Science.gov

Sample records for based enrichment method

  1. Partition enrichment of nucleotide sequences (PINS)--a generally applicable, sequence based method for enrichment of complex DNA samples.

    PubMed

    Kvist, Thomas; Sondt-Marcussen, Line; Mikkelsen, Marie Just

    2014-01-01

    The dwindling cost of DNA sequencing is driving transformative changes in various biological disciplines including medicine, thus resulting in an increased need for routine sequencing. Preparation of samples suitable for sequencing is the starting point of any practical application, but enrichment of the target sequence over background DNA is often laborious and of limited sensitivity thereby limiting the usefulness of sequencing. The present paper describes a new method, Probability directed Isolation of Nucleic acid Sequences (PINS), for enrichment of DNA, enabling the sequencing of a large DNA region surrounding a small known sequence. A 275,000 fold enrichment of a target DNA sample containing integrated human papilloma virus is demonstrated. Specifically, a sample containing 0.0028 copies of target sequence per ng of total DNA was enriched to 786 copies per ng. The starting concentration of 0.0028 target copies per ng corresponds to one copy of target in a background of 100,000 complete human genomes. The enriched sample was subsequently amplified using rapid genome walking and the resulting DNA sequence revealed not only the sequence of a the truncated virus, but also 1026 base pairs 5' and 50 base pairs 3' to the integration site in chromosome 8. The demonstrated enrichment method is extremely sensitive and selective and requires only minimal knowledge of the sequence to be enriched and will therefore enable sequencing where the target concentration relative to background is too low to allow the use of other sample preparation methods or where significant parts of the target sequence is unknown.

  2. Comparative study on gene set and pathway topology-based enrichment methods.

    PubMed

    Bayerlová, Michaela; Jung, Klaus; Kramer, Frank; Klemm, Florian; Bleckmann, Annalen; Beißbarth, Tim

    2015-10-22

    Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions. In contrast, the new group of so called pathway topology-based methods integrates the topological structure of a pathway into the analysis. We comparatively investigated gene set and pathway topology-based enrichment approaches, considering three gene set and four topological methods. These methods were compared in two extensive simulation studies and on a benchmark of 36 real datasets, providing the same pathway input data for all methods. In the benchmark data analysis both types of methods showed a comparable ability to detect enriched pathways. The first simulation study was conducted with KEGG pathways, which showed considerable gene overlaps between each other. In this study with original KEGG pathways, none of the topology-based methods outperformed the gene set approach. Therefore, a second simulation study was performed on non-overlapping pathways created by unique gene IDs. Here, methods accounting for pathway topology reached higher accuracy than the gene set methods, however their sensitivity was lower. We conducted one of the first comprehensive comparative works on evaluating gene set against pathway topology-based enrichment methods. The topological methods showed better performance in the simulation scenarios with non-overlapping pathways, however, they were not conclusively better in the other scenarios. This suggests that simple gene set approach might be sufficient to detect an enriched pathway under realistic circumstances. Nevertheless, more extensive studies and further benchmark data are needed to systematically evaluate these methods and to assess what gain and cost pathway topology information introduces into enrichment analysis. Both

  3. Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere

    PubMed Central

    Ottesen, Andrea R.; Gonzalez, Antonio; Bell, Rebecca; Arce, Caroline; Rideout, Steven; Allard, Marc; Evans, Peter; Strain, Errol; Musser, Steven; Knight, Rob; Brown, Eric; Pettengill, James B.

    2013-01-01

    The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite

  4. A regulating method for reducing nitrogen loss based on enriched ammonia-oxidizing bacteria during composting.

    PubMed

    Zhang, Yun; Zhao, Yue; Chen, Yanni; Lu, Qian; Li, Mingxiao; Wang, Xueqin; Wei, Yuquan; Xie, Xinyu; Wei, Zimin

    2016-12-01

    In this study, enriched ammonia-oxidizing bacteria (AOB) were acquired by domesticated cultivation, followed by inoculation into the co-composting of rice straw and chicken manure. The effect of inoculation on nitrogen loss, the succession of bacterial community and the correlation between the key bacteria and environmental factors were investigated. The results showed that inoculation could reduce ammonia emission and nitrogen loss by transforming ammonium into nitrite. Inoculation also increased the amount and abundance of bacterial community. Redundancy analysis showed that indigenous and exogenous bacteria in inoculation group, compared with those in control group, were positively correlated with nitrite but negatively correlated with ammonium, demonstrating that the former contributed to the lower ammonia emission and nitrogen loss. Based on these results, the application of enriched AOB was proposed as a new method of resource recycle and improvement of composting technology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. StageTip-based HAMMOC, an efficient and inexpensive phosphopeptide enrichment method for plant shotgun phosphoproteomics.

    PubMed

    Nakagami, Hirofumi

    2014-01-01

    Phosphopeptide enrichment is the most critical step for successful LC-MS/MS-based shotgun phosphoproteomics. Recent technological improvements have made selective phosphopeptide enrichment from non-fractionated whole cell lysate digests with a single-step procedure possible. Here, a handy protocol is described for phosphopeptide enrichment from plant materials using hydroxy acid-modified metal oxide chromatography (HAMMMOC) with a stop-and-go-extraction tip (StageTip).

  6. Pros and cons of methylation-based enrichment methods for ancient DNA

    PubMed Central

    Seguin-Orlando, Andaine; Gamba, Cristina; Sarkissian, Clio Der; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D.; Lopez, Patricio; McDonald, H. Gregory; Scott, Eric; Tikhonov, Alexei; Stafford,, Thomas W.; Alfarhan, Ahmed H.; Alquraishi, Saleh A.; Al-Rasheid, Khaled A. S.; Shapiro, Beth; Willerslev, Eske; Prokhortchouk, Egor; Orlando, Ludovic

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions. PMID:26134828

  7. Pros and cons of methylation-based enrichment methods for ancient DNA.

    PubMed

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D; Lopez, Patricio; McDonald, H Gregory; Scott, Eric; Tikhonov, Alexei; Stafford, Thomas W; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Shapiro, Beth; Willerslev, Eske; Prokhortchouk, Egor; Orlando, Ludovic

    2015-07-02

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

  8. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods.

    PubMed

    Bernacki, Katarzyna; Kalyanaraman, Chakrapani; Jacobson, Matthew P

    2005-10-01

    Motivated by their participation in the McMaster Data-Mining and Docking Competition, the authors developed 2 new computational technologies and applied them to docking against Escherichia coli dihydrofolate reductase: a receptor preparation procedure that incorporates rotamer optimization of side chains and a physics-based rescoring procedure for estimating relative binding affinities of the protein-ligand complexes. Both methods use the same energy function, consisting of the all-atom OPLS-AA force field and a generalized Born solvent model, which treats the protein receptor and small-molecule ligands in a consistent manner. Thus, the energy function is similar to that used in more sophisticated approaches, such as free-energy perturbation and the molecular mechanics Poisson-Boltzmann/surface area, but sampling during the rescoring procedure is limited to simple energy minimization of the ligand. The use of a highly efficient minimization algorithm permitted the authors to apply this rescoring procedure to hundreds of thousands of protein-ligand complexes during the competition, using a modest Linux cluster. To test these methods, they used the 12 competitive inhibitors identified in the training set, plus methotrexate, as positive controls in enrichment studies with both the training and test sets, each containing 50,000 compounds. The key conclusion is that combining the receptor preparation and rescoring methods makes it possible to identify most of the positive controls within the top few tenths of a percent of the rank-ordered training and test set libraries.

  9. Nonprotein Based Enrichment Method to Analyze Peptide Cross-Linking in Protein Complexes

    PubMed Central

    Yan, Funing; Che, Fa-Yun; Rykunov, Dmitry; Nieves, Edward; Fiser, Andras; Weiss, Louis M.; Angeletti, Ruth Hogue

    2009-01-01

    Cross-linking analysis of protein complexes and structures by tandem mass spectrometry (MS/MS) has advantages in speed, sensitivity, specificity, and the capability of handling complicated protein assemblies. However, detection and accurate assignment of the cross-linked peptides are often challenging due to their low abundance and complicated fragmentation behavior in collision-induced dissociation (CID). To simplify the MS analysis and improve the signal-to-noise ratio of the cross-linked peptides, we developed a novel peptide enrichment strategy that utilizes a cross-linker with a cryptic thiol group and using beads modified with a photocleavable cross-linker. The functional cross-linkers were designed to react with the primary amino groups in proteins. Human serum albumin was used as a model protein to detect intra- and intermolecular cross-linkages. Use of this protein-free selective retrieval method eliminates the contamination that can result from avidin–biotin based retrieval systems and simplifies data analysis. These features may make the method suitable to investigate protein–protein interactions in biological samples. PMID:19642656

  10. Validation of Flow Cytometry and Magnetic Bead-Based Methods to Enrich CNS Single Cell Suspensions for Quiescent Microglia.

    PubMed

    Volden, T A; Reyelts, C D; Hoke, T A; Arikkath, J; Bonasera, S J

    2015-12-01

    Microglia are resident mononuclear phagocytes within the CNS parenchyma that intimately interact with neurons and astrocytes to remodel synapses and extracellular matrix. We briefly review studies elucidating the molecular pathways that underlie microglial surveillance, activation, chemotaxis, and phagocytosis; we additionally place these studies in a clinical context. We describe and validate an inexpensive and simple approach to obtain enriched single cell suspensions of quiescent parenchymal and perivascular microglia from the mouse cerebellum and hypothalamus. Following preparation of regional CNS single cell suspensions, we remove myelin debris, and then perform two serial enrichment steps for cells expressing surface CD11b. Myelin depletion and CD11b enrichment are both accomplished using antigen-specific magnetic beads in an automated cell separation system. Flow cytometry of the resultant suspensions shows a significant enrichment for CD11b(+)/CD45(+) cells (perivascular microglia) and CD11b(+)/CD45(-) cells (parenchymal microglia) compared to starting suspensions. Of note, cells from these enriched suspensions minimally express Aif1 (aka Iba1), suggesting that the enrichment process does not evoke significant microglial activation. However, these cells readily respond to a functional challenge (LPS) with significant changes in the expression of molecules specifically associated with microglia. We conclude that methods employing a combination of magnetic-bead based sorting and flow cytometry produce suspensions highly enriched for microglia that are appropriate for a variety of molecular and cellular assays.

  11. A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data

    PubMed Central

    Fruzangohar, Mario; Ebrahimie, Esmaeil; Adelson, David L.

    2017-01-01

    Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer’s disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology. PMID:28199395

  12. A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data.

    PubMed

    Fruzangohar, Mario; Ebrahimie, Esmaeil; Adelson, David L

    2017-01-01

    Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer's disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology.

  13. A Laser-Based Method for On-Site Analysis of UF6 at Enrichment Plants

    SciTech Connect

    Anheier, Norman C.; Cannon, Bret D.; Martinez, Alonzo; Barrett, Christopher A.; Taubman, Matthew S.; Anderson, Kevin K.; Smith, Leon E.

    2014-11-23

    The International Atomic Energy Agency’s (IAEA’s) long-term research and development plan calls for more cost-effective and efficient safeguard methods to detect and deter misuse of gaseous centrifuge enrichment plants (GCEPs). The IAEA’s current safeguards approaches at GCEPs are based on a combination of routine and random inspections that include environmental sampling and destructive assay (DA) sample collection from UF6 in-process material and selected cylinders. Samples are then shipped offsite for subsequent laboratory analysis. In this paper, a new DA sample collection and onsite analysis approach that could help to meet challenges in transportation and chain of custody for UF6 DA samples is introduced. This approach uses a handheld sampler concept and a Laser Ablation, Laser Absorbance Spectrometry (LAARS) analysis instrument, both currently under development at the Pacific Northwest National Laboratory. A LAARS analysis instrument could be temporarily or permanently deployed in the IAEA control room of the facility, in the IAEA data acquisition cabinet, for example. The handheld PNNL DA sampler design collects and stabilizes a much smaller DA sample mass compared to current sampling methods. The significantly lower uranium mass reduces the sample radioactivity and the stabilization approach diminishes the risk of uranium and hydrogen fluoride release. These attributes enable safe sample handling needed during onsite LAARS assay and may help ease shipping challenges for samples to be processed at the IAEA’s offsite laboratory. The LAARS and DA sampler implementation concepts will be described and preliminary technical viability results presented.

  14. Phosphopeptide enrichment: Development of magnetic solid phase extraction method based on polydopamine coating and Ti(4+)-IMAC.

    PubMed

    Piovesana, Susy; Capriotti, Anna Laura; Cavaliere, Chiara; Ferraris, Francesca; Samperi, Roberto; Ventura, Salvatore; Laganà, Aldo

    2016-02-25

    Protein post translational modifications currently represent one of the main challenges with proteomic analysis, due to the important biological role they play within cells. Protein phosphorylation is one of the most important, with several approaches developed for phosphopeptides enrichment and analysis, essential for comprehensive phosphoproteomic analysis. However, the development of new materials for phosphopeptides enrichment may overcome previous drawbacks and improve enrichment of such peptides. In this regard, new magnetic stationary phases based on polydopamine coating and Ti(4+) immobilization exploit the potential of IMAC enrichment and couple it with the versatility of magnetic solid phase extraction. In this work the use of such stationary phase was extended from the MALDI proof of concept stage with the development of an optimized method for phosphopeptides enrichment compatible with typical shotgun proteomics experimental workflows. Different loading and elution buffers were tested to improve phosphopeptides recovery and enrichment selectivity. Finally, the analysis of isolated peptides pointed out that polydopamine alone is an ideal support matrix for polar post translational modifications because it enables to reduce unspecific binding and preferentially binds hydrophilic peptides. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles

    PubMed Central

    Rider, Mark A.; Hurwitz, Stephanie N.; Meckes, David G.

    2016-01-01

    Initially thought to be a means for cells to eliminate waste, secreted extracellular vesicles, known as exosomes, are now understood to mediate numerous healthy and pathological processes. Though abundant in biological fluids, purifying exosomes has been challenging because their biophysical properties overlap with other secreted cell products. Easy-to-use commercial kits for harvesting exosomes are now widely used, but the relative low-purity and high-cost of the preparations restricts their utility. Here we describe a method for purifying exosomes and other extracellular vesicles by adapting methods for isolating viruses using polyethylene glycol. This technique, called ExtraPEG, enriches exosomes from large volumes of media rapidly and inexpensively using low-speed centrifugation, followed by a single small-volume ultracentrifugation purification step. Total protein and RNA harvested from vesicles is sufficient in quantity and quality for proteomics and sequencing analyses, demonstrating the utility of this method for biomarker discovery and diagnostics. Additionally, confocal microscopy studies suggest that the biological activity of vesicles is not impaired. The ExtraPEG method can be easily adapted to enrich for different vesicle populations, or as an efficient precursor to subsequent purification techniques, providing a means to harvest exosomes from many different biological fluids and for a wide variety of purposes. PMID:27068479

  16. A combined enrichment/polymerase chain reaction based method for the routine screening of Streptococcus agalactiae in pregnant women

    PubMed Central

    Munari, F.M.; De-Paris, F.; Salton, G.D.; Lora, P.S.; Giovanella, P.; Machado, A.B.M.P.; Laybauer, L.S.; Oliveira, K.R.P.; Ferri, C.; Silveira, J.L.S.; Laurino, C.C.F.C.; Xavier, R.M.; Barth, A.L.; Echeverrigaray, S.; Laurino, J.P.

    2012-01-01

    Group B Streptococcus (GBS) is the most common cause of life-threatening infection in neonates. Guidelines from CDC recommend universal screening of pregnant women for rectovaginal GBS colonization. The objective of this study was to compare the performance of a combined enrichment/PCR based method targeting the atr gene in relation to culture using enrichment with selective broth medium (standard method) to identify the presence of GBS in pregnant women. Rectovaginal GBS samples from women at ≥36 weeks of pregnancy were obtained with a swab and analyzed by the two methods. A total of 89 samples were evaluated. The prevalence of positive results for GBS detection was considerable higher when assessed by the combined enrichment/PCR method than with the standard method (35.9% versus 22.5%, respectively). The results demonstrated that the use of selective enrichment broth followed by PCR targeting the atr gene is a highly sensitive, specific and accurate test for GBS screening in pregnant women, allowing the detection of the bacteria even in lightly colonized patients. This PCR methodology may provide a useful diagnostic tool for GBS detection and contributes for a more accurate and effective intrapartum antibiotic and lower newborn mortality and morbidity. PMID:24031826

  17. Modeling Damage in Composite Materials Using an Enrichment Based Multiscale Method

    DTIC Science & Technology

    2015-03-01

    into the structural enrichment technique. 1 Approved for public release ; distribution is unlimited. Figure 1. Multiscale Homogenization Approach... Enrichment Approach 7 Approved for public release ; distribution is unlimited. Implementation of Damaged Microstructure We now focus, in this section, on...RVEs 216.8 75.4 Enrichment w/o Damaged RVEs 273.5 69.0 Enrichment with Damaged RVEs 349.7 60.4 11 Approved for public release ; distribution is

  18. Inhibition of recombinase polymerase amplification by background DNA: a lateral flow-based method for enriching target DNA.

    PubMed

    Rohrman, Brittany; Richards-Kortum, Rebecca

    2015-02-03

    Recombinase polymerase amplification (RPA) may be used to detect a variety of pathogens, often after minimal sample preparation. However, previous work has shown that whole blood inhibits RPA. In this paper, we show that the concentrations of background DNA found in whole blood prevent the amplification of target DNA by RPA. First, using an HIV-1 RPA assay with known concentrations of nonspecific background DNA, we show that RPA tolerates more background DNA when higher HIV-1 target concentrations are present. Then, using three additional assays, we demonstrate that the maximum amount of background DNA that may be tolerated in RPA reactions depends on the DNA sequences used in the assay. We also show that changing the RPA reaction conditions, such as incubation time and primer concentration, has little effect on the ability of RPA to function when high concentrations of background DNA are present. Finally, we develop and characterize a lateral flow-based method for enriching the target DNA concentration relative to the background DNA concentration. This sample processing method enables RPA of 10(4) copies of HIV-1 DNA in a background of 0-14 μg of background DNA. Without lateral flow sample enrichment, the maximum amount of background DNA tolerated is 2 μg when 10(6) copies of HIV-1 DNA are present. This method requires no heating or other external equipment, may be integrated with upstream DNA extraction and purification processes, is compatible with the components of lysed blood, and has the potential to detect HIV-1 DNA in infant whole blood with high proviral loads.

  19. A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing

    PubMed Central

    Bent, Zachary W.; Poorey, Kunal; LaBauve, Annette E.; Hamblin, Rachelle; Williams, Kelly P.

    2016-01-01

    When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich for pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs. PMID:28002481

  20. A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing

    DOE PAGES

    Bent, Zachary W.; Poorey, Kunal; LaBauve, Annette E.; ...

    2016-12-21

    When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich formore » pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs.« less

  1. GOMA: functional enrichment analysis tool based on GO modules

    PubMed Central

    Huang, Qiang; Wu, Ling-Yun; Wang, Yong; Zhang, Xiang-Sun

    2013-01-01

    Analyzing the function of gene sets is a critical step in interpreting the results of high-throughput experiments in systems biology. A variety of enrichment analysis tools have been developed in recent years, but most output a long list of significantly enriched terms that are often redundant, making it difficult to extract the most meaningful functions. In this paper, we present GOMA, a novel enrichment analysis method based on the new concept of enriched functional Gene Ontology (GO) modules. With this method, we systematically revealed functional GO modules, i.e., groups of functionally similar GO terms, via an optimization model and then ranked them by enrichment scores. Our new method simplifies enrichment analysis results by reducing redundancy, thereby preventing inconsistent enrichment results among functionally similar terms and providing more biologically meaningful results. PMID:23237213

  2. Method for laser induced isotope enrichment

    DOEpatents

    Pronko, Peter P.; Vanrompay, Paul A.; Zhang, Zhiyu

    2004-09-07

    Methods for separating isotopes or chemical species of an element and causing enrichment of a desired isotope or chemical species of an element utilizing laser ablation plasmas to modify or fabricate a material containing such isotopes or chemical species are provided. This invention may be used for a wide variety of materials which contain elements having different isotopes or chemical species.

  3. Enrichment of phosphorylated peptides and proteins by selective precipitation methods.

    PubMed

    Rainer, Matthias; Bonn, Günther K

    2015-01-01

    Protein phosphorylation is one of the most prominent post-translational modifications involved in the regulation of cellular processes. Fundamental understanding of biological processes requires appropriate bioanalytical methods for selectively enriching phosphorylated peptides and proteins. Most of the commonly applied enrichment approaches include chromatographic materials including Fe(3+)-immobilized metal-ion affinity chromatography or metal oxides. In the last years, the introduction of several non-chromatographic isolation technologies has increasingly attracted the interest of many scientists. Such approaches are based on the selective precipitation of phosphorylated peptides and proteins by applying various metal cations. The excellent performance of precipitation-based enrichment methods can be explained by the absence of any stationary phase, resin or sorbent, which usually leads to unspecific binding. This review provides an overview of recently published methods for the selective precipitation of phosphorylated peptides and proteins.

  4. A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data.

    PubMed

    Polishchuk, Maya; Paz, Inbal; Kohen, Refael; Mesika, Rona; Yakhini, Zohar; Mandel-Gutfreund, Yael

    2017-04-15

    RNA binding proteins (RBPs) play an important role in regulating many processes in the cell. RBPs often recognize their RNA targets in a specific manner. In addition to the RNA primary sequence, the structure of the RNA has been shown to play a central role in RNA recognition by RBPs. In recent years, many experimental approaches, both in vitro and in vivo, were developed and employed to identify and characterize RBP targets and extract their binding specificities. In vivo binding techniques, such as CrossLinking and ImmunoPrecipitation (CLIP)-based methods, enable the characterization of protein binding sites on RNA targets. However, these methods do not provide information regarding the structural preferences of the protein. While methods to obtain the structure of RNA are available, inferring both the sequence and the structure preferences of RBPs remains a challenge. Here we present SMARTIV, a novel computational tool for discovering combined sequence and structure binding motifs from in vivo RNA binding data relying on the sequences of the target sites, the ranking of their binding scores and their predicted secondary structure. The combined motifs are provided in a unified representation that is informative and easy for visual perception. We tested the method on CLIP-seq data from different platforms for a variety of RBPs. Overall, we show that our results are highly consistent with known binding motifs of RBPs, offering additional information on their structural preferences. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

    PubMed

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.

  6. Effect of cooking method on the fatty acid content of reduced-fat and PUFA-enriched pork patties formulated with a konjac-based oil bulking system.

    PubMed

    Salcedo-Sandoval, Lorena; Cofrades, Susana; Ruiz-Capillas, Claudia; Jiménez-Colmenero, Francisco

    2014-12-01

    The effect of cooking methods (electric grilling and pan-frying in olive oil) on the composition of reduced-fat and reduced-fat/PUFA enriched pork patties was studied. Fat reduction was performed by replacing pork backfat (38% and 100%) with konjac gel and PUFA-enrichment by replacing pork backfat (49%) with a konjac-based oil bulking system stabilizing a healthier oil combination (olive, linseed and fish oils). Cooking losses (13%-27%) were affected (p<0.05) by formulation and cooking procedure. Compared with raw products, cooked samples had higher (p<0.05) concentrations of MUFAs and PUFAs (both n-3 and n-6); the difference was greater (p<0.05) in the pan-fried patties. Fatty acid retention was generally better in pan-fried than in grilled samples. When cooked, the PUFA levels in the medium-fat/improved sample containing the oil bulking system ranged between 1.4 and 1.6g/100g (0.47-0.51 from n-3 PUFAs), with EPA+DHA concentrations of around 75mg/100g. Konjac materials were successfully used to produce pork patties with a better lipid composition. Copyright © 2014. Published by Elsevier Ltd.

  7. Method for isotope enrichment by photoinduced chemiionization

    DOEpatents

    Dubrin, James W.

    1985-01-01

    Isotope enrichment, particularly .sup.235 U enrichment, is achieved by irradiating an isotopically mixed vapor feed with radiant energy at a wavelength or wavelengths chosen to selectively excite the species containing a desired isotope to a predetermined energy level. The vapor feed if simultaneously reacted with an atomic or molecular reactant species capable of preferentially transforming the excited species into an ionic product by a chemiionization reaction. The ionic product, enriched in the desired isotope, is electrostatically or electromagnetically extracted from the reaction system.

  8. FDR-FET: an optimizing gene set enrichment analysis method

    PubMed Central

    Ji, Rui-Ru; Ott, Karl-Heinz; Yordanova, Roumyana; Bruccoleri, Robert E

    2011-01-01

    Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as “gene sets”. Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher’s exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications. PMID:21918636

  9. FDR-FET: an optimizing gene set enrichment analysis method.

    PubMed

    Ji, Rui-Ru; Ott, Karl-Heinz; Yordanova, Roumyana; Bruccoleri, Robert E

    2011-01-01

    Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as "gene sets". Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher's exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications.

  10. The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method

    PubMed Central

    Narihiro, Takashi; Suzuki, Aya; Yoshimune, Kazuaki; Hori, Tomoyuki; Hoshino, Tamotsu; Yumoto, Isao; Yokota, Atsushi; Kimura, Nobutada; Kamagata, Yoichi

    2014-01-01

    Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature. PMID:24859309

  11. Enrichment of the finite element method with reproducing kernel particle method

    SciTech Connect

    Chen, Y.; Liu, W.K.; Uras, R.A.

    1995-07-01

    Based on the reproducing kernel particle method on enrichment procedure is introduced to enhance the effectiveness of the finite element method. The basic concepts for the reproducing kernel particle method are briefly reviewed. By adopting the well-known completeness requirements, a generalized form of the reproducing kernel particle method is developed. Through a combination of these two methods their unique advantages can be utilized. An alternative approach, the multiple field method is also introduced.

  12. QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

    PubMed Central

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

  13. Application of seismic multi-attribute fusion method based on D-S evidence theory in prediction of CBM-enriched area

    NASA Astrophysics Data System (ADS)

    Qi, Xue-Mei; Zhang, Shao-Cong

    2012-03-01

    D-S evidence theory provides a good approach to fuse uncertain information. In this article, we introduce seismic multi-attribute fusion based on D-S evidence theory to predict the coalbed methane (CBM) concentrated areas. First, we choose seismic attributes that are most sensitive to CBM content changes with the guidance of CBM content measured at well sites. Then the selected seismic attributes are fused using D-S evidence theory and the fusion results are used to predict CBM-enriched area. The application shows that the predicted CBM content and the measured values are basically consistent. The results indicate that using D-S evidence theory in seismic multi-attribute fusion to predict CBM-enriched areas is feasible.

  14. [Comparative studies of methods of salmonella enrichment (author's transl)].

    PubMed

    Pietzsch, O; Kretschmer, F J; Bulling, E

    1975-07-01

    Eight different methods of salmonella enrichment were compared in two series of experiments involving 100 samples of whole-egg powder and 80 samples of frozen whole liquid egg, respectively. 66 out of a total of 100 samples of whole-egg powder had been artificially infected with varying numbers of S. typhi-murium; 60 out of 80 samples of frozen whole liquid egg were found to be naturally infected with various salmonella species. 3 of the 8 methods (Table 1) were compared within an international collaborative study with 14 laboratories in 11 countries participating. A reduction of the pre-enrichment period from 18 to 6 hours and of volumes used in pre-enrichment and selective enrichment from 10 and 100 ml, respectively to 1 and 10 ml, respectively were found to have adverse influence upon the result of isolations, in particular in the case of weakly infected samples. In contrast, extended incubation over 48 hours as well as preparation of two sub-cultures on solid selective media following incubation of enrichment cultures over 18-24 hours and 42-48 hours, respectively always resulted in a certain increase of salmonella yield which, however, exhibited gradual differences for the individual methods examined. Preparation of a 2nd sub-culture meant, in particular, a decisive improvement of the result of isolations from artificially infected samples if selenite-cystine enrichment volumes were 10 and 100 ml, respectively. The best results could be obtained by means of the following methods of enrichment: Pre-enrichment of material in buffered peptone water at 37 degrees C over 18 hours; pipetting of 10 ml inoculated and incubated pre-enriched material into 100 ml selenite-cystine or tetrathionate enrichment medium according to MULLER-KAUFFMANN; onward incubation of the enrichment culture at 43 degrees C over 48 hours; and preparation of sub-cultures on solid selective media after 24 and 48 hours. The method using tetrathionate enrichment medium was found to be most

  15. An effective and in-situ method based tresyl-functionalized porous polymer material for enrichment and digestion of membrane proteins and its application in extraction tips.

    PubMed

    Wang, Jiaxi; Gao, Mingxia; Yan, Guoquan; Zhang, Xiangmin

    2015-06-23

    Membrane proteins are one of promising targets for drug discovery because of the unique properties in physiological processes. Due to their low abundance and extremely hydrophobic nature, the analysis of membrane proteins is still a great challenge. In this work, an effective and in-situ method were developed to enrich and digest membrane proteins by adopting tresyl-functionalized porous polymer material. With tresyl groups, the material can effectively immobilize membrane proteins via covalent bonding on the surface. The material became a facile carrier to enrich membrane proteins from the rat liver in detergents and organic solvents owing to its outstanding binding capacity and excellent biocompatibility. Moreover, it was further applied in extraction tips to capture and in-situ digest the pretreatment membrane proteins in two different solutions. A total of 600 membrane proteins (51% of total protein groups) and 359 transmembrane proteins were identified by nano-LC-ESI-MS/MS in 4% sodium dodecyl sulfate (SDS), and similar results were achieved in the 60% methanol solution. All these results demonstrated that the new approach is of great promise for large-scale characterization of membrane proteins.

  16. Feeding enrichment methods for Pacific walrus calves.

    PubMed

    Kastelein, Ronald A; Jennings, Nancy; Postma, Jacobus

    2007-05-01

    In the wild, walrus calves are occupied with many behaviors necessary for survival. In captivity there is usually less to occupy them. Therefore it is necessary to develop other ways to occupy the animals to prevent negative behavior. In the present study, food in four different types of dispensers were tested on two walrus calves: fish in ice, fish in a nine-hole container, fish in a two-hole container, and fish in ice in a one-hole container. All four methods of offering fish had an effect on the animals' behavior. There were differences in the way the two animals responded to each of the four dispensers. The dispensers occupied one animal on average between 32-95% of the 90-min test periods, and the other animal for between 14-57% of the test periods. Due to the effect of learning and rapid development of the calves, which were shifting from a 100% formula diet to a 100% fish diet during the study period, the four methods cannot be compared. Besides the time feeding methods occupy animals, the practicality of a dispenser determines how often it will be used by the keepers. Of the four dispenser types tested in the present study, the nine-hole container was the most practical and was still used frequently by the keepers years after the study. Zoo Biol 0:1-12, 2007. (c) 2007 Wiley-Liss, Inc.

