumina high-throughput RNA-Seq of 35- and 76-nucleotide sequences produced in the MAQC project and simulation reads. Reads were mapped with human genome obtained from UCSC Genome Browser Database. For precise evaluation, we investigated Spearman correlation between the normalization results from RNA-Seq and MAQC qRT-PCR values for 996 genes. Based on this work, we showed that out of the eight non-abundance estimation normalization methods, RC, UQ, Med, TMM, DESeq, and Q gave similar normalization results for all data sets. For RNA-Seq of a 35-nucleotide sequence, RPKM showed the highest correlation results, but for RNA-Seq of a 76-nucleotide sequence, least correlation was observed than the other methods. ERPKM did not improve results than RPKM. Between two abundance estimation normalization methods, for RNA-Seq of a 35-nucleotide sequence, higher correlation was obtained with Sailfish than that with RSEM, which was better than without using abundance estimation methods. However, for RNA-Seq of a 76-nucleotide sequence, the results achieved by RSEM were similar to without applying abundance estimation methods, and were much better than with Sailfish. Furthermore, we found that adding a poly-A tail increased alignment numbers, but did not improve normalization results. Spearman correlation analysis revealed that RC, UQ

  18. Cadmium, lead and mercury levels in feeding yeast produced in Czechoslovakia.

    Science.gov (United States)

    Cibulka, J; Turecki, T; Miholová, D; Mader, P; Száková, J; Brabec, M

    1992-04-01

    Ninety-six samples of the feeding yeast known as VITEX were analyzed for Cd, Pb and Hg content during 1987-1989. Cadmium content ranged from 0.30 to 5.12 mg/kg(-1), lead content from 0.21 to 3.01 mg/kg(-1) and mercury content from 0.008 to 0.187 mg/kg(-1). Our findings meet the current government standards (max. allowed Pb = 5.00, Cd = 0.50 and Hg = 0.100 mg/kg(-1)) only for lead, and with five exceptions, for mercury. With two exceptions, all cadmium levels found in the samples exceeded the limit. One raw material - the wood chips - was shown to be the main source of cadmium in the technological process. Relatively high Hg contents were measured in the wood chips (up to 0.155 mg/kg(-1)); the highest Hg level (1.105 mg/kg(-1)) however was found in a sample of KOH.

  19. MALDI-TOF MS as a tool to identify foodborne yeasts and yeast-like fungi.

    Science.gov (United States)

    Quintilla, Raquel; Kolecka, Anna; Casaregola, Serge; Daniel, Heide M; Houbraken, Jos; Kostrzewa, Markus; Boekhout, Teun; Groenewald, Marizeth

    2018-02-02

    Since food spoilage by yeasts causes high economic losses, fast and accurate identifications of yeasts associated with food and food-related products are important for the food industry. In this study the efficiency of the matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify food related yeasts was evaluated. A CBS in-house MALDI-TOF MS database was created and later challenged with a blinded test set of 146 yeast strains obtained from food and food related products. Ninety eight percent of the strains were correctly identified with log score values>1.7. One strain, Mrakia frigida, gained a correct identification with a score value1.7. Ambiguous identifications were observed due to two incorrect reference mass spectra's found in the commercial database BDAL v.4.0, namely Candida sake DSM 70763 which was re-identified as Candida oleophila, and Candida inconspicua DSM 70631 which was re-identified as Pichia membranifaciens. MALDI-TOF MS can distinguish between most of the species, but for some species complexes, such as the Kazachstania telluris and Mrakia frigida complexes, MALDI-TOF MS showed limited resolution and identification of sibling species was sometimes problematic. Despite this, we showed that the MALDI-TOF MS is applicable for routine identification and validation of foodborne yeasts, but a further update of the commercial reference databases is needed. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout.

    Directory of Open Access Journals (Sweden)

    Sixin Liu

    Full Text Available Fish under intensive rearing conditions experience various stressors which have negative impacts on survival, growth, reproduction and fillet quality. Identifying and characterizing the molecular mechanisms underlying stress responses will facilitate the development of strategies that aim to improve animal welfare and aquaculture production efficiency. In this study, we used RNA-seq to identify transcripts which are differentially expressed in the rainbow trout liver in response to handling and confinement stress. These stressors were selected due to their relevance in aquaculture production. Total RNA was extracted from the livers of individual fish in five tanks having eight fish each, including three tanks of fish subjected to a 3 hour handling and confinement stress and two control tanks. Equal amount of total RNA of six individual fish was pooled by tank to create five RNA-seq libraries which were sequenced in one lane of Illumina HiSeq 2000. Three sequencing runs were conducted to obtain a total of 491,570,566 reads which were mapped onto the previously generated stress reference transcriptome to identify 316 differentially expressed transcripts (DETs. Twenty one DETs were selected for qPCR to validate the RNA-seq approach. The fold changes in gene expression identified by RNA-seq and qPCR were highly correlated (R(2 = 0.88. Several gene ontology terms including transcription factor activity and biological process such as glucose metabolic process were enriched among these DETs. Pathways involved in response to handling and confinement stress were implicated by mapping the DETs to reference pathways in the KEGG database.Raw RNA-seq reads have been submitted to the NCBI Short Read Archive under accession number SRP022881.All customized scripts described in this paper are available from Dr. Guangtu Gao or the corresponding author.

  1. Modular 3D printed lab-on-a-chip bio-reactor for the biochemical energy cascade of microorganisms

    Science.gov (United States)

    Podwin, Agnieszka; Dziuban, Jan A.

    2017-10-01

    The paper presents the sandwiched polymer 3D printed lab-on-a-chip bio-reactor for the biochemical energy cascade of microorganisms. Euglenas and yeast were separately and simultaneously cultured for 10 d in the chip. As a result of the experiments, euglenas, light-initialized and nourished by CO2—a product of ethanol fermentation handled by yeast—generated oxygen, based on the photosynthesis process. The presence of oxygen in the bio-reactor was confirmed by the colorimetric method—a bicarbonate (pH) indicator. Preliminary studies towards the obtainment of an effective source of oxygen are promising and further research should be done to enable the utility of the bio-reactor in, for instance, microbial fuel cells.

  2. Modular 3D printed lab-on-a-chip bio-reactor for the biochemical energy cascade of microorganisms

    International Nuclear Information System (INIS)

    Podwin, Agnieszka; Dziuban, Jan A

    2017-01-01

    The paper presents the sandwiched polymer 3D printed lab-on-a-chip bio-reactor for the biochemical energy cascade of microorganisms. Euglenas and yeast were separately and simultaneously cultured for 10 d in the chip. As a result of the experiments, euglenas, light-initialized and nourished by CO 2 —a product of ethanol fermentation handled by yeast—generated oxygen, based on the photosynthesis process. The presence of oxygen in the bio-reactor was confirmed by the colorimetric method—a bicarbonate (pH) indicator. Preliminary studies towards the obtainment of an effective source of oxygen are promising and further research should be done to enable the utility of the bio-reactor in, for instance, microbial fuel cells. (paper)

  3. Yeast Isolation for Bioethanol Production

    Directory of Open Access Journals (Sweden)

    EKA RURIANI

    2012-09-01

    Full Text Available We have isolated 12 yeast isolates from five different rotten fruits by using a yeast glucose chloramphenicol agar (YGCA medium supplemented with tetracycline. From pre-screening assay, four isolates exhibited higher substrate (glucose-xylose consumption efficiency in the reaction tube fermentation compared to Saccharomyces cerevisiae dan Saccharomyces ellipsoids as the reference strains. Based on the fermentation process in gooseneck flasks, we observed that two isolates (K and SB showed high fermentation efficiency both in sole glucose and mixed glucose-xylose substrate. Moreover, isolates K and SB produced relatively identical level of ethanol concentration compared to the reference strains. Isolates H and MP could only produce high levels of ethanol in glucose fermentation, while only half of that amount of ethanol was detected in glucose-xylose fermentation. Isolate K and SB were identified as Pichia kudriavzeevii (100% based on large sub unit (LSU ribosomal DNA D1/D2 region.

  4. Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast.

    Science.gov (United States)

    Yu, Chuanhe; Gan, Haiyun; Zhang, Zhiguo

    2018-01-01

    DNA replication initiates at DNA replication origins after unwinding of double-strand DNA(dsDNA) by replicative helicase to generate single-stranded DNA (ssDNA) templates for the continuous synthesis of leading-strand and the discontinuous synthesis of lagging-strand. Therefore, methods capable of detecting strand-specific information will likely yield insight into the association of proteins at leading and lagging strand of DNA replication forks and the regulation of leading and lagging strand synthesis during DNA replication. The enrichment and Sequencing of Protein-Associated Nascent DNA (eSPAN), which measure the relative amounts of proteins at nascent leading and lagging strands of DNA replication forks, is a step-wise procedure involving the chromatin immunoprecipitation (ChIP) of a protein of interest followed by the enrichment of protein-associated nascent DNA through BrdU immunoprecipitation. The isolated ssDNA is then subjected to strand-specific sequencing. This method can detect whether a protein is enriched at leading or lagging strand of DNA replication forks. In addition to eSPAN, two other strand-specific methods, (ChIP-ssSeq), which detects potential protein-ssDNA binding and BrdU-IP-ssSeq, which can measure synthesis of both leading and lagging strand, were developed along the way. These methods can provide strand-specific and complementary information about the association of the target protein with DNA replication forks as well as synthesis of leading and lagging strands genome wide. Below, we describe the detailed eSPAN, ChIP-ssSeq, and BrdU-IP-ssSeq protocols.

  5. Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii.

    Science.gov (United States)

    Ortiz-Merino, Raúl A; Kuanyshev, Nurzhan; Byrne, Kevin P; Varela, Javier A; Morrissey, John P; Porro, Danilo; Wolfe, Kenneth H; Branduardi, Paola

    2018-03-01

    Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH and a fermentative metabolism with a high growth rate. Here we used mRNA sequencing (RNA-seq) to analyze Z. parabailii 's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than under control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/Aft2, previously described as lactic acid responsive in Saccharomyces cerevisiae Furthermore, formate dehydrogenase ( FDH ) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii in comparison to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production. IMPORTANCE Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression under conditions of interest and relating gene expression patterns

  6. Error Control for Network-on-Chip Links

    CERN Document Server

    Fu, Bo

    2012-01-01

    As technology scales into nanoscale regime, it is impossible to guarantee the perfect hardware design. Moreover, if the requirement of 100% correctness in hardware can be relaxed, the cost of manufacturing, verification, and testing will be significantly reduced. Many approaches have been proposed to address the reliability problem of on-chip communications. This book focuses on the use of error control codes (ECCs) to improve on-chip interconnect reliability. Coverage includes detailed description of key issues in NOC error control faced by circuit and system designers, as well as practical error control techniques to minimize the impact of these errors on system performance. Provides a detailed background on the state of error control methods for on-chip interconnects; Describes the use of more complex concatenated codes such as Hamming Product Codes with Type-II HARQ, while emphasizing integration techniques for on-chip interconnect links; Examines energy-efficient techniques for integrating multiple error...

  7. Energy efficiency and CO{sub 2} -eq emissions of forest chip supply chains in Finland 2020

    Energy Technology Data Exchange (ETDEWEB)

    Kariniemi, A.; Kaerhae, K. (Metsaeteho Oy, Helsinki (Finland)), Email: arto.kariniemi@metsateho.fi, Email: kalle.karha@metsateho.fi

    2009-07-01

    The research carried out by Metsaeteho Oy calculated what would be the total fuel consumption and CO{sub 2}-eq emissions of forest chip production if the use of forest chips is 24 TWhin 2020 in Finland in accordance with the target set of Long-term Climate and Energy Strategy. CO{sub 2}-eq emissions were determined with Metsaeteho OY's updated Emissions Calculation Model. If the production and consumption of forest chips in Finland are 24 TWh in 2020, then the total CO{sub 2}-eq emissions would be around 245000 tonnes. The volume of diesel consumption was 79 million litres and petrol 1,5 millions litres. Electric rail transportation and chipping at the mill site consumed 15 GWh of electricity. The supply chain with the lowest CO{sub 2}-eq emissions was logging residues comminuted at plant. Conversely, the highest CO{sub 2}-eq emissions came from stump wood when operating with terminal comminuting. Some 3% of the energy content was consumed during the forest chip production. Energy input/output ratio in the total volume was 0.030 MWh/MWh which varied from 0.022 to 0.044 between the supply systems researched. Hence, forest chip production gave a net of some 97% of the energy content delivered at the plant. (orig.)

  8. Yeast viability and concentration analysis using lens-free computational microscopy and machine learning

    Science.gov (United States)

    Feizi, Alborz; Zhang, Yibo; Greenbaum, Alon; Guziak, Alex; Luong, Michelle; Chan, Raymond Yan Lok; Berg, Brandon; Ozkan, Haydar; Luo, Wei; Wu, Michael; Wu, Yichen; Ozcan, Aydogan

    2017-03-01

    Research laboratories and the industry rely on yeast viability and concentration measurements to adjust fermentation parameters such as pH, temperature, and pressure. Beer-brewing processes as well as biofuel production can especially utilize a cost-effective and portable way of obtaining data on cell viability and concentration. However, current methods of analysis are relatively costly and tedious. Here, we demonstrate a rapid, portable, and cost-effective platform for imaging and measuring viability and concentration of yeast cells. Our platform features a lens-free microscope that weighs 70 g and has dimensions of 12 × 4 × 4 cm. A partially-coherent illumination source (a light-emitting-diode), a band-pass optical filter, and a multimode optical fiber are used to illuminate the sample. The yeast sample is directly placed on a complementary metal-oxide semiconductor (CMOS) image sensor chip, which captures an in-line hologram of the sample over a large field-of-view of >20 mm2. The hologram is transferred to a touch-screen interface, where a trained Support Vector Machine model classifies yeast cells stained with methylene blue as live or dead and measures cell viability as well as concentration. We tested the accuracy of our platform against manual counting of live and dead cells using fluorescent exclusion staining and a bench-top fluorescence microscope. Our regression analysis showed no significant difference between the two methods within a concentration range of 1.4 × 105 to 1.4 × 106 cells/mL. This compact and cost-effective yeast analysis platform will enable automatic quantification of yeast viability and concentration in field settings and resource-limited environments.

  9. Readout chip for the CMS pixel detector upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Rossini, Marco, E-mail: marco.rossini@phys.ethz.ch

    2014-11-21

    For the CMS experiment a new pixel detector is planned for installation during the extended shutdown in winter 2016/2017. Among the changes of the detector modified front end electronics will be used for higher efficiency at peak luminosity of the LHC and faster readout. The first prototype versions of the new readout chip have been designed and produced. The results of qualification and calibration for the new chip are presented in this paper.

  10. The yeast stands alone: the future of protein biologic production.

    Science.gov (United States)

    Love, Kerry R; Dalvie, Neil C; Love, J Christopher

    2017-12-22

    Yeasts are promising alternative hosts for the manufacturing of recombinant protein therapeutics because they simply and efficiently meet needs for both platform and small-market drugs. Fast accumulation of biomass and low-cost media reduce the cost-of-goods when using yeast, which in turn can enable agile, small-volume manufacturing facilities. Small, tractable yeast genomes are amenable to rapid process development, facilitating strain and product quality by design. Specifically, Pichia pastoris is becoming a widely accepted yeast for biopharmaceutical manufacturing in much of the world owing to a clean secreted product and the rapidly expanding understanding of its cell biology as a host organism. We advocate for a near term partnership spanning industry and academia to promote open source, timely development of yeast hosts. Copyright © 2017. Published by Elsevier Ltd.

  11. Implantable Biomedical Signal Monitoring Using RF Energy Harvestingand On-Chip Antenna

    Directory of Open Access Journals (Sweden)

    Jiann-Shiun Yuan

    2015-08-01

    Full Text Available This paper presents the design of an energy harvesting wireless and battery-less silicon-on-chip (SoC device that can be implanted in the human body to monitor certain health conditions. The proposed architecture has been designed on TSMC 0.18μm CMOS ICs and is an integrated system with a rectenna (antenna and rectifier and transmitting circuit, all on a single chip powered by an external transmitter and that is small enough to be inserted in the human eye, heart or brain. The transmitting and receiving antennas operate in the 5.8- GHz ISM band and have a -10dB gain. The distinguishing feature of this design is the rectenna that comprises of a singlestage diode connected NMOS rectifier and a 3-D on-chip antenna that occupies only 2.5 × 1 × 2.8 mm3 of chip area and has the ability to communicate within proximity of 5 cm while giving 10% efficiency. The external source is a reader that powers up the RF rectifier in the implantable chip triggering it to start sending data back to the reader enabling an efficient method of health evaluation for the patient.

  12. MiSeq: A Next Generation Sequencing Platform for Genomic Analysis.

    Science.gov (United States)

    Ravi, Rupesh Kanchi; Walton, Kendra; Khosroheidari, Mahdieh

    2018-01-01

    MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.