  17. Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques

    PubMed Central

    Thomson, John P.; Hunter, Jennifer M.; Nestor, Colm E.; Dunican, Donncha S.; Terranova, Rémi; Moggs, Jonathan G.; Meehan, Richard R.

    2013-01-01

    The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hmC. PMID:24214958

  18. Quantification of Listeria monocytogenes in minimally processed leafy vegetables using a combined method based on enrichment and 16S rRNA real-time PCR.

    PubMed

    Aparecida de Oliveira, Maria; Abeid Ribeiro, Eliana Guimarães; Morato Bergamini, Alzira Maria; Pereira De Martinis, Elaine Cristina

    2010-02-01

    Modern lifestyle markedly changed eating habits worldwide, with an increasing demand for ready-to-eat foods, such as minimally processed fruits and leafy greens. Packaging and storage conditions of those products may favor the growth of psychrotrophic bacteria, including the pathogen Listeria monocytogenes. In this work, minimally processed leafy vegetables samples (n = 162) from retail market from Ribeirão Preto, São Paulo, Brazil, were tested for the presence or absence of Listeria spp. by the immunoassay Listeria Rapid Test, Oxoid. Two L. monocytogenes positive and six artificially contaminated samples of minimally processed leafy vegetables were evaluated by the Most Probable Number (MPN) with detection by classical culture method and also culture method combined with real-time PCR (RTi-PCR) for 16S rRNA genes of L. monocytogenes. Positive MPN enrichment tubes were analyzed by RTi-PCR with primers specific for L. monocytogenes using the commercial preparation ABSOLUTE QPCR SYBR Green Mix (ABgene, UK). Real-time PCR assay presented good exclusivity and inclusivity results and no statistical significant difference was found in comparison with the conventional culture method (p < 0.05). Moreover, RTi-PCR was fast and easy to perform, with MPN results obtained in ca. 48 h for RTi-PCR in comparison to 7 days for conventional method.

  19. Enrichment Assay Methods for a UF6 Cylinder Verification Station

    SciTech Connect

    Smith, Leon E.; Jordan, David V.; Misner, Alex C.; Mace, Emily K.; Orton, Christopher R.

    2010-11-30

    International Atomic Energy Agency (IAEA) inspectors currently perform periodic inspections at uranium enrichment plants to verify UF6 cylinder enrichment declarations. Measurements are typically performed with handheld high-resolution sensors on a sampling of cylinders taken to be representative of the facility’s entire cylinder inventory. These enrichment assay methods interrogate only a small fraction of the total cylinder volume, and are time-consuming and expensive to execute for inspectors. Pacific Northwest National Laboratory (PNNL) is developing an unattended measurement system capable of automated enrichment measurements over the full volume of Type 30B and Type 48 cylinders. This Integrated Cylinder Verification System (ICVS) could be located at key measurement points to positively identify each cylinder, measure its mass and enrichment, store the collected data in a secure database, and maintain continuity of knowledge on measured cylinders until IAEA inspector arrival. The focus of this paper is the development of nondestructive assay (NDA) methods that combine “traditional” enrichment signatures (e.g. 185-keV emission from U-235) and more-penetrating “non-traditional” signatures (e.g. high-energy neutron-induced gamma rays spawned primarily from U-234 alpha emission) collected by medium-resolution gamma-ray spectrometers (i.e. sodium iodide or lanthanum bromide). The potential of these NDA methods for the automated assay of feed, tail and product cylinders is explored through MCNP modeling and with field measurements on a cylinder population ranging from 0.2% to 5% in U-235 enrichment.

  20. 77 FR 13367 - General Electric-Hitachi Global Laser Enrichment, LLC, Proposed Laser-Based Uranium Enrichment...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-06

    ... COMMISSION General Electric-Hitachi Global Laser Enrichment, LLC, Proposed Laser-Based Uranium Enrichment...- Hitachi Global Laser Enrichment, LLC (GLE) Uranium Enrichment Facility. On June 26, 2009, GLE submitted a license application that proposes the construction, operation, and decommissioning of a laser-based...

  1. Microchip method for the enrichment of specific DNA sequences

    DOEpatents

    Mirzabekov, Andrei Darievich; Lysov, Yuri Petrovich; Shick, Valentine Vladimirovich; Dubiley, Svetlana Alekseevna

    1998-01-01

    A method for enriching specific genetic material sequences is provided, whereby oligonucleotide molecules complementary to the desired genetic material is first used to isolate the genetic material from a first source of genomic material. Then the genetic material is used as a label to isolate similar genetic sequences from other sources.

  2. Microchip method for the enrichment of specific DNA sequences

    DOEpatents

    Mirzabekov, A.D.; Lysov, Y.P.; Shick, V.V.; Dubiley, S.A.

    1998-12-22

    A method for enriching specific genetic material sequences is provided, whereby oligonucleotide molecules complementary to the desired genetic material is first used to isolate the genetic material from a first source of genomic material. Then the genetic material is used as a label to isolate similar genetic sequences from other sources. 4 figs.

  3. Glycoprotein enrichment method using a selective magnetic nano-probe platform (MNP) functionalized with lectins.

    PubMed

    Cova, Marta; Oliveira-Silva, Rui; Ferreira, José Alexandre; Ferreira, Rita; Amado, Francisco; Daniel-da-Silva, Ana Luísa; Vitorino, Rui

    2015-01-01

    Protein post-translational modifications (PTMs) have increasingly become a research field of incredible importance to fully understand the regulation of biological processes in health and disease. Among PTMs, glycosylation is one of the most studied for which contributed the development and improvement of enrichment techniques. Nowadays, glycoprotein enrichment methods are based on lectin affinity, covalent interactions, and hydrophilic interaction liquid chromatography (HILIC). Nonetheless, the nanotechnology era has fetched new methods to enrich glycoproteins from complex samples as human biological fluids. For instance, magnetic nanoparticles (MNPs) are being used as an interesting enrichment approach allowing a better characterization of glycoproteins and glycopeptides.In this chapter, we describe an enrichment method based on MNPs functionalized with lectins (Concavalin A, wheat germ agglutinin, and Maackia amurensis lectin) to enrich specific sets of glycoproteins from biological fluids. Moreover, it is proposed a bioinformatic strategy to deal with data retrieved from mass spectrometry analysis of enriched samples aiming the identification of relevant biological processes modulated by a given stimuli and, ultimately, of new biomarkers for disease screening/management.

  4. Method for production of an isotopically enriched compound

    DOEpatents

    Watrous, Matthew G.

    2012-12-11

    A method is presented for producing and isolating an isotopically enriched compound of a desired isotope from a parent radionuclide. The method includes forming, or placing, a precipitate containing a parent radionuclide of the desired daughter isotope in a first reaction zone and allowing sufficient time for the parent to decay into the desired gaseous daughter radioisotope. The method further contemplates collecting the desired daughter isotope as a solid in a second reaction zone through the application of temperatures below the freezing point of the desired isotope to a second reaction zone that is connected to the first reaction zone. Specifically, a method is presented for producing isotopically enriched compounds of xenon, including the radioactive isotope Xe-131m and the stable isotope Xe-131.

  5. Isotopic backmixing in a large-scale enrichment column in a chemical enrichment method

    SciTech Connect

    Takeda, K.; Nishigaki, Y.; Onitsuka, H. )

    1990-03-01

    The Asahi chemical enrichment pilot plant with four large-scale 1-mm-diam enrichment columns has been operated using the super process since June 1987. Uranium with 3.3% enrichment was recovered in April 1988, and higher efficiencies have been observed in the pilot plant than in the bench-scale plant, which has 0.1-mm-diam enrichment columns. A possible reason is that the isotopic backmixing in the pilot plant is much smaller than in the bench-scale plant. Quantitative and statistical studies imply that both the extracolumn volume ratio and wall effect contribute to the smaller backmixing.

  6. A generalized finite element method with global-local enrichment functions for confined plasticity problems

    NASA Astrophysics Data System (ADS)

    Kim, D.-J.; Duarte, C. A.; Proenca, S. P.

    2012-11-01

    The main feature of partition of unity methods such as the generalized or extended finite element method is their ability of utilizing a priori knowledge about the solution of a problem in the form of enrichment functions. However, analytical derivation of enrichment functions with good approximation properties is mostly limited to two-dimensional linear problems. This paper presents a procedure to numerically generate proper enrichment functions for three-dimensional problems with confined plasticity where plastic evolution is gradual. This procedure involves the solution of boundary value problems around local regions exhibiting nonlinear behavior and the enrichment of the global solution space with the local solutions through the partition of unity method framework. This approach can produce accurate nonlinear solutions with a reduced computational cost compared to standard finite element methods since computationally intensive nonlinear iterations can be performed on coarse global meshes after the creation of enrichment functions properly describing localized nonlinear behavior. Several three-dimensional nonlinear problems based on the rate-independent J 2 plasticity theory with isotropic hardening are solved using the proposed procedure to demonstrate its robustness, accuracy and computational efficiency.

  7. Coupling enrichment methods with proteomics for understanding and treating disease.

    PubMed

    Kumar, Amit; Baycin-Hizal, Deniz; Shiloach, Joseph; Bowen, Michael A; Betenbaugh, Michael J

    2015-02-01

    Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of drugs to treat human disease, including target and drug evaluation, understanding mechanisms of drug action, and biomarker discovery. Currently, the genetic sequences of many major organisms are available, which have helped greatly in characterizing proteomes in model animal systems and humans. Through proteomics, global profiles of different disease states can be characterized (e.g. changes in types and relative levels as well as changes in PTMs such as glycosylation or phosphorylation). Although intracellular proteomics can provide a broad overview of physiology of cells and tissues, it has been difficult to quantify the low abundance proteins which can be important for understanding the diseased states and treatment progression. For this reason, there is increasing interest in coupling comparative proteomics methods with subcellular fractionation and enrichment techniques for membranes, nucleus, phosphoproteome, glycoproteome as well as low abundance serum proteins. In this review, we will provide examples of where the utilization of different proteomics-coupled enrichment techniques has aided target and biomarker discovery, understanding the drug targeting mechanism, and mAb discovery. Taken together, these improvements will help to provide a better understanding of the pathophysiology of various diseases including cancer, autoimmunity, inflammation, cardiovascular disease, and neurological conditions, and in the design and development of better medicines for treating these afflictions.

  8. A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples

    SciTech Connect

    Zhang, Qibin; Qian, Weijun; Knyushko, Tanya V.; Clauss, Therese RW; Purvine, Samuel O.; Moore, Ronald J.; Sacksteder, Colette A.; Chin, Mark H.; Smith, Desmond J.; Camp, David G.; Bigelow, Diana J.; Smith, Richard D.

    2007-06-01

    Elevated levels of protein tyrosine nitration have been found in various neurodegenerative diseases and aging related pathologies; however, the lack of an efficient enrichment method has prevented the analysis of this important low level protein modification. We have developed an efficient method for specific enrichment of nitrotyrosine containing peptides that permits nitrotyrosine peptides and specific nitration sites to be unambiguously identified with LC-MS/MS. The method is based on the derivatization of nitrotyrosine into free sulfhydryl groups followed by high efficiency enrichment of sulfhydryl-containing peptides with thiopropyl sepharose beads. The derivatization process starts with acetylation with acetic anhydride to block all primary amines, followed by reduction of nitrotyrosine to aminotyrosine, then derivatization of aminotyrosine with N-Succinimidyl S-Acetylthioacetate (SATA), and finally deprotecting of S-acetyl on SATA to form free sulfhydryl groups. This method was evaluated using nitrotyrosine containing peptides, in-vitro nitrated human histone 1.2, and bovine serum albumin (BSA). 91% and 62% of the identified peptides from enriched histone and BSA samples were nitrotyrosine derivatized peptides, respectively, suggesting relative high specificity of the enrichment method. The application of this method to in-vitro nitrated mouse brain homogenate resulted in 35% of identified peptides containing nitrotyrosine (compared to only 5.9% observed from the global analysis of unenriched sample), and a total of 150 unique nitrated peptides covering 102 proteins were identified with a false discovery rate estimated at 3.3% from duplicate LC-MS/MS analyses of a single enriched sample.

  9. A novel method for obtaining highly enriched Schwann cell populations from mature monkey nerves based on in vitro pre‑degeneration.

    PubMed

    Wang, Gangyang; Ma, Zhengwen; Cao, Lingling; Yan, Guofeng; Wang, Yang; Jin, Yuqing; Shen, Hua; Zhang, Yiping; Xu, Xiaoming; Chen, Xuejin; Shen, Zunli

    2017-09-05

    Schwann cells (SCs) are indispensable for cell therapy and tissue engineering of the peripheral nervous system. Easy access to activated, highly proliferative SCs is necessary for clinical applications. The present study developed a fast, efficient method for obtaining highly purified SCs from the peripheral nerve of a mature Rhesus monkey. The common peroneal nerves of 4‑year‑old Rhesus monkeys were harvested and subjected to in vitro pre‑degeneration in a modified SC culture medium (SCCM). The nerve pieces were subsequently treated enzymatically to dissociate the cells and then cultured for 2 days in SCCM. Cultured cells were treated with purification medium containing Ara‑C to assist in restricting the overgrowth of fibroblast‑like cells, for 24 h. After another 24‑h cultivation period, the cells were subsequently treated with a multiplex collagenase, which enabled SC detachment over fibroblast detachment, and thereby facilitated SC isolation. Finally, SCs were cultured in SCCM. The cell yield was determined by cell counting following enzyme digestion and SC purity was determined from the percentage of SCs with respect to the total number of cells. Following purification, 96.3±3.9% of cells were identified as SCs. In vitro pre‑degeneration in the presence of basic‑fibroblast growth factor, heregulin β1 and forskolin maximized the purity and yield of SCs that could be obtained from monkey peroneal nerves. The present study identified a novel technique that can efficiently isolate and purify SCs from mature monkey nerves based on in vitro pre‑degeneration.

  10. Improved Methods for the Enrichment and Analysis of Glycated Peptides

    SciTech Connect

    Zhang, Qibin; Schepmoes, Athena A; Brock, Jonathan W; Wu, Si; Moore, Ronald J; Purvine, Samuel O; Baynes, John; Smith, Richard D; Metz, Thomas O

    2008-12-15

    Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an on-line wash of column-bound glycated peptides using 50 mM ammonium acetate. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (≥3) precursor-ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activation after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. In general, acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor-ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number glycated peptides identified by LC-MS/MS.

  11. Improved Methods for the Enrichment and Analysis of Glycated Peptides

    PubMed Central

    Zhang, Qibin; Schepmoes, Athena A.; Brock, Jonathan W. C.; Wu, Si; Moore, Ronald J.; Purvine, Samuel O.; Baynes, John W.; Smith, Richard D.; Metz, Thomas O.

    2009-01-01

    Nonenzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron-transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an online wash of column-bound glycated peptides using 50 mM ammonium acetate, followed by elution with 100 mM acetic acid. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (≥3) precursor ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activation after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. Acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number of glycated peptides and corresponding glycated proteins identified by LC–MS/MS. PMID:18989935

  12. Method and apparatus for measuring enrichment of UF6

    DOEpatents

    Hill, Thomas Roy [Santa Fe, NM; Ianakiev, Kiril Dimitrov [Los Alamos, NM

    2011-06-07

    A system and method are disclosed for determining the enrichment of .sup.235U in Uranium Hexafluoride (UF6) utilizing synthesized X-rays which are directed at a container test zone containing a sample of UF6. A detector placed behind the container test zone then detects and counts the X-rays which pass through the container and the UF6. In order to determine the portion of the attenuation due to the UF6 gas alone, this count rate may then be compared to a calibration count rate of X-rays passing through a calibration test zone which contains a vacuum, the test zone having experienced substantially similar environmental conditions as the actual test zone. Alternatively, X-rays of two differing energy levels may be alternately directed at the container, where either the container or the UF6 has a high sensitivity to the difference in the energy levels, and the other having a low sensitivity.

  13. A new 17O-isotopic enrichment method for the NMR characterisation of phosphate compounds.

    PubMed

    Flambard, Alexandrine; Montagne, Lionel; Delevoye, Laurent

    2006-08-28

    Heating phosphate compounds under (17)O-enriched water vapour is an easy and rapid method to prepare homogeneously enriched and pure samples for the acquisition of (17)O NMR spectra with a good sensitivity.

  14. Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment.

    PubMed

    Giganti, David; Guillemain, Hélène; Spadoni, Jean-Louis; Nilges, Michael; Zagury, Jean-François; Montes, Matthieu

    2010-06-28

    In the early stage of drug discovery programs, when the structure of a complex involving a target and a small molecule is available, structure-based virtual ligand screening methods are generally preferred. However, ligand-based strategies like shape-similarity search methods can also be applied. Shape-similarity search methods consist in exploring a pseudo-binding-site derived from the known small molecule used as a reference. Several of these methods use conformational sampling algorithms which are also shared by corresponding docking methods: for example Surflex-dock/Surflex-sim, FlexX/FlexS, ICM, and OMEGA-FRED/OMEGA-ROCS. Using 11 systems issued from the challenging "own" subsets of the Directory of Useful Decoys (DUD-own), we evaluated and compared the performance of the above-cited programs in terms of molecular alignment accuracy, enrichment in active compounds, and enrichment in different chemotypes (scaffold-hopping). Since molecular alignment is a crucial aspect of performance for the different methods, we have assessed its impact on enrichment. We have also illustrated the paradox of retrieving active compounds with good scores even if they are inaccurately positioned. Finally, we have highlighted possible positive aspects of using shape-based approaches in drug-discovery protocols when the structure of the target in complex with a small molecule is known.

  15. Hybrid Enrichment Assay Methods for a UF6 Cylinder Verification Station: FY10 Progress Report

    SciTech Connect

    Smith, Leon E.; Jordan, David V.; Orton, Christopher R.; Misner, Alex C.; Mace, Emily K.

    2010-08-01

    Pacific Northwest National Laboratory (PNNL) is developing the concept of an automated UF6 cylinder verification station that would be located at key measurement points to positively identify each cylinder, measure its mass and enrichment, store the collected data in a secure database, and maintain continuity of knowledge on measured cylinders until the arrival of International Atomic Energy Agency (IAEA) inspectors. At the center of this unattended system is a hybrid enrichment assay technique that combines the traditional enrichment-meter method (based on the 186 keV peak from 235U) with non-traditional neutron-induced high-energy gamma-ray signatures (spawned primarily by 234U alpha emissions and 19F(alpha, neutron) reactions). Previous work by PNNL provided proof-of-principle for the non-traditional signatures to support accurate, full-volume interrogation of the cylinder enrichment, thereby reducing the systematic uncertainties in enrichment assay due to UF6 heterogeneity and providing greater sensitivity to material substitution scenarios. The work described here builds on that preliminary evaluation of the non-traditional signatures, but focuses on a prototype field system utilizing NaI(Tl) and LaBr3(Ce) spectrometers, and enrichment analysis algorithms that integrate the traditional and non-traditional signatures. Results for the assay of Type-30B cylinders ranging from 0.2 to 4.95 wt% 235U, at an AREVA fuel fabrication plant in Richland, WA, are described for the following enrichment analysis methods: 1) traditional enrichment meter signature (186 keV peak) as calculated using a square-wave convolute (SWC) algorithm; 2) non-traditional high-energy gamma-ray signature that provides neutron detection without neutron detectors and 3) hybrid algorithm that merges the traditional and non-traditional signatures. Uncertainties for each method, relative to the declared enrichment for each cylinder, are calculated and compared to the uncertainties from an attended

  16. Heat-transfer resistance measurement method (HTM)-based cell detection at trace levels using a progressive enrichment approach with highly selective cell-binding surface imprints.

    PubMed

    Bers, Karolien; Eersels, Kasper; van Grinsven, Bart; Daemen, Mat; Bogie, Jeroen F J; Hendriks, Jerome J A; Bouwmans, Evelien E; Püttmann, Christiane; Stein, Christoph; Barth, Stefan; Bos, Gerard M J; Germeraad, Wilfred T V; De Ceuninck, Ward; Wagner, Patrick

    2014-04-01

    Surface-imprinted polymers allow for specific cell detection based on simultaneous recognition of the cell shape, cell size, and cell membrane functionalities by macromolecular cell imprints. In this study, the specificity of detection and the detection sensitivity for target cells within a pool of non-target cells were analyzed for a cell-specific surface-imprinted polymer combined with a heat-transfer-based read-out technique (HTM). A modified Chinese hamster ovarian cell line (CHO-ldlD) was used as a model system on which the transmembrane protein mucin-1 (MUC1) could be excessively expressed and for which the occurrence of MUC1 glycosylation could be controlled. In specific cancer cells, the overexpressed MUC1 protein typically shows an aberrant apical distribution and glycosylation. We show that surface-imprinted polymers discriminate between cell types that (1) only differ in the expression of a specific membrane protein (MUC1) or (2) only differ in the membrane protein being glycosylated or not. Moreover, surface-imprinted polymers of cells carrying different glycoforms of the same membrane protein do target both types of cells. These findings illustrate the high specificity of cell detection that can be reached by the structural imprinting of cells in polymer layers. Competitiveness between target and non-target cells was proven to negatively affect the detection sensitivity of target cells. Furthermore, we show that the detection sensitivity can be increased significantly by repetitively exposing the surface to the sample and eliminating non-specifically bound cells by flushing between consecutive cell exposures.

  17. Adaptive enriched Galerkin methods for miscible displacement problems with entropy residual stabilization

    NASA Astrophysics Data System (ADS)

    Lee, Sanghyun; Wheeler, Mary F.

    2017-02-01

    We present a novel approach to the simulation of miscible displacement by employing adaptive enriched Galerkin finite element methods (EG) coupled with entropy residual stabilization for transport. In particular, numerical simulations of viscous fingering instabilities in heterogeneous porous media and Hele-Shaw cells are illustrated. EG is formulated by enriching the conforming continuous Galerkin finite element method (CG) with piecewise constant functions. The method provides locally and globally conservative fluxes, which are crucial for coupled flow and transport problems. Moreover, EG has fewer degrees of freedom in comparison with discontinuous Galerkin (DG) and an efficient flow solver has been derived which allows for higher order schemes. Dynamic adaptive mesh refinement is applied in order to reduce computational costs for large-scale three dimensional applications. In addition, entropy residual based stabilization for high order EG transport systems prevents spurious oscillations. Numerical tests are presented to show the capabilities of EG applied to flow and transport.

  18. Highly Selective Enrichment of Glycopeptides Based on Zwitterionically Functionalized Soluble Nanopolymers

    NASA Astrophysics Data System (ADS)

    Cao, Weiqian; Huang, Jiangming; Jiang, Biyun; Gao, Xing; Yang, Pengyuan

    2016-07-01

    Efficient glycopeptides enrichment prior to mass spectrometry analysis is essential for glycoproteome study. ZIC-HILIC (zwitterionic hydrophilic interaction liquid chromatography) based glycopeptides enrichment approaches have been attracting more attention for several benefits like easy operating, high enrichment specificity and intact glycopeptide retained. In this study, Poly (amidoamine) dendrimer (PAMAM) was adopted for the synthesis of zwitterionically functionalized (ZICF) materials for glycopeptide enrichment. The multiple branched structure and good solubility of ZICF-PAMAM enables a sufficient interaction with glycopeptides. The ZICF-PAMAM combined with the FASP-mode enrichment strategy exhibits more superior performance compared with the existing methods. It has the minimum detectable concentration of femtomolar level and high recovery rate of over 90.01%, and can efficiently enrich glycopeptides from complex biological samples even for merely 0.1 μL human serum. The remarkable glycopeptides enrichment capacity of ZICF-PAMAM highlights the potential application in in-depth glycoproteome research, which may open up new opportunities for the development of glycoproteomics.

  19. Highly Selective Enrichment of Glycopeptides Based on Zwitterionically Functionalized Soluble Nanopolymers

    PubMed Central

    Cao, Weiqian; Huang, Jiangming; Jiang, Biyun; Gao, Xing; Yang, Pengyuan

    2016-01-01

    Efficient glycopeptides enrichment prior to mass spectrometry analysis is essential for glycoproteome study. ZIC-HILIC (zwitterionic hydrophilic interaction liquid chromatography) based glycopeptides enrichment approaches have been attracting more attention for several benefits like easy operating, high enrichment specificity and intact glycopeptide retained. In this study, Poly (amidoamine) dendrimer (PAMAM) was adopted for the synthesis of zwitterionically functionalized (ZICF) materials for glycopeptide enrichment. The multiple branched structure and good solubility of ZICF-PAMAM enables a sufficient interaction with glycopeptides. The ZICF-PAMAM combined with the FASP-mode enrichment strategy exhibits more superior performance compared with the existing methods. It has the minimum detectable concentration of femtomolar level and high recovery rate of over 90.01%, and can efficiently enrich glycopeptides from complex biological samples even for merely 0.1 μL human serum. The remarkable glycopeptides enrichment capacity of ZICF-PAMAM highlights the potential application in in-depth glycoproteome research, which may open up new opportunities for the development of glycoproteomics. PMID:27412817

  20. A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

    PubMed Central

    Feehery, George R.; Yigit, Erbay; Oyola, Samuel O.; Langhorst, Bradley W.; Schmidt, Victor T.; Stewart, Fiona J.; Dimalanta, Eileen T.; Amaral-Zettler, Linda A.; Davis, Theodore; Quail, Michael A.; Pradhan, Sriharsa

    2013-01-01

    DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we used a methyl-CpG binding domain (MBD) to separate methylated host DNA from microbial DNA based on differences in CpG methylation density. MBD fused to the Fc region of a human antibody (MBD-Fc) binds strongly to protein A paramagnetic beads, forming an effective one-step enrichment complex that was used to remove human or fish host DNA from bacterial and protistan DNA for subsequent sequencing and analysis. We report enrichment of DNA samples from human saliva, human blood, a mock malaria-infected blood sample and a black molly fish. When reads were mapped to reference genomes, sequence reads aligning to host genomes decreased 50-fold, while bacterial and Plasmodium DNA sequences reads increased 8–11.5-fold. The Shannon-Wiener diversity index was calculated for 149 bacterial species in saliva before and after enrichment. Unenriched saliva had an index of 4.72, while the enriched sample had an index of 4.80. The similarity of these indices demonstrates that bacterial species diversity and relative phylotype abundance remain conserved in enriched samples. Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types. PMID:24204593

  1. Method for enriching a middle isotope using vibration-vibration pumping

    DOEpatents

    Rich, Joseph W.; Homicz, Gregory F.; Bergman, Richard C.

    1989-01-01

    Method for producing isotopically enriched material by vibration-vibration excitation of gaseous molecules wherein a middle mass isotope of an isotopic mixture including lighter and heavier mass isotopes preferentially populates a higher vibrational mode and chemically reacts to provide a product in which it is enriched. The method can be used for vibration-vibration enrichment of .sup.17 O in a CO reactant mixture.

  2. Enrichment Assay Methods Development for the Integrated Cylinder Verification System

    SciTech Connect

    Smith, Leon E.; Misner, Alex C.; Hatchell, Brian K.; Curtis, Michael M.

    2009-10-22

    International Atomic Energy Agency (IAEA) inspectors currently perform periodic inspections at uranium enrichment plants to verify UF6 cylinder enrichment declarations. Measurements are typically performed with handheld high-resolution sensors on a sampling of cylinders taken to be representative of the facility's entire product-cylinder inventory. Pacific Northwest National Laboratory (PNNL) is developing a concept to automate the verification of enrichment plant cylinders to enable 100 percent product-cylinder verification and potentially, mass-balance calculations on the facility as a whole (by also measuring feed and tails cylinders). The Integrated Cylinder Verification System (ICVS) could be located at key measurement points to positively identify each cylinder, measure its mass and enrichment, store the collected data in a secure database, and maintain continuity of knowledge on measured cylinders until IAEA inspector arrival. The three main objectives of this FY09 project are summarized here and described in more detail in the report: (1) Develop a preliminary design for a prototype NDA system, (2) Refine PNNL's MCNP models of the NDA system, and (3) Procure and test key pulse-processing components. Progress against these tasks to date, and next steps, are discussed.

  3. Using Case Method to Enrich Students' Learning Outcomes

    ERIC Educational Resources Information Center

    Nkhoma, Mathews; Sriratanaviriyakul, Narumon; Quang, Huy Le

    2017-01-01

    There is a need to examine the effect of using discussion cases to enrich students' learning outcomes. A research framework was created to study this multidimensional relationship, via the instruments of interactivity, students' time devotion and students' engagement in order to find which factors could improve learning outcomes, including…

  4. Novel co-enrichment method for isolation of magnetotactic bacteria.

    PubMed

    Sorty, Ajay M; Shaikh, Nasir R

    2015-04-01

    A novel co-enrichment technique was designed for enrichment of magnetotactic bacteria from soil, water, and sediments. Delayed addition of iron uptake inducer and the iron source proved amenable to induce magnetosome synthesis by MTB followed by their separation from consortium using magnetic flux. We successfully enriched and isolated both North seeking as well as South seeking magnetotactic bacteria from Lonar Lake (Buldhana), Moti Lake (Jalna), Ghanewadi Lake (Jalna), Ganesh Lake (Miraj), Rankala Lake (Kolhapur), and industrial metal-contaminated glaying soils (Jalna) and a soil (Karad), (MS, India) exposed to high-voltage electric current. The hanging drop preparations and growth under magnetic stress on low-agar media allowed conformation of magnetotactic behavior of the isolates. Both Gram positive and Gram negative MTB were isolated with diverse morphologies. South seeking population was more predominant. The soil inhabitants showed little dwelling property which was more prominent in case of aquatic inhabitants. The use of in situ pH and salt concentrations during enrichment and isolation found suited. The simultaneous growth of whole consortium in the system ensured the in situ simulation of microenvironment needful for proper growth of fastidious MTB.

  5. Large-scale All-electron Density Functional Theory Calculations using Enriched Finite Element Method

    NASA Astrophysics Data System (ADS)

    Kanungo, Bikash; Gavini, Vikram

    We present a computationally efficient method to perform large-scale all-electron density functional theory calculations by enriching the Lagrange polynomial basis in classical finite element (FE) discretization with atom-centered numerical basis functions, which are obtained from the solutions of the Kohn-Sham (KS) problem for single atoms. We term these atom-centered numerical basis functions as enrichment functions. The integrals involved in the construction of the discrete KS Hamiltonian and overlap matrix are computed using an adaptive quadrature grid based on gradients in the enrichment functions. Further, we propose an efficient scheme to invert the overlap matrix by exploiting its LDL factorization and employing spectral finite elements along with Gauss-Lobatto quadrature rules. Finally, we use a Chebyshev polynomial based acceleration technique to compute the occupied eigenspace in each self-consistent iteration. We demonstrate the accuracy, efficiency and scalability of the proposed method on various metallic and insulating benchmark systems, with systems ranging in the order of 10,000 electrons. We observe a 50-100 fold reduction in the overall computational time when compared to classical FE calculations while being commensurate with the desired chemical accuracy. We acknowledge the support of NSF (Grant No. 1053145) and ARO (Grant No. W911NF-15-1-0158) in conducting this work.