  13. Plasmid construction using recombination activity in the fission yeast Schizosaccharomyces pombe.

    Directory of Open Access Journals (Sweden)

    Ayako Chino

    Full Text Available BACKGROUND: Construction of plasmids is crucial in modern genetic manipulation. As of now, the common method for constructing plasmids is to digest specific DNA sequences with restriction enzymes and to ligate the resulting DNA fragments with DNA ligase. Another potent method to construct plasmids, known as gap-repair cloning (GRC, is commonly used in the budding yeast Saccharomyces cerevisiae. GRC makes use of the homologous recombination activity that occurs within the yeast cells. Due to its flexible design and efficiency, GRC has been frequently used for constructing plasmids with complex structures as well as genome-wide plasmid collections. Although there have been reports indicating GRC feasibility in the fission yeast Schizosaccharomyces pombe, this species is not commonly used for GRC as systematic studies of reporting GRC efficiency in S. pombe have not been performed till date. METHODOLOGY/PRINCIPAL FINDINGS: We investigated GRC efficiency in S. pombe in this study. We first showed that GRC was feasible in S. pombe by constructing a plasmid that contained the LEU2 auxotrophic marker gene in vivo and showed sufficient efficiency with short homology sequences (>25 bp. No preference was shown for the sequence length from the cut site in the vector plasmid. We next showed that plasmids could be constructed in a proper way using 3 DNA fragments with 70% efficiency without any specific selections being made. The GRC efficiency with 3 DNA fragments was dramatically increased >95% in lig4Delta mutant cell, where non-homologous end joining is deficient. Following this approach, we successfully constructed plasmid vectors with leu1+, ade6+, his5+, and lys1+ markers with the low-copy stable plasmid pDblet as a backbone by applying GRC in S. pombe. CONCLUSIONS/SIGNIFICANCE: We concluded that GRC was sufficiently feasible in S. pombe for genome-wide gene functional analysis as well as for regular plasmid construction. Plasmids with different

  14. Silicon Chip-to-Chip Mode-Division Multiplexing

    DEFF Research Database (Denmark)

    Baumann, Jan Markus; Porto da Silva, Edson; Ding, Yunhong

    2018-01-01

    A chip-to-chip mode-division multiplexing connection is demonstrated using a pair of multiplexers/demultiplexers fabricated on the silicon-on-insulator platform. Successful mode multiplexing and demultiplexing is experimentally demonstrated, using the LP01, LP11a and LP11b modes.......A chip-to-chip mode-division multiplexing connection is demonstrated using a pair of multiplexers/demultiplexers fabricated on the silicon-on-insulator platform. Successful mode multiplexing and demultiplexing is experimentally demonstrated, using the LP01, LP11a and LP11b modes....

  15. Effects of Dietary Yeast (Saccharomyces cerevisia Supplementation in Practical Diets of Tilapia (Oreochromis niloticus

    Directory of Open Access Journals (Sweden)

    José E. P. Cyrino

    2012-01-01

    Full Text Available A 51-day feeding trial was carried out to determine the effects of various dietary levels of brewer’s yeast, Saccharomyces cerevisiae, in the growth performance, body composition and nutrient utilization in Nile tilapia, Oreochromis niloticus, juveniles. Fish (7.6 ± 0.3 g were stocked into eighteen 1,000-L tanks (100 fish per tank; n = 3 and fed to apparent satiation six isonitrogenous (27% crude protein and isoenergetic (19 kJ/g diets, formulated to contain different dried yeast levels (0%, 10%, 15%, 20%, 30% or 40% diet in substitution to fishmeal. Body weight tripled at the end of the feeding trial for fish fed up to 20% dietary yeast incorporation. Daily growth coefficient (DGC, % body weight/day decreased with increasing dietary yeast level (P < 0.0001. Voluntary feed intake (VFI, %BW/day did not vary significantly with increasing yeast level. Fish fed 40% yeast showed significant reduction in protein efficiency rate, protein retention and nitrogen gain. Increasing levels of dietary yeast did not significantly affect protein or lipid digestibility. Dietary dried yeast was seemingly palatable to tilapia juveniles and was suitable up to 15% inclusion to promote growth and efficient diet utilization, without affecting body composition.

  16. Chip shape and secondary fragmentation through TBM excavation

    International Nuclear Information System (INIS)

    Tsusaka, Kimikazu; Tanimoto, Chikaosa; Ueno, Takaaki; Koizumi, Yu; Nakane, Tatsuto

    2008-01-01

    The chips through TBM tunneling are well-known for one of useful indices to reflect the geological conditions. The flat and elongated chips whose width are equal to the spacing of cutter trace indicate the cutting face with less joints and good practice of TBM excavation with less secondary fragmentation rate. Through a case history in granitic rock, the authors proposed the new index, which is the ratio of length of major axis to thickness. Also the authors studied the relationship between the index and the excavation efficiencies. In conclusion, it was clarified that chips with the new index over 3.5 were generally observed when a TBM drove with less than 30% the secondary fragmentation rate. (author)

  17. Nuclear Magnetic Resonance Spectroscopy-Based Identification of Yeast.

    Science.gov (United States)

    Himmelreich, Uwe; Sorrell, Tania C; Daniel, Heide-Marie

    2017-01-01

    Rapid and robust high-throughput identification of environmental, industrial, or clinical yeast isolates is important whenever relatively large numbers of samples need to be processed in a cost-efficient way. Nuclear magnetic resonance (NMR) spectroscopy generates complex data based on metabolite profiles, chemical composition and possibly on medium consumption, which can not only be used for the assessment of metabolic pathways but also for accurate identification of yeast down to the subspecies level. Initial results on NMR based yeast identification where comparable with conventional and DNA-based identification. Potential advantages of NMR spectroscopy in mycological laboratories include not only accurate identification but also the potential of automated sample delivery, automated analysis using computer-based methods, rapid turnaround time, high throughput, and low running costs.We describe here the sample preparation, data acquisition and analysis for NMR-based yeast identification. In addition, a roadmap for the development of classification strategies is given that will result in the acquisition of a database and analysis algorithms for yeast identification in different environments.

  18. Yeast Communities of Chestnut Soils under Vineyards in Dagestan

    Science.gov (United States)

    Abdullabekova, D. A.; Magomedova, E. S.; Magomedov, G. G.; Aliverdieva, D. A.; Kachalkin, A. V.

    2017-12-01

    The study of yeast communities in chestnut soils (Kastanozems) under vineyards in the Republic of Dagestan made it possible to isolate 20 yeast species. Most of the yeasts under vineyards belonged to ascomycetes, among which species of the Saccharomycetaceae family (in particular, Saccharomyces cerevisiae) comprised a significant part. The obtained results indicate that the soils under vineyards keep the pool of microbial diversity and ensure preservation of many species typical for grapes. The method of enrichment culture on grape juice medium proved to be more efficient than other methods of analysis with respect to the number of isolated species and the rate of their detection. However, implementation of different techniques to study yeasts' diversity can give somewhat different results; a set of methods should be used for an integrated analysis.

  19. Genetic and phenotypic characteristics of baker's yeast: relevance to baking.

    Science.gov (United States)

    Randez-Gil, Francisca; Córcoles-Sáez, Isaac; Prieto, José A

    2013-01-01

    Yeasts rarely encounter ideal physiological conditions during their industrial life span; therefore, their ability to adapt to changing conditions determines their usefulness and applicability. This is especially true for baking strains of Saccharomyces cerevisiae. The success of this yeast in the ancient art of bread making is based on its capacity to rapidly transform carbohydrates into CO2 rather than its unusual resistance to environmental stresses. Moreover, baker's yeast must exhibit efficient respiratory metabolism during yeast manufacturing, which determines biomass yield. However, optimal growth conditions often have negative consequences in other commercially important aspects, such as fermentative power or stress tolerance. This article reviews the genetic and physiological characteristics of baking yeast strains, emphasizing the activation of regulatory mechanisms in response to carbon source and stress signaling and their importance in defining targets for strain selection and improvement.

  20. METHOD FOR THE PRODUCTION OF HETEROLOGOUS POLYPEPTIDES IN TRANSFORMED YEAST CELLS

    DEFF Research Database (Denmark)

    2000-01-01

    The invention describes industrial fermentation of a $i(Saccharomyces) yeast species for production of a heterologous product encoded by a plasmid or DNA contained in said $i(Saccharomyces) yeast species with method utilizes the substrate more efficiently and without fermentative metabolism...... resulting in formation of ethanol and other unwanted primary products of fermentative activity whereby high yields of the heterologous product are obtained. The $i(Saccharomyces) yeast species is preferably a Crabtree negative $i(Saccharomyces species) in particular $i(Saccharomyces kluyveri)....

  1. Conventional and Non-Conventional Yeasts in Beer Production

    Directory of Open Access Journals (Sweden)

    Angela Capece

    2018-06-01

    Full Text Available The quality of beer relies on the activity of fermenting yeasts, not only for their good fermentation yield-efficiency, but also for their influence on beer aroma, since most of the aromatic compounds are intermediate metabolites and by-products of yeast metabolism. Beer production is a traditional process, in which Saccharomyces is the sole microbial component, and any deviation is considered a flaw. However, nowadays the brewing sector is faced with an increasing demand for innovative products, and it is diffusing the use of uncharacterized autochthonous starter cultures, spontaneous fermentation, or non-Saccharomyces starters, which leads to the production of distinctive and unusual products. Attempts to obtain products with more complex sensory characteristics have led one to prospect for non-conventional yeasts, i.e., non-Saccharomyces yeasts. These generally are characterized by low fermentation yields and are more sensitive to ethanol stress, but they provide a distinctive aroma and flavor. Furthermore, non-conventional yeasts can be used for the production of low-alcohol/non-alcoholic and light beers. This review aims to present the main findings about the role of traditional and non-conventional yeasts in brewing, demonstrating the wide choice of available yeasts, which represents a new biotechnological approach with which to target the characteristics of beer and to produce different or even totally new beer styles.