  6. What Is the Best NGS Enrichment Method for the Molecular Diagnosis of Monogenic Diabetes and Obesity?

    PubMed Central

    Philippe, Julien; Derhourhi, Mehdi; Durand, Emmanuelle; Vaillant, Emmanuel; Dechaume, Aurélie; Rabearivelo, Iandry; Dhennin, Véronique; Vaxillaire, Martine; De Graeve, Franck; Sand, Olivier; Froguel, Philippe; Bonnefond, Amélie

    2015-01-01

    Molecular diagnosis of monogenic diabetes and obesity is of paramount importance for both the patient and society, as it can result in personalized medicine associated with a better life and it eventually saves health care spending. Genetic clinical laboratories are currently switching from Sanger sequencing to next-generation sequencing (NGS) approaches but choosing the optimal protocols is not easy. Here, we compared the sequencing coverage of 43 genes involved in monogenic forms of diabetes and obesity, and variant detection rates, resulting from four enrichment methods based on the sonication of DNA (Agilent SureSelect, RainDance technologies), or using enzymes for DNA fragmentation (Illumina Nextera, Agilent HaloPlex). We analyzed coding exons and untranslated regions of the 43 genes involved in monogenic diabetes and obesity. We found that none of the methods achieves yet full sequencing of the gene targets. Nonetheless, the RainDance, SureSelect and HaloPlex enrichment methods led to the best sequencing coverage of the targets; while the Nextera method resulted in the poorest sequencing coverage. Although the sequencing coverage was high, we unexpectedly found that the HaloPlex method missed 20% of variants detected by the three other methods and Nextera missed 10%. The question of which NGS technique for genetic diagnosis yields the highest diagnosis rate is frequently discussed in the literature and the response is still unclear. Here, we showed that the RainDance enrichment method as well as SureSelect, which are both based on the sonication of DNA, resulted in a good sequencing quality and variant detection, while the use of enzymes to fragment DNA (HaloPlex or Nextera) might not be the best strategy to get an accurate sequencing. PMID:26599467

  7. What Is the Best NGS Enrichment Method for the Molecular Diagnosis of Monogenic Diabetes and Obesity?

    PubMed

    Philippe, Julien; Derhourhi, Mehdi; Durand, Emmanuelle; Vaillant, Emmanuel; Dechaume, Aurélie; Rabearivelo, Iandry; Dhennin, Véronique; Vaxillaire, Martine; De Graeve, Franck; Sand, Olivier; Froguel, Philippe; Bonnefond, Amélie

    2015-01-01

    Molecular diagnosis of monogenic diabetes and obesity is of paramount importance for both the patient and society, as it can result in personalized medicine associated with a better life and it eventually saves health care spending. Genetic clinical laboratories are currently switching from Sanger sequencing to next-generation sequencing (NGS) approaches but choosing the optimal protocols is not easy. Here, we compared the sequencing coverage of 43 genes involved in monogenic forms of diabetes and obesity, and variant detection rates, resulting from four enrichment methods based on the sonication of DNA (Agilent SureSelect, RainDance technologies), or using enzymes for DNA fragmentation (Illumina Nextera, Agilent HaloPlex). We analyzed coding exons and untranslated regions of the 43 genes involved in monogenic diabetes and obesity. We found that none of the methods achieves yet full sequencing of the gene targets. Nonetheless, the RainDance, SureSelect and HaloPlex enrichment methods led to the best sequencing coverage of the targets; while the Nextera method resulted in the poorest sequencing coverage. Although the sequencing coverage was high, we unexpectedly found that the HaloPlex method missed 20% of variants detected by the three other methods and Nextera missed 10%. The question of which NGS technique for genetic diagnosis yields the highest diagnosis rate is frequently discussed in the literature and the response is still unclear. Here, we showed that the RainDance enrichment method as well as SureSelect, which are both based on the sonication of DNA, resulted in a good sequencing quality and variant detection, while the use of enzymes to fragment DNA (HaloPlex or Nextera) might not be the best strategy to get an accurate sequencing.

  8. Prospects of lithium enrichment on 7Li isotope by method of controlled ions electro-migration

    NASA Astrophysics Data System (ADS)

    Martoyan, G. A.; Kalugin, M. M.; Gabrielyan, A. V.; Martoyan, A. G.

    2016-01-01

    This paper deals with a new electro-membrane method of enrichment of 7Li isotope. The data are presented on the importance and application fields regarding the use of 7Li isotopes. Existing methods and criteria of separation of lithium isotopes are discussed. The principle of new technology, regimes of enrichment experiments, and analysis details of obtained products are briefly described.

  9. Enriching semantic knowledge bases for opinion mining in big data applications.

    PubMed

    Weichselbraun, A; Gindl, S; Scharl, A

    2014-10-01

    This paper presents a novel method for contextualizing and enriching large semantic knowledge bases for opinion mining with a focus on Web intelligence platforms and other high-throughput big data applications. The method is not only applicable to traditional sentiment lexicons, but also to more comprehensive, multi-dimensional affective resources such as SenticNet. It comprises the following steps: (i) identify ambiguous sentiment terms, (ii) provide context information extracted from a domain-specific training corpus, and (iii) ground this contextual information to structured background knowledge sources such as ConceptNet and WordNet. A quantitative evaluation shows a significant improvement when using an enriched version of SenticNet for polarity classification. Crowdsourced gold standard data in conjunction with a qualitative evaluation sheds light on the strengths and weaknesses of the concept grounding, and on the quality of the enrichment process.

  10. Foraging-Based Enrichment Promotes More Varied Behaviour in Captive Australian Fur Seals (Arctocephalus pusillus doriferus)

    PubMed Central

    Hocking, David P.; Salverson, Marcia; Evans, Alistair R.

    2015-01-01

    During wild foraging, Australian fur seals (Arctocephalus pusillus doriferus) encounter many different types of prey in a wide range of scenarios, yet in captive environments they are typically provided with a narrower range of opportunities to display their full repertoire of behaviours. This study aimed to quantitatively explore the effect of foraging-based enrichment on the behaviour and activity patterns displayed by two captive Australian fur seals at Melbourne Zoo, Australia. Food was presented as a scatter in open water, in a free-floating ball device, or in a static box device, with each treatment separated by control trials with no enrichment. Both subjects spent more time interacting with the ball and static box devices than the scatter feed. The total time spent pattern swimming was reduced in the enrichment treatments compared to the controls, while the time spent performing random swimming behaviours increased. There was also a significant increase in the total number of bouts of behaviour performed in all three enrichment treatments compared to controls. Each enrichment method also promoted a different suit of foraging behaviours. Hence, rather than choosing one method, the most effective way to increase the diversity of foraging behaviours, while also increasing variation in general activity patterns, is to provide seals with a wide range of foraging scenarios where food is encountered in different ways. PMID:25946412

  11. Growth of 18O isotopically enriched ZnO nanorods by two novel VPT methods

    NASA Astrophysics Data System (ADS)

    Gray, Ciarán; Trefflich, Lukas; Röder, Robert; Ronning, Carsten; Henry, Martin O.; McGlynn, Enda

    2017-02-01

    We have developed two novel vapour phase transport methods to grow ZnO nanorod arrays isotopically enriched with 18O. Firstly, a three-step process used to grow natural and Zn-enriched ZnO nanorods has been further modified, by replacing the atmospheric O2 with enriched 18O2, in order to grow 18O-enriched ZnO nanorods using this vapour-solid method on chemical bath deposited buffer layers. In addition, 18O-enriched ZnO nanorods were successfully grown using 18O isotopically enriched ZnO source powders in a vapour-liquid-solid growth method. Scanning electron microscopy studies confirmed the success of both growth methods in terms of nanorod morphology, although in the case of the vapour-liquid-solid samples, the nanorods' c-axes were not vertically aligned due to the use of a non-epitaxial substrate. Raman and PL studies indicated clearly that O-enrichment was successful in both cases, although the results indicate that the enrichment is at a lower level in our samples compared to previous reports with the same nominal enrichment levels. The results of our studies also allow us to comment on both levels of enrichment achieved and on novel effects of the high temperature growth environment on the nanorod growth, as well as suggesting possible mechanisms for such effects. Very narrow photoluminescence line widths, far narrower than those reported previously in the literature for isotopically enriched bulk ZnO, are seen in both the vapour-solid and vapour-liquid-solid nanorod samples demonstrating their excellent optical quality and their potential for use in detailed optical studies of defects and impurities using low temperature photoluminescence.

  12. A new enrichment method for isolation of Bacillus thuringiensis from diverse sample types.

    PubMed

    Patel, Ketan D; Bhanshali, Forum C; Chaudhary, Avani V; Ingle, Sanjay S

    2013-05-01

    New or more efficient methodologies having different principles are needed, as one method could not be suitable for isolation of organisms from samples of diverse types and from various environments. In present investigation, growth kinetics study revealed a higher germination rate, a higher growth rate, and maximum sporulation of Bacillus thuringiensis (Bt) compared to other Bacillus species. Considering these facts, a simple and efficient enrichment method was devised which allowed propagation of spores and vegetative cells of Bt and thereby increased Bt cell population proportionately. The new enrichment method yielded Bt from 44 out of 58 samples. Contrarily, Bt was isolated only from 16 and 18 samples by sodium acetate selection and dry heat pretreatment methods, respectively. Moreover, the percentages of Bt colonies isolated by the enrichment method were higher comparatively. Vegetative whole cell protein profile analysis indicated isolation of diverse population of Bt from various samples. Bt strains isolated by the enrichment method represented novel serovars and possibly new cry2 gene.

  13. Microdroplet-based PCR enrichment for large-scale targeted sequencing.

    PubMed

    Tewhey, Ryan; Warner, Jason B; Nakano, Masakazu; Libby, Brian; Medkova, Martina; David, Patricia H; Kotsopoulos, Steve K; Samuels, Michael L; Hutchison, J Brian; Larson, Jonathan W; Topol, Eric J; Weiner, Michael P; Harismendy, Olivier; Olson, Jeff; Link, Darren R; Frazer, Kelly A

    2009-11-01

    Targeted enrichment of specific loci of the human genome is a promising approach to enable sequencing-based studies of genetic variation in large populations. Here we describe an enrichment approach based on microdroplet PCR, which enables 1.5 million amplifications in parallel. We sequenced six samples enriched by microdroplet or traditional singleplex PCR using primers targeting 435 exons of 47 genes. Both methods generated similarly high-quality data: 84% of the uniquely mapping reads fell within the targeted sequences; coverage was uniform across approximately 90% of targeted bases; sequence variants were called with >99% accuracy; and reproducibility between samples was high (r(2) = 0.9). We scaled the microdroplet PCR to 3,976 amplicons totaling 1.49 Mb of sequence, sequenced the resulting sample with both Illumina GAII and Roche 454, and obtained data with equally high specificity and sensitivity. Our results demonstrate that microdroplet technology is well suited for processing DNA for massively parallel enrichment of specific subsets of the human genome for targeted sequencing.

  14. Unattended Environmental Sampling and Laser-based Enrichment Assay for Detection of Undeclared HEU Production in Enrichment Plants

    SciTech Connect

    Anheier, Norman C.; Bushaw, Bruce A.

    2010-04-15

    Nuclear power is enjoying rapid growth as government energy policies and public demand shift toward carbon neutral energy production. Accompanying the growth in nuclear power is the requirement for increased nuclear fuel production, including a significant expansion in uranium enrichment capacity. Essential to the success of the nuclear energy renaissance is the development and implementation of sustainable, proliferation-resistant nuclear power generation. Unauthorized production of highly enriched uranium (HEU) remains the primary proliferation concern for modern gaseous centrifuge enrichment plants (GCEPs). While to date there has been no indication of declared, safeguarded GCEPs producing HEU, the massive separative work unit (SWU) processing power of modern GCEPs presents a significant latent risk of nuclear breakout and suggests the need for more timely detection of potential facility misuse. The Pacific Northwest National Laboratory is developing an unattended safeguards instrument, combining continuous aerosol particulate collection with uranium isotope assay, to provide timely HEU detection within a GCEP. This approach is based on laser vaporization of aerosol particulates, followed by laser spectroscopy to characterize the uranium enrichment level. We demonstrate enrichment assay, with relative isotope abundance uncertainty <5%, on individual micron-sized particles that are trace components within a mixture ‘background’ particles

  15. Isolation method (direct plating or enrichment) does not affect antimicrobial susceptibility of Campylobacter from chicken carcasses

    USDA-ARS?s Scientific Manuscript database

    To determine if Campylobacter isolation method influenced antimicrobial susceptibility results, the minimum inhibitory concentrations (MIC) of nine antimicrobials were compared for 291 pairs of Campylobacter isolates recovered from chicken carcass rinse samples using direct plating and an enrichment...

  16. Adaptation of the doubly labeled water method for subjects consuming isotopically enriched water.

    PubMed

    Gretebeck, R J; Schoeller, D A; Socki, R A; Davis-Street, J; Gibson, E K; Schulz, L O; Lane, H W

    1997-02-01

    The use of doubly labeled water (DLW) to measure energy expenditure is subject to error if the background abundance of the oxygen and hydrogen isotope tracers changes during the test period. This study evaluated the accuracy and precision of different methods by which such background isotope changes can be corrected, including a modified method that allows prediction of the baseline that would be achieved if subjects were to consume water from a given source indefinitely. Subjects in this study were eight women (4 test subjects and 4 control subjects) who consumed for 28 days water enriched to resemble drinking water aboard the United States space shuttle. Test subjects and control subjects were given a DLW dose on days 1 and 15, respectively. The change to an enriched water source produced a bias in expenditure calculations that exceeded 2.9 MJ/day (35%), relative to calculations from intake-balance. The proposed correction based on the predicted final abundance of 18O and deuterium after equilibration to the new water source eliminated this bias, as did the traditional use of a control group. This new modified correction method is advantageous under field conditions when subject numbers are limited.

  17. Benchmarking methods and data sets for ligand enrichment assessment in virtual screening.

    PubMed

    Xia, Jie; Tilahun, Ermias Lemma; Reid, Terry-Elinor; Zhang, Liangren; Wang, Xiang Simon

    2015-01-01

    Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of benchmarking methods as well as data sets and highlight three main types of biases found in benchmarking sets, i.e. "analogue bias", "artificial enrichment" and "false negative". In addition, we introduce our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structure-based VS approaches, and its implementations to three important human histone deacetylases (HDACs) isoforms, i.e. HDAC1, HDAC6 and HDAC8. The leave-one-out cross-validation (LOO CV) demonstrates that the benchmarking sets built by our algorithm are maximum-unbiased as measured by property matching, ROC curves and AUCs. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. An Innovative Non-Destructive and Computational Method for Uranium Activity and Enrichment Verification of UF{sub 6} Cylinder

    SciTech Connect

    El-Mongy, Sayed A.; Allam, K.M.; Farid, Osama M.

    2006-07-01

    Verification of {sup 235}U enrichment in uranium hexafluoride (UF{sub 6}) cylinders is often achieved by destructive and non-destructive assay techniques. These techniques are time consuming, need suitable and similar standard, in addition to loss of the nuclear material in the case of destructive analysis. This paper introduce an innovative approach for verifying of {sup 235}U enrichment in UF{sub 6} cylinder. The approach is based on measuring dose rate ({mu}Sv/h) resulted from the emitted gamma rays of {sup 235}U at the surface of the cylinder and then calculating the activity of uranium and enrichment percentage inside the cylinder by a three dimensional model. Attenuation of the main {sup 235}U gamma transitions due to the cylinder wall (5A Type of Ni alloy) was also calculated and corrected for. The method was applied on UF{sub 6} cylinders enriched with 19.75% of {sup 235}U. The calculated enrichment was found to be 18% with 9% uncertainty. By the suggested method, the calculated total uranium activity inside one of the investigated UF{sub 6} cylinder was found close to the target (certified) value (5.6 GBq) with 9% uncertainty. The method is being developed by taking into consideration other parameters. (authors)

  19. Enhancing the Identification of Phosphopeptides from Putative Basophilic Kinase Substrates Using Ti (IV) Based IMAC Enrichment*

    PubMed Central

    Zhou, Houjiang; Low, Teck Y.; Hennrich, Marco L.; van der Toorn, Henk; Schwend, Thomas; Zou, Hanfa; Mohammed, Shabaz; Heck, Albert J. R.

    2011-01-01

    Metal and metal oxide chelating-based phosphopeptide enrichment technologies provide powerful tools for the in-depth profiling of phosphoproteomes. One weakness inherent to current enrichment strategies is poor binding of phosphopeptides containing multiple basic residues. The problem is exacerbated when strong cation exchange (SCX) is used for pre-fractionation, as under low pH SCX conditions phosphorylated peptides with multiple basic residues elute with the bulk of the tryptic digest and therefore require more stringent enrichment. Here, we report a systematic evaluation of the characteristics of a novel phosphopeptide enrichment approach based on a combination of low pH SCX and Ti4+-immobilized metal ion affinity chromatography (IMAC) comparing it one-to-one with the well established low pH SCX-TiO2 enrichment method. We also examined the effect of 1,1,1,3,3,3-hexafluoroisopropanol (HFP), trifluoroacetic acid (TFA), or 2,5-dihydroxybenzoic acid (DHB) in the loading buffer, as it has been hypothesized that high levels of TFA and the perfluorinated solvent HFP improve the enrichment of phosphopeptides containing multiple basic residues. We found that Ti4+-IMAC in combination with TFA in the loading buffer, outperformed all other methods tested, enabling the identification of around 5000 unique phosphopeptides containing multiple basic residues from 400 μg of a HeLa cell lysate digest. In comparison, ∼2000 unique phosphopeptides could be identified by Ti4+-IMAC with HFP and close to 3000 by TiO2. We confirmed, by motif analysis, the basic phosphopeptides enrich the number of putative basophilic kinases substrates. In addition, we performed an experiment using the SCX/Ti4+-IMAC methodology alongside the use of collision-induced dissociation (CID), higher energy collision induced dissociation (HCD) and electron transfer dissociation with supplementary activation (ETD) on considerably more complex sample, consisting of a total of 400 μg of triple dimethyl labeled

  20. Comparison of polymerase chain reaction methods and plating for analysis of enriched cultures of Listeria monocytogenes when using the ISO11290-1 method.

    PubMed

    Dalmasso, Marion; Bolocan, Andrei Sorin; Hernandez, Marta; Kapetanakou, Anastasia E; Kuchta, Tomáš; Manios, Stavros G; Melero, Beatriz; Minarovičová, Jana; Muhterem, Meryem; Nicolau, Anca Ioana; Rovira, Jordi; Skandamis, Panagiotis N; Stessl, Beatrix; Wagner, Martin; Jordan, Kieran; Rodríguez-Lázaro, David

    2014-03-01

    Analysis for Listeria monocytogenes by ISO11290-1 is time-consuming, entailing two enrichment steps and subsequent plating on agar plates, taking five days without isolate confirmation. The aim of this study was to determine if a polymerase chain reaction (PCR) assay could be used for analysis of the first and second enrichment broths, saving four or two days, respectively. In a comprehensive approach involving six European laboratories, PCR and traditional plating of both enrichment broths from the ISO11290-1 method were compared for the detection of L. monocytogenes in 872 food, raw material and processing environment samples from 13 different dairy and meat food chains. After the first and second enrichments, total DNA was extracted from the enriched cultures and analysed for the presence of L. monocytogenes DNA by PCR. DNA extraction by chaotropic solid-phase extraction (spin column-based silica) combined with real-time PCR (RTi-PCR) was required as it was shown that crude DNA extraction applying sonication lysis and boiling followed by traditional gel-based PCR resulted in fewer positive results than plating. The RTi-PCR results were compared to plating, as defined by the ISO11290-1 method. For first and second enrichments, 90% of the samples gave the same results by RTi-PCR and plating, whatever the RTi-PCR method used. For the samples that gave different results, plating was significantly more accurate for detection of positive samples than RTi-PCR from the first enrichment, but RTi-PCR detected a greater number of positive samples than plating from the second enrichment, regardless of the RTi-PCR method used. RTi-PCR was more accurate for non-food contact surface and food contact surface samples than for food and raw material samples especially from the first enrichment, probably because of sample matrix interference. Even though RTi-PCR analysis of the first enrichment showed less positive results than plating, in outbreak scenarios where a rapid result is

  1. Enrichment process of biogas using simultaneous Absorption - Adsorption methods

    NASA Astrophysics Data System (ADS)

    Kusrini, Eny; Lukita, Maya; Gozan, Misri; Susanto, Bambang Heru; Nasution, Dedy Alharis; Rahman, Arif; Gunawan, Cindy

    2017-03-01

    Removal of CO2 in biogas is an essential methods to the purification and upgrading of biogas. Natural Clinoptilolite zeolites were evaluated as sorbents for purification of biogas that produced from palm oil mill effluent (POME) by anerobic-digestion method. The absorption and adsorption experiments were conducted in a fixed-bed two column adsorption unit by simultaneous absorption-adsorption method. The Ca(OH)2 solution with concentration of 0.062 M was used as absorption method. Sorbent for removal of CO2 in biogas have been prepared by modifying of Clinoptilolite zeolites with an acid (HCl, 2M) and alkaline (NaOH, 2M), calcined at 450°C and then coated using chitosan (0.5 w/v%) in order to increase their adsorption capacity. The removal of CO2 in biogas was achieved about ˜83% using 2.5 g of sorbent zeolite (2M)/chitosan dosage for each column, breakthrough time of 30 min, and flow rate of 100 mL/min. Clinoptilolite zeolites with modifications of an acid-alkaline and chitosan (zeolite (2M)/chitosan) are promising sorbents due to the amine groups from chitosan and high surface-volume ratio are one of important factors in a simultaneous absorption-adsorption method.

  2. Specific Affinity Enrichment of Electrochemically Cleaved Peptides Based on Cu(II)-Mediated Spirolactone Tagging

    PubMed Central

    2017-01-01

    Specific digestion of proteins is an essential step for mass spectrometry-based proteomics, and the chemical labeling of the resulting peptides is often used for peptide enrichment or the introduction of desirable tags. Electrochemical oxidation yielding specific cleavage C-terminal to tyrosine (Tyr) and tryptophan (Trp) residues provides a potential alternative to enzymatic digestion and a possibility for further chemical labeling by introducing reactive spirolactone moieties. However, spirolactone-containing peptides suffer from low stability due to hydrolysis and intramolecular side reactions. We found that Cu(II) ions stabilize the spirolactone and prevent intramolecular side reactions during chemical labeling, allowing efficient chemical tagging with a reduced excess of labeling reagent without intramolecular side reactions. On the basis of this reaction, we developed an analytical procedure combining electrochemical digestion, Cu(II)-mediated spirolactone biotinylation, and enrichment by avidin affinity chromatography with mass spectrometry. The method was optimized with the tripeptide LWL and subsequently applied to chicken egg white lysozyme, in which one biotinylated electrochemistry (EC)-cleaved peptide was identified after affinity enrichment. This proof-of-principle shows that specific enrichment of electrochemically cleaved spirolactone-containing peptides can be used for protein identification and notably that inclusion of Cu(II) ions is essential for stabilizing spirolactones for subsequent biotinylation. PMID:28593756

  3. Combining multiple tools outperforms individual methods in gene set enrichment analyses

    PubMed Central

    Ng, Milica; Wilson, Nicholas J.; Sheridan, Julie M.; Huynh, Huy; Wilson, Michael J.

    2017-01-01

    Abstract Motivation: Gene set enrichment (GSE) analysis allows researchers to efficiently extract biological insight from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of GSE analysis methods and hence it has become increasingly difficult for researchers to select an optimal GSE tool based on their particular dataset. Moreover, the majority of GSE analysis methods do not allow researchers to simultaneously compare gene set level results between multiple experimental conditions. Results: The ensemble of genes set enrichment analyses (EGSEA) is a method developed for RNA-sequencing data that combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. EGSEA’s gene set database contains around 25 000 gene sets from sixteen collections. It has multiple visualization capabilities that allow researchers to view gene sets at various levels of granularity. EGSEA has been tested on simulated data and on a number of human and mouse datasets and, based on biologists’ feedback, consistently outperforms the individual tools that have been combined. Our evaluation demonstrates the superiority of the ensemble approach for GSE analysis, and its utility to effectively and efficiently extrapolate biological functions and potential involvement in disease processes from lists of differentially regulated genes. Availability and Implementation: EGSEA is available as an R package at http://www.bioconductor.org/packages/EGSEA/. The gene sets collections are available in the R package EGSEAdata from http://www.bioconductor.org/packages/EGSEAdata/. Contacts:monther.alhamdoosh@csl.com.au ormritchie@wehi.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27694195

  4. Combining multiple tools outperforms individual methods in gene set enrichment analyses.

    PubMed

    Alhamdoosh, Monther; Ng, Milica; Wilson, Nicholas J; Sheridan, Julie M; Huynh, Huy; Wilson, Michael J; Ritchie, Matthew E

    2017-02-01

    Gene set enrichment (GSE) analysis allows researchers to efficiently extract biological insight from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of GSE analysis methods and hence it has become increasingly difficult for researchers to select an optimal GSE tool based on their particular dataset. Moreover, the majority of GSE analysis methods do not allow researchers to simultaneously compare gene set level results between multiple experimental conditions. The ensemble of genes set enrichment analyses (EGSEA) is a method developed for RNA-sequencing data that combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. EGSEA's gene set database contains around 25 000 gene sets from sixteen collections. It has multiple visualization capabilities that allow researchers to view gene sets at various levels of granularity. EGSEA has been tested on simulated data and on a number of human and mouse datasets and, based on biologists' feedback, consistently outperforms the individual tools that have been combined. Our evaluation demonstrates the superiority of the ensemble approach for GSE analysis, and its utility to effectively and efficiently extrapolate biological functions and potential involvement in disease processes from lists of differentially regulated genes. EGSEA is available as an R package at http://www.bioconductor.org/packages/EGSEA/ . The gene sets collections are available in the R package EGSEAdata from http://www.bioconductor.org/packages/EGSEAdata/ . monther.alhamdoosh@csl.com.au mritchie@wehi.edu.au. Supplementary data are available at Bioinformatics online.

  5. Unattended Monitoring of HEU Production in Gaseous Centrifuge Enrichment Plants using Automated Aerosol Collection and Laser-based Enrichment Assay

    SciTech Connect

    Anheier, Norman C.; Bushaw, Bruce A.

    2010-08-11

    Nuclear power is enjoying rapid growth as government energy policies and public demand shift toward low carbon energy production. Pivotal to the global nuclear power renaissance is the development and deployment of robust safeguards instrumentation that allows the limited resources of the IAEA to keep pace with the expansion of the nuclear fuel cycle. Undeclared production of highly enriched uranium (HEU) remains a primary proliferation concern for modern gaseous centrifuge enrichment plants (GCEPs), due to their massive separative work unit (SWU) processing power and comparably short cascade equilibrium timescale. The Pacific Northwest National Laboratory is developing an unattended safeguards instrument, combining continuous aerosol particulate collection with uranium isotope assay, to provide timely detection of HEU production within a GCEP. This approach is based on laser vaporization of aerosol particulates, followed by laser spectroscopy to characterize the uranium enrichment level. Our prior investigation demonstrated single-shot detection sensitivity approaching the femtogram range and relative isotope ratio uncertainty better than 10% using gadolinium as a surrogate for uranium. In this paper we present measurement results on standard samples containing traces of depleted, natural, and low enriched uranium, as well as measurements on aerodynamic size uranium particles mixed in background materials (e.g., dust, minerals, soils). Improvements and optimizations in the detection electronics, signal timing, calibration, and laser alignment have lead to significant improvements in detection sensitivity and enrichment accuracy, contributing to an overall reduction in the false alarm probability. The sample substrate media was also found to play a significant role in facilitating laser-induced vaporization and the production of energetic plasma conditions, resulting in ablation optimization and further improvements in the isotope abundance sensitivity.

  6. Whole-system nutrient enrichment increases secondary production in a detritus-based ecosystem

    Treesearch

    W.F. Cross; J.B. Wallace; A.D. Rosemond; S.L. Eggert

    2006-01-01

    Although the effects of nutrient enrichment on consumer-resource dynamics are relatively well studied in ecosystems based on living plants, little is known about the manner in which enrichment influences the dynamics and productivity of consumers and resources in detritus-based ecosystems. Because nutrients can stimulate loss of carbon at the base of detrital food webs...

  7. Method for enriching a gaseous isotopic mixture with at least one isotope

    SciTech Connect

    de Mevergnies, M.N.; Fettweis, P.

    1982-02-02

    There is described a method for enriching a gas-like isotopic mixture with at least one isotope, in which a mixture of Cf2Cl2 and O2 is irradiated by means of a pulsed and focalized laser beam having an optical frequency corresponding to a wave number lying in the band from 920 to 945 cm-1 to enrich the residual Cf2Cl2 with 37Cl, in the band from 1050 to 1075 cm-1 to produce CoF2 enriched with 13C and/or in the band from 1080 to 1095 cm-1 to enrich the residual Cf2Cl2 with 35Cl and 13C.

  8. Enriched Title-Based Keyword Index Generation Using dBase II.

    ERIC Educational Resources Information Center

    Rajendran, P. P.

    1986-01-01

    Describes the use of a database management system (DBMS)--dBaseII--to create an enriched title-based keyword index for a collection of news items at the Renewable Energy Resources Information Center of the Asian Institute of Technology. The use of DBMSs in libraries in developing countries is emphasized. (Author/LRW)

  9. Enriched Title-Based Keyword Index Generation Using dBase II.

    ERIC Educational Resources Information Center

    Rajendran, P. P.

    1986-01-01

    Describes the use of a database management system (DBMS)--dBaseII--to create an enriched title-based keyword index for a collection of news items at the Renewable Energy Resources Information Center of the Asian Institute of Technology. The use of DBMSs in libraries in developing countries is emphasized. (Author/LRW)

  10. Batch methods for enriching trace impurities in hydrogen gas for their further analysis

    DOEpatents

    Ahmed, Shabbir; Lee, Sheldon H.D.; Kumar, Romesh; Papdias, Dionissios D.

    2014-07-15

    Provided herein are batch methods and devices for enriching trace quantities of impurities in gaseous mixtures, such as hydrogen fuel. The methods and devices rely on concentrating impurities using hydrogen transport membranes wherein the time period for concentrating the sample is calculated on the basis of optimized membrane characteristics, comprising its thickness and permeance, with optimization of temperature, and wherein the enrichment of trace impurities is proportional to the pressure ratio P.sub.hi/P.sub.lo and the volume ratio V.sub.1/V.sub.2, with following detection of the impurities using commonly-available detection methods.

  11. WaveSeq: A Novel Data-Driven Method of Detecting Histone Modification Enrichments Using Wavelets

    PubMed Central

    Mitra, Apratim; Song, Jiuzhou

    2012-01-01

    Background Chromatin immunoprecipitation followed by next-generation sequencing is a genome-wide analysis technique that can be used to detect various epigenetic phenomena such as, transcription factor binding sites and histone modifications. Histone modification profiles can be either punctate or diffuse which makes it difficult to distinguish regions of enrichment from background noise. With the discovery of histone marks having a wide variety of enrichment patterns, there is an urgent need for analysis methods that are robust to various data characteristics and capable of detecting a broad range of enrichment patterns. Results To address these challenges we propose WaveSeq, a novel data-driven method of detecting regions of significant enrichment in ChIP-Seq data. Our approach utilizes the wavelet transform, is free of distributional assumptions and is robust to diverse data characteristics such as low signal-to-noise ratios and broad enrichment patterns. Using publicly available datasets we showed that WaveSeq compares favorably with other published methods, exhibiting high sensitivity and precision for both punctate and diffuse enrichment regions even in the absence of a control data set. The application of our algorithm to a complex histone modification data set helped make novel functional discoveries which further underlined its utility in such an experimental setup. Conclusions WaveSeq is a highly sensitive method capable of accurate identification of enriched regions in a broad range of data sets. WaveSeq can detect both narrow and broad peaks with a high degree of accuracy even in low signal-to-noise ratio data sets. WaveSeq is also suited for application in complex experimental scenarios, helping make biologically relevant functional discoveries. PMID:23029045

  12. Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria

    PubMed Central

    Ballhausen, Max-Bernhard; van Veen, Johannes A.; Hundscheid, Maria P. J.; de Boer, Wietse

    2015-01-01

    Mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. However, with exception of the soil bacterial genus Collimonas, occurrence of this feeding strategy has not been well examined. Evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. In this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. A short-term method based on baiting for bacteria that can rapidly adhere to fungal hyphae and a long-term method based on the enrichment of bacteria on fungal hyphae via repeated transfer. Hyphae-adhering bacteria were isolated, identified by 16S rDNA sequencing and tested for antifungal activity and the ability to feed on fungi as the sole source of carbon. Both methods yielded a range of potentially mycophagous bacterial isolates with little phylogenetic overlap. We also found indications for feeding preferences among the potentially mycophagous bacteria. Our results indicate that mycophagy could be an important growth strategy for rhizosphere bacteria. To our surprise, we found several potential plant pathogenic bacteria among the mycophagous isolates. We discuss the possible benefits that these bacteria might gain from colonizing fungal hyphae. PMID:26733962

  13. 3D hierarchical interface-enriched finite element method: Implementation and applications

    NASA Astrophysics Data System (ADS)

    Soghrati, Soheil; Ahmadian, Hossein

    2015-10-01

    A hierarchical interface-enriched finite element method (HIFEM) is proposed for the mesh-independent treatment of 3D problems with intricate morphologies. The HIFEM implements a recursive algorithm for creating enrichment functions that capture gradient discontinuities in nonconforming finite elements cut by arbitrary number and configuration of materials interfaces. The method enables the mesh-independent simulation of multiphase problems with materials interfaces that are in close proximity or contact while providing a straightforward general approach for evaluating the enrichments. In this manuscript, we present a detailed discussion on the implementation issues and required computational geometry considerations associated with the HIFEM approximation of thermal and mechanical responses of 3D problems. A convergence study is provided to investigate the accuracy and convergence rate of the HIFEM and compare them with standard FEM benchmark solutions. We will also demonstrate the application of this mesh-independent method for simulating the thermal and mechanical responses of two composite materials systems with complex microstructures.

  14. Comparison of direct-plating and enrichment methods for isolation of Vibrio cholerae from diarrhea patients.

    PubMed Central

    Lesmana, M; Richie, E; Subekti, D; Simanjuntak, C; Walz, S E

    1997-01-01

    A direct-plating method on thiosulfate citrate bile salts sucrose agar (DIR-TCBS) in conjunction with enrichment in alkaline peptone water (APW) incubated for both 6 h and 24 h followed by subculture onto TCBS (APW6h-TCBS and APW24h-TCBS, respectively) was performed on 16,034 rectal swab samples for isolating Vibrio cholerae. A total of 2,932 (18.3%) rectal swab samples were positive for V. cholerae O1 biotype El Tor, with the Ogawa serotype constituting 99.2% of the isolates. There were no significant differences in V. cholerae O1 isolation rates between the three culture systems nor between the combinations of any two systems. However, direct plating plus enrichment demonstrated a significantly higher V. cholerae O1 isolation rate than DIR-TCBS alone (P < 0.02). Conversely, enrichment procedure, alone or in combination with DIR-TCBS, yielded significantly more (P < 0.0001) V. cholerae non-O1 isolates than DIR-TCBS alone. The length of incubation time of the enrichment broth, 6 h, offers no significant advantages over 24 h for the isolation of V. cholerae O1 and non-O1. A 24-h enrichment broth incubation period has the practical advantage of being easy to integrate into a normal laboratory workday, whereas 6-h broth enrichment, although more commonly recommended, requires that arrangements be made for after-hours subculture. PMID:9196208

  15. Key genes and pathways in thyroid cancer based on gene set enrichment analysis.

    PubMed

    He, Wenwu; Qi, Bin; Zhou, Qiuxi; Lu, Chuansen; Huang, Qi; Xian, Lei; Chen, Mingwu

    2013-09-01

    The incidence of thyroid cancer and its associated morbidity has shown the most rapid increase among all cancers since 1982, but the mechanisms involved in thyroid cancer, particularly significant key genes induced in thyroid cancer, remain undefined. In many studies, gene probes have been used to search for key genes involved in causing and facilitating thyroid cancer. As a result, many possible virulence genes and pathways have been identified. However, these studies lack a case contrast for selecting the most possible virulence genes and pathways, as well as conclusive results with which to clarify the mechanisms of cancer development. In the present study, we used gene set enrichment and meta-analysis to select key genes and pathways. Based on gene set enrichment, we identified 5 downregulated and 4 upregulated mixed pathways in 6 tissue datasets. Based on the meta-analysis, there were 17 common pathways in the tissue datasets. One pathway, the p53 signaling pathway, which includes 13 genes, was identified by both the gene set enrichment analysis and meta-analysis. Genes are important elements that form key pathways. These pathways can induce the development of thyroid cancer later in life. The key pathways and genes identified in the present study can be used in the next stage of research, which will involve gene elimination and other methods of experimentation.

  16. A Pharmacology-Based Enrichment Program for Undergraduates Promotes Interest in Science

    PubMed Central

    Godin, Elizabeth A.; Wormington, Stephanie V.; Perez, Tony; Barger, Michael M.; Snyder, Kate E.; Richman, Laura Smart; Schwartz-Bloom, Rochelle; Linnenbrink-Garcia, Lisa

    2015-01-01

    There is a strong need to increase the number of undergraduate students who pursue careers in science to provide the “fuel” that will power a science and technology–driven U.S. economy. Prior research suggests that both evidence-based teaching methods and early undergraduate research experiences may help to increase retention rates in the sciences. In this study, we examined the effect of a program that included 1) a Summer enrichment 2-wk minicourse and 2) an authentic Fall research course, both of which were designed specifically to support students' science motivation. Undergraduates who participated in the pharmacology-based enrichment program significantly improved their knowledge of basic biology and chemistry concepts; reported high levels of science motivation; and were likely to major in a biological, chemical, or biomedical field. Additionally, program participants who decided to major in biology or chemistry were significantly more likely to choose a pharmacology concentration than those majoring in biology or chemistry who did not participate in the enrichment program. Thus, by supporting students' science motivation, we can increase the number of students who are interested in science and science careers. PMID:26538389

  17. A Pharmacology-Based Enrichment Program for Undergraduates Promotes Interest in Science.

    PubMed

    Godin, Elizabeth A; Wormington, Stephanie V; Perez, Tony; Barger, Michael M; Snyder, Kate E; Richman, Laura Smart; Schwartz-Bloom, Rochelle; Linnenbrink-Garcia, Lisa

    2015-01-01

    There is a strong need to increase the number of undergraduate students who pursue careers in science to provide the "fuel" that will power a science and technology-driven U.S. economy. Prior research suggests that both evidence-based teaching methods and early undergraduate research experiences may help to increase retention rates in the sciences. In this study, we examined the effect of a program that included 1) a Summer enrichment 2-wk minicourse and 2) an authentic Fall research course, both of which were designed specifically to support students' science motivation. Undergraduates who participated in the pharmacology-based enrichment program significantly improved their knowledge of basic biology and chemistry concepts; reported high levels of science motivation; and were likely to major in a biological, chemical, or biomedical field. Additionally, program participants who decided to major in biology or chemistry were significantly more likely to choose a pharmacology concentration than those majoring in biology or chemistry who did not participate in the enrichment program. Thus, by supporting students' science motivation, we can increase the number of students who are interested in science and science careers.

  18. BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

    PubMed

    Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

    2015-02-21

    Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis. We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

  19. Assessment of the latest NGS enrichment capture methods in clinical context.

    PubMed

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-02-11

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.

  20. Assessment of the latest NGS enrichment capture methods in clinical context

    PubMed Central

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-01-01

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelectQXT, against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelectQXT showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach. PMID:26864517

  1. An enriched finite element method to fractional advection-diffusion equation

    NASA Astrophysics Data System (ADS)

    Luan, Shengzhi; Lian, Yanping; Ying, Yuping; Tang, Shaoqiang; Wagner, Gregory J.; Liu, Wing Kam

    2017-03-01

    In this paper, an enriched finite element method with fractional basis [ 1,x^{α }] for spatial fractional partial differential equations is proposed to obtain more stable and accurate numerical solutions. For pure fractional diffusion equation without advection, the enriched Galerkin finite element method formulation is demonstrated to simulate the exact solution successfully without any numerical oscillation, which is advantageous compared to the traditional Galerkin finite element method with integer basis [ 1,x] . For fractional advection-diffusion equation, the oscillatory behavior becomes complex due to the introduction of the advection term which can be characterized by a fractional element Peclet number. For the purpose of addressing the more complex numerical oscillation, an enriched Petrov-Galerkin finite element method is developed by using a dimensionless fractional stabilization parameter, which is formulated through a minimization of the residual of the nodal solution. The effectiveness and accuracy of the enriched finite element method are demonstrated by a series of numerical examples of fractional diffusion equation and fractional advection-diffusion equation, including both one-dimensional and two-dimensional, steady-state and time-dependent cases.

  2. An enriched finite element method to fractional advection-diffusion equation

    NASA Astrophysics Data System (ADS)

    Luan, Shengzhi; Lian, Yanping; Ying, Yuping; Tang, Shaoqiang; Wagner, Gregory J.; Liu, Wing Kam

    2017-08-01

    In this paper, an enriched finite element method with fractional basis [ 1,x^{α }] for spatial fractional partial differential equations is proposed to obtain more stable and accurate numerical solutions. For pure fractional diffusion equation without advection, the enriched Galerkin finite element method formulation is demonstrated to simulate the exact solution successfully without any numerical oscillation, which is advantageous compared to the traditional Galerkin finite element method with integer basis [ 1,x] . For fractional advection-diffusion equation, the oscillatory behavior becomes complex due to the introduction of the advection term which can be characterized by a fractional element Peclet number. For the purpose of addressing the more complex numerical oscillation, an enriched Petrov-Galerkin finite element method is developed by using a dimensionless fractional stabilization parameter, which is formulated through a minimization of the residual of the nodal solution. The effectiveness and accuracy of the enriched finite element method are demonstrated by a series of numerical examples of fractional diffusion equation and fractional advection-diffusion equation, including both one-dimensional and two-dimensional, steady-state and time-dependent cases.

  3. Nanoprobe-based immobilized metal affinity chromatography for sensitive and complementary enrichment of multiply phosphorylated peptides.

    PubMed

    Wu, Huan-Ting; Hsu, Chuan-Chih; Tsai, Chia-Feng; Lin, Po-Chiao; Lin, Chun-Cheng; Chen, Yu-Ju

    2011-07-01

    Magnetic nanoparticles (MNP, <100 nm) have rapidly evolved as sensitive affinity probes for phosphopeptide enrichment. By taking advantage of the easy magnetic separation and flexible surface modification of the MNP, we developed a surface-blocked, nanoprobe-based immobilized metal ion affinity chromatography (NB-IMAC) method for the enhanced purification of multiply phosphorylated peptides. The NB-IMAC method allowed rapid and specific one-step enrichment by blocking the surface of titanium (IV) ion-charged nitrilotriacetic acid-conjugated MNP (Ti⁴-NTA-PEG@MNP) with low molecular weight polyethylene glycol. The MNP demonstrated highly sensitive and unbiased extraction of both mono- and multiply phosphorylated peptides from diluted β-casein (2 × 10⁻¹⁰  M). Without chemical derivation or fractionation, 1283 phosphopeptides were identified from 400 μg of Raji B cells with 80% purification specificity. We also showed the first systematic comparison on the particle size effect between nano-sclae IMAC and micro-scale IMAC. Inductively coupled plasma-mass spectrometry (ICP-MS) analysis revealed that MNP had a 4.6-fold higher capacity for metal ions per unit weight than did the magnetic micro-sized particle (MMP, 2-10 μm), resulting in the identification of more phosphopeptides as well as a higher percentage of multiply phosphorylated peptides (31%) at the proteome scale. Furthermore, NB-IMAC complements chromatography-based IMAC and TiO₂ methods because <13% of mono- and 12% of multiply phosphorylated peptide identifications overlapped among the 2700 phosphopeptides identified by the three methods. Notably, the number of multiply phosphorylated peptides was enriched twofold and threefold by NB-IMAC relative to micro-scale IMAC and TiO₂, respectively. NB-IMAC is an innovative material for increasing the identification coverage in phosphoproteomics. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment

    PubMed Central

    Pradeep, Prachi; Struble, Craig; Neumann, Terrence; Sem, Daniel S.; Merrill, Stephen J.

    2016-01-01

    Molecular docking is a computational technique which predicts the binding energy and the preferred binding mode of a ligand to a protein target. Virtual screening is a tool which uses docking to investigate large chemical libraries to identify ligands that bind favorably to a protein target. We have developed a novel scoring based distributed protein docking application to improve enrichment in virtual screening. The application addresses the issue of time and cost of screening in contrast to conventional systematic parallel virtual screening methods in two ways. Firstly, it automates the process of creating and launching multiple independent dockings on a high performance computing cluster. Secondly, it uses a Nȧive Bayes scoring function to calculate binding energy of un-docked ligands to identify and preferentially dock (Autodock predicted) better binders. The application was tested on four proteins using a library of 10,573 ligands. In all the experiments, (i). 200 of the 1000 best binders are identified after docking only ∼ 14% of the chemical library, (ii). 9 or 10 best-binders are identified after docking only ∼ 19% of the chemical library, and (iii). no significant enrichment is observed after docking ∼ 70% of the chemical library. The results show significant increase in enrichment of potential drug leads in early rounds of virtual screening. PMID:26671816

  5. A New Exhaustive Method and Strategy for Finding Motifs in ChIP-Enriched Regions

    PubMed Central

    Jia, Caiyan; Carson, Matthew B.; Wang, Yang; Lin, Youfang; Lu, Hui

    2014-01-01

    ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with next-generation parallel sequencing, allows for the genome-wide identification of protein-DNA interactions. This technology poses new challenges for the development of novel motif-finding algorithms and methods for determining exact protein-DNA binding sites from ChIP-enriched sequencing data. State-of-the-art heuristic, exhaustive search algorithms have limited application for the identification of short (, ) motifs (, ) contained in ChIP-enriched regions. In this work we have developed a more powerful exhaustive method (FMotif) for finding long (, ) motifs in DNA sequences. In conjunction with our method, we have adopted a simple ChIP-enriched sampling strategy for finding these motifs in large-scale ChIP-enriched regions. Empirical studies on synthetic samples and applications using several ChIP data sets including 16 TF (transcription factor) ChIP-seq data sets and five TF ChIP-exo data sets have demonstrated that our proposed method is capable of finding these motifs with high efficiency and accuracy. The source code for FMotif is available at http://211.71.76.45/FMotif/. PMID:24475069

  6. A new method to track seed dispersal and recruitment using 15N isotope enrichment.

    PubMed

    Carlo, Tomás A; Tewksbury, Joshua J; Martínez Del Río, Carlos

    2009-12-01

    Seed dispersal has a powerful influence on population dynamics, genetic structuring, evolutionary rates, and community ecology. Yet, patterns of seed dispersal are difficult to measure due to methodological shortcomings in tracking dispersed seeds from sources of interest. Here we introduce a new method to track seed dispersal: stable isotope enrichment. It consists of leaf-feeding plants with sprays of 15N-urea during the flowering stage such that seeds developed after applications are isotopically enriched. We conducted a greenhouse experiment with Solanum americanum and two field experiments with wild Capsicum annuum in southern Arizona, USA, to field-validate the method. First, we show that plants sprayed with 15N-urea reliably produce isotopically enriched progeny, and that delta 15N (i.e., the isotopic ratio) of seeds and seedlings is a linear function of the 15N-urea concentration sprayed on mothers. We demonstrate that three urea dosages can be used to distinctly enrich plants and unambiguously differentiate their offspring after seeds are dispersed by birds. We found that, with high urea dosages, the resulting delta 15N values in seedlings are 10(3) - 10(4) times higher than the delta 15N values of normal plants. This feature allows tracking not only where seeds arrive, but in locations where seeds germinate and recruit, because delta 15N enrichment is detectable in seedlings that have increased in mass by at least two orders of magnitude before fading to normal delta 15N values. Last, we tested a mixing model to analyze seed samples in bulk. We used the delta 15N values of batches (i.e., combined seedlings or seeds captured in seed traps) to estimate the number of enriched seeds coming from isotopically enriched plants in the field. We confirm that isotope enrichment, combined with batch-sampling, is a cheap, reliable, and user-friendly method for bulk-processing seeds and is thus excellent for the detection of rare dispersal events. This method could

  7. Benchmarking Methods and Data Sets for Ligand Enrichment Assessment in Virtual Screening

    PubMed Central

    Xia, Jie; Tilahun, Ermias Lemma; Reid, Terry-Elinor; Zhang, Liangren; Wang, Xiang Simon

    2014-01-01

    Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of benchmarking methods as well as data sets and highlight three main types of biases found in benchmarking sets, i.e. “analogue bias”, “artificial enrichment” and “false negative”. In addition, we introduced our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structure-based VS approaches, and its implementations to three important human histone deacetylase (HDAC) isoforms, i.e. HDAC1, HDAC6 and HDAC8. The Leave-One-Out Cross-Validation (LOO CV) demonstrates that the benchmarking sets built by our algorithm are maximum-unbiased in terms of property matching, ROC curves and AUCs. PMID:25481478

  8. Nucleotide analogs and new buffers improve a generalized method to enrich for low abundance mutations.

    PubMed Central

    Day, J P; Hammer, R P; Bergstrom, D; Barany, F

    1999-01-01

    A high sensitivity method for detecting low level mutations is under development. A PCR reaction is performed in which a restriction site is introduced in wild-type DNA by alteration of specific bases. Digestion of wild-type DNA by the cognate restriction endonuclease (RE) enriches for products with mutations within the recognition site. After reamplification, mutations are identified by a ligation detection reaction (LDR). This PCR/RE/LDR assay was initially used to detect PCR error in known wild-type samples. PCR error was measured in low |Deltap K a| buffers containing tricine, EPPS and citrate, as well as otherwise identical buffers containing Tris. PCR conditions were optimized to minimize PCR error using perfect match primers at the Msp I site in the p53 tumor suppressor gene at codon 248. However, since mutations do not always occur within pre-existing restriction sites, a generalized PCR/RE/LDR method requires the introduction of a new restriction site. In principle, PCR with mismatch primers can alter specific bases in a sequence and generate a new restriction site. However, extension from 3' mismatch primers may generate misextension products. We tested conversion of the Msp I (CCGG) site to a Taq I site (TCGA). Conversion was unsuccessful using a natural base T mismatch primer set. Conversion was successful when modified primers containing the 6 H,8 H -3, 4-dihydropyrimido[4,5- c ][1,2]oxazine-7-one (Q6) base at 3'-ends were used in three cycles of preconversion PCR prior to conversion PCR using the 3' natural base T primers. The ability of the pyrimidine analog Q6 to access both a T-like and C-like tautomer appears to greatly facilitate the conversion. PMID:10101189

  9. Enrichment, Amplification, and Sequence-Based Typing of Salmonella enterica and Other Foodborne Pathogens.

    PubMed

    Edlind, Tom; Brewster, Jeffrey D; Paoli, George C

    2017-01-01

    Detection of Salmonella enterica in foods typically involves microbiological enrichment, molecular-based assay, and subsequent isolation and identification of a pure culture. This is ideally followed by strain typing, which provides information critical to the investigation of outbreaks and the attribution of their sources. Pulsed-field gel electrophoresis is the "gold standard" for S. enterica strain typing, but its limitations have encouraged the search for alternative methods, including whole genome sequencing. Both methods typically require a pure culture, which adds to the cost and turnaround time. A more rapid and cost-effective method with sufficient discriminatory power would benefit food industries, regulatory agencies, and public health laboratories. To address this need, a novel enrichment, amplification, and sequence-based typing (EAST) approach was developed involving (i) overnight enrichment and total DNA preparation, (ii) amplification of polymorphic tandem repeat-containing loci with electrophoretic detection, and (iii) DNA sequencing and bioinformatic analysis to identify related strains. EAST requires 3 days or less and provides a strain resolution that exceeds serotyping and is comparable to pulsed-field gel electrophoresis. Evaluation with spiked ground turkey demonstrated its sensitivity (with a starting inoculum of ≤1 CFU/g) and specificity (with unique or nearly unique alleles relative to databases of >1,000 strains). In tests with unspiked retail chicken parts, 3 of 11 samples yielded S. enterica -specific PCR products. Sequence analysis of three distinct typing targets (SeMT1, SeCRISPR1, and SeCRISPR2) revealed consistent similarities to specific serotype Schwarzengrund, Montevideo, and Typhimurium strains. EAST provides a time-saving and cost-effective approach for detecting and typing foodborne S. enterica , and postenrichment steps can be commercially outsourced to facilitate its implementation. Initial studies with Listeria

  10. Electronic and optoelectronic devices based on chirality-enriched wafer-scale single-wall carbon nanotube thin films

    NASA Astrophysics Data System (ADS)

    Gao, Weilu; He, Xiaowei; Xie, Lijuan; Zhang, Qi; Haroz, Erik; Doorn, Stephen K.; Kono, Junichiro

    2015-03-01

    The unique and rich material properties of single-wall carbon nanotubes (SWCNTs) make them attractive for nano-electronic and optoelectronic applications. Slight changes in tube diameter and wrapping angle, defined by the chirality indices (n, m), can dramatically modify the bandstructure, which can be utilized for designing devices with tailored properties. However, it remains to be a challenge to fabricate macroscopic, single-chirality devices. Here, we introduce a simple way of producing chirality-enriched wafer-scale SWCNT films by combining recently developed solution-based polymer-modified sorting method and vacuum filtration. The produced thin films can be easily transferred onto any substrate to have a CMOS compatible wafer. We fabricated a transistor of (6,5)-enriched SWCNTs with an on/off ratio >103. Large-scale photothermoelectric-effect-based and photovoltaic-effect-based photodetectors made of (6,6)- and (6,5)-enriched films, respectively, will also be discussed.

  11. Monitoring the enrichment of virgin olive oil with natural antioxidants by using a new capillary electrophoresis method.

    PubMed

    Nevado, Juan José Berzas; Robledo, Virginia Rodríguez; Callado, Carolina Sánchez-Carnerero

    2012-07-15

    The enrichment of virgin olive oil (VOO) with natural antioxidants contained in various herbs (rosemary, thyme and oregano) was studied. Three different enrichment procedures were used for the solid-liquid extraction of antioxidants present in the herbs to VOO. One involved simply bringing the herbs into contact with the VOO for 190 days; another keeping the herb-VOO mixture under stirring at room temperature (25°C) for 11 days; and the third stirring at temperatures above room level (35-40°C). The efficiency of each procedure was assessed by using a reproducible, efficient, reliable analytical capillary zone electrophoresis (CZE) method to separate and determine selected phenolic compounds (rosmarinic and caffeic acid) in the oil. Prior to electrophoretic separation, the studied antioxidants were isolated from the VOO matrix by using an optimised preconcentration procedure based on solid phase extraction (SPE). The CZE method was optimised and validated. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. NMR method for measuring carbon-13 isotopic enrichment of metabolites in complex solutions.

    PubMed

    Lewis, Ian A; Karsten, Ryan H; Norton, Mark E; Tonelli, Marco; Westler, William M; Markley, John L

    2010-06-01

    Isotope-based methods are commonly used for metabolic flux analysis and metabolite quantification in biological extracts. Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical tool for these studies because NMR can unambiguously identify compounds and accurately measure (13)C enrichment. We have developed a new pulse sequence, isotope-edited total correlation spectroscopy (ITOCSY), that filters two-dimensional (1)H-(1)H NMR spectra from (12)C- and (13)C-containing molecules into separate, quantitatively equivalent spectra. The ITOCSY spectra of labeled and unlabeled molecules are directly comparable and can be assigned using existing bioinformatics tools. In this study, we evaluate ITOCSY using synthetic mixtures of standards and extracts from Escherichia coli . We show that ITOCSY has low technical error (6.6% for metabolites ranging from 0.34 to 6.2 mM) and can detect molecules at concentrations less than 10 muM. We propose ITOCSY as a practical NMR strategy for metabolic flux analysis, isotope dilution experiments, and other methods that rely on carbon-13 labeling.

  13. NMR Method for Measuring Carbon-13 Isotopic Enrichment of Metabolites in Complex Solutions

    PubMed Central

    2010-01-01

    Isotope-based methods are commonly used for metabolic flux analysis and metabolite quantification in biological extracts. Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical tool for these studies because NMR can unambiguously identify compounds and accurately measure 13C enrichment. We have developed a new pulse sequence, isotope-edited total correlation spectroscopy (ITOCSY), that filters two-dimensional 1H−1H NMR spectra from 12C- and 13C-containing molecules into separate, quantitatively equivalent spectra. The ITOCSY spectra of labeled and unlabeled molecules are directly comparable and can be assigned using existing bioinformatics tools. In this study, we evaluate ITOCSY using synthetic mixtures of standards and extracts from Escherichia coli. We show that ITOCSY has low technical error (6.6% for metabolites ranging from 0.34 to 6.2 mM) and can detect molecules at concentrations less than 10 μM. We propose ITOCSY as a practical NMR strategy for metabolic flux analysis, isotope dilution experiments, and other methods that rely on carbon-13 labeling. PMID:20459129

  14. Cellular enrichment through microfluidic fractionation based on cell biomechanical properties

    PubMed Central

    Wang, Gonghao; Turbyfield, Cory; Crawford, Kaci; Alexeev, Alexander; Sulchek, Todd

    2017-01-01

    The biomechanical properties of populations of diseased cells are shown to have differences from healthy populations of cells, yet the overlap of these biomechanical properties can limit their use in disease cell enrichment and detection. We report a new microfluidic cell enrichment technology that continuously fractionates cells through differences in biomechanical properties, resulting in highly pure cellular subpopulations. Cell fractionation is achieved in a microfluidic channel with an array of diagonal ridges that are designed to segregate biomechanically distinct cells to different locations in the channel. Due to the imposition of elastic and viscous forces during cellular compression, which are a function of cell biomechanical properties including size and viscoelasticity, larger, stiffer and less viscos cells migrate parallel to the diagonal ridges and exhibit positive lateral displacement. On the other hand, smaller, softer and more viscous cells migrate perpendicular to the diagonal ridges due to circulatory flow induced by the ridges and result in negative lateral displacement. Multiple outlets are then utilized to collect cells with finer gradation of differences in cell biomechanical properties. The result is that cell fractionation dramatically improves cell separation efficiency compared to binary outputs and enables the measurement of subtle biomechanical differences within a single cell type. As a proof-of-concept demonstration, we mix two different leukemia cell lines (K562 and HL60) and utilize cell fractionation to achieve over 45-fold enhancement of cell populations, with high purity cellular enrichment (90% to 99%) of each cell line. In addition, we demonstrate cell fractionation of a single cell type (K562 cells) into subpopulations and characterize the variations of biomechanical properties of the separated cells with atomic force microscopy. These results will be beneficial to obtaining label-free separation of cellular mixtures, or to

  15. Cellular enrichment through microfluidic fractionation based on cell biomechanical properties.

    PubMed

    Wang, Gonghao; Turbyfield, Cory; Crawford, Kaci; Alexeev, Alexander; Sulchek, Todd

    2015-10-01

    The biomechanical properties of populations of diseased cells are shown to have differences from healthy populations of cells, yet the overlap of these biomechanical properties can limit their use in disease cell enrichment and detection. We report a new microfluidic cell enrichment technology that continuously fractionates cells through differences in biomechanical properties, resulting in highly pure cellular subpopulations. Cell fractionation is achieved in a microfluidic channel with an array of diagonal ridges that are designed to segregate biomechanically distinct cells to different locations in the channel. Due to the imposition of elastic and viscous forces during cellular compression, which are a function of cell biomechanical properties including size and viscoelasticity, larger, stiffer and less viscos cells migrate parallel to the diagonal ridges and exhibit positive lateral displacement. On the other hand, smaller, softer and more viscous cells migrate perpendicular to the diagonal ridges due to circulatory flow induced by the ridges and result in negative lateral displacement. Multiple outlets are then utilized to collect cells with finer gradation of differences in cell biomechanical properties. The result is that cell fractionation dramatically improves cell separation efficiency compared to binary outputs and enables the measurement of subtle biomechanical differences within a single cell type. As a proof-of-concept demonstration, we mix two different leukemia cell lines (K562 and HL60) and utilize cell fractionation to achieve over 45-fold enhancement of cell populations, with high purity cellular enrichment (90% to 99%) of each cell line. In addition, we demonstrate cell fractionation of a single cell type (K562 cells) into subpopulations and characterize the variations of biomechanical properties of the separated cells with atomic force microscopy. These results will be beneficial to obtaining label-free separation of cellular mixtures, or to

  16. Modeling and Analysis Methods for an On-line Enrichment Monitor

    SciTech Connect

    Smith, Leon E.; Jarman, Kenneth D.; Wittman, Richard S.; Zalavadia, Mital A.; March-Leuba, Jose A.