  2. PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

    Science.gov (United States)

    Zhang, Yanju; Lameijer, Eric-Wubbo; 't Hoen, Peter A C; Ning, Zemin; Slagboom, P Eline; Ye, Kai

    2012-02-15

    RNA-seq is a powerful technology for the study of transcriptome profiles that uses deep-sequencing technologies. Moreover, it may be used for cellular phenotyping and help establishing the etiology of diseases characterized by abnormal splicing patterns. In RNA-Seq, the exact nature of splicing events is buried in the reads that span exon-exon boundaries. The accurate and efficient mapping of these reads to the reference genome is a major challenge. We developed PASSion, a pattern growth algorithm-based pipeline for splice site detection in paired-end RNA-Seq reads. Comparing the performance of PASSion to three existing RNA-Seq analysis pipelines, TopHat, MapSplice and HMMSplicer, revealed that PASSion is competitive with these packages. Moreover, the performance of PASSion is not affected by read length and coverage. It performs better than the other three approaches when detecting junctions in highly abundant transcripts. PASSion has the ability to detect junctions that do not have known splicing motifs, which cannot be found by the other tools. Of the two public RNA-Seq datasets, PASSion predicted ≈ 137,000 and 173,000 splicing events, of which on average 82 are known junctions annotated in the Ensembl transcript database and 18% are novel. In addition, our package can discover differential and shared splicing patterns among multiple samples. The code and utilities can be freely downloaded from https://trac.nbic.nl/passion and ftp://ftp.sanger.ac.uk/pub/zn1/passion.

  3. Systematic identification of yeast cell cycle transcription factors using multiple data sources

    Directory of Open Access Journals (Sweden)

    Li Wen-Hsiung

    2008-12-01

    Full Text Available Abstract Background Eukaryotic cell cycle is a complex process and is precisely regulated at many levels. Many genes specific to the cell cycle are regulated transcriptionally and are expressed just before they are needed. To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs that regulate the expression of cell cycle-regulated genes. Results We developed a method to identify cell cycle TFs in yeast by integrating current ChIP-chip, mutant, transcription factor binding site (TFBS, and cell cycle gene expression data. We identified 17 cell cycle TFs, 12 of which are known cell cycle TFs, while the remaining five (Ash1, Rlm1, Ste12, Stp1, Tec1 are putative novel cell cycle TFs. For each cell cycle TF, we assigned specific cell cycle phases in which the TF functions and identified the time lag for the TF to exert regulatory effects on its target genes. We also identified 178 novel cell cycle-regulated genes, among which 59 have unknown functions, but they may now be annotated as cell cycle-regulated genes. Most of our predictions are supported by previous experimental or computational studies. Furthermore, a high confidence TF-gene regulatory matrix is derived as a byproduct of our method. Each TF-gene regulatory relationship in this matrix is supported by at least three data sources: gene expression, TFBS, and ChIP-chip or/and mutant data. We show that our method performs better than four existing methods for identifying yeast cell cycle TFs. Finally, an application of our method to different cell cycle gene expression datasets suggests that our method is robust. Conclusion Our method is effective for identifying yeast cell cycle TFs and cell cycle-regulated genes. Many of our predictions are validated by the literature. Our study shows that integrating multiple data sources is a powerful approach to studying complex biological systems.

  4. Optimization Of A High-Throughput Transcriptomic (HTTr) Bioactivity Screen In MCF7 Cells Using Targeted RNA-Seq (SOT)

    Science.gov (United States)

    Recent advances in targeted RNA-Seq technology allow researchers to efficiently and cost-effectively obtain whole transcriptome profiles using picograms of mRNA from human cell lysates. Low mRNA input requirements and sample multiplexing capabilities has made time- and concentrat...

  5. Active role of a human genomic insert in replication of a yeast artificial chromosome.

    Science.gov (United States)

    van Brabant, A J; Fangman, W L; Brewer, B J

    1999-06-01

    Yeast artificial chromosomes (YACs) are a common tool for cloning eukaryotic DNA. The manner by which large pieces of foreign DNA are assimilated by yeast cells into a functional chromosome is poorly understood, as is the reason why some of them are stably maintained and some are not. We examined the replication of a stable YAC containing a 240-kb insert of DNA from the human T-cell receptor beta locus. The human insert contains multiple sites that serve as origins of replication. The activity of these origins appears to require the yeast ARS consensus sequence and, as with yeast origins, additional flanking sequences. In addition, the origins in the human insert exhibit a spacing, a range of activation efficiencies, and a variation in times of activation during S phase similar to those found for normal yeast chromosomes. We propose that an appropriate combination of replication origin density, activation times, and initiation efficiencies is necessary for the successful maintenance of YAC inserts.

  6. NBLDA: negative binomial linear discriminant analysis for RNA-Seq data.

    Science.gov (United States)

    Dong, Kai; Zhao, Hongyu; Tong, Tiejun; Wan, Xiang

    2016-09-13

    RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to RNA-Seq data, they are not ideal due to the discrete nature of RNA-Seq data. The Poisson distribution and negative binomial distribution are commonly used to model count data. Recently, Witten (Annals Appl Stat 5:2493-2518, 2011) proposed a Poisson linear discriminant analysis for RNA-Seq data. The Poisson assumption may not be as appropriate as the negative binomial distribution when biological replicates are available and in the presence of overdispersion (i.e., when the variance is larger than or equal to the mean). However, it is more complicated to model negative binomial variables because they involve a dispersion parameter that needs to be estimated. In this paper, we propose a negative binomial linear discriminant analysis for RNA-Seq data. By Bayes' rule, we construct the classifier by fitting a negative binomial model, and propose some plug-in rules to estimate the unknown parameters in the classifier. The relationship between the negative binomial classifier and the Poisson classifier is explored, with a numerical investigation of the impact of dispersion on the discriminant score. Simulation results show the superiority of our proposed method. We also analyze two real RNA-Seq data sets to demonstrate the advantages of our method in real-world applications. We have developed a new classifier using the negative binomial model for RNA-seq data classification. Our simulation results show that our proposed classifier has a better performance than existing works. The proposed classifier can serve as an effective tool for classifying RNA-seq data. Based on the comparison results, we have provided some guidelines for scientists to decide which method should be used in the discriminant analysis of RNA-Seq data

  7. Identification and Characterization of Yeast Isolates from Pharmaceutical Waste Water

    Directory of Open Access Journals (Sweden)

    Marjeta Recek

    2002-01-01

    Full Text Available In order to develop an efficient an system for waste water pretreatment, the isolation of indigenous population of microorganisms from pharmaceutical waste water was done. We obtained pure cultures of 16 yeast isolates that differed slightly in colony morphology. Ten out of 16 isolates efficiently reduced COD in pharmaceutical waste water. Initial physiological characterization failed to match the 10 yeast isolates to either Pichia anomala or Pichia ciferrii. Restriction analysis of rDNA (rDNA-RFLP using three different restriction enzymes: HaeIII, MspI and CfoI, showed identical patterns of the isolates and Pichia anomala type strain. Separation of chromosomal DNAs of yeast isolates by the pulsed field gel electrophoresis revealed that the 10 isolates could be grouped into 6 karyotypes. Growth characteristics of the 6 isolates with distinct karyotypes were then studied in batch cultivation in pharmaceutical waste water for 80 hours.

  8. Self-powered integrated systems-on-chip (energy chip)

    KAUST Repository

    Hussain, Muhammad Mustafa

    2010-04-23

    In today\\'s world, consumer driven technology wants more portable electronic gadgets to be developed, and the next big thing in line is self-powered handheld devices. Therefore to reduce the power consumption as well as to supply sufficient power to run those devices, several critical technical challenges need to be overcome: a. Nanofabrication of macro/micro systems which incorporates the direct benefit of light weight (thus portability), low power consumption, faster response, higher sensitivity and batch production (low cost). b. Integration of advanced nano-materials to meet the performance/cost benefit trend. Nano-materials may offer new functionalities that were previously underutilized in the macro/micro dimension. c. Energy efficiency to reduce power consumption and to supply enough power to meet that low power demand. We present a pragmatic perspective on a self-powered integrated System on Chip (SoC). We envision the integrated device will have two objectives: low power consumption/dissipation and on-chip power generation for implementation into handheld or remote technologies for defense, space, harsh environments and medical applications. This paper provides insight on materials choices, intelligent circuit design, and CMOS compatible integration.

  9. Self-powered integrated systems-on-chip (energy chip)

    Science.gov (United States)

    Hussain, M. M.; Fahad, H.; Rojas, J.; Hasan, M.; Talukdar, A.; Oommen, J.; Mink, J.

    2010-04-01

    In today's world, consumer driven technology wants more portable electronic gadgets to be developed, and the next big thing in line is self-powered handheld devices. Therefore to reduce the power consumption as well as to supply sufficient power to run those devices, several critical technical challenges need to be overcome: a. Nanofabrication of macro/micro systems which incorporates the direct benefit of light weight (thus portability), low power consumption, faster response, higher sensitivity and batch production (low cost). b. Integration of advanced nano-materials to meet the performance/cost benefit trend. Nano-materials may offer new functionalities that were previously underutilized in the macro/micro dimension. c. Energy efficiency to reduce power consumption and to supply enough power to meet that low power demand. We present a pragmatic perspective on a self-powered integrated System on Chip (SoC). We envision the integrated device will have two objectives: low power consumption/dissipation and on-chip power generation for implementation into handheld or remote technologies for defense, space, harsh environments and medical applications. This paper provides insight on materials choices, intelligent circuit design, and CMOS compatible integration.

  10. voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data

    Directory of Open Access Journals (Sweden)

    Gokmen Zararsiz

    2017-10-01

    Full Text Available RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used to build diagnostic classifiers particularly for cancer diseases. Microarray based classifiers are not directly applicable to RNA-Seq data due to its discrete nature. Overdispersion is another problem that requires careful modeling of mean and variance relationship of the RNA-Seq data. In this study, we present voomDDA classifiers: variance modeling at the observational level (voom extensions of the nearest shrunken centroids (NSC and the diagonal discriminant classifiers. VoomNSC is one of these classifiers and brings voom and NSC approaches together for the purpose of gene-expression based classification. For this purpose, we propose weighted statistics and put these weighted statistics into the NSC algorithm. The VoomNSC is a sparse classifier that models the mean-variance relationship using the voom method and incorporates voom’s precision weights into the NSC classifier via weighted statistics. A comprehensive simulation study was designed and four real datasets are used for performance assessment. The overall results indicate that voomNSC performs as the sparsest classifier. It also provides the most accurate results together with power-transformed Poisson linear discriminant analysis, rlog transformed support vector machines and random forests algorithms. In addition to prediction purposes, the voomNSC classifier can be used to identify the potential diagnostic biomarkers for a condition of interest. Through this work, statistical learning methods proposed for microarrays can be reused for RNA-Seq data. An interactive web application is freely available at http://www.biosoft.hacettepe.edu.tr/voomDDA/.

  11. voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data.

    Science.gov (United States)

    Zararsiz, Gokmen; Goksuluk, Dincer; Klaus, Bernd; Korkmaz, Selcuk; Eldem, Vahap; Karabulut, Erdem; Ozturk, Ahmet

    2017-01-01

    RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used to build diagnostic classifiers particularly for cancer diseases. Microarray based classifiers are not directly applicable to RNA-Seq data due to its discrete nature. Overdispersion is another problem that requires careful modeling of mean and variance relationship of the RNA-Seq data. In this study, we present voomDDA classifiers: variance modeling at the observational level (voom) extensions of the nearest shrunken centroids (NSC) and the diagonal discriminant classifiers. VoomNSC is one of these classifiers and brings voom and NSC approaches together for the purpose of gene-expression based classification. For this purpose, we propose weighted statistics and put these weighted statistics into the NSC algorithm. The VoomNSC is a sparse classifier that models the mean-variance relationship using the voom method and incorporates voom's precision weights into the NSC classifier via weighted statistics. A comprehensive simulation study was designed and four real datasets are used for performance assessment. The overall results indicate that voomNSC performs as the sparsest classifier. It also provides the most accurate results together with power-transformed Poisson linear discriminant analysis, rlog transformed support vector machines and random forests algorithms. In addition to prediction purposes, the voomNSC classifier can be used to identify the potential diagnostic biomarkers for a condition of interest. Through this work, statistical learning methods proposed for microarrays can be reused for RNA-Seq data. An interactive web application is freely available at http://www.biosoft.hacettepe.edu.tr/voomDDA/.

  12. Decapsulation Method for Flip Chips with Ceramics in Microelectronic Packaging

    Science.gov (United States)

    Shih, T. I.; Duh, J. G.

    2008-06-01

    The decapsulation of flip chips bonded to ceramic substrates is a challenging task in the packaging industry owing to the vulnerability of the chip surface during the process. In conventional methods, such as manual grinding and polishing, the solder bumps are easily damaged during the removal of underfill, and the thin chip may even be crushed due to mechanical stress. An efficient and reliable decapsulation method consisting of thermal and chemical processes was developed in this study. The surface quality of chips after solder removal is satisfactory for the existing solder rework procedure as well as for die-level failure analysis. The innovative processes included heat-sink and ceramic substrate removal, solder bump separation, and solder residue cleaning from the chip surface. In the last stage, particular temperatures were selected for the removal of eutectic Pb-Sn, high-lead, and lead-free solders considering their respective melting points.

  13. Flip chip assembly of thinned chips for hybrid pixel detector applications

    International Nuclear Information System (INIS)

    Fritzsch, T; Zoschke, K; Rothermund, M; Oppermann, H; Woehrmann, M; Ehrmann, O; Lang, K D; Huegging, F

    2014-01-01

    There is a steady trend to ultra-thin microelectronic devices. Especially for future particle detector systems a reduced readout chip thickness is required to limit the loss of tracking precision due to scattering. The reduction of silicon thickness is performed at wafer level in a two-step thinning process. To minimize the risk of wafer breakage the thinned wafer needs to be handled by a carrier during the whole process chain of wafer bumping. Another key process is the flip chip assembly of thinned readout chips onto thin sensor tiles. Besides the prevention of silicon breakage the minimization of chip warpage is one additional task for a high yield and reliable flip chip process. A new technology using glass carrier wafer will be described in detail. The main advantage of this technology is the combination of a carrier support during wafer processing and the chip support during flip chip assembly. For that a glass wafer is glue-bonded onto the backside of the thinned readout chip wafer. After the bump deposition process the glass-readout chip stack is diced in one step. Finally the glass carrier chip is released by laser illumination after flip chip assembly of the readout chip onto sensor tile. The results of the flip chip assembly process development for the ATLAS IBL upgrade are described more in detail. The new ATLAS FEI4B chip with a size of 20 × 19 mm 2 is flip chip bonded with a thickness of only 150 μm, but the capability of this technology has been demonstrated on hybrid modules with a reduced readout chip thickness of down to 50 μm which is a major step for ultra-thin electronic systems

  14. Some Metabolites Act as Second Messengers in Yeast Chronological Aging

    Directory of Open Access Journals (Sweden)

    Karamat Mohammad

    2018-03-01

    Full Text Available The concentrations of some key metabolic intermediates play essential roles in regulating the longevity of the chronologically aging yeast Saccharomyces cerevisiae. These key metabolites are detected by certain ligand-specific protein sensors that respond to concentration changes of the key metabolites by altering the efficiencies of longevity-defining cellular processes. The concentrations of the key metabolites that affect yeast chronological aging are controlled spatially and temporally. Here, we analyze mechanisms through which the spatiotemporal dynamics of changes in the concentrations of the key metabolites influence yeast chronological lifespan. Our analysis indicates that a distinct set of metabolites can act as second messengers that define the pace of yeast chronological aging. Molecules that can operate both as intermediates of yeast metabolism and as second messengers of yeast chronological aging include reduced nicotinamide adenine dinucleotide phosphate (NADPH, glycerol, trehalose, hydrogen peroxide, amino acids, sphingolipids, spermidine, hydrogen sulfide, acetic acid, ethanol, free fatty acids, and diacylglycerol. We discuss several properties that these second messengers of yeast chronological aging have in common with second messengers of signal transduction. We outline how these second messengers of yeast chronological aging elicit changes in cell functionality and viability in response to changes in the nutrient, energy, stress, and proliferation status of the cell.

  15. SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

    Directory of Open Access Journals (Sweden)

    Patel Viren

    2010-09-01

    Full Text Available Abstract Background The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research. Results SeqAnt (Sequence Annotator is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds. Conclusion SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.

  16. Cell-surface display of enzymes by the yeast Saccharomyces cerevisiae for synthetic biology.

    Science.gov (United States)

    Tanaka, Tsutomu; Kondo, Akihiko

    2015-02-01

    In yeast cell-surface displays, functional proteins, such as cellulases, are genetically fused to an anchor protein and expressed on the cell surface. Saccharomyces cerevisiae, which is often utilized as a cell factory for the production of fuels, chemicals, and proteins, is the most commonly used yeast for cell-surface display. To construct yeast cells with a desired function, such as the ability to utilize cellulose as a substrate for bioethanol production, cell-surface display techniques for the efficient expression of enzymes on the cell membrane need to be combined with metabolic engineering approaches for manipulating target pathways within cells. In this Minireview, we summarize the recent progress of biorefinery fields in the development and application of yeast cell-surface displays from a synthetic biology perspective and discuss approaches for further enhancing cell-surface display efficiency. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  17. Optic nerve signals in a neuromorphic chip II: Testing and results.