    2016-05-30

    The International Atomic Energy Agency (IAEA) has developed an On-Line Enrichment Monitor (OLEM) as one possible component in a new generation of safeguards measures for uranium enrichment plants. The OLEM measures 235U emissions from the UF6 gas flowing through a unit header pipe using NaI(Tl) spectrometers, and corrects for gas density changes using pressure and temperature sensors in order to determine the enrichment of the gas as a function of time. In parallel with the OLEM instrument development, a Virtual OLEM (VOLEM) software tool has been developed that is capable of producing synthetic gamma-ray, pressure, and temperature data representative of a wide range of enrichment plant operating conditions. VOLEM complements instrument development activities and allows the study of OLEM for scenarios that will be difficult or impossible to evaluate empirically. Uses of VOLEM include: investigation of hardware design options; inter-comparison of candidate gamma-ray spectral analysis and enrichment estimation algorithms; uncertainty budget analysis and performance prediction for typical and atypical operational scenarios; and testing of the OLEM data acquisition, analysis and reporting software. This paper describes the technical foundations of VOLEM and illustrates how it can be used. An overview of the nominal instrument design and deployment scenario for OLEM is provided, with emphasis on the key online-assay measurement challenge: accurately determining the portion of the total 235U signal that comes from a background that includes solid uranium deposits on the piping walls. Monte Carlo modeling tools, data analysis algorithms and uncertainty quantification methods are described. VOLEM is then used to quantitatively explore the uncertainty budgets and predicted instrument performance for a plausible range of typical plant operating parameters, and one set of candidate analysis algorithms. Additionally, a series of VOLEM case studies illustrates how an online

  17. Review of the magnetic isotope method for isotopic separation and enrichment

    SciTech Connect

    Turro, N.J.

    1985-01-01

    In the Progress Report of November 19, 1985 a detailed review of the theory of the magnetic isotope method for isotope separation and enrichment was presented. Here we present only the major qualitative features of the theory of the magnetic isotope effect, and we indicate how these aspects can be exploited to design experiments which demonstrate the feasibility and practicability of the magnetic isotope method.

  18. Assay of protein and peptide adducts of cholesterol ozonolysis products by hydrophobic and click enrichment methods.

    PubMed

    Windsor, Katherine; Genaro-Mattos, Thiago C; Miyamoto, Sayuri; Stec, Donald F; Kim, Hye-Young H; Tallman, Keri A; Porter, Ned A

    2014-10-20

    Cholesterol undergoes ozonolysis to afford a variety of oxysterol products, including cholesterol-5,6-epoxide (CholEp) and the isomeric aldehydes secosterol A (seco A) and secosterol B (seco B). These oxysterols display numerous important biological activities, including protein adduction; however, much remains to be learned about the identity of the reactive species and the range of proteins modified by these oxysterols. Here, we synthesized alkynyl derivatives of cholesterol-derived oxysterols and employed a straightforward detection method to establish secosterols A and B as the most protein-reactive of the oxysterols tested. Model adduction studies with an amino acid, peptides, and proteins provide evidence for the potential role of secosterol dehydration products in protein adduction. Hydrophobic separation methods-Folch extraction and solid phase extraction (SPE)-were successfully applied to enrich oxysterol-adducted peptide species, and LC-MS/MS analysis of a model peptide-seco adduct revealed a unique fragmentation pattern (neutral loss of 390 Da) for that species. Coupling a hydrophobic enrichment method with proteomic analysis utilizing characteristic fragmentation patterns facilitates the identification of secosterol-modified peptides and proteins in an adducted protein. More broadly, these improved enrichment methods may give insight into the role of oxysterols and ozone exposure in the pathogenesis of a variety of diseases, including atherosclerosis, Alzheimer's disease, Parkinson's disease, and asthma.

  19. A simple method for the absolute determination of uranium enrichment by high-resolution gamma spectrometry.

    PubMed

    Korob, R O; Blasiyh Nuño, G A

    2006-05-01

    A simple method for the determination of uranium enrichment using high-resolution gamma spectrometry is presented in this paper. The method relies solely on the gamma-ray emission probabilities of 235U and 234mPa, and an iterative procedure for the least squares fit of a polynomial to a set of experimentally determined data. To ensure the reliability of the 234mPa gamma-ray emission probabilities employed, a new determination of these probabilities was carried out using a combination of gamma spectrometry and Cerenkov counting of a purified 234Th solution. Using these new data, a maximum difference of approximately 5% has been found between the experimental and declared uranium enrichment in a set of solid and liquid samples containing uranium compounds.

  20. Method for isotope replenishment in an exchange liquid used in a laser induced isotope enrichment process

    SciTech Connect

    Keyser, G.M.; Mader, D.L.; O'Neill, J.A.

    1986-11-04

    A method is described for deuterium or tritium isotope replenishment of an exchange liquid in a process for concentrating deuterium or tritium by means of a laser induced selective photodissociation of a deuterium or tritium containing working compound mixed with its protiated or deuterated analog. The working compound is selected from the group consisting of a dueterated or tritiated analog of a dihalomethane, a trihalomethane, a 1,2-dihaloethylene, a trihaloethylene, a tetrahaloethane, and a pentahaloethane. The method comprises: selectively laser photodissociating the working compound to give an isotope enriched compound and an isotope depleted working compound; contacting the isotope depleted working compound mixture countercurrently with an exchange liquid having approximately the isotope concentration of an external source feed stream of water of D/sub 2/O in a first contacting column. The countercurrent contacting provides an isotope replenishment of the working compound as it moves up the column and an isotope depletion of the exchange liquid as it moves down the column. The exchange liquid consists essentially of a mixture of water of D/sub 2/O and a strong base catalyst; removing isotope deplated exchange liquid from the bottom of the first column; contacting the isotope depleted exchange liquid countercurrently with the feed stream in a second contacting apparatus thereby providing isotope replenishment of the exchange liquid and isotope depletion of the feed stream without causing salting out of the base catalyst; and removing the isotope replenished exchange liquid from one end of the second apparatus for use in the first column and removing isotope depleted water of D/sub 2/O steam from the other end of the second apparatus.

  1. Protein expression and isotopic enrichment based on induction of the Entner-Doudoroff pathway in Escherichia coli.

    PubMed

    Refaeli, Bosmat; Goldbourt, Amir

    2012-10-12

    The Entner-Doudoroff pathway is known to exist in many organisms including bacteria, archea and eukarya. Although the common route for carbon catabolism in Escherichia coli is the Embden-Meyerhof-Parnas pathway, it was shown that gluconate catabolism in E. coli occurs via the Entner-Doudoroff pathway. We demonstrate here that by supplying BL21(DE3) competent E.coli cells with gluconate in a minimal growth medium, protein expression can be induced. Nuclear magnetic resonance data of over-expressed ubiquitin show that by using [1-(13)C]-gluconate as the only carbon source, and (15)N-enriched ammonium chloride, sparse isotopic enrichment in the form of a spin-pair carbonyl-amide backbone enrichment is obtained. The specific amino acid labeling pattern is analyzed and is shown to be compatible with Entner-Doudoroff metabolism. Isotopic enrichment serves as a key factor in the biophysical characterization of proteins by various methods including nuclear magnetic resonance, mass spectrometry, infrared spectroscopy and more. Therefore, the method presented here can be applied to study proteins by obtaining sparse enrichment schemes that are not based on the regular glycolytic pathway, or to study the Entner-Doudoroff metabolism during protein expression. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. Rare earth element enrichment using membrane based solvent extraction

    NASA Astrophysics Data System (ADS)

    Makertiharta, I. G. B. N.; Dharmawijaya, P. T.; Zunita, M.; Wenten, I. G.

    2017-01-01

    The chemical, catalytic, electrical, magnetic, and optical properties of rare earth elements are required in broad applications. Rare earth elements have similar physical and chemical properties thus it is difficult to separate one from each other. Rare earth element is relatively abundant in earth's crust but rarely occur in high concentrated deposits. Traditionally, ion-exchange and solvent extraction techniques have been developed to separate and purify single rare earth solutions or compounds. Recently, membrane starts to gain attention for rare earth separation by combining membrane and proven technologies such as solvent extraction. Membrane-based process offers selective, reliable, energy efficient and easy to scale up separation. During membrane-based separation process, one phase passes through membrane pores while the other phase is rejected. There is no direct mixing of two phases thus the solvent loss is very low. Membrane can also lower solvent physical properties requirement (viscosity, density) and backmixing, eliminate flooding phenomenon and provide large interfacial area for mass transfer. This paper will summarize research efforts in developing membrane technology for rare earth element separation. Special attention will be given to solvent extraction related process as the commonly used method for rare earth element separation. Furthermore, membrane configuration and its potentials will also be discussed.

  3. Magnetic bead-based hydrophilic interaction liquid chromatography for glycopeptide enrichments.

    PubMed

    Yeh, Chia-Hao; Chen, Shu-Hui; Li, Ding-Tzai; Lin, Hong-Ping; Huang, Hung-Jen; Chang, Chi-I; Shih, Wen-Ling; Chern, Chi-Liang; Shi, Fong-Ku; Hsu, Jue-Liang

    2012-02-10

    Purification of glycopeptides prior to the analysis by mass spectrometry (MS) is demanded due to ion suppression effect during ionization caused by the co-presence of non-glycosylated peptides. Among various purification methods, hydrophilic interaction liquid chromatography (HILIC) has become a popular method in recent years. In this work, we reported a novel magnetic bead-based zwitterionic HILIC (ZIC-HILIC) material which was fabricated by coating a zwitterionic polymer synthesized by spontaneous acid-catalyzed polymerization of 4-vinyl-pyridinium ethanesulfonate monomer on iron oxide magnetic nanoparticles. The resulting magnetic ZIC-HILIC nanoparticles were shown to provide high specificity and high recovery yield (95-100%) for the enrichment of glycopeptides from a standard glycoprotein, fetuin, using a simple magnetic bar. In addition, we proposed a two-step HILIC enrichment strategy using magnetic ZIC-HILIC nanoparticles for a large scale analysis of glycoproteins in complex biological samples. Using this approach, we identified 85 N-glycosylation sites in 53 glycoproteins from urine samples. Two novel glycosylation sites on N513 of uromodulin and N470 of lysosomal alpha-glucosidase which have not yet been reported were identified by two-step HILIC approach. Furthermore, all these identified sites were confirmed by studies conducted using PNGase F deglycosylation and 18O enzymatic labeling. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Assay of Protein and Peptide Adducts of Cholesterol Ozonolysis Products by Hydrophobic and Click Enrichment Methods

    PubMed Central

    2015-01-01

    Cholesterol undergoes ozonolysis to afford a variety of oxysterol products, including cholesterol-5,6-epoxide (CholEp) and the isomeric aldehydes secosterol A (seco A) and secosterol B (seco B). These oxysterols display numerous important biological activities, including protein adduction; however, much remains to be learned about the identity of the reactive species and the range of proteins modified by these oxysterols. Here, we synthesized alkynyl derivatives of cholesterol-derived oxysterols and employed a straightforward detection method to establish secosterols A and B as the most protein-reactive of the oxysterols tested. Model adduction studies with an amino acid, peptides, and proteins provide evidence for the potential role of secosterol dehydration products in protein adduction. Hydrophobic separation methods—Folch extraction and solid phase extraction (SPE)—were successfully applied to enrich oxysterol-adducted peptide species, and LC-MS/MS analysis of a model peptide–seco adduct revealed a unique fragmentation pattern (neutral loss of 390 Da) for that species. Coupling a hydrophobic enrichment method with proteomic analysis utilizing characteristic fragmentation patterns facilitates the identification of secosterol-modified peptides and proteins in an adducted protein. More broadly, these improved enrichment methods may give insight into the role of oxysterols and ozone exposure in the pathogenesis of a variety of diseases, including atherosclerosis, Alzheimer’s disease, Parkinson’s disease, and asthma. PMID:25185119

  5. Targeted sequencing with enrichment PCR: a novel diagnostic method for the detection of EGFR mutations

    PubMed Central

    Kang, Suki; Kim, Baek Gil; Han, Hyun Ho; Lee, Joo Hyun; Kim, Ji Eun; Shim, Hyo Sup; Cho, Nam Hoon

    2015-01-01

    Epidermal growth factor receptor (EGFR) is an important mediator of tumor cell survival and proliferation. The detection of EGFR mutations can predict prognoses and indicate when treatment with EGFR tyrosine kinase inhibitors should be used. As such, the development of highly sensitive methods for detecting EGFR mutations is important. Targeted next-generation sequencing is an effective method for diagnosing mutations. We compared the abilities of enrichment PCR followed by ultra-deep pyrosequencing (UDP), UDP alone, and PNA-mediated RT-PCR clamping to detect low-frequency EGFR mutations in tumor cell lines and tissue samples. Using enrichment PCR-UDP, we were able to detect the E19del and L858R mutations at minimum frequencies of 0.01% and 0.05%, respectively, in the PC-9 and H197 tumor cell lines. We also confirmed the sensitivity of detecting the E19del mutation by performing a titration analysis in FFPE tumor samples. The lowest mutation frequency detected was 0.0692% in tissue samples. EGFR mutations with frequencies as low as 0.01% were detected using enrichment PCR-UDP, suggesting that this method is a valuable tool for detecting rare mutations, especially in scarce tissue samples or those with small quantities of DNA. PMID:25915533

  6. Filter-based pathogen enrichment technology for detection of multiple viable foodborne pathogens in 1 day.

    PubMed

    Murakami, Taku

    2012-09-01

    Conventional foodborne pathogen assays currently used in the food industry often require long culture enrichments to increase pathogen levels so they can be detected. Even using sensitive real-time PCR assays, culture enrichment at least overnight is necessary especially for detection of pathogens with slow growth rates such as Listeria monocytogenes. To eliminate this cumbersome enrichment step and detect minute amounts of pathogens within 1 day, filter-based pathogen enrichment technology was developed utilizing a unique combination of glass fiber depth filter and porous filter aid materials to efficiently separate pathogens from food homogenates and avoid filter clogging by food particles. After pathogen immobilization in depth filters, only viable pathogens were selectively collected in a small volume of growth medium via microbial multiplication and migration; nonviable pathogens remained inside the filters. By assaying viable pathogens using real-time PCRs, multiple species of foodborne pathogens were detected, including L. monocytogenes, Salmonella enterica, and Escherichia coli O157:H7, at around 1 CFU/ml or 1 CFU/g in various food samples. This filter-based pathogen enrichment technology is a unique bacterial enrichment alternative to the conventional culture enrichment step and can significantly shorten the time necessary to obtain assay results.

  7. Isotopic enrichment in herbivorous insects: a comparative field-based study of variation.

    PubMed

    Spence, Kenneth O; Rosenheim, Jay A

    2005-11-01

    Researchers will be able to use stable isotope analysis to study community structure in an efficient way, without a need for extensive calibrations, if isotopic enrichment values are consistent, or if variation in enrichment values can be predicted. In this study, we generated an experimental data set of delta15N and delta13C enrichment means for 22 terrestrial herbivorous arthropods feeding on 18 different host plants. Mean enrichments observed across a single trophic transfer (plants to herbivores) were -0.53+/-0.26 per thousand for delta13C (range: -3.47 per thousand to 1.89 per thousand) and 1.88+/-0.37 per thousand for delta15N (range: -0.20 per thousand to 6.59 per thousand). The mean delta13C enrichment was significantly lower than that reported in recent literature surveys, whereas the mean delta15N enrichment was not significantly different. The experimental data set provided no support for recent hypotheses advanced to explain variation in enrichment values, including the proposed roles for consumer feeding mode, development type, and diet C:N ratio. A larger data set, formed by combining our experimental data with data from the literature, did suggest possible roles for feeding mode, nitrogen recycling, herbivore life stage, and host plant type. Our results indicate that species enrichment values are variable even in this relatively narrow defined group of organisms and that our ability to predict enrichment values of terrestrial herbivorous arthropods based on physiological, ecological, or taxonomic traits is low. The primary implications are that (1) mean enrichment may have to be measured empirically for each trophic link of interest, rather than relying on estimates from a broad survey of animal taxa and (2) the advantage of using stable isotope analysis to probe animal communities that are recalcitrant to other modes of study will be somewhat diminished as a consequence.

  8. Different EV enrichment methods suitable for clinical settings yield different subpopulations of urinary extracellular vesicles from human samples

    PubMed Central

    Royo, Felix; Zuñiga-Garcia, Patricia; Sanchez-Mosquera, Pilar; Egia, Ainara; Perez, Amparo; Loizaga, Ana; Arceo, Raquel; Lacasa, Isabel; Rabade, Ainara; Arrieta, Edurne; Bilbao, Roberto; Unda, Miguel; Carracedo, Arkaitz; Falcon-Perez, Juan M.

    2016-01-01

    Urine sample analysis is irreplaceable as a non-invasive method for disease diagnosis and follow-up. However, in urine samples, non-degraded protein and RNA may be only found in urinary extracellular vesicles (uEVs). In recent years, various methods of uEV enrichment using low volumes of urine and unsophisticated equipment have been developed, with variable success. We compared the results of the differential ultracentrifugation procedure with 4 of these methods. The methods tested were a lectin-based purification, Exoquick (System Biosciences), Total Exosome Isolation from Invitrogen and an in-house modified procedure employing the Exosomal RNA Kit from Norgen Biotek Corp. The analysis of selected gene transcripts and protein markers of extracellular vesicles (EVs) revealed that each method isolates a different mixture of uEV protein markers. In our conditions, the extraction with Norgen's reagent achieved the best performance in terms of gene transcript and protein detection and reproducibility. By using this method, we were able to detect alterations of EVs protein markers in urine samples from prostate cancer adenoma patients. Taken together, our results show that the isolation of uEVs is feasible from small volumes of urine and avoiding ultracentrifugation, making easier the analysis in a clinical facility. However, caution should be taken in the selection of the enrichment method since they have a differential affinity for protein uEVs markers and by extension for different subpopulation of EVs. PMID:26895490

  9. A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation.

    PubMed

    Yigit, Erbay; Feehery, George R; Langhorst, Bradley W; Stewart, Fiona J; Dimalanta, Eileen T; Pradhan, Sriharsa; Slatko, Barton; Gardner, Andrew F; McFarland, James; Sumner, Christine; Davis, Theodore B

    2016-07-01

    "Microbiome" is used to describe the communities of microorganisms and their genes in a particular environment, including communities in association with a eukaryotic host or part of a host. One challenge in microbiome analysis concerns the presence of host DNA in samples. Removal of host DNA before sequencing results in greater sequence depth of the intended microbiome target population. This unit describes a novel method of microbial DNA enrichment in which methylated host DNA such as human genomic DNA is selectively bound and separated from microbial DNA before next-generation sequencing (NGS) library construction. This microbiome enrichment technique yields a higher fraction of microbial sequencing reads and improved read quality resulting in a reduced cost of downstream data generation and analysis. © 2016 by John Wiley & Sons, Inc.

  10. Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership.

    PubMed

    Iacucci, Ernesto; Zingg, Hans H; Perkins, Theodore J

    2012-01-01

    High-throughput molecular biology studies, such as microarray assays of gene expression, two-hybrid experiments for detecting protein interactions, or ChIP-Seq experiments for transcription factor binding, often result in an "interesting" set of genes - say, genes that are co-expressed or bound by the same factor. One way of understanding the biological meaning of such a set is to consider what processes or functions, as defined in an ontology, are over-represented (enriched) or under-represented (depleted) among genes in the set. Usually, the significance of enrichment or depletion scores is based on simple statistical models and on the membership of genes in different classifications. We consider the more general problem of computing p-values for arbitrary integer additive statistics, or weighted membership functions. Such membership functions can be used to represent, for example, prior knowledge on the role of certain genes or classifications, differential importance of different classifications or genes to the experimenter, hierarchical relationships between classifications, or different degrees of interestingness or evidence for specific genes. We describe a generic dynamic programming algorithm that can compute exact p-values for arbitrary integer additive statistics. We also describe several optimizations for important special cases, which can provide orders-of-magnitude speed up in the computations. We apply our methods to datasets describing oxidative phosphorylation and parturition and compare p-values based on computations of several different statistics for measuring enrichment. We find major differences between p-values resulting from these statistics, and that some statistics recover "gold standard" annotations of the data better than others. Our work establishes a theoretical and algorithmic basis for far richer notions of enrichment or depletion of gene sets with respect to gene ontologies than has previously been available.

  11. Porous membrane ultrafiltration-A novel method for enrichment of the active compounds from micro-plasma samples

    NASA Astrophysics Data System (ADS)

    Liu, Qingshan; Yin, Xiaoying; Sha, Biying; You, Jingjing

    2014-10-01

    To enrich the active compounds from plasma samples, a novel and simple method has been developed using a porous membrane envelope based on the ultrafiltration technique combining with high-performance liquid chromatography. The ultrafiltration device is a sealed porous membrane envelope prepared with a polypropylene sheet to effectively separate the active small molecules and large biomolecules, and a sample carrier is held inside the envelope to load plasma samples. The enrichment of hyperoside and isoquercitrin from rat plasma was used as an example. Significant factors of this method, such as membrane types, the desorption solvent, and the desorption time were optimized for the ultrafiltration method. Under the optimal conditions, correlation coefficients of 0.999 and 0.998 were obtained for hyperoside and isoquercitrin, respectively, with a linear range between 0.5 and 100 μg/mL. The absolute extraction recoveries from 83.2% to 86.8% were achieved. The detection limits of the method for hyperoside and isoquercitrin were 0.22 and 0.20 μg/mL, respectively. Compared with protein precipitation, solid-phase extraction and commercial ultrafiltration membrane methods, our proposed method demonstrates lower detection limits and lower cost for extraction. Also, it consumes less plasma samples and is found to be applicable to biological samples.

  12. Porous membrane ultrafiltration-A novel method for enrichment of the active compounds from micro-plasma samples.

    PubMed

    Liu, Qingshan; Yin, Xiaoying; Sha, Biying; You, Jingjing

    2014-10-15

    To enrich the active compounds from plasma samples, a novel and simple method has been developed using a porous membrane envelope based on the ultrafiltration technique combining with high-performance liquid chromatography. The ultrafiltration device is a sealed porous membrane envelope prepared with a polypropylene sheet to effectively separate the active small molecules and large biomolecules, and a sample carrier is held inside the envelope to load plasma samples. The enrichment of hyperoside and isoquercitrin from rat plasma was used as an example. Significant factors of this method, such as membrane types, the desorption solvent, and the desorption time were optimized for the ultrafiltration method. Under the optimal conditions, correlation coefficients of 0.999 and 0.998 were obtained for hyperoside and isoquercitrin, respectively, with a linear range between 0.5 and 100μg/mL. The absolute extraction recoveries from 83.2% to 86.8% were achieved. The detection limits of the method for hyperoside and isoquercitrin were 0.22 and 0.20μg/mL, respectively. Compared with protein precipitation, solid-phase extraction and commercial ultrafiltration membrane methods, our proposed method demonstrates lower detection limits and lower cost for extraction. Also, it consumes less plasma samples and is found to be applicable to biological samples.

  13. Epoxy based oxygen enriched porous carbons for CO2 capture

    NASA Astrophysics Data System (ADS)

    Tiwari, Deepak; Bhunia, Haripada; Bajpai, Pramod K.

    2017-08-01

    Oxygen enriched carbon adsorbents were successfully synthesized for the first time from template zeolite and epoxy resin as precursor using a nanocasting technique. Carbonization and CO2 activation were performed at various temperatures (500-800 °C) to prepare different carbon structure adsorbents. Several characterization techniques were used to characterize the textural structure, oxygen content and surface functional groups of the adsorbents. The carbon adsorbents show high oxygen content (47.51%), highest surface area (SBET = 686.37 m2 g-1) and pore volume (0.60 cm3 g-1), respectively. The materials were evaluated thermogravimetrically at different adsorption temperatures (30-100 °C) and CO2 concentrations (6-100%). Adsorbent prepared at 700 °C exhibited highest CO2 uptake of 0.91 mmol g-1 due to high surface basicity. Further, regeneration studies of adsorbent exhibited easy regenerability and stability over four multiple adsorptions-desorption cycles. Kinetic models for CO2 adsorption at various CO2 concentrations and temperatures were studied and it was found that the fractional order provided best fitting for the adsorption behavior with an error of less than 3%. The experimental data for CO2 adsorption were analyzed using different isothermal models and found that the Freundlich isothermal model presented perfect fit among all isotherm models depicting heterogeneous adsorbent surface. The isosteric heat of adsorption was estimated to be 11.75 kJ mol-1, indicating physiosorption process. Overall, the above results suggested that the synthesized adsorbent using nanocasting technique provides a feasible way for CO2 capture from point source due to their environmentally benign nature, low cost and stable adsorption capacity.

  14. Imaging based enrichment criteria using deep learning algorithms for efficient clinical trials in MCI

    PubMed Central

    Ithapu, Vamsi K.; Okonkwo, Ozioma C.; Chappell, Richard J.; Dowling, N. Maritza; Johnson, Sterling C.

    2015-01-01

    The Mild Cognitive Impairment (MCI) stage of AD may be optimal for clinical trials to test potential treatments for preventing or delaying decline to dementia. However, MCI is heterogeneous in that not all cases progress to dementia within the time frame of a trial, and some may not have underlying AD pathology. Identifying those MCIs who are most likely to decline during a trial and thus most likely to benefit from treatment will improve trial efficiency and power to detect treatment effects. To this end, employing multi-modal imaging-derived inclusion criteria may be especially beneficial. Here, we present a novel multi-modal imaging marker that predicts future cognitive and neural decline from [F-18]fluorodeoxyglucose positron emission tomography (PET), amyloid florbetapir PET, and structural magnetic resonance imaging (MRI), based on a new deep learning algorithm (randomized denoising autoencoder marker, rDAm). Using ADNI2 MCI data, we show that employing rDAm as a trial enrichment criterion reduces the required sample estimates by at least five times compared to the no-enrichment regime, and leads to smaller trials with high statistical power, compared to existing methods. PMID:26093156

  15. Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing.

    PubMed

    Sakaguchi, Shota; Ueno, Saneyoshi; Tsumura, Yoshihiko; Setoguchi, Hiroaki; Ito, Motomi; Hattori, Chie; Nozoe, Shogo; Takahashi, Daiki; Nakamasu, Riku; Sakagami, Taishi; Lannuzel, Guillaume; Fogliani, Bruno; Wulff, Adrien S; L'Huillier, Laurent; Isagi, Yuji

    2017-05-01

    High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing. Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully. This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species).

  16. Material classification and automatic content enrichment of images using supervised learning and knowledge bases

    NASA Astrophysics Data System (ADS)

    Mallepudi, Sri Abhishikth; Calix, Ricardo A.; Knapp, Gerald M.

    2011-02-01

    In recent years there has been a rapid increase in the size of video and image databases. Effective searching and retrieving of images from these databases is a significant current research area. In particular, there is a growing interest in query capabilities based on semantic image features such as objects, locations, and materials, known as content-based image retrieval. This study investigated mechanisms for identifying materials present in an image. These capabilities provide additional information impacting conditional probabilities about images (e.g. objects made of steel are more likely to be buildings). These capabilities are useful in Building Information Modeling (BIM) and in automatic enrichment of images. I2T methodologies are a way to enrich an image by generating text descriptions based on image analysis. In this work, a learning model is trained to detect certain materials in images. To train the model, an image dataset was constructed containing single material images of bricks, cloth, grass, sand, stones, and wood. For generalization purposes, an additional set of 50 images containing multiple materials (some not used in training) was constructed. Two different supervised learning classification models were investigated: a single multi-class SVM classifier, and multiple binary SVM classifiers (one per material). Image features included Gabor filter parameters for texture, and color histogram data for RGB components. All classification accuracy scores using the SVM-based method were above 85%. The second model helped in gathering more information from the images since it assigned multiple classes to the images. A framework for the I2T methodology is presented.

  17. Signatures and Methods for the Automated Nondestructive Assay of UF6 Cylinders at Uranium Enrichment Plants

    SciTech Connect

    Smith, Leon E.; Mace, Emily K.; Misner, Alex C.; Shaver, Mark W.

    2010-08-08

    International Atomic Energy Agency (IAEA) inspectors currently perform periodic inspections at uranium enrichment plants to verify UF6 cylinder enrichment declarations. Measurements are typically performed with handheld high-resolution sensors on a sampling of cylinders taken to be representative of the facility’s entire cylinder inventory. These measurements are time-consuming, expensive, and assay only a small fraction of the total cylinder volume. An automated nondestructive assay system capable of providing enrichment measurements over the full volume of the cylinder could improve upon current verification practices in terms of manpower and assay accuracy. Such a station would use sensors that can be operated in an unattended mode at an industrial facility: medium-resolution scintillators for gamma-ray spectroscopy (e.g., NaI(Tl)) and moderated He-3 neutron detectors. This sensor combination allows the exploitation of additional, more-penetrating signatures beyond the traditional 185-keV emission from U-235: neutrons produced from F-19(α,n) reactions (spawned primarily from U 234 alpha emission) and high-energy gamma rays (extending up to 8 MeV) induced by neutrons interacting in the steel cylinder. This paper describes a study of these non-traditional signatures for the purposes of cylinder enrichment verification. The signatures and the radiation sensors designed to collect them are described, as are proof-of-principle cylinder measurements and analyses. Key sources of systematic uncertainty in the non-traditional signatures are discussed, and the potential benefits of utilizing these non-traditional signatures, in concert with an automated form of the traditional 185-keV-based assay, are discussed.

  18. Protein expression and isotopic enrichment based on induction of the Entner-Doudoroff pathway in Escherichia coli

    SciTech Connect

    Refaeli, Bosmat; Goldbourt, Amir

    2012-10-12

    Highlights: Black-Right-Pointing-Pointer The Entner-Doudoroff pathway is induced during protein expression in E. coli. Black-Right-Pointing-Pointer 1-{sup 13}C-gluconate and {sup 15}NH{sub 4}Cl provide a carbonyl-amide protein backbone labeling scheme. Black-Right-Pointing-Pointer The enrichment pattern is determined by nuclear magnetic resonance. -- Abstract: The Entner-Doudoroff pathway is known to exist in many organisms including bacteria, archea and eukarya. Although the common route for carbon catabolism in Escherichia coli is the Embden-Meyerhof-Parnas pathway, it was shown that gluconate catabolism in E. coli occurs via the Entner-Doudoroff pathway. We demonstrate here that by supplying BL21(DE3) competent E.coli cells with gluconate in a minimal growth medium, protein expression can be induced. Nuclear magnetic resonance data of over-expressed ubiquitin show that by using [1-{sup 13}C]-gluconate as the only carbon source, and {sup 15}N-enriched ammonium chloride, sparse isotopic enrichment in the form of a spin-pair carbonyl-amide backbone enrichment is obtained. The specific amino acid labeling pattern is analyzed and is shown to be compatible with Entner-Doudoroff metabolism. Isotopic enrichment serves as a key factor in the biophysical characterization of proteins by various methods including nuclear magnetic resonance, mass spectrometry, infrared spectroscopy and more. Therefore, the method presented here can be applied to study proteins by obtaining sparse enrichment schemes that are not based on the regular glycolytic pathway, or to study the Entner-Doudoroff metabolism during protein expression.