    Science.gov (United States)

    Zaghloul, Kareem A; Boahen, Kwabena

    2004-04-01

    Seeking to match the brain's computational efficiency, we draw inspiration from its neural circuits. To model the four main output (ganglion) cell types found in the retina, we morphed outer and inner retina circuits into a 96 x 60-photoreceptor, 3.5 x 3.3 mm2, 0.35 microm-CMOS chip. Our retinomorphic chip produces spike trains for 3600 ganglion cells (GCs), and consumes 62.7 mW at 45 spikes/s/GC. This chip, which is the first silicon retina to successfully model inner retina circuitry, approaches the spatial density of the retina. We present experimental measurements showing that the chip's subthreshold current-mode circuits realize luminance adaptation, bandpass spatiotemporal filtering, temporal adaptation and contrast gain control. The four different GC outputs produced by our chip encode light onset or offset in a sustained or transient fashion, producing a quadrature-like representation. The retinomorphic chip's circuit design is described in a companion paper [Zaghloul and Boahen (2004)].

  18. Smart Chips for Smart Surroundings -- 4S

    NARCIS (Netherlands)

    Schuler, Eberhard; König, Ralf; Becker, Jürgen; Rauwerda, G.K.; van de Burgwal, M.D.; Smit, Gerardus Johannes Maria; Cardoso, João M.P.; Hübner, Michael

    2011-01-01

    The overall mission of the 4S project (Smart Chips for Smart Surroundings) was to define and develop efficient flexible, reconfigurable core building blocks, including the supporting tools, for future Ambient System Devices. Reconfigurability offers the needed flexibility and adaptability, it

  19. On-Chip Bondwire Magnetics with Ferrite-Epoxy Glob Coating for Power Systems on Chip

    Directory of Open Access Journals (Sweden)

    Jian Lu

    2008-01-01

    Full Text Available A novel concept of on-chip bondwire inductors and transformers with ferrite epoxy glob coating is proposed to offer a cost effective approach realizing power systems on chip (SOC. We have investigated the concept both experimentally and with finite element modeling. A Q factor of 30–40 is experimentally demonstrated for the bondwire inductors which represents an improvement by a factor of 3–30 over the state-of-the-art MEMS micromachined inductors. Transformer parameters including self- and mutual inductance and coupling factors are extracted from both modeled and measured S-parameters. More importantly, the bondwire magnetic components can be easily integrated into SOC manufacturing processes with minimal changes and open enormous possibilities for realizing cost-effective, high-current, high-efficiency power SOCs.

  20. Production of dry wood chips in connection with a district heating plant

    Directory of Open Access Journals (Sweden)

    Yrjölä Jukka

    2004-01-01

    Full Text Available Moisture and its variation in wood chips make the control of burning in small scale heating appliances difficult resulting in emissions and loss of efficiency. If the quality of wood chips would be better, i. e. dried and sieved fuel with more uniform size distribution would be avail able, the burning could be much cleaner and efficiency higher. In addition higher power out put could be obtained and the investment costs of the burning appliances would be lower. The production of sieved and dried wood chip with good quality could be accomplished in connection with a district heating plant. Then the plant would make profit, in addition to the district heat, from the dried wood chips sold to the neighboring buildings and enterprises sep a rated from the district heating net using wood chips in energy production. The peak power of a district heating plant is required only a short time during the coldest days of the winter. Then the excess capacity during the milder days can be used as heat source for drying of wood chips to be marketed. Then wood chips are sieved and the fuel with best quality is sold and the reject is used as fuel in the plant it self. In a larger district heating plant, quality of the fuel does not need to be so high In this paper the effect of moisture on the fuel chain and on the boiler is discussed. Energy and mass balance calculations as a tool of system design is described and the characteristics of proposed dry chips production method is discussed.

  1. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

    Science.gov (United States)

    Zhang, Wenqian; Yu, Ying; Hertwig, Falk; Thierry-Mieg, Jean; Zhang, Wenwei; Thierry-Mieg, Danielle; Wang, Jian; Furlanello, Cesare; Devanarayan, Viswanath; Cheng, Jie; Deng, Youping; Hero, Barbara; Hong, Huixiao; Jia, Meiwen; Li, Li; Lin, Simon M; Nikolsky, Yuri; Oberthuer, André; Qing, Tao; Su, Zhenqiang; Volland, Ruth; Wang, Charles; Wang, May D; Ai, Junmei; Albanese, Davide; Asgharzadeh, Shahab; Avigad, Smadar; Bao, Wenjun; Bessarabova, Marina; Brilliant, Murray H; Brors, Benedikt; Chierici, Marco; Chu, Tzu-Ming; Zhang, Jibin; Grundy, Richard G; He, Min Max; Hebbring, Scott; Kaufman, Howard L; Lababidi, Samir; Lancashire, Lee J; Li, Yan; Lu, Xin X; Luo, Heng; Ma, Xiwen; Ning, Baitang; Noguera, Rosa; Peifer, Martin; Phan, John H; Roels, Frederik; Rosswog, Carolina; Shao, Susan; Shen, Jie; Theissen, Jessica; Tonini, Gian Paolo; Vandesompele, Jo; Wu, Po-Yen; Xiao, Wenzhong; Xu, Joshua; Xu, Weihong; Xuan, Jiekun; Yang, Yong; Ye, Zhan; Dong, Zirui; Zhang, Ke K; Yin, Ye; Zhao, Chen; Zheng, Yuanting; Wolfinger, Russell D; Shi, Tieliu; Malkas, Linda H; Berthold, Frank; Wang, Jun; Tong, Weida; Shi, Leming; Peng, Zhiyu; Fischer, Matthias

    2015-06-25

    Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.

  2. Gene expression profiling of human breast tissue samples using SAGE-Seq.

    Science.gov (United States)

    Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

    2010-12-01

    We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

  3. ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.

    Directory of Open Access Journals (Sweden)

    Brett A McKinney

    Full Text Available Relief-F is a nonparametric, nearest-neighbor machine learning method that has been successfully used to identify relevant variables that may interact in complex multivariate models to explain phenotypic variation. While several tools have been developed for assessing differential expression in sequence-based transcriptomics, the detection of statistical interactions between transcripts has received less attention in the area of RNA-seq analysis. We describe a new extension and assessment of Relief-F for feature selection in RNA-seq data. The ReliefSeq implementation adapts the number of nearest neighbors (k for each gene to optimize the Relief-F test statistics (importance scores for finding both main effects and interactions. We compare this gene-wise adaptive-k (gwak Relief-F method with standard RNA-seq feature selection tools, such as DESeq and edgeR, and with the popular machine learning method Random Forests. We demonstrate performance on a panel of simulated data that have a range of distributional properties reflected in real mRNA-seq data including multiple transcripts with varying sizes of main effects and interaction effects. For simulated main effects, gwak-Relief-F feature selection performs comparably to standard tools DESeq and edgeR for ranking relevant transcripts. For gene-gene interactions, gwak-Relief-F outperforms all comparison methods at ranking relevant genes in all but the highest fold change/highest signal situations where it performs similarly. The gwak-Relief-F algorithm outperforms Random Forests for detecting relevant genes in all simulation experiments. In addition, Relief-F is comparable to the other methods based on computational time. We also apply ReliefSeq to an RNA-Seq study of smallpox vaccine to identify gene expression changes between vaccinia virus-stimulated and unstimulated samples. ReliefSeq is an attractive tool for inclusion in the suite of tools used for analysis of mRNA-Seq data; it has power to

  4. Dietary glucose regulates yeast consumption in adult Drosophila males.

    Science.gov (United States)

    Lebreton, Sébastien; Witzgall, Peter; Olsson, Marie; Becher, Paul G

    2014-01-01

    The adjustment of feeding behavior in response to hunger and satiety contributes to homeostatic regulation in animals. The fruit fly Drosophila melanogaster feeds on yeasts growing on overripe fruit, providing nutrients required for adult survival, reproduction and larval growth. Here, we present data on how the nutritional value of food affects subsequent yeast consumption in Drosophila adult males. After a period of starvation, flies showed intensive yeast consumption. In comparison, flies stopped feeding after having access to a nutritive cornmeal diet. Interestingly, dietary glucose was equally efficient as the complex cornmeal diet. In contrast, flies fed with sucralose, a non-metabolizable sweetener, behaved as if they were starved. The adipokinetic hormone and insulin-like peptides regulate metabolic processes in insects. We did not find any effect of the adipokinetic hormone pathway on this modulation. Instead, the insulin pathway was involved in these changes. Flies lacking the insulin receptor (InR) did not respond to nutrient deprivation by increasing yeast consumption. Together these results show the importance of insulin in the regulation of yeast consumption in response to starvation in adult D. melanogaster males.

  5. GC-Content Normalization for RNA-Seq Data

    Science.gov (United States)

    2011-01-01

    Background Transcriptome sequencing (RNA-Seq) has become the assay of choice for high-throughput studies of gene expression. However, as is the case with microarrays, major technology-related artifacts and biases affect the resulting expression measures. Normalization is therefore essential to ensure accurate inference of expression levels and subsequent analyses thereof. Results We focus on biases related to GC-content and demonstrate the existence of strong sample-specific GC-content effects on RNA-Seq read counts, which can substantially bias differential expression analysis. We propose three simple within-lane gene-level GC-content normalization approaches and assess their performance on two different RNA-Seq datasets, involving different species and experimental designs. Our methods are compared to state-of-the-art normalization procedures in terms of bias and mean squared error for expression fold-change estimation and in terms of Type I error and p-value distributions for tests of differential expression. The exploratory data analysis and normalization methods proposed in this article are implemented in the open-source Bioconductor R package EDASeq. Conclusions Our within-lane normalization procedures, followed by between-lane normalization, reduce GC-content bias and lead to more accurate estimates of expression fold-changes and tests of differential expression. Such results are crucial for the biological interpretation of RNA-Seq experiments, where downstream analyses can be sensitive to the supplied lists of genes. PMID:22177264

  6. A hidden Ising model for ChIP-chip data analysis

    KAUST Repository

    Mo, Q.

    2010-01-28

    Motivation: Chromatin immunoprecipitation (ChIP) coupled with tiling microarray (chip) experiments have been used in a wide range of biological studies such as identification of transcription factor binding sites and investigation of DNA methylation and histone modification. Hidden Markov models are widely used to model the spatial dependency of ChIP-chip data. However, parameter estimation for these models is typically either heuristic or suboptimal, leading to inconsistencies in their applications. To overcome this limitation and to develop an efficient software, we propose a hidden ferromagnetic Ising model for ChIP-chip data analysis. Results: We have developed a simple, but powerful Bayesian hierarchical model for ChIP-chip data via a hidden Ising model. Metropolis within Gibbs sampling algorithm is used to simulate from the posterior distribution of the model parameters. The proposed model naturally incorporates the spatial dependency of the data, and can be used to analyze data with various genomic resolutions and sample sizes. We illustrate the method using three publicly available datasets and various simulated datasets, and compare it with three closely related methods, namely TileMap HMM, tileHMM and BAC. We find that our method performs as well as TileMap HMM and BAC for the high-resolution data from Affymetrix platform, but significantly outperforms the other three methods for the low-resolution data from Agilent platform. Compared with the BAC method which also involves MCMC simulations, our method is computationally much more efficient. Availability: A software called iChip is freely available at http://www.bioconductor.org/. Contact: moq@mskcc.org. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org.

  7. TRANSIT--A Software Tool for Himar1 TnSeq Analysis.

    Directory of Open Access Journals (Sweden)

    Michael A DeJesus

    2015-10-01

    Full Text Available TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. We demonstrate the utility of this software by analyzing TnSeq datasets of M. tuberculosis grown on glycerol and cholesterol. We show that TRANSIT can be used to discover genes which have been previously implicated for growth on these carbon sources. TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux platforms. The source code is distributed under the GNU GPL v3 license and can be obtained from the following GitHub repository: https://github.com/mad-lab/transit.

  8. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

    Science.gov (United States)

    Ou, Jianhong; Liu, Haibo; Yu, Jun; Kelliher, Michelle A; Castilla, Lucio H; Lawson, Nathan D; Zhu, Lihua Julie

    2018-03-01

    ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset. This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html .

  9. An Integrated Approach for RNA-seq Data Normalization.

    Science.gov (United States)

    Yang, Shengping; Mercante, Donald E; Zhang, Kun; Fang, Zhide

    2016-01-01

    DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization. In this article, we propose an integrated approach for RNA-seq data normalization. Comparisons show that the proposed normalization can improve power for downstream differentially expressed gene detection and generate more biologically meaningful results in gene profiling. In addition, our findings show that due to the effects of copy number changes, some housekeeping genes are not always suitable internal controls for studying gene expression. Using information from DNA copy number, integrated approach is successful in reducing noises due to both biological and nonbiological causes in RNA-seq data, thus increasing the accuracy of gene profiling.

  10. Mammalian amyloidogenic proteins promote prion nucleation in yeast.

    Science.gov (United States)

    Chandramowlishwaran, Pavithra; Sun, Meng; Casey, Kristin L; Romanyuk, Andrey V; Grizel, Anastasiya V; Sopova, Julia V; Rubel, Aleksandr A; Nussbaum-Krammer, Carmen; Vorberg, Ina M; Chernoff, Yury O

    2018-03-02

    Fibrous cross-β aggregates (amyloids) and their transmissible forms (prions) cause diseases in mammals (including humans) and control heritable traits in yeast. Initial nucleation of a yeast prion by transiently overproduced prion-forming protein or its (typically, QN-rich) prion domain is efficient only in the presence of another aggregated (in most cases, QN-rich) protein. Here, we demonstrate that a fusion of the prion domain of yeast protein Sup35 to some non-QN-rich mammalian proteins, associated with amyloid diseases, promotes nucleation of Sup35 prions in the absence of pre-existing aggregates. In contrast, both a fusion of the Sup35 prion domain to a multimeric non-amyloidogenic protein and the expression of a mammalian amyloidogenic protein that is not fused to the Sup35 prion domain failed to promote prion nucleation, further indicating that physical linkage of a mammalian amyloidogenic protein to the prion domain of a yeast protein is required for the nucleation of a yeast prion. Biochemical and cytological approaches confirmed the nucleation of protein aggregates in the yeast cell. Sequence alterations antagonizing or enhancing amyloidogenicity of human amyloid-β (associated with Alzheimer's disease) and mouse prion protein (associated with prion diseases), respectively, antagonized or enhanced nucleation of a yeast prion by these proteins. The yeast-based prion nucleation assay, developed in our work, can be employed for mutational dissection of amyloidogenic proteins. We anticipate that it will aid in the identification of chemicals that influence initial amyloid nucleation and in searching for new amyloidogenic proteins in a variety of proteomes. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Mastering multi-depth bio-chip patterns with DVD LBRs

    Science.gov (United States)

    Carson, Doug

    2017-08-01

    Bio chip and bio disc are rapidly growing technologies used in medical, health and other industries. While there are numerous unique designs and features, these products all rely on precise three-dimensional micro-fluidic channels or arrays to move, separate and combine samples under test. These bio chip and bio disc consumables are typically manufactured by molding these parts to a precise three-dimensional pattern on a negative metal stamper, or they can be made in smaller quantities using an appropriate curable resin and a negative mold/stamper. Stampers required for bio chips have been traditionally made using either micro machining or XY stepping lithography. Both of these technologies have their advantages as well as limitations when it comes to creating micro-fluidic patterns. Significant breakthroughs in continuous maskless lithography have enabled accurate and efficient manufacturing of micro-fluidic masters using LBRs (Laser Beam Recorders) and DRIE (Deep Reactive Ion Etching). The important advantages of LBR continuous lithography vs. XY stepping lithography and micro machining are speed and cost. LBR based continuous lithography is >100x faster than XY stepping lithography and more accurate than micro machining. Several innovations were required in order to create multi-depth patterns with sub micron accuracy. By combining proven industrial LBRs with DCA's G3-VIA pattern generator and DRIE, three-dimensional bio chip masters and stampers are being manufactured efficiently and accurately.

  12. Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

    LENUS (Irish Health Repository)

    Guida, Alessandro

    2011-12-22

    Abstract Background Candida parapsilosis is one of the most common causes of Candida infection worldwide. However, the genome sequence annotation was made without experimental validation and little is known about the transcriptional landscape. The transcriptional response of C. parapsilosis to hypoxic (low oxygen) conditions, such as those encountered in the host, is also relatively unexplored. Results We used next generation sequencing (RNA-seq) to determine the transcriptional profile of C. parapsilosis growing in several conditions including different media, temperatures and oxygen concentrations. We identified 395 novel protein-coding sequences that had not previously been annotated. We removed > 300 unsupported gene models, and corrected approximately 900. We mapped the 5\\' and 3\\' UTR for thousands of genes. We also identified 422 introns, including two introns in the 3\\' UTR of one gene. This is the first report of 3\\' UTR introns in the Saccharomycotina. Comparing the introns in coding sequences with other species shows that small numbers have been gained and lost throughout evolution. Our analysis also identified a number of novel transcriptional active regions (nTARs). We used both RNA-seq and microarray analysis to determine the transcriptional profile of cells grown in normoxic and hypoxic conditions in rich media, and we showed that there was a high correlation between the approaches. We also generated a knockout of the UPC2 transcriptional regulator, and we found that similar to C. albicans, Upc2 is required for conferring resistance to azole drugs, and for regulation of expression of the ergosterol pathway in hypoxia. Conclusion We provide the first detailed annotation of the C. parapsilosis genome, based on gene predictions and transcriptional analysis. We identified a number of novel ORFs and other transcribed regions, and detected transcripts from approximately 90% of the annotated protein coding genes. We found that the transcription factor

  13. Site-specific genomic (SSG and random domain-localized (RDL mutagenesis in yeast

    Directory of Open Access Journals (Sweden)