  19. Pedagogical Quality Enrichment in OER-Based Courseware: Guiding Principles

    ERIC Educational Resources Information Center

    Misra, Pradeep Kumar

    2013-01-01

    This is a critical phase for Open Educational Resources (OER) movement: on one side the number of OER is increasing rapidly, and on other side debates about quality of OER-based courseware are heating up. These debates emanate from the fact that OER-based courseware are supposed to help users to follow a logical learning path and get an engaging,…

  20. Highly sensitive and rapid detection of Pseudomonas aeruginosa based on magnetic enrichment and magnetic separation.

    PubMed

    Tang, Yongjun; Zou, Jun; Ma, Chao; Ali, Zeeshan; Li, Zhiyang; Li, Xiaolong; Ma, Ninging; Mou, Xianbo; Deng, Yan; Zhang, Liming; Li, Kai; Lu, Guangming; Yang, Haowen; He, Nongyue

    2013-01-01

    A method for highly sensitive and rapid detection of Pseudomonas aeruginosa, based on magnetic enrichment and magnetic separation, is described in this paper. The magnetic nanoparticles (MNPs) were applied to adsorb genome DNA after the sample was lysed. The DNA binding MNPs were directly subjected to polymerase chain reaction (PCR) to amplify gyrB specific sequence of Pseudomonas aeruginosa. The biotin labeled PCR products were detected by chemiluminescence when they were successively incubated with the probes-modified MNPs and alkaline phosphatase (ALP) labeled streptavidin (SA). Agarose gel electrophoresis analyses approved the method of in situ PCR to be highly reliable. The factors which could affect the chemiluminiscence were studied in detail. The results showed that the MNPs of 400 nm in diameter are beneficial to the detection. The sequence length and the binding site of the probe with a target sequence have obvious effects on the detection. The optimal concentration of the probes, hybridization temperature and hybridization time were 10 μM, 60 ºC and 60 mins, respectively. The method of in situ PCR based on MNPs can greatly improve the utilization rate of the DNA template ultimately enhancing the detection sensitivity. Experiment results proved that the primer and probe had high specificity, and Pseudomonas aeruginosa was successfully detected with detection limits as low as 10 cfu/mL by this method, while the detection of a single Pseudomonas aeruginosa can also be achieved.

  1. Nutrient enrichment differentially affects body sizes of primary consumers and predators in a detritus-based stream

    Treesearch

    John M. Davis; Amy D. Rosemond; Sue L. Eggert; Wyatt F. Cross; J. Bruce. Wallace

    2010-01-01

    We assessed how a 5-yr nutrient enrichment affected the responses of different size classes of primary consumers and predators in a detritus-based headwater stream. We hypothesized that alterations in detritus availability because of enrichment would decrease the abundance and biomass of large-bodied consumers. In contrast, we found that 2 yr of enrichment increased...

  2. Selective enrichment of phenols from coal liquefaction oil by solid phase extraction method

    SciTech Connect

    Tian, M.; Feng, J.

    2009-07-01

    This study focuses on the solid phase extraction method for the enrichment and separation of phenol from coal liquefaction oil. The phenols' separation efficiency was compared on different solid phase extraction (SPE) cartridges, and the effect of solvents with different polarity and solubility parameter on amino-bonded silica was compared for selection of optimal elution solution. The result showed that amino-bonded silica has the highest selectivity and best extraction capability due to two factors, weak anion exchange adsorption and polar attraction adsorption.

  3. Fast critical assembly safeguards: NDA methods for highly enriched uranium. Summary report, October 1978-September 1979

    SciTech Connect

    Bellinger, F.O.; Winslow, G.H.

    1980-12-01

    Nondestructive assay (NDA) methods, principally passive gamma measurements and active neutron interrogation, have been studied for their safeguards effectiveness and programmatic impact as tools for making inventories of highly enriched uranium fast critical assembly fuel plates. It was concluded that no NDA method is the sole answer to the safeguards problem, that each of those emphasized here has its place in an integrated safeguards system, and that each has minimum facility impact. It was found that the 185-keV area, as determined with a NaI detector, was independent of highly-enriched uranium (HEU) plate irradiation history, though the random neutron driver methods used here did not permit accurate assay of irradiated plates. Containment procedures most effective for accurate assaying were considered, and a particular geometry is recommended for active interrogation by a random driver. A model, pertinent to that geometry, which relates the effects of multiplication and self-absorption, is described. Probabilities of failing to detect that plates are missing are examined.

  4. Examining How Middle School Science Teachers Implement a Multimedia-Enriched Problem-Based Learning Environment

    ERIC Educational Resources Information Center

    Liu, Min; Wivagg, Jennifer; Geurtz, Renata; Lee, Shih-Ting; Chang, Hyeseung Maria

    2012-01-01

    This study examined how a group of ten middle school teachers implemented a technology enriched problem-based learning (PBL) environment. The goal was to understand their motivation, document their implementation techniques, and identify factors that teachers considered important in using technology-based PBL tools in their teaching. The analysis…

  5. Ultratrace DNA Detection Based on the Condensing-Enrichment Effect of Superwettable Microchips.

    PubMed

    Xu, Li-Ping; Chen, Yanxia; Yang, Gao; Shi, Wanxin; Dai, Bing; Li, Guannan; Cao, Yanhua; Wen, Yongqiang; Zhang, Xueji; Wang, Shutao

    2015-11-18

    A sensitive nucleic acid detection platform based on superhydrophilic microwells spotted on a superhydrophobic substrate is fabricated. Due to the wettability differences, ultratrace DNA molecules are enriched and the fluorescent signals are amplified to allow more sensitive detection. The biosensing interface based on superwettable materials provides a simple and cost-effective way for ultratrace DNA sensing.

  6. Chasing Phosphoarginine Proteins: Development of a Selective Enrichment Method Using a Phosphatase Trap*

    PubMed Central

    Trentini, Débora Broch; Fuhrmann, Jakob; Mechtler, Karl; Clausen, Tim

    2014-01-01

    Arginine phosphorylation is an emerging post-translational protein modification implicated in the bacterial stress response. Although early reports suggested that arginine phosphorylation also occurs in higher eukaryotes, its overall prevalence was never studied using modern mass spectrometry methods, owing to technical difficulties arising from the acid lability of phosphoarginine. As shown recently, the McsB and YwlE proteins from Bacillus subtilis function as a highly specific protein arginine kinase and phosphatase couple, shaping the phosphoarginine proteome. Using a B. subtilis ΔywlE strain as a source for arginine-phosphorylated proteins, we were able to adapt mass spectrometry (MS) protocols to the special chemical properties of the arginine modification. Despite this progress, the analysis of protein arginine phosphorylation in eukaryotes is still challenging, given the great abundance of serine/threonine phosphorylations that would compete with phosphoarginine during the phosphopeptide enrichment procedure, as well as during data-dependent MS acquisition. We thus set out to establish a method for the selective enrichment of arginine-phosphorylated proteins as an initial step in the phosphoproteomic analysis. For this purpose, we developed a substrate-trapping mutant of the YwlE phosphatase that retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. By testing a number of active site substitutions, we identified a YwlE mutant (C9A) that stably binds to arginine-phosphorylated proteins. We further improved the substrate-trapping efficiency by impeding the oligomerization of the phosphatase mutant. The engineered YwlE trap efficiently captured arginine-phosphorylated proteins from complex B. subtilis ΔywlE cell extracts, thus facilitating identification of phosphoarginine sites in the large pool of cellular protein modifications. In conclusion, we present a novel tool for the selective enrichment and

  7. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.

    PubMed

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R; Krogh, Anders; Vinther, Jeppe

    2015-05-01

    Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA-RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing. © 2015 Poulsen et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

    PubMed Central

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R.; Krogh, Anders; Vinther, Jeppe

    2015-01-01

    Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA–RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing. PMID:25805860

  9. microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes

    PubMed Central

    Yoon, Jung-Ki; Ahn, Jinwoo; Kim, Han Sang; Han, Soo Min; Jang, Hoon; Lee, Min Goo; Lee, Ji Hyun; Bang, Duhee

    2015-01-01

    Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we developed a simple and efficient microarray-based MIP preparation protocol using only one enzyme with double-stranded probes and improved target capture yields by designing probes with overlapping targets and unique barcodes. To test our strategy, we produced 11 510 microarray-based duplex MIPs (microDuMIPs) and captured 3554 exons of 228 genes in a HapMap genomic DNA sample (NA12878). Under our protocol, capture performance and precision of calling were compatible to conventional MIP capture methods, yet overlapping targets and unique barcodes allowed us to precisely genotype with as little as 50 ng of input genomic DNA without library preparation. microDuMIP method is simpler and cheaper, allowing broader applications and accurate target sequencing with a scalable number of targets. PMID:25414325

  10. MARCC (Matrix-Assisted Reader Chromatin Capture): An Antibody-Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications.

    PubMed

    Su, Zhangli; Denu, John M

    2015-07-01

    Combinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody-free method named MARCC (Matrix-Assisted Reader Chromatin Capture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin-interacting protein modules, or so-called reader domains, which can bind in a combinatorial modification-dependent manner. The enriched chromatin can be quantified by immunoblotting or mass spectrometry for the co-existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next-generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications. Copyright © 2015 John Wiley & Sons, Inc.

  11. Reduced order variational multiscale enrichment method for thermo-mechanical problems

    NASA Astrophysics Data System (ADS)

    Zhang, Shuhai; Oskay, Caglar

    2017-06-01

    This manuscript presents the formulation and implementation of the reduced order variational multiscale enrichment (ROVME) method for thermo-mechanical problems. ROVME is extended to model the inelastic behavior of heterogeneous structures, in which the constituent properties are temperature sensitive. The temperature-dependent coefficient tensors of the reduced order method are approximated in an efficient manner, retaining the computational efficiency of the reduced order model in the presence of spatial/temporal temperature variations. A Newton-Raphson iterative scheme is formulated and implemented for the numerical evaluation of nonlinear system of equations associated with the proposed ROVME method. Numerical verifications are performed to assess the efficiency and accuracy of the proposed computational framework. The results of the verifications reveal that ROVME retains reasonable accuracy and achieves high efficiency in the presence of hermo-mechanical loads.

  12. Reduced order variational multiscale enrichment method for thermo-mechanical problems

    NASA Astrophysics Data System (ADS)

    Zhang, Shuhai; Oskay, Caglar

    2017-02-01

    This manuscript presents the formulation and implementation of the reduced order variational multiscale enrichment (ROVME) method for thermo-mechanical problems. ROVME is extended to model the inelastic behavior of heterogeneous structures, in which the constituent properties are temperature sensitive. The temperature-dependent coefficient tensors of the reduced order method are approximated in an efficient manner, retaining the computational efficiency of the reduced order model in the presence of spatial/temporal temperature variations. A Newton-Raphson iterative scheme is formulated and implemented for the numerical evaluation of nonlinear system of equations associated with the proposed ROVME method. Numerical verifications are performed to assess the efficiency and accuracy of the proposed computational framework. The results of the verifications reveal that ROVME retains reasonable accuracy and achieves high efficiency in the presence of hermo-mechanical loads.

  13. Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data

    PubMed Central

    Wang, Haiying; Zheng, Huiru; Simpson, David; Azuaje, Francisco

    2006-01-01

    Background Retinal photoreceptors are highly specialised cells, which detect light and are central to mammalian vision. Many retinal diseases occur as a result of inherited dysfunction of the rod and cone photoreceptor cells. Development and maintenance of photoreceptors requires appropriate regulation of the many genes specifically or highly expressed in these cells. Over the last decades, different experimental approaches have been developed to identify photoreceptor enriched genes. Recent progress in RNA analysis technology has generated large amounts of gene expression data relevant to retinal development. This paper assesses a machine learning methodology for supporting the identification of photoreceptor enriched genes based on expression data. Results Based on the analysis of publicly-available gene expression data from the developing mouse retina generated by serial analysis of gene expression (SAGE), this paper presents a predictive methodology comprising several in silico models for detecting key complex features and relationships encoded in the data, which may be useful to distinguish genes in terms of their functional roles. In order to understand temporal patterns of photoreceptor gene expression during retinal development, a two-way cluster analysis was firstly performed. By clustering SAGE libraries, a hierarchical tree reflecting relationships between developmental stages was obtained. By clustering SAGE tags, a more comprehensive expression profile for photoreceptor cells was revealed. To demonstrate the usefulness of machine learning-based models in predicting functional associations from the SAGE data, three supervised classification models were compared. The results indicated that a relatively simple instance-based model (KStar model) performed significantly better than relatively more complex algorithms, e.g. neural networks. To deal with the problem of functional class imbalance occurring in the dataset, two data re-sampling techniques were

  14. Comparison of Listeria monocytogenes recoveries from spiked mung bean sprouts by the enrichment methods of three regulatory agencies.

    PubMed

    Cauchon, Kaitlin E; Hitchins, Anthony D; Smiley, R Derike

    2017-09-01

    Three selective enrichment methods, the United States Food and Drug Administration's (FDA method), the United States Department of Agriculture Food Safety Inspection Service's (USDA method), and the EN ISO 11290-1 standard method, were assessed for their suitability for recovery of Listeria monocytogenes from spiked mung bean sprouts. Three parameters were evaluated; the enrichment L. monocytogenes population from singly-spiked sprouts, the enrichment L. monocytogenes population from doubly-spiked (L. monocytogenes and Listeria innocua) sprouts, and the population differential resulting from the enrichment of doubly-spiked sprouts. Considerable L. monocytogenes inter-strain variation was observed. The mean enrichment L. monocytogenes populations for singly-spiked sprouts were 6.1 ± 1.2, 4.9 ± 1.2, and 6.9 ± 2.3 log CFU/mL for the FDA, USDA, and EN ISO 11290-1 methods, respectively. The mean L. monocytogenes populations for doubly-spiked sprouts were 4.7 ± 1.1, 5.5 ± 1.3, and 4.6 ± 1.4 log CFU/mL for the FDA, USDA, and ISO 11290-1 enrichment methods, respectively. The corresponding mean population differentials were 2.8 ± 1.1, 3.3 ± 1.3, and 3.6 ± 1.4 Δlog CFU/mL for the same three enrichment methods, respectively. The presence of L. innocua and resident microorganisms on the sprouts negatively impacted final levels of L. monocytogenes with all three enrichment methods. Published by Elsevier Ltd.

  15. Wide dynamic range enrichment method of semiconducting single-walled carbon nanotubes with weak field centrifugation

    NASA Astrophysics Data System (ADS)

    Reis, Wieland G.; Tomović, Željko; Weitz, R. Thomas; Krupke, Ralph; Mikhael, Jules

    2017-03-01

    The potential of single–walled carbon nanotubes (SWCNTs) to outperform silicon in electronic application was finally enabled through selective separation of semiconducting nanotubes from the as-synthesized statistical mix with polymeric dispersants. Such separation methods provide typically high semiconducting purity samples with narrow diameter distribution, i.e. almost single chiralities. But for a wide range of applications high purity mixtures of small and large diameters are sufficient or even required. Here we proof that weak field centrifugation is a diameter independent method for enrichment of semiconducting nanotubes. We show that the non-selective and strong adsorption of polyarylether dispersants on nanostructured carbon surfaces enables simple separation of diverse raw materials with different SWCNT diameter. In addition and for the first time, we demonstrate that increased temperature enables higher purity separation. Furthermore we show that the mode of action behind this electronic enrichment is strongly connected to both colloidal stability and protonation. By giving simple access to electronically sorted SWCNTs of any diameter, the wide dynamic range of weak field centrifugation can provide economical relevance to SWCNTs.

  16. Wide dynamic range enrichment method of semiconducting single-walled carbon nanotubes with weak field centrifugation

    PubMed Central

    Reis, Wieland G.; Tomović, Željko; Weitz, R. Thomas; Krupke, Ralph; Mikhael, Jules

    2017-01-01

    The potential of single–walled carbon nanotubes (SWCNTs) to outperform silicon in electronic application was finally enabled through selective separation of semiconducting nanotubes from the as-synthesized statistical mix with polymeric dispersants. Such separation methods provide typically high semiconducting purity samples with narrow diameter distribution, i.e. almost single chiralities. But for a wide range of applications high purity mixtures of small and large diameters are sufficient or even required. Here we proof that weak field centrifugation is a diameter independent method for enrichment of semiconducting nanotubes. We show that the non-selective and strong adsorption of polyarylether dispersants on nanostructured carbon surfaces enables simple separation of diverse raw materials with different SWCNT diameter. In addition and for the first time, we demonstrate that increased temperature enables higher purity separation. Furthermore we show that the mode of action behind this electronic enrichment is strongly connected to both colloidal stability and protonation. By giving simple access to electronically sorted SWCNTs of any diameter, the wide dynamic range of weak field centrifugation can provide economical relevance to SWCNTs. PMID:28317942

  17. A modified enrichment method to construct microsatellite library from plateau pika genome (Ochotona curzoniae).

    PubMed

    Geng, Jianing; Li, Kexin; Zhang, Yanming; Hu, Songnian

    2010-03-01

    A microsatellite-enriched library of plateau pika (Ochotona curzoniae) was constructed according to the strong affinity between biotin and streptavidin. Firstly, genomic DNA was fragmented by ultrasonication, which is a major improvement over traditional methods. Linker-ligated DNA fragments were hybridized with biotinylated microsatellite probes, and then were subjected to streptavidin-coated magnetic beads. PCR amplification was performed to obtain double-stranded DNA fragments containing microsatellites. Ligation and transformation were carried out by using the pGEM-T Vector System I and Escherichia coli DH10B competent cells. Sequencing results showed that 80.2% of clones contained microsatellite repeat motif. Several modifications make this protocol time-efficient and technically easier than the traditional ones; particularly, composition and relative abundance of microsatellite repeats in plateau pika genome were truly represented through the optimized PCR conditions. This method has also been successfully applied to construct microsatellite-enriched genomic libraries of Chinese hamster (Cricetulus griseus) and small abalone [Haliotis diversicolor (Reeve)] with high rates of positive clones, demonstrating its feasibility and stability. 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

  18. Size-selective separation and overall-amplification of cell-free fetal DNA fragments using PCR-based enrichment.

    PubMed

    Yang, Qiwei; Du, Zhenwu; Song, Yang; Gao, Sujie; Yu, Shan; Zhu, He; Ren, Ming; Zhang, Guizhen

    2017-01-19

    This study aimed to establish a method for the selective amplification of cell-free fetal DNA (cffDNA) in maternal plasma and preserve the integrity of DNA fragments during amplification, thereby providing a sufficient amount of cffDNA to meet the requirement of routine non-invasive prenatal testing. We amplified DNA molecules in a one-reaction system without considering their particular sequences and lengths (overall amplification) by using PCR-based enrichment. We then modified PCR conditions to verify the effect of denaturation temperature on DNA amplification on various lengths of DNA (selective overall amplification). Finally, we used an optimum temperature range to amplify cffDNA selectively. Amplification results were validated by electrophoresis and real-time quantitative PCR. Our PCR-based enrichment efficiently amplified all DNA fragments with differing lengths within a single reaction system, as well as preserving the integrity of the DNA fragments. cffDNA was significantly amplified along with the selective amplification of small fragment maternal plasma DNA in an appropriate range of denaturation temperatures. We have established a PCR-based method for the simultaneous enrichment and amplification of cffDNA in order to meet the requirements of high cffDNA quantity for routine non-invasive prenatal testing.

  19. Size-selective separation and overall-amplification of cell-free fetal DNA fragments using PCR-based enrichment

    PubMed Central

    Yang, Qiwei; Du, Zhenwu; Song, Yang; Gao, Sujie; Yu, Shan; Zhu, He; Ren, Ming; Zhang, Guizhen

    2017-01-01

    This study aimed to establish a method for the selective amplification of cell-free fetal DNA (cffDNA) in maternal plasma and preserve the integrity of DNA fragments during amplification, thereby providing a sufficient amount of cffDNA to meet the requirement of routine non-invasive prenatal testing. We amplified DNA molecules in a one-reaction system without considering their particular sequences and lengths (overall amplification) by using PCR-based enrichment. We then modified PCR conditions to verify the effect of denaturation temperature on DNA amplification on various lengths of DNA (selective overall amplification). Finally, we used an optimum temperature range to amplify cffDNA selectively. Amplification results were validated by electrophoresis and real-time quantitative PCR. Our PCR-based enrichment efficiently amplified all DNA fragments with differing lengths within a single reaction system, as well as preserving the integrity of the DNA fragments. cffDNA was significantly amplified along with the selective amplification of small fragment maternal plasma DNA in an appropriate range of denaturation temperatures. We have established a PCR-based method for the simultaneous enrichment and amplification of cffDNA in order to meet the requirements of high cffDNA quantity for routine non-invasive prenatal testing. PMID:28102322

  20. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.

    PubMed

    Cui, Pin; Löber, Ulrike; Alquezar-Planas, David E; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N; Lenz, Dorina; Helgen, Kristofer M; Roca, Alfred L; Hartman, Stefanie; Greenwood, Alex D

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

  1. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

    PubMed Central

    Alquezar-Planas, David E.; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N.; Lenz, Dorina; Helgen, Kristofer M.; Roca, Alfred L.; Hartman, Stefanie

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

  2. Direct Detection and Prediction of All Pneumococcal Serogroups by Target Enrichment-Based Next-Generation Sequencing

    PubMed Central

    Liyanapathirana, Veranja; Ang, Irene; Fung, Kitty S. C.; Ng, T. K.; Zhou, Haokui; Tsang, Dominic N. C.

    2014-01-01

    Despite the availability of standard methods for pneumococcal serotyping, there is room for improvement in the available methods, in terms of throughput, multiplexing capacity, and the number of serotypes identified. We describe a target enrichment-based next-generation sequencing method applied to nasopharyngeal samples for direct detection and serogroup prediction of all known serotypes of Streptococcus pneumoniae, 32 to the serotype level and the rest to the closely related serogroup level. The method was applied to detect and to predict the serogroups of pneumococci directly in clinical samples and from sweeps of primary culture DNA, with increased detection rates versus culture-based identification and agreement with the serotypes/serogroups determined by conventional serotyping methods. We propose this method, in conjunction with traditional serotyping methods, as an alternative to rapid detection and serotyping of pneumococci. PMID:25274995

  3. Recent advances in enrichment and separation strategies for mass spectrometry-based phosphoproteomics

    PubMed Central

    Yang, Chenxi; Zhong, Xuefei; Li, Lingjun

    2016-01-01

    Due to the significance of protein phosphorylation in various biological processes and signaling events, new analytical techniques for enhanced phosphoproteomics have been rapidly introduced in recent years. The combinatorial use of the phospho-specific enrichment techniques and prefractionation methods prior to MS analysis enables comprehensive profiling of the phosphoproteome and facilitates deciphering the critical roles that phosphorylation plays in signaling pathways in various biological systems. This review places special emphasis on the recent five-year (2009–2013) advances for enrichment and separation techniques that have been utilized for phosphopeptides prior to MS analysis. PMID:24687451

  4. Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods

    PubMed Central

    Reynès, Christelle; Host, Hélène; Camproux, Anne-Claude; Laconde, Guillaume; Leroux, Florence; Mazars, Anne; Deprez, Benoit; Fahraeus, Robin; Villoutreix, Bruno O.; Sperandio, Olivier

    2010-01-01

    Protein-protein interactions (PPIs) may represent one of the next major classes of therapeutic targets. So far, only a minute fraction of the estimated 650,000 PPIs that comprise the human interactome are known with a tiny number of complexes being drugged. Such intricate biological systems cannot be cost-efficiently tackled using conventional high-throughput screening methods. Rather, time has come for designing new strategies that will maximize the chance for hit identification through a rationalization of the PPI inhibitor chemical space and the design of PPI-focused compound libraries (global or target-specific). Here, we train machine-learning-based models, mainly decision trees, using a dataset of known PPI inhibitors and of regular drugs in order to determine a global physico-chemical profile for putative PPI inhibitors. This statistical analysis unravels two important molecular descriptors for PPI inhibitors characterizing specific molecular shapes and the presence of a privileged number of aromatic bonds. The best model has been transposed into a computer program, PPI-HitProfiler, that can output from any drug-like compound collection a focused chemical library enriched in putative PPI inhibitors. Our PPI inhibitor profiler is challenged on the experimental screening results of 11 different PPIs among which the p53/MDM2 interaction screened within our own CDithem platform, that in addition to the validation of our concept led to the identification of 4 novel p53/MDM2 inhibitors. Collectively, our tool shows a robust behavior on the 11 experimental datasets by correctly profiling 70% of the experimentally identified hits while removing 52% of the inactive compounds from the initial compound collections. We strongly believe that this new tool can be used as a global PPI inhibitor profiler prior to screening assays to reduce the size of the compound collections to be experimentally screened while keeping most of the true PPI inhibitors. PPI-HitProfiler is

  5. Aptamer-based microfluidic device for enrichment, sorting, and detection of multiple cancer cells.

    PubMed

    Xu, Ye; Phillips, Joseph A; Yan, Jilin; Li, Qingge; Fan, Z Hugh; Tan, Weihong

    2009-09-01

    The ability to diagnose cancer based on the detection of rare cancer cells in blood or other bodily fluids is a significant challenge. To address this challenge, we have developed a microfluidic device that can simultaneously sort, enrich, and then detect multiple types of cancer cells from a complex sample. The device, which is made from poly(dimethylsiloxane) (PDMS), implements cell-affinity chromatography based on the selective cell-capture of immobilized DNA-aptamers and yields a 135-fold enrichment of rare cells in a single run. This enrichment is achieved because the height of the channel is on the order of a cell diameter. The sorted cells grow at the comparable rate as cultured cells and are 96% pure based on flow cytometry determination. Thus, by using our aptamer based device, cell capture is achieved simply and inexpensively, with no sample pretreatment before cell analysis. Enrichment and detection of multiple rare cancer cells can be used to detect cancers at the early stages, diagnose metastatic relapse, stratify patients for therapeutic purposes, monitor response to drugs and therapies, track tumor progression, and gain a deeper understanding of the biology of circulating tumor cells (CTCs).

  6. Aptamer-based microfluidic device for enrichment, sorting, and detection of multiple cancer cells

    PubMed Central

    Xu, Ye; Phillips, Joseph A.; Yan, Jilin; Li, Qingge

    2011-01-01

    The ability to diagnose cancer based on the detection of rare cancer cells in blood or other bodily fluids is a significant challenge. To address this challenge, we have developed a microfluidic device that can simultaneously sort, enrich, and then detect multiple types of cancer cells from a complex sample. The device, which is made from poly(dimethylsiloxane) (PDMS), implements cell-affinity chromatography based on the selective cell-capture of immobilized DNA-aptamers and yields a 135-fold enrichment of rare cells in a single run. This enrichment is achieved because the height of the channel is on the order of a cell diameter. The sorted cells grow at the comparable rate as cultured cells and are 96% pure based on flow cytometry determination. Thus, by using our aptamer based device, cell capture is achieved simply and inexpensively, with no sample pretreatment before cell analysis. Enrichment and detection of multiple rare cancer cells can be used to detect cancers at the early stages, diagnose metastatic relapse, stratify patients for therapeutic purposes, monitor response to drugs and therapies, track tumor progression, and gain a deeper understanding of the biology of circulating tumor cells (CTCs). PMID:19715365

  7. Remediating and Enriching Performance Learning. Implementing Competency Based Education in Community Colleges, 8.

    ERIC Educational Resources Information Center

    Loomis, Katherine A.; And Others

    Part of a series on implementing competency-based education, this monograph discusses some diagnostic and prescriptive techniques which can be used in the day-to-day management of performance learning to determine which students need remediation or enrichment. Using analogies from detective work, the monograph suggests ways of assessing students'…

  8. Inquiry-Based Science and Technology Enrichment Program for Middle School-Aged Female Students

    ERIC Educational Resources Information Center

    Kim, Hanna

    2016-01-01

    This study investigates the effects of an intensive 1-week Inquiry-Based Science and Technology Enrichment Program (InSTEP) designed for middle school-aged female students. InSTEP uses a guided/open inquiry approach that is deepened and redefined as eight sciences and engineering practices in the Next Generation Science Standards, which aimed at…

  9. Remediating and Enriching Performance Learning. Implementing Competency Based Education in Community Colleges, 8.

    ERIC Educational Resources Information Center

    Loomis, Katherine A.; And Others

    Part of a series on implementing competency-based education, this monograph discusses some diagnostic and prescriptive techniques which can be used in the day-to-day management of performance learning to determine which students need remediation or enrichment. Using analogies from detective work, the monograph suggests ways of assessing students'…

  10. Apparent galactose appearance rate in human galactosemia based on plasma [(13)C]galactose isotopic enrichment.

    PubMed

    Ning, C; Fenn, P T; Blair, I A; Berry, G T; Segal, S

    2000-08-01

    Determination of endogenous galactose formation in galactosemic subjects provides important information in understanding the etiology of the long-term complications. To accomplish this task a sensitive method for measurement of isotopic enrichment of plasma galactose was developed. The aldononitrile pentaacetate derivative of galactose was utilized for gas chromatography/mass spectrometry analysis. Using a phenyl-methylsilicone capillary column, adequate separation of galactose from glucose was obtained by temperature programming of the chromatography. The specific fragmentation pattern of m/z 212, 225, 314 from d-[(12)C]galactose and m/z 213, 226, 315 from l-[(13)C]galactose was used for the galactose enrichment measurement by atom percent excess (APE). There was good correlation between expected enrichment and determined APEs at galactose concentrations of 1, 2, and 5 micromol/L with a coefficient of variation ranging from 0.22 to 7.17%. The method provides an accurate estimation of plasma [(13)C]galactose enrichment from which the galactose production rate can be calculated. The steady-state plasma l-[(13)C]galactose isotopic enrichment of three individuals with galactosemia, two males ages 33 and 13, and one female age 9, during constant infusion of l-[(13)C]galactose was 55, 41, and 55%, allowing the estimation of the apparent galactose appearance rate of 0.62, 1.09, and 0.82 mg/kg/h, respectively. The reanalysis of three previous studies by the present method found that APE values determined by the method then employed, butylboronate acetate derivatization, were systemically lower than those determined with aldononitrile pentaacetate derivatization, making for an overestimation of the apparent galactose appearance rate. The small plasma sample volumes needed make it feasible to perform these studies in infants and young children with galactosemia. Copyright 2000 Academic Press.

  11. Screening essential genes of Mycobacterium tuberculosis with the pathway enrichment method.

    PubMed

    Xu, Guangyu; Ni, Zhaohui; Shi, Yue; Sun, Xiaoyu; Wang, Huaidong; Wei, Chengguo; Wang, Guoqing; Li, Fan

    2014-11-01

    The number of effective drugs for the prevention and control of tuberculosis is very limited. Therefore, high-throughput screening for Mycobacterium tuberculosis drug targets is critical. In addition, determining the essential gene cluster is important for both understanding a survival mechanism and finding novel molecular targets for anti-tuberculosis drugs. In this study, we applied the pathway enrichment method to perform high throughput screening of genes encoding key molecules for potential drug targets for M. tuberculosis. Our results indicated 122 genes that existed in more than three pathways, while four existed in 11 pathways. We predicted 55 genes that are potentially essential genes. Four of them, namely, Rv0363c, Rv0408, Rv0409 and Rv0794c, had the highest probability to be essential genes, and thus further experimental validation is warranted.

  12. Behavioral analysis of Wistar rats fed with a flaxseed based diet added to an environmental enrichment.

    PubMed

    Azevedo de Meneses, J; Junqueira Lopes, C A; Coca Velarde, L G; Teles Boaventura, G

    2011-01-01

    Flaxseed has a high content of n-3 fatty acids and its intake associated with an environmental enrichment may promote distinct behavioral results upon habituation and animal behavior. This work aimed to evaluating animal behavior under the use of these two tools in the Open Field Test. Thirty-six male Wistar rats were divided into 6 groups (n = 6): FEEG, receiving chow made up of flaxseed and kept in enriched environment; FSEG, receiving flaxseed based diet and kept in a standard environment; CEEG, receiving casein based diet and kept in enriched environment; CSEG, receiving casein based chow and kept in standard environment; MCEEG, receiving chow made up of casein but modified so as to provide the same content of fibers and lipids found in flaxseed diet and kept in enriched environment; MCSEG, receiving modified casein based diet and kept in standard environment. All animals were kept under controlled temperature, collective cages and dark/light cycle, receiving chow and water ad libitum, except for MCEEG and MCSEG, which were pair fed with FEEG and FSEG, respectively. Chow intake and animal body weight were evaluated twice in a week. Animals were maintained in these groups from the first until the second month of life, by the time when 3 day tests in Open Field Test began. Finishing the tests, animals were sacrificed and their brains were obtained in order to calculate the relative brain weight. Our results show an interplay between flaxseed and environmental enrichment in habituation to a new environment, making the animals more manageable and less stressed.

  13. GC-based analysis of plant stanyl fatty acid esters in enriched foods.

    PubMed

    Barnsteiner, Andreas; Lubinus, Tim; di Gianvito, Angelica; Schmid, Wolfgang; Engel, Karl-Heinz

    2011-05-25

    Approaches for the capillary gas chromatographic (GC) based analysis of intact plant stanyl esters in enriched foods were developed. Reference compounds were synthesized by enzyme-catalyzed transesterifications. Their identities were confirmed by means of mass spectrometry. Using a medium polar trifluoropropylmethyl polysiloxane stationary phase, long-chain plant stanyl esters could be separated according to their stanol moieties and their fatty acid chains. Thermal degradation during GC analysis was compensated by determining response factors; calibrations were performed for ten individual plant stanyl esters. For the analysis of low-fat products (skimmed milk drinking yogurts), the GC separation was combined with a "fast extraction" under acidic conditions. For fat-based foods (margarines), online coupled LC-GC offered an elegant and efficient way to avoid time-consuming sample preparation steps. The robust and rapid methods allow conclusions on both, the stanol profiles and the fatty acid moieties, and thus provide a basis for the authentication of this type of functional food ingredients.

  14. A study on the vibration-based self-monitoring capabilities of nano-enriched composite laminated beams

    NASA Astrophysics Data System (ADS)

    García, David; Trendafilova, Irina; Inman, Daniel J.

    2016-04-01

    This is an exploratory investigation on the self-sensing capabilities of nano-enriched glass/fibre laminates for damage detection purposes through changes in the dynamic responses, which are estimated by measuring the changes in voltage due to a dynamic strain. The deformation of the nano-enriched structure introduces changes in the resistance/voltage of the nanocomposites. The measured voltage signals contain information of the vibratory response of the laminated beam. This research uses a vibration-based data driven methodology for damage detection applied for the estimated vibratory signals using the conductivity properties of the embedded nano-particles. The structure considered in this study is a glass/fibre laminated beam enriched with carbon black nanoparticles (CB). The structure is subjected to a direct electric current and the voltage signal is measured. The vibration based monitoring method used is generally based on singular spectrum analysis applied on the estimated vibratory response. The voltage response signal is divided into a certain number of principal components which contain the oscillatory components distributed by their content of variance in the voltage signal. The components with more variance are used to define a reference state based on the status of the healthy structure. Consequently, the estimated vibratory signals from beams with a simulated damage are compared to the healthy state which eventually results in the damage detection procedure. The damage was simulated firstly by adding an additional mass on the beam tip and secondly by drilling a hole on the beam tip. The results demonstrate the potential for using the voltage estimated vibratory signals for self-sensing damage detection purposes in carbon nano-enriched glass/fibre structures.

  15. Effect of Dietary Fiber Enrichment and Different Cooking Methods on Quality of Chicken Nuggets.

    PubMed

    Pathera, Ashok K; Riar, C S; Yadav, Sanjay; Sharma, D P

    2017-01-01

    The effect of dietary fiber enrichment (wheat bran) and cooking methods (oven, steam and microwave) on functional and physico-chemical properties of raw nuggets formulation as well as nutritional, color and textural properties of chicken nuggets were analyzed in this study. Among different cooking methods used for nuggets preparation, steam cooked nuggets had significantly (p<0.05) higher water holding capacity (56.65%), cooking yield (97.16%) and total dietary fiber content (4.32%) in comparison to oven and microwave cooked nuggets. The effect of cooking methods and wheat bran incorporation was also noticed on textural properties of the nuggets. Hardness, firmness and toughness values of oven and steam cooked nuggets were significantly (p<0.05) higher than microwave cooked nuggets. Among nuggets prepared by different cooking methods, cohesiveness of microwave cooked nuggets was found to be significantly (p<0.05) highest, whereas, oven cooked nuggets had significantly (p<0.05) highest gumminess and chewiness values. Steam cooked nuggets were found to be better among all nuggets due to their higher cooking yield and dietary fiber content.

  16. Effect of Dietary Fiber Enrichment and Different Cooking Methods on Quality of Chicken Nuggets

    PubMed Central

    Yadav, Sanjay; Sharma, D. P.

    2017-01-01

    The effect of dietary fiber enrichment (wheat bran) and cooking methods (oven, steam and microwave) on functional and physico-chemical properties of raw nuggets formulation as well as nutritional, color and textural properties of chicken nuggets were analyzed in this study. Among different cooking methods used for nuggets preparation, steam cooked nuggets had significantly (p<0.05) higher water holding capacity (56.65%), cooking yield (97.16%) and total dietary fiber content (4.32%) in comparison to oven and microwave cooked nuggets. The effect of cooking methods and wheat bran incorporation was also noticed on textural properties of the nuggets. Hardness, firmness and toughness values of oven and steam cooked nuggets were significantly (p<0.05) higher than microwave cooked nuggets. Among nuggets prepared by different cooking methods, cohesiveness of microwave cooked nuggets was found to be significantly (p<0.05) highest, whereas, oven cooked nuggets had significantly (p<0.05) highest gumminess and chewiness values. Steam cooked nuggets were found to be better among all nuggets due to their higher cooking yield and dietary fiber content. PMID:28747827

  17. Determination of the Avogadro constant by the XRCD method using a 28Si-enriched sphere

    NASA Astrophysics Data System (ADS)

    Kuramoto, Naoki; Mizushima, Shigeki; Zhang, Lulu; Fujita, Kazuaki; Azuma, Yasushi; Kurokawa, Akira; Okubo, Sho; Inaba, Hajime; Fujii, Kenichi

    2017-10-01

    To determine the Avogadro constant N A by the x-ray crystal density method, the density of a 28Si-enriched crystal was determined by absolute measurements of the mass and volume of a 1 kg sphere manufactured from the crystal. The mass and volume were determined by an optical interferometer and a vacuum mass comparator, respectively. The sphere surface was characterized by x-ray photoelectron spectroscopy and spectroscopic ellipsometry to derive the mass and volume of the Si core of the sphere excluding the surface layers. From the mass and volume, the density of the Si core was determined with a relative standard uncertainty of 2.3  ×  10‑8. By combining the Si core density with the lattice constant and the molar mass of the sphere reported by the International Avogadro Coordination (IAC) project in 2015, a new value of 6.022 140 84(15)  ×  1023 mol‑1 was obtained for N A with a relative standard uncertainty of 2.4  ×  10‑8. To make the N A value determined in this work usable for a future adjustment of the fundamental constants by the CODATA Task Group on Fundamental Constants, the correlation of the new N A value with the N A values determined in our previous works was examined. The correlation coefficients with the values of N A determined by IAC in 2011 and 2015 were estimated to be 0.07 and 0.28, respectively. The correlation of the new N A value with the N A value determined by IAC in 2017 using a different 28Si-enriched crystal was also examined, and the correlation coefficient was estimated to be 0.21.

  18. Real-time PCR detection of Listeria monocytogenes in infant formula and lettuce following macrophage-based isolation and enrichment.

    PubMed

    Day, J B; Basavanna, U

    2015-01-01

    To develop a rapid detection procedure for Listeria monocytogenes in infant formula and lettuce using a macrophage-based enrichment protocol and real-time PCR. A macrophage cell culture system was employed for the isolation and enrichment of L. monocytogenes from infant formula and lettuce for subsequent identification using real-time PCR. Macrophage monolayers were exposed to infant formula and lettuce contaminated with a serial dilution series of L. monocytogenes. As few as approx. 10 CFU ml(-1) or g(-1) of L. monocytogenes were detected in infant formula and lettuce after 16 h postinfection by real-time PCR. Internal positive PCR controls were utilized to eliminate the possibility of false-negative results. Co-inoculation with Listeria innocua did not reduce the L. monocytogenes detection sensitivity. Intracellular L. monocytogenes could also be isolated on Listeria selective media from infected macrophage lysates for subsequent confirmation. The detection method is highly sensitive and specific for L. monocytogenes in infant formula and lettuce and establishes a rapid identification time of 20 and 48 h for presumptive and confirmatory identification, respectively. The method is a promising alternative to many currently used q-PCR detection methods which employ traditional selective media for enrichment of contaminated food samples. Macrophage enrichment of L. monocytogenes eliminates PCR inhibitory food elements and contaminating food microflora which produce cleaner samples that increase the rapidity and sensitivity of detection. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

  19. Enrichment of steroid hormones in water with porous and hydrophobic polymer-based SPE followed by HPLC-UV determination.

    PubMed

    Hu, Yinfen; Zhang, Man; Tong, Changlun; Wu, Jianmin; Liu, Weiping

    2013-10-01

    There have been great concerns about the persistence of steroid hormones in surface water. Since the concentrations of these compounds in water samples are usually at a trace level, the efficient enrichment of steroid hormones is vital for further analysis. In this work, a porous and hydrophobic polymer was synthesized and characterized. The composition of solvent used as porogen in the synthetic process was shown to have an effect on the morphology of the polymer, which was successfully used as an SPE sorbent for simultaneously enriching steroid hormones in surface water samples. The recoveries of the steroid hormones on the custom-made polymer ranged from 93.4 to 106.2%, whereas those on commercialized ENVI-18, LC-18, and Oasis HLB ranged from 54.8 to 104.9, 66 to 93.6, and 77.2 to 106%, respectively. Five types of steroid hormones were simultaneously measured using HPLC-UV after they were enriched by the custom-made sorbent. Based on these findings, the SPE-HPLC method was developed. The LODs of this method for estriol, estradiol, estrone, androstenedione, progesterone were 0.07, 0.43, 0.61, 0.27, and 0.42 μg/L, respectively, while precision and reproducibility RSDs were <6.40 and 7.49%, respectively. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing1

    PubMed Central

    Sakaguchi, Shota; Ueno, Saneyoshi; Tsumura, Yoshihiko; Setoguchi, Hiroaki; Ito, Motomi; Hattori, Chie; Nozoe, Shogo; Takahashi, Daiki; Nakamasu, Riku; Sakagami, Taishi; Lannuzel, Guillaume; Fogliani, Bruno; Wulff, Adrien S.; L’Huillier, Laurent; Isagi, Yuji

    2017-01-01

    Premise of the study: High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. Methods: Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing. Results: Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully. Discussion: This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species). PMID:28529832

  1. Comparison of simple sucrose and percoll based methodologies for synaptosome enrichment.

    PubMed

    Tenreiro, P; Rebelo, S; Martins, F; Santos, M; Coelho, E D; Almeida, M; Alves de Matos, A P; da Cruz E Silva, O A B

    2017-01-15

    Synaptosomes are isolated nerve terminals. They represent an extremely attractive in vitro model system to study synaptic physiology since they preserve morphological and functional characteristics of the synapse. As such they have been used to investigate synaptic dysfunctions associated with neuropathologies like Alzheimer's disease. In the present work two simple methodologies for isolating synaptosomal-enriched fractions were compared for the first time. The starting points of both protocols were rat cortical or hippocampal homogenized tissues that underwent several differential centrifugation steps followed by a final purification of synaptosomal-enriched fractions using either a Percoll gradient or a Sucrose gradient. Comparison of the fractions obtained was carried out, using both biochemical and electron microscopy approaches. In the biochemical analysis the protein levels of pre-synaptic, post-synaptic, nuclear and mitochondrial markers were evaluated. Additional characterization of the synaptosomal-enriched fractions was performed using transmission electron microscopy. In summary, the results indicate that under the conditions tested the Sucrose based protocol is more efficient for the isolation of synaptosomal-enriched fractions from both neuronal tissues, being particularly efficient for hippocampus that is a less abundant brain tissue. Further, the sucrose protocol apparently results in a higher yield of viable synaptosomes suitable for further assays, including structural and functional studies of synapses; making this an attractive procedure to study processes associated with neuropathologies. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Isolation and enrichment of low abundant particles with insulator-based dielectrophoresis

    PubMed Central

    LaLonde, Alexandra; Romero-Creel, Maria F.; Saucedo-Espinosa, Mario A.; Lapizco-Encinas, Blanca H.

    2015-01-01

    Isolation and enrichment of low-abundant particles are essential steps in many bio-analytical and clinical applications. In this work, the capability of an insulator-based dielectrophoresis (iDEP) device for the detection and stable capture of low abundant polystyrene particles and yeast cells was evaluated. Binary and tertiary mixtures of particles and cells were tested, where the low-abundant particles had concentration ratios on the order of 1:10 000 000 compared to the other particles present in the mixture. The results demonstrated successful and stable capture and enrichment of rare particles and cells (trapping efficiencies over 99%), where particles remained trapped in a stable manner for up to 4 min. A device with four reservoirs was employed for the separation and enrichment of rare particles, where the particles of interest were first selectively concentrated and then effectively directed to a side port for future collection and analysis. The present study demonstrates that simple iDEP devices have appropriate screening capacity and can be used for handling samples containing rare particles; achieving both enrichment and isolation of low-abundant particles and cells. PMID:26674134

  3. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis.

    PubMed

    Zheng, Qi; Wang, Xiu-Jie

    2008-07-01

    Gene Ontology (GO) analysis has become a commonly used approach for functional studies of large-scale genomic or transcriptomic data. Although there have been a lot of software with GO-related analysis functions, new tools are still needed to meet the requirements for data generated by newly developed technologies or for advanced analysis purpose. Here, we present a Gene Ontology Enrichment Analysis Software Toolkit (GOEAST), an easy-to-use web-based toolkit that identifies statistically overrepresented GO terms within given gene sets. Compared with available GO analysis tools, GOEAST has the following improved features: (i) GOEAST displays enriched GO terms in graphical format according to their relationships in the hierarchical tree of each GO category (biological process, molecular function and cellular component), therefore, provides better understanding of the correlations among enriched GO terms; (ii) GOEAST supports analysis for data from various sources (probe or probe set IDs of Affymetrix, Illumina, Agilent or customized microarrays, as well as different gene identifiers) and multiple species (about 60 prokaryote and eukaryote species); (iii) One unique feature of GOEAST is to allow cross comparison of the GO enrichment status of multiple experiments to identify functional correlations among them. GOEAST also provides rigorous statistical tests to enhance the reliability of analysis results. GOEAST is freely accessible at http://omicslab.genetics.ac.cn/GOEAST/

  4. Virus Enrichment for Single Virus Infection by Using 3D Insulator Based Dielectrophoresis

    PubMed Central

    Masuda, Taisuke; Maruyama, Hisataka; Honda, Ayae; Arai, Fumihito

    2014-01-01

    We developed an active virus filter (AVF) that enables virus enrichment for single virus infection, by using insulator-based dielectrophoresis (iDEP). A 3D-constricted flow channel design enabled the production of an iDEP force in the microfluidic chip. iDEP using a chip with multiple active virus filters (AVFs) was more accurate and faster than using a chip with a single AVF, and improved the efficiency of virus trapping. We utilized maskless photolithography to achieve the precise 3D gray-scale exposure required for fabrication of constricted flow channel. Influenza virus (A PR/8) was enriched by a negative DEP force when sinusoidal wave was applied to the electrodes within an amplitude range of 20 Vp-p and a frequency of 10 MHz. AVF-mediated virus enrichment can be repeated simply by turning the current ON or OFF. Furthermore, the negative AVF can inhibit virus adhesion onto the glass substrate. We then trapped and transported one of the enriched viruses by using optical tweezers. This microfluidic chip facilitated the effective transport of a single virus from AVFs towards the cell-containing chamber without crossing an electrode. We successfully transported the virus to the cell chamber (v = 10 µm/s) and brought it infected with a selected single H292 cell. PMID:24918921

  5. Rheology, fatty acid profile and quality characteristics of nutrient enriched pizza base.

    PubMed

    Gupta, Chaitali Sen; Milind; Jeyarani, T; Rajiv, Jyotsna

    2015-05-01

    Enrichment of thick bread type pizza base (PZB) was done by substituting wheat flour (WF) with 5, 10 and 15 % soya protein isolate (SPI). The rheological characteristics of WF showed that water absorption increased, extensibility and peak viscosity decreased when level of SPI increased from 5 to 15 %. Baking studies showed that spread ratio decreased and hardness values of PZB increased with the increase in amount of SPI from 5 to15 %. Beyond 10 % SPI, the overall quality of PZB was adversely affected. To the optimal blend of 10 % SPI, 5 % psyllium husk (PH) was added and the hydrogenated fat was replaced by canola oil (CAN) in enriched PZB. The enriched PZB treated with combination of additives had 1.7 and 1.6 times more protein and dietary fiber than the control PZB. Fatty acid analysis showed that the enriched PZB had 58.65 % oleic, 6.58 % linolenic acid and 31.28 % polyunsaturated fatty acid and no Trans fat was present.

  6. Feasibility study of an alkaline-based chemical treatment for the purification of polyhydroxybutyrate produced by a mixed enriched culture.

    PubMed

    Jiang, Yang; Mikova, Gizela; Kleerebezem, Robbert; van der Wielen, Luuk Am; Cuellar, Maria C

    2015-12-01

    This study focused on investigating the feasibility of purifying polyhydroxybutyrate (PHB) from mixed culture biomass by alkaline-based chemical treatment. The PHB-containing biomass was enriched on acetate under non-sterile conditions. Alkaline treatment (0.2 M NaOH) together with surfactant SDS (0.2 w/v% SDS) could reach 99% purity, with more than 90% recovery. The lost PHB could be mostly attributed to PHB hydrolysis during the alkaline treatment. PHB hydrolysis could be moderated by increasing the crystallinity of the PHB granules, for example, by biomass pretreatment (e.g. freezing or lyophilization) or by effective cell lysis (e.g. adjusting alkali concentration). The suitability of the purified PHB by alkaline treatment for polymer applications was evaluated by molecular weight and thermal stability. A solvent based purification method was also performed for comparison purposes. As result, PHB produced by mixed enriched cultures was found suitable for thermoplastic applications when purified by the solvent method. While the alkaline method resulted in purity, recovery yield and molecular weight comparable to values reported in literature for PHB produced by pure cultures, it was found unsuitable for thermoplastic applications. Given the potential low cost and favorable environmental impact of this method, it is expected that PHB purified by alkaline method may be suitable for other non-thermal polymer applications, and as a platform chemical.

  7. Development of gel-filter method for high enrichment of low-molecular weight proteins from serum.

    PubMed

    Chen, Lingsheng; Zhai, Linhui; Li, Yanchang; Li, Ning; Zhang, Chengpu; Ping, Lingyan; Chang, Lei; Wu, Junzhu; Li, Xiangping; Shi, Deshun; Xu, Ping

    2015-01-01

    The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa) difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2) from 10 μL serum. Among them, 559 (n = 2) proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses.

  8. Development of Gel-Filter Method for High Enrichment of Low-Molecular Weight Proteins from Serum

    PubMed Central

    Chen, Lingsheng; Zhai, Linhui; Li, Yanchang; Li, Ning; Zhang, Chengpu; Ping, Lingyan; Chang, Lei; Wu, Junzhu; Li, Xiangping; Shi, Deshun; Xu, Ping

    2015-01-01

    The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa) difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2) from 10 μL serum. Among them, 559 (n = 2) proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses. PMID:25723528

  9. Method for Recovery and Immunoaffinity Enrichment of Membrane Proteins Illustrated with Metastatic Ovarian Cancer Tissues

    PubMed Central

    Schneider, Luke V.; Likhte, Varsha; Wright, William H.; Chu, Frances; Cambron, Emma; Baldwin-Burnett, Anne; Krakow, Jessica; Smejkal, Gary B.

    2012-01-01

    Integral membrane proteins play key biological roles in cell signaling, transport, and pathogen invasion. However, quantitative clinical assays for this critical class of proteins remain elusive and are generally limited to serum-soluble extracellular fragments. Furthermore, classic proteomic approaches to membrane protein analysis typically involve proteolytic digestion of the soluble pieces, resulting in separation of intra- and extracellular segments and significant informational loss. In this paper, we describe the development of a new method for the quantitative extraction of intact integral membrane proteins (including GPCRs) from solid metastatic ovarian tumors using pressure cycling technology in combination with a new (ProteoSolve-TD) buffer system. This new extraction buffer is compatible with immunoaffinity methods (e.g., ELISA and immunoaffinity chromatography), as well as conventional proteomic techniques (e.g., 2D gels, western blots). We demonstrate near quantitative recovery of membrane proteins EDG2, EDG4, FASLG, KDR, and LAMP-3 by western blots. We have also adapted commercial ELISAs for serum-soluble membrane protein fragments (e.g., sVEGFR2) to measure the tissue titers of their transmembrane progenitors. Finally, we demonstrate the compatibility of the new buffers with immunoaffinity enrichment/mass spectrometric characterization of tissue proteins. PMID:22919487

  10. Pruned-enriched Rosenbluth method: Simulations of {theta} polymers of chain length up to 1000000

    SciTech Connect

    Grassberger, P. |

    1997-09-01

    We present an algorithm for simulating flexible chain polymers. It combines the Rosenbluth-Rosenbluth method with recursive enrichment. Although it can be applied also in more general situations, it is most efficient for three-dimensional {theta} polymers on the simple-cubic lattice. There it allows high statistics simulations of chains of length up to N=10{sup 6}. For storage reasons, this is feasable only for polymers in a finite volume. For free {theta} polymers in infinite volume, we present very high statistics runs with N=10000. These simulations fully agree with previous simulations made by Hegger and Grassberger [J. Chem. Phys. {bold 102}, 6681 (1995)] with a similar but less efficient algorithm, showing that logarithmic corrections to mean field behavior are much stronger than predicted by field theory. But the finite volume simulations show that the density inside a collapsed globule scales with the distance from the {theta} point as predicted by mean field theory, in contrast to claims in the work mentioned above. In addition to the simple-cubic lattice, we also studied two versions of the bond fluctuation model, but with much shorter chains. Finally, we show that our method can be applied also to off-lattice models, and illustrate this with simulations of a model studied in detail by Freire {ital et al.} [Macromolecules {bold 19}, 452 (1986) and later work]. {copyright} {ital 1997} {ital The American Physical Society}

  11. Membrane filtration immobilization technique-a simple and novel method for primary isolation and enrichment of bacteriophages.

    PubMed

    Ghugare, G S; Nair, A; Nimkande, V; Sarode, P; Rangari, P; Khairnar, K

    2017-02-01

    To develop a method for the isolation and enrichment of bacteriophages selectively against specific bacteria coupled with a membrane filtration technique. Rapid isolation and concentration of host-specific bacteriophages was achieved by exposure of the sample suspected to contain bacteriophages to a specific host immobilized on a 0·45 μm membrane in a membrane filtration unit. The principle behind this method is the exploitation of host-specific interaction of bacteriophages with their host and maximizing this interaction using a classic membrane filtration method. This provides a chance for each bacteriophage in the sample to interact with the specific host on the membrane filter fitted with a vacuum pump. Specific bacteriophages of the host are retained on the membrane along with its host cells due to the effect of adsorption and these adsorbed bacteriophages (along with their hosts) on the filter disc are then amplified and enriched in regular nutritive broth tryptose soya broth by incubation. With the help of the plaque assay method, host-specific phages of various bacterial species were isolated, segregated and enriched. The phage concentration method coupled with membrane filtration immobilization of host bacteria was able to isolate and enrich the host-specific bacteriophages by several fold using a lower quantity of an environmental water sample, or other phage suspensions. Enrichment of phages from single plaques was also achieved. The isolation and detection of host-specific bacteriophages from a low density bacteriophage water sample in a single step by the use of a simple and basic microbiological technique can be achieved. Enrichment of phages from low phage titre suspensions is also achieved very effectively. © 2016 The Society for Applied Microbiology.

  12. Nutrient enrichment reduces constraints on material flows in a detritus-based food web.

    PubMed

    Cross, Wyatt F; Wallace, J Bruce; Rosemond, Amy D

    2007-10-01

    Most aquatic and terrestrial ecosystems are experiencing increased nutrient availability, which is affecting their structure and function. By altering community composition and productivity of consumers, enrichment can indirectly cause changes in the pathways and magnitude of material flows in food webs. These changes, in turn, have major consequences for material storage and cycling in the ecosystem. Understanding mechanisms and predicting consequences of nutrient-induced changes in material flows requires a quantitative food web approach that combines information on consumer energetics and consumer-resource stoichiometry. We examined effects of a whole-system experimental nutrient enrichment on the trophic basis of production and the magnitude and pathways of carbon (C), nitrogen (N), and phosphorus (P) flows in a detritus-based stream food web. We compared the response of the treated stream to an adjacent reference stream throughout the study. Dietary composition and elemental flows varied considerably among invertebrate functional feeding groups. During nutrient enrichment, increased flows of leaf litter and amorphous detritus to shredders and gatherers accounted for most of the altered flows of C from basal resources to consumers. Nutrient enrichment had little effect on patterns of material flows but had large positive effects on the magnitude of C, N, and P flows to consumers (mean increase of 97% for all elements). Nutrient-specific food webs revealed similar flows of N and P to multiple functional groups despite an order of magnitude difference among groups in consumption of C. Secondary production was more strongly related to consumption of nutrients than C, and increased material flows were positively related to the degree of consumer-resource C:P and C:N imbalances. Nutrient enrichment resulted in an increased proportion of detrital C inputs consumed by primary consumers (from -15% to 35%) and a decreased proportion of invertebrate prey consumed by

  13. Stirred suspension bioreactors as a novel method to enrich germ cells from pre-pubertal pig testis

    PubMed Central

    Dores, Camila; Rancourt, Derrick; Dobrinski, Ina

    2015-01-01

    To study spermatogonial stem cells the heterogeneous testicular cell population first needs to be enriched for undifferentiated spermatogonia, which contain the stem cell population. When working with non-rodent models, this step requires working with large numbers of cells. Available cell separation methods rely on differential properties of testicular cell types such as expression of specific cell surface proteins, size, density or differential adhesion to substrates to separate germ cells from somatic cells. The objective of this study was to develop an approach that allowed germ cell enrichment while providing efficiency of handling large cell numbers. Here we report the use of stirred suspension bioreactors to exploit the adhesion properties of Sertoli cells to enrich cells obtained from pre-pubertal porcine testes for undifferentiated spermatogonia. We also compared the bioreactor approach with an established differential plating method and the combination of both: stirred suspension bioreactor followed by differential plating. After 66 hours of culture, germ cell enrichment in stirred suspension bioreactors provided 7.3±1.0 fold (n=9), differential plating 9.8±2.4 fold (n=6) and combination of both methods resulted in 9.1±0.3 fold enrichment of germ cells from the initial germ cell population (n=3). To document functionality of cells recovered from the bioreactor, we demonstrated that cells retained their functional ability to reassemble seminiferous tubules de novo after grafting to mouse hosts and to support spermatogenesis. These results demonstrate that the stirred suspension bioreactor allows enrichment of germ cells in a controlled and scalable environment providing an efficient method when handling large cell numbers while reducing variability due to handling. PMID:25877677

  14. Iron oxide nanoparticle coating of organic polymer-based monolithic columns for phosphopeptide enrichment.

    PubMed

    Krenkova, Jana; Foret, Frantisek

    2011-08-01

    A new monolithic capillary column with an iron oxide nanoparticle coating has been developed for selective and efficient enrichment of phosphopeptides. Iron oxide nanoparticles were prepared by a co-precipitation method and stabilized by citrate ions. A stable coating of nanoparticles was obtained via multivalent electrostatic interactions of citrate ions on the surface of iron oxide nanoparticles with a quaternary amine functionalized poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith. A high dynamic binding capacity of 86 μmol/mL column volume was measured with an adenosine-5'-triphosphate. Performance of the monolithic column was demonstrated with the efficient and selective enrichment of phosphopeptides from peptide mixtures of α-casein and β-casein digests and their MALDI/MS characterization in off-line mode. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. A Convenient and Efficient Method to Enrich and Maintain Highly Proliferative Human Fetal Liver Stem Cells.

    PubMed

    Guo, Xuan; Wang, Shu; Dou, Ya-ling; Guo, Xiang-fei; Chen, Zhao-li; Wang, Xin-wei; Shen, Zhi-qiang; Qiu, Zhi-gang; Jin, Min; Li, Jun-wen

    2015-06-01

    Pluripotent human hepatic stem cells have broad research and clinical applications, which are, however, restricted by both limited resources and technical difficulties with respect to isolation of stem cells from the adult or fetal liver. In this study, we developed a convenient and efficient method involving a two-step in situ collagenase perfusion, gravity sedimentation, and Percoll density gradient centrifugation to enrich and maintain highly proliferative human fetal liver stem cells (hFLSCs). Using this method, the isolated hFLSCs entered into the exponential growth phase within 10 days and maintained sufficient proliferative activity to permit subculture for at least 20 passages without differentiation. Immunocytochemistry, immunofluorescence, and flow cytometry results showed that these cells expressed stem cell markers, such as c-kit, CD44, epithelial cell adhesion molecule (EpCAM), oval cell marker-6 (OV-6), epithelial marker cytokeratin 18 (CK18), biliary ductal marker CK19, and alpha-fetoprotein (AFP). Gene expression analysis showed that these cells had stable mRNA expression of c-Kit, EpCAM, neural cell adhesion molecule (NCAM), CK19, CK18, AFP, and claudin 3 (CLDN-3) throughout each passage while maintaining low levels of ALB, but with complete absence of cytochrome P450 3A4 (C3A4), phosphoenolpyruvate carboxykinase (PEPCK), telomeric repeat binding factor (TRF), and connexin 26 (CX26) expression. When grown in appropriate medium, these isolated liver stem cells could differentiate into hepatocytes, cholangiocytes, osteoblasts, adipocytes, or endothelial cells. Thus, we have demonstrated a more economical and efficient method to isolate hFLSCs than magnetic-activated cell sorting (MACS). This novel approach may provide an excellent tool to isolate highly proliferative hFLSCs for tissue engineering and regenerative therapies.

  16. Effect of Different Mixing and Placement Methods on the Compressive Strength of Calcium-Enriched Mixture

    PubMed Central

    Sahebi, Safoora; Sadatshojaee, Nooshin; Jafari, Zahra

    2015-01-01

    Introduction: The aim of this experimental laboratory study was to evaluate the effect of different mixing and placement techniques on compressive strength (CS) of calcium-enriched mixture (CEM) cement. Methods and Materials: CEM powder was mixed with its liquid either by hand mixing or amalgamator mixing. The mixture was loaded to cylindrical acrylic molds with 6.0±0.1 mm height and 4.0±1 mm diameter. Half of the specimens in each group were selected randomly and ultrasonic energy was applied to them for 30 sec. All samples were incubated for 7 days at 37°C. The CS test was performed by means of a universal testing machine. The data were analyzed by the two-way analysis of variance (ANOVA) and Tukey’s post hoc tests. The level of significance was set at 0.05. Results: The maximum CS was seen in the amalgamator-mixed samples that did not receive ultrasonic agitation. The CS value of amalgamator-mixed samples was significantly higher than manually-mixed ones (P=0.003). Ultrasonic vibration did not change the CS of specimens. Conclusion: According to the results, mixing with amalgamator increases the CS of CEM cement, while ultrasonic vibration had no positive effect. PMID:25834593

  17. Numerical modeling of undersea acoustics using a partition of unity method with plane waves enrichment

    NASA Astrophysics Data System (ADS)

    Hospital-Bravo, Raúl; Sarrate, Josep; Díez, Pedro

    2016-05-01

    A new 2D numerical model to predict the underwater acoustic propagation is obtained by exploring the potential of the Partition of Unity Method (PUM) enriched with plane waves. The aim of the work is to obtain sound pressure level distributions when multiple operational noise sources are present, in order to assess the acoustic impact over the marine fauna. The model takes advantage of the suitability of the PUM for solving the Helmholtz equation, especially for the practical case of large domains and medium frequencies. The seawater acoustic absorption and the acoustic reflectance of the sea surface and sea bottom are explicitly considered, and perfectly matched layers (PML) are placed at the lateral artificial boundaries to avoid spurious reflexions. The model includes semi-analytical integration rules which are adapted to highly oscillatory integrands with the aim of reducing the computational cost of the integration step. In addition, we develop a novel strategy to mitigate the ill-conditioning of the elemental and global system matrices. Specifically, we compute a low-rank approximation of the local space of solutions, which in turn reduces the number of degrees of freedom, the CPU time and the memory footprint. Numerical examples are presented to illustrate the capabilities of the model and to assess its accuracy.

  18. Variational multiscale enrichment method with mixed boundary conditions for elasto-viscoplastic problems

    NASA Astrophysics Data System (ADS)

    Zhang, Shuhai; Oskay, Caglar

    2015-04-01

    This manuscript presents the formulation and implementation of the variational multiscale enrichment (VME) method for the analysis of elasto-viscoplastic problems. VME is a global-local approach that allows accurate fine scale representation at small subdomains, where important physical phenomena are likely to occur. The response within far-fields is idealized using a coarse scale representation. The fine scale representation not only approximates the coarse grid residual, but also accounts for the material heterogeneity. A one-parameter family of mixed boundary conditions that range from Dirichlet to Neumann is employed to study the effect of the choice of the boundary conditions at the fine scale on accuracy. The inelastic material behavior is modeled using Perzyna type viscoplasticity coupled with flow stress evolution idealized by the Johnson-Cook model. Numerical verifications are performed to assess the performance of the proposed approach against the direct finite element simulations. The results of verification studies demonstrate that VME with proper boundary conditions accurately model the inelastic response accounting for material heterogeneity.

  19. Transversally enriched pipe element method (TEPEM): An effective numerical approach for blood flow modeling.

    PubMed

    Mansilla Alvarez, Luis; Blanco, Pablo; Bulant, Carlos; Dari, Enzo; Veneziani, Alessandro; Feijóo, Raúl

    2017-04-01

    In this work, we present a novel approach tailored to approximate the Navier-Stokes equations to simulate fluid flow in three-dimensional tubular domains of arbitrary cross-sectional shape. The proposed methodology is aimed at filling the gap between (cheap) one-dimensional and (expensive) three-dimensional models, featuring descriptive capabilities comparable with the full and accurate 3D description of the problem at a low computational cost. In addition, this methodology can easily be tuned or even adapted to address local features demanding more accuracy. The numerical strategy employs finite (pipe-type) elements that take advantage of the pipe structure of the spatial domain under analysis. While low order approximation is used for the longitudinal description of the physical fields, transverse approximation is enriched using high order polynomials. Although our application of interest is computational hemodynamics and its relevance to pathological dynamics like atherosclerosis, the approach is quite general and can be applied in any internal fluid dynamics problem in pipe-like domains. Numerical examples covering academic cases as well as patient-specific coronary arterial geometries demonstrate the potentialities of the developed methodology and its performance when compared against traditional finite element methods. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  20. Multimetric assessment of nutrient enrichment in impounded rivers based on benthic macroinvertebrates.

    PubMed

    Camargo, Julio A; Alonso, Alvaro; de la Puente, Marcos

    2004-01-01

    In this investigation we evaluated the performance of multiple metrics, based on benthic macroinvertebrates, to assess nutrient enrichment in impounded rivers. Field studies were conducted in the upper reaches of four impounded mountain rivers (Tormes, Riaza, Eresma and Miraflores Rivers) of Central Spain. The watersheds of these rivers are underlain by siliceous rocks. Two sampling sites, upstream and downstream from the reservoir, were established in stony riffles of each impounded river. We used a total of 34 metrics, representing five different metric groups: measures of abundance and richness, percentages of taxonomic groups, percentages of functional feeding groups, measures of dominance and diversity, and biotic indices. Evaluation of different metrics was mainly based on correlation analyses between concentrations of nutrients (NO3-N, NH4-N, PO4-P) and values of individual metrics. Deep releases from the reservoirs were the primary cause responsible for the nutrient enrichment at downstream sampling sites. Chironomidae density, Gastropoda density, % Chironomidae, % Gastropoda, % collector-gatherers and scrapers, proportion of the two most dominant taxa, and Camargo's dominance index exhibited the highest positive correlation coefficients. Conversely, Plecoptera density, Trichoptera density, EPT richness, % Plecoptera, % Trichoptera, % collector-filterers, % predators, % shredders, Simpson's and Camargo's diversity indices, and the average BMWQ score (biotic index) exhibited the highest negative correlation coefficients. Overall it is concluded that the multimetric approach may be a useful technique for the biological assessment of nutrient enrichment in fluvial ecosystems, particularly in upper reaches of siliceous rivers.

  1. Magnetic-based multi-layer microparticles for endothelial progenitor cell isolation, enrichment, and detachment.

    PubMed

    Wadajkar, Aniket S; Santimano, Sonia; Tang, Liping; Nguyen, Kytai T

    2014-01-01

    Although endothelial progenitor cells (EPCs) are useful in many applications including cell-based therapies, their use is still limited due to issues associated with cell culture techniques like a low isolation efficiency, use of harmful proteolytic enzymes in cell cultures, and difficulty in ex vivo expansion. Here, we report a tool to simultaneously isolate, enrich, and detach EPCs without the use of harmful chemicals. In particular, we developed magnetic-based multi-layer microparticles (MLMPs) that (1) magnetically isolate EPCs via anti-CD34 antibodies to avoid the use of Ficoll and harsh shear forces; (2) provide a 3D surface for cell attachment and growth; (3) produce sequential releases of growth factors (GFs) to enrich ex vivo expansion of cells; and (4) detach cells without using trypsin. MLMPs were successful in isolating EPCs from a cell suspension and provided a sequential release of GFs for EPC proliferation and differentiation. The cell enrichment profiles indicated steady cell growth on MLMPs in comparison to commercial Cytodex3 microbeads. Further, the cells were detached from MLMPs by lowering the temperature below 32 °C. Results indicate that the MLMPs have potential to be an effective tool towards efficient cell isolation, fast expansion, and non-chemical detachment. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Evaluation of a RF-Based Approach for Tracking UF6 Cylinders at a Uranium Enrichment Plant

    SciTech Connect

    Pickett, Chris A; Younkin, James R; Kovacic, Donald N; Laughter, Mark D; Hines, Jairus B; Boyer, Brian; Martinez, B.

    2008-01-01

    Approved industry-standard cylinders are used globally to handle and store uranium hexafluoride (UF{sub 6}) feed, product, tails, and samples at uranium enrichment plants. The International Atomic Energy Agency (IAEA) relies on time-consuming physical inspections to verify operator declarations and detect possible diversion of UF{sub 6}. Development of a reliable, automated, and tamper-resistant system for near real-time tracking and monitoring UF{sub 6} cylinders (as they move within an enrichment facility) would greatly improve the inspector function. This type of system can reduce the risk of false or misreported cylinder tare weights, diversion of nuclear material, concealment of excess production, utilization of undeclared cylinders, and misrepresentation of the cylinders contents. This paper will describe a proof-of-concept approach that was designed to evaluate the feasibility of using radio frequency (RF)-based technologies to track individual UF{sub 6} cylinders throughout a portion of their life cycle, and thus demonstrate the potential for improved domestic accountability of materials, and a more effective and efficient method for application of site-level IAEA safeguards. The evaluation system incorporates RF-based identification devices (RFID) which provide a foundation for establishing a reliable, automated, and near real-time tracking system that can be set up to utilize site-specific, rules-based detection algorithms. This paper will report results from a proof-of-concept demonstration at a real enrichment facility that is specifically designed to evaluate both the feasibility of using RF to track cylinders and the durability of the RF equipment to survive the rigors of operational processing and handling. The paper also discusses methods for securely attaching RF devices and describes how the technology can effectively be layered with other safeguard systems and approaches to build a robust system for detecting cylinder diversion. Additionally

  3. Radiometric method for pyrazinamide susceptibility testing of Mycobacterium tuberculosis in egg-yolk-enriched BACTEC 12A medium

    SciTech Connect

    Woodley, C.L.; Smithwick, R.W.

    1988-01-01

    A radiometric method for testing the susceptibility of Mycobacterium tuberculosis to pyrazinamide in egg-yolk-enriched 12A medium (pH 5.5) is described. We obtained 100% agreement between the 7H10 agar method with 25 microgram of pyrazinamide per ml and the modified radiometric method with a drug concentration of 50 microgram/ml in tests of 90 clinical isolates.

  4. An optimised version of the secretome protein enrichment with click sugars (SPECS) method leads to enhanced coverage of the secretome.

    PubMed

    Serdaroglu, Alperen; Müller, Stephan A; Schepers, Ute; Bräse, Stefan; Weichert, Wilko; Lichtenthaler, Stefan F; Kuhn, Peer-Hendrik

    2017-03-01

    The secretome, the entirety of all soluble proteins either being secreted or proteolytically released by a cell, plays a key role in inter-cellular communication of multi-cellular organisms. Pathological alterations contribute to diseases such as hypertension, cancer, autoimmune disorders or neurodegenerative diseases. Hence, studying disease-related perturbations of the secretome and the secretome itself covers an important aspect of cellular physiology. We recently developed the secretome protein enrichment with click sugars (SPECS) method that enables the analysis of secretomes of in vitro cell cultures even in the presence of FCS with MS. So far, SPECS facilitated the identification of protease substrates of BACE1, SPPL3 and ADAM10. Though, the SPECS method has already enabled deep insights into secretome biology, we aimed to improve the SPECS protocol to obtain even more information from MS-based secretome analysis and reduce the amount of input material. Here, we optimised the reaction buffer, the pH and replaced Dibenzocyclooctyne (DBCO) PEG12-biotin with the more water-soluble variant DBCO-sulpho-biotin to finally provide an optimised protocol of the recently published SPECS protocol. Overall, the number of quantified glycoproteins and their average sequence coverage was increased by 1.6- and 2.4-fold, respectively. Thus, the opzimised SPECS protocol allows reducing the input material by half without losing information. These improvements make the SPECS method more sensitive and more universal applicable to cell types with limited availability.

  5. Ecological distribution of extremely thermophilic bacteria belonging to the genus Calditerricola using the novel enrichment MPN-PCR method.

    PubMed

    Bienes, Kathrina Mae; Ito, Minoru; Shiotsuka, Kota; Yamaguchi, Sachi; Fujioka, Taiki; Tashiro, Yukihiro; Sakai, Kenji

    2017-08-07

    A unique compost called Satsuma soil is produced from sewage sludge by a hyperthermal composting process in Kagoshima City, Japan. The composting process is carried out at a controlled temperature of at least 80°C and the resulting compost might be useful for recycling sustainable agricultural products. The extremely thermophilic bacterial genus Calditerricola was initially isolated from the high-temperature compost. Likewise, the bacteria were previously isolated from material sludge. It is believed that bacteria in this genus might be involved in the hyperthermal composting process. Calditerricola bacteria are distributed not only in compost, but also in all of its material sludge, and are more abundant in material sludge than in compost. Moreover, based on investigations of samples near geothermal areas in high temperature conditions, such as volcanoes, Calditerricola was presumed to originate in the volcanic ash of Mt. Sakurajima in Kagoshima City, Japan. However, its precise origin and ecology are unclear. Thus, in this study, a new molecular biological method called enrichment most probable number (MPN)-PCR (eMPN-PCR) was established and used to quantitatively investigate the population and distribution of the extreme thermophile Calditerricola in environmental samples using genus-specific PCR primers. The eMPN-PCR method was an effective quantitative detection method with high sensitivity, yielding MPN estimates that were highly correlated with colony forming unit (CFU) estimates but a low detection threshold value. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  6. Ceria-based nanocomposites for the enrichment and identification of phosphopeptides.

    PubMed

    Fatima, Batool; Najam-ul-Haq, Muhammad; Jabeen, Fahmida; Majeed, Saadat; Ashiq, Muhammad N; Musharraf, S Ghulam; Shad, Muhammad A; Xu, Guobao

    2013-09-07

    Nanocomposites are given preference over the individual materials due to the combined properties of the components involved. Ceria has a high efficiency in phosphopeptide enrichment as well as in dephosphorylation. Iron oxide and tin oxide are chosen as counter metal oxides to synthesize the ceria nanocomposites using a co-precipitation method. The nanocomposites are characterized by Fourier-transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). Tryptic β-casein digest shows the feasibility of phosphopeptide enrichment by the two nanocomposites. Selectivity studies show their performance in comparison to ceria. Being more selective in the extended mass range, both nanocomposites are applied to spiked human serum and non-fat milk digest. The ceria nanocomposites are also capable of being used as material-enhanced laser desorption/ionization (MELDI) carrier/affinity materials for real biological samples with varying degrees of complexity. The enriched content is analyzed by MALDI-TOF MS. All the phosphopeptides in all variants of casein are identified. The sequence coverage of caseins is also interpreted. Nanocomposites thus offer a high selectivity and sensitivity, which make them promising materials for biomarker discoveries and the identification of phosphorylation pathways for new post translational modifications (PTMs).

  7. Sonication-based isolation and enrichment of Chlorella protothecoides chloroplasts for illumina genome sequencing

    SciTech Connect

    Angelova, Angelina; Park, Sang-Hycuk; Kyndt, John; Fitzsimmons, Kevin; Brown, Judith K

    2013-09-01

    With the increasing world demand for biofuel, a number of oleaginous algal species are being considered as renewable sources of oil. Chlorella protothecoides Krüger synthesizes triacylglycerols (TAGs) as storage compounds that can be converted into renewable fuel utilizing an anabolic pathway that is poorly understood. The paucity of algal chloroplast genome sequences has been an important constraint to chloroplast transformation and for studying gene expression in TAGs pathways. In this study, the intact chloroplasts were released from algal cells using sonication followed by sucrose gradient centrifugation, resulting in a 2.36-fold enrichment of chloroplasts from C. protothecoides, based on qPCR analysis. The C. protothecoides chloroplast genome (cpDNA) was determined using the Illumina HiSeq 2000 sequencing platform and found to be 84,576 Kb in size (8.57 Kb) in size, with a GC content of 30.8 %. This is the first report of an optimized protocol that uses a sonication step, followed by sucrose gradient centrifugation, to release and enrich intact chloroplasts from a microalga (C. prototheocoides) of sufficient quality to permit chloroplast genome sequencing with high coverage, while minimizing nuclear genome contamination. The approach is expected to guide chloroplast isolation from other oleaginous algal species for a variety of uses that benefit from enrichment of chloroplasts, ranging from biochemical analysis to genomics studies.

  8. Erythrocyte Enrichment in Hematopoietic Progenitor Cell Cultures Based on Magnetic Susceptibility of the Hemoglobin

    PubMed Central

    Jin, Xiaoxia; Abbot, Stewart; Zhang, Xiaokui; Kang, Lin; Voskinarian-Berse, Vanessa; Zhao, Rui; Kameneva, Marina V.; Moore, Lee R.; Chalmers, Jeffrey J.; Zborowski, Maciej

    2012-01-01

    Using novel media formulations, it has been demonstrated that human placenta and umbilical cord blood-derived CD34+ cells can be expanded and differentiated into erythroid cells with high efficiency. However, obtaining mature and functional erythrocytes from the immature cell cultures with high purity and in an efficient manner remains a significant challenge. A distinguishing feature of a reticulocyte and maturing erythrocyte is the increasing concentration of hemoglobin and decreasing cell volume that results in increased cell magnetophoretic mobility (MM) when exposed to high magnetic fields and gradients, under anoxic conditions. Taking advantage of these initial observations, we studied a noninvasive (label-free) magnetic separation and analysis process to enrich and identify cultured functional erythrocytes. In addition to the magnetic cell separation and cell motion analysis in the magnetic field, the cell cultures were characterized for cell sedimentation rate, cell volume distributions using differential interference microscopy, immunophenotyping (glycophorin A), hemoglobin concentration and shear-induced deformability (elongation index, EI, by ektacytometry) to test for mature erythrocyte attributes. A commercial, packed column high-gradient magnetic separator (HGMS) was used for magnetic separation. The magnetically enriched fraction comprised 80% of the maturing cells (predominantly reticulocytes) that showed near 70% overlap of EI with the reference cord blood-derived RBC and over 50% overlap with the adult donor RBCs. The results demonstrate feasibility of label-free magnetic enrichment of erythrocyte fraction of CD34+ progenitor-derived cultures based on the presence of paramagnetic hemoglobin in the maturing erythrocytes. PMID:22952572

  9. Erythrocyte enrichment in hematopoietic progenitor cell cultures based on magnetic susceptibility of the hemoglobin.

    PubMed

    Jin, Xiaoxia; Abbot, Stewart; Zhang, Xiaokui; Kang, Lin; Voskinarian-Berse, Vanessa; Zhao, Rui; Kameneva, Marina V; Moore, Lee R; Chalmers, Jeffrey J; Zborowski, Maciej

    2012-01-01

    Using novel media formulations, it has been demonstrated that human placenta and umbilical cord blood-derived CD34+ cells can be expanded and differentiated into erythroid cells with high efficiency. However, obtaining mature and functional erythrocytes from the immature cell cultures with high purity and in an efficient manner remains a significant challenge. A distinguishing feature of a reticulocyte and maturing erythrocyte is the increasing concentration of hemoglobin and decreasing cell volume that results in increased cell magnetophoretic mobility (MM) when exposed to high magnetic fields and gradients, under anoxic conditions. Taking advantage of these initial observations, we studied a noninvasive (label-free) magnetic separation and analysis process to enrich and identify cultured functional erythrocytes. In addition to the magnetic cell separation and cell motion analysis in the magnetic field, the cell cultures were characterized for cell sedimentation rate, cell volume distributions using differential interference microscopy, immunophenotyping (glycophorin A), hemoglobin concentration and shear-induced deformability (elongation index, EI, by ektacytometry) to test for mature erythrocyte attributes. A commercial, packed column high-gradient magnetic separator (HGMS) was used for magnetic separation. The magnetically enriched fraction comprised 80% of the maturing cells (predominantly reticulocytes) that showed near 70% overlap of EI with the reference cord blood-derived RBC and over 50% overlap with the adult donor RBCs. The results demonstrate feasibility of label-free magnetic enrichment of erythrocyte fraction of CD34+ progenitor-derived cultures based on the presence of paramagnetic hemoglobin in the maturing erythrocytes.

  10. LENS: web-based lens for enrichment and network studies of human proteins

    PubMed Central

    2015-01-01

    Background Network analysis is a common approach for the study of genetic view of diseases and biological pathways. Typically, when a set of genes are identified to be of interest in relation to a disease, say through a genome wide association study (GWAS) or a different gene expression study, these genes are typically analyzed in the context of their protein-protein interaction (PPI) networks. Further analysis is carried out to compute the enrichment of known pathways and disease-associations in the network. Having tools for such analysis at the fingertips of biologists without the requirement for computer programming or curation of data would accelerate the characterization of genes of interest. Currently available tools do not integrate network and enrichment analysis and their visualizations, and most of them present results in formats not most conducive to human cognition. Results We developed the tool Lens for Enrichment and Network Studies of human proteins (LENS) that performs network and pathway and diseases enrichment analyses on genes of interest to users. The tool creates a visualization of the network, provides easy to read statistics on network connectivity, and displays Venn diagrams with statistical significance values of the network's association with drugs, diseases, pathways, and GWASs. We used the tool to analyze gene sets related to craniofacial development, autism, and schizophrenia. Conclusion LENS is a web-based tool that does not require and download or plugins to use. The tool is free and does not require login for use, and is available at http://severus.dbmi.pitt.edu/LENS. PMID:26680011

  11. Microfluidic, Label-Free Enrichment of Prostate Cancer Cells in Blood Based on Acoustophoresis

    PubMed Central

    Augustsson, Per; Magnusson, Cecilia; Nordin, Maria; Lilja, Hans; Laurell, Thomas

    2012-01-01

    Circulating tumor cells (CTC) are shed in peripheral blood at advanced metastatic stages of solid cancers. Surface-marker-based detection of CTC predicts recurrence and survival in colorectal, breast, and prostate cancer. However, scarcity and variation in size, morphology, expression profile, and antigen exposure impairs reliable detection and characterization of CTC. We have developed a non-contact, label-free microfluidic acoustophoresis method to separate prostate cancer cells from white blood cells (WBC) through forces generated by ultrasonic resonances in microfluidic channels. Implementation of cell pre-alignment in a temperature-stabilized (±0.5°C) acoustophoresis microchannel dramatically enhanced the discriminatory capacity and enabled the separation of 5-μm microspheres from 7-μm microspheres with 99% purity. Next, we determined the feasibility of employing label-free microfluidic acoustophoresis to discriminate and divert tumor cells from WBCs using erythrocyte-lysed blood from healthy volunteers spiked with tumor cells from three prostate cancer cell-lines (DU145, PC3, LNCaP). For cells fixed with paraformaldehyde, cancer cell recovery ranged from 93.6% to 97.9% with purity ranging from 97.4% to 98.4%. There was no detectable loss of cell viability or cell proliferation subsequent to the exposure of viable tumor cells to acoustophoresis. For non-fixed, viable cells, tumor cell recovery ranged from 72.5% to 93.9% with purity ranging from 79.6% to 99.7%. These data contribute proof-in-principle that label-free microfluidic acoustophoresis can be used to enrich both viable and fixed cancer cells from WBCs with very high recovery and purity. PMID:22897670

  12. Innovative method for the enrichment of high-polarity bioactive molecules present at low concentrations in complex matrices.

    PubMed

    Liu, Qing-Shan; He, Jie; Zhou, Wen-Bin; Gu, Yu-Long; Huang, Huoqiang; Li, Ke-Qin; Yin, Xiao-Ying

    2017-02-01

    Ginsenoside Rg1 is a valuable bioactive molecule but its high polarity and low concentration in complex mixtures makes it a challenge to separate Ginsenoside Rg1 from other saponins with similar structures, resulting in low extraction efficiency. The successful development of effective Rg1 molecularly imprinted polymers that exhibit high selectivity and adsorption may offer an improved method for the enrichment of active compounds. In this work, molecularly imprinted polymers were prepared with two different methods, precipitation polymerization or surface imprinted polymerization. Comparison of the adsorption abilities showed higher adsorption of the surface molecularly imprinted polymers prepared by surface imprinted polymerization, 46.80 mg/g, compared to the 27.74 mg/g observed for the molecularly imprinted polymers prepared by precipitation polymerization. Therefore, for higher adsorption of the highly polar Rg1, surface imprinted polymerization is a superior technique to make Rg1 molecularly imprinted polymers. The prepared surface molecularly imprinted polymers were tested as a solid-phase extraction column to directionally enrich Rg1 and its analogues from ginseng tea and total ginseng extracts. The column with surface molecularly imprinted polymers showed higher enrichment efficiency and better selectivity than a C18 solid-phase extraction column. Overall, a new, innovative method was developed to efficiently enrich high-polarity bioactive molecules present at low concentrations in complex matrices.

  13. Changes in the composition and structure of Mediterranean rocky-shore communities following a gradient of nutrient enrichment: descriptive study and test of proposed methods to assess water quality regarding macroalgae.

    PubMed

    Arévalo, Raquel; Pinedo, Susana; Ballesteros, Enric

    2007-01-01

    Changes in the species composition and structure of Mediterranean macroalgal-dominated communities from the upper sublittoral zone are described along a gradient of nutrient enrichment coming from a urban sewage outfall. Ulva-dominated communities only appear close to the sewage outfall. Corallina-dominated communities replace ulvacean algae at intermediate levels of nutrient enrichment. Cystoseira-dominated communities thrive in the reference site but already appear at nutrient levels that are threefold higher than those reported from unpolluted sites. Assemblage variability of Cystoseira-dominated communities decreases along the gradient of nutrient enrichment. Methods based on the functional-form groups of macroalgae to assess the water quality provide equivocal results at intermediate levels of nutrient enrichment because species belonging to the same group can display a completely different response to pollution. Alternatively, methods based on indicator species showed correlated evidence among species abundances and pollution levels and seem to have better performances in water quality assessment.

  14. HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.

    PubMed

    Deng, Yue; Gao, Lin; Wang, Bingbo; Guo, Xingli

    2015-01-01

    Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the controlled vocabulary. The Human Phenotype Ontology (HPO) provides a standardized and controlled vocabulary covering phenotypic abnormalities in human diseases, and becomes a comprehensive resource for computational analysis of human disease phenotypes. Most of the existing HPO-based software tools cannot be used offline and provide only few similarity measures. Therefore, there is a critical need for developing a comprehensive and offline software for phenotypic features similarity based on HPO. HPOSim is an R package for analyzing phenotypic similarity for genes and diseases based on HPO data. Seven commonly used semantic similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets are also implemented, including hypergeometric enrichment analysis and network ontology analysis (NOA). HPOSim can be used to predict disease genes and explore disease-related function of gene modules. HPOSim is open source and freely available at SourceForge (https://sourceforge.net/p/hposim/).

  15. HPOSim: An R Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology

    PubMed Central

    Deng, Yue; Gao, Lin; Wang, Bingbo; Guo, Xingli

    2015-01-01

    Background Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the controlled vocabulary. The Human Phenotype Ontology (HPO) provides a standardized and controlled vocabulary covering phenotypic abnormalities in human diseases, and becomes a comprehensive resource for computational analysis of human disease phenotypes. Most of the existing HPO-based software tools cannot be used offline and provide only few similarity measures. Therefore, there is a critical need for developing a comprehensive and offline software for phenotypic features similarity based on HPO. Results HPOSim is an R package for analyzing phenotypic similarity for genes and diseases based on HPO data. Seven commonly used semantic similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets are also implemented, including hypergeometric enrichment analysis and network ontology analysis (NOA). Conclusions HPOSim can be used to predict disease genes and explore disease-related function of gene modules. HPOSim is open source and freely available at SourceForge (https://sourceforge.net/p/hposim/). PMID:25664462

  16. Salmonella in foods: new enrichment procedure for TECRA Salmonella Visual Immunoassay using a single rv(R10) only, TT only, or dual rv(R10) and TT selective enrichment broths (AOAC official method 998.09): collaborative study.

    PubMed

    Hughes, Denise; Dailianis, Angela E; Hill, Louise; Curiale, Michael S; Gangar, Vidhya

    2003-01-01

    A collaborative study was conducted to compare a new enrichment procedure for the TECRA Salmonella Visual Immunoassay (TSVIA) with the reference method given in the U.S. Food and Drug Administration's Bacteriological Analytical Manual (7th Ed.). Three food types (milk powder, pepper, and soy flour) were analyzed in Australia and 3 food types (milk chocolate, dried egg, and raw turkey) were analyzed in the United States. Thirty-eight collaborators participated in the study. The TECRA method was evaluated using both Rappaport-Vassiliadis R10 (RV(R10)) and tetrathionate (TT) broths for selective enrichment. M broth cultures arising from each of the 2 selective enrichment broths were tested in the TSVIA using 2 individual wells, one for each selective broth, and a single well to test the pooled selective enrichment broths. The results for the pooled enrichment broths were reported elsewhere. This study presents the results for the use of single enrichment broths, i.e., RV(R10) only or TT only, with the TSVIA. No significant differences (p > 0.05) were observed for the pairwise comparison of the proportion of positive samples for either RV(R10) or TT used as a single enrichment broth for the TSVIA with that for the reference method.

  17. Top-down Feedback Exacerbates Effects of Nutrient Enrichment in Detritus-based Ecosystems via Increased Loss of Basal Carbon

    NASA Astrophysics Data System (ADS)

    Rosemond, A. D.; Suberkropp, K.; Cross, W. F.; Greenwood, J. L.; Eggert, S. L.; Taylor, N.; Wallace, J.

    2005-05-01

    In primary producer-based food webs faced with chronic nutrient enrichment, increased plant biomass may ultimately be suppressed by consumers. Effects of chronic enrichment of detritus-based ecosystems may be fundamentally different, with consumers exacerbating, rather than suppressing, the effects of enrichment on basal resources. We have continuously enriched a headwater stream at the Coweeta LongTerm Ecological Research site (North Carolina, USA) with N & P (to ca. 400 ug/L dissolved inorganic nitrogen and 50 ug/L soluble reactive phosphorus) for 4.5 yrs and quantified leaf breakdown rates, microbial production, invertebrate production, and leaf litter standing crop in the enriched stream and in an adjacent reference stream. Whereas nutrient enrichment largely increases basal carbon in primary producer-based systems, detrital carbon in the treatment stream was drastically diminished relative to the reference stream. During each successive year of enrichment, rates of leaf breakdown were progressively faster and standing crops of detrital carbon were progressively lower. This `ramping up' of loss rates of carbon appear to be driven by increased consumption by invertebrates, rather than increased microbial activity. Our results illustrate that fundamentally