    Honigberg Saul M

    2004-04-01

    Full Text Available Abstract Background A valuable weapon in the arsenal available to yeast geneticists is the ability to introduce specific mutations into yeast genome. In particular, methods have been developed to introduce deletions into the yeast genome using PCR fragments. These methods are highly efficient because they do not require cloning in plasmids. Results We have modified the existing method for introducing deletions in the yeast (S. cerevisiae genome using PCR fragments in order to target point mutations to this genome. We describe two PCR-based methods for directing point mutations into the yeast genome such that the final product contains no other disruptions. In the first method, site-specific genomic (SSG mutagenesis, a specific point mutation is targeted into the genome. In the second method, random domain-localized (RDL mutagenesis, a mutation is introduced at random within a specific domain of a gene. Both methods require two sequential transformations, the first transformation integrates the URA3 marker into the targeted locus, and the second transformation replaces URA3 with a PCR fragment containing one or a few mutations. This PCR fragment is synthesized using a primer containing a mutation (SSG mutagenesis or is synthesized by error-prone PCR (RDL mutagenesis. In SSG mutagenesis, mutations that are proximal to the URA3 site are incorporated at higher frequencies than distal mutations, however mutations can be introduced efficiently at distances of at least 500 bp from the URA3 insertion. In RDL mutagenesis, to ensure that incorporation of mutations occurs at approximately equal frequencies throughout the targeted region, this region is deleted at the same time URA3 is integrated. Conclusion SSG and RDL mutagenesis allow point mutations to be easily and efficiently incorporated into the yeast genome without disrupting the native locus.

  14. Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts.

    Science.gov (United States)

    Gonçalves, Margarida; Pontes, Ana; Almeida, Pedro; Barbosa, Raquel; Serra, Marta; Libkind, Diego; Hutzler, Mathias; Gonçalves, Paula; Sampaio, José Paulo

    2016-10-24

    Beer is one of the oldest alcoholic beverages and is produced by the fermentation of sugars derived from starches present in cereal grains. Contrary to lager beers, made by bottom-fermenting strains of Saccharomyces pastorianus, a hybrid yeast, ale beers are closer to the ancient beer type and are fermented by S. cerevisiae, a top-fermenting yeast. Here, we use population genomics to investigate (1) the closest relatives of top-fermenting beer yeasts; (2) whether top-fermenting yeasts represent an independent domestication event separate from those already described; (3) whether single or multiple beer yeast domestication events can be inferred; and (4) whether top-fermenting yeasts represent non-recombinant or recombinant lineages. Our results revealed that top-fermenting beer yeasts are polyphyletic, with a main clade composed of at least three subgroups, dominantly represented by the German, British, and wheat beer strains. Other beer strains were phylogenetically close to sake, wine, or bread yeasts. We detected genetic signatures of beer yeast domestication by investigating genes previously linked to brewing and using genome-wide scans. We propose that the emergence of the main clade of beer yeasts is related with a domestication event distinct from the previously known cases of wine and sake yeast domestication. The nucleotide diversity of the main beer clade more than doubled that of wine yeasts, which might be a consequence of fundamental differences in the modes of beer and wine yeast domestication. The higher diversity of beer strains could be due to the more intense and different selection regimes associated to brewing. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. A high-throughput method for quantifying metabolically active yeast cells

    DEFF Research Database (Denmark)

    Nandy, Subir Kumar; Knudsen, Peter Boldsen; Rosenkjær, Alexander

    2015-01-01

    By redesigning the established methylene blue reduction test for bacteria and yeast, we present a cheap and efficient methodology for quantitative physiology of eukaryotic cells applicable for high-throughput systems. Validation of themethod in fermenters and highthroughput systems proved....... The drop in metabolic activity associated with the diauxic shift in yeast proved more pronounced for the MBRT-derived curve compared with OD curves, consistent with a dramatic shift in the ratio between live and dead cells at this metabolic event. This method provides a tool with numerous applications, e.......g. characterizing the death phase of stationary phase cultures, or in drug screens with pathogenic yeasts....

  16. Prions in yeast

    OpenAIRE

    Bezdíčka, Martin

    2013-01-01

    The thesis describes yeast prions and their biological effects on yeast in general. It defines the basic characteristics of yeast prions, that distinguish prions from other proteins. The thesis introduces various possibilities of prion formation, and propagation as well as specific types of yeast prions, including various functions of most studied types of prions. The thesis also focuses on chaperones that affect the state of yeast prions in cells. Lastly, the thesis indicates similarities be...

  17. Drying characteristics of willow chips and stems

    NARCIS (Netherlands)

    Gigler, J.K.; Loon, van W.K.P.; Seres, I.; Meerdink, G.; Coumans, W.J.

    2000-01-01

    In supply chains of willow (Salix viminalis) biomass to energy plants, drying is advisable in order to enable safe long-term storage, increase boiler efficiency and reduce gaseous emissions. To gain insight into the drying process, drying characteristics of willow chips and stems were investigated

  18. Non-Conventional Yeast Strains Increase the Aroma Complexity of Bread

    Science.gov (United States)

    Rezaei, Mohammad Naser; Steensels, Jan; Courtin, Christophe M.; Verstrepen, Kevin J.

    2016-01-01

    Saccharomyces cerevisiae is routinely used yeast in food fermentations because it combines several key traits, including fermentation efficiency and production of desirable flavors. However, the dominance of S. cerevisiae in industrial fermentations limits the diversity in the aroma profiles of the end products. Hence, there is a growing interest in non-conventional yeast strains that can help generate the diversity and complexity desired in today’s diversified and consumer-driven markets. Here, we selected a set of non-conventional yeast strains to examine their potential for bread fermentation. Here, we tested ten non-conventional yeasts for bread fermentation, including two Saccharomyces species that are not currently used in bread making and 8 non-Saccharomyces strains. The results show that Torulaspora delbrueckii and Saccharomyces bayanus combine satisfactory dough fermentation with an interesting flavor profile. Sensory analysis and HS-SPME-GC-MS analysis confirmed that these strains produce aroma profiles that are very different from that produced by a commercial bakery strain. Moreover, bread produced with these yeasts was preferred by a majority of a trained sensory panel. These results demonstrate the potential of T. delbrueckii and S. bayanus as alternative yeasts for bread dough leavening, and provide a general experimental framework for the evaluation of more yeasts and bacteria. PMID:27776154

  19. Non-Conventional Yeast Strains Increase the Aroma Complexity of Bread.

    Science.gov (United States)

    Aslankoohi, Elham; Herrera-Malaver, Beatriz; Rezaei, Mohammad Naser; Steensels, Jan; Courtin, Christophe M; Verstrepen, Kevin J

    2016-01-01

    Saccharomyces cerevisiae is routinely used yeast in food fermentations because it combines several key traits, including fermentation efficiency and production of desirable flavors. However, the dominance of S. cerevisiae in industrial fermentations limits the diversity in the aroma profiles of the end products. Hence, there is a growing interest in non-conventional yeast strains that can help generate the diversity and complexity desired in today's diversified and consumer-driven markets. Here, we selected a set of non-conventional yeast strains to examine their potential for bread fermentation. Here, we tested ten non-conventional yeasts for bread fermentation, including two Saccharomyces species that are not currently used in bread making and 8 non-Saccharomyces strains. The results show that Torulaspora delbrueckii and Saccharomyces bayanus combine satisfactory dough fermentation with an interesting flavor profile. Sensory analysis and HS-SPME-GC-MS analysis confirmed that these strains produce aroma profiles that are very different from that produced by a commercial bakery strain. Moreover, bread produced with these yeasts was preferred by a majority of a trained sensory panel. These results demonstrate the potential of T. delbrueckii and S. bayanus as alternative yeasts for bread dough leavening, and provide a general experimental framework for the evaluation of more yeasts and bacteria.

  20. Non-Conventional Yeast Strains Increase the Aroma Complexity of Bread.

    Directory of Open Access Journals (Sweden)

    Elham Aslankoohi

    Full Text Available Saccharomyces cerevisiae is routinely used yeast in food fermentations because it combines several key traits, including fermentation efficiency and production of desirable flavors. However, the dominance of S. cerevisiae in industrial fermentations limits the diversity in the aroma profiles of the end products. Hence, there is a growing interest in non-conventional yeast strains that can help generate the diversity and complexity desired in today's diversified and consumer-driven markets. Here, we selected a set of non-conventional yeast strains to examine their potential for bread fermentation. Here, we tested ten non-conventional yeasts for bread fermentation, including two Saccharomyces species that are not currently used in bread making and 8 non-Saccharomyces strains. The results show that Torulaspora delbrueckii and Saccharomyces bayanus combine satisfactory dough fermentation with an interesting flavor profile. Sensory analysis and HS-SPME-GC-MS analysis confirmed that these strains produce aroma profiles that are very different from that produced by a commercial bakery strain. Moreover, bread produced with these yeasts was preferred by a majority of a trained sensory panel. These results demonstrate the potential of T. delbrueckii and S. bayanus as alternative yeasts for bread dough leavening, and provide a general experimental framework for the evaluation of more yeasts and bacteria.

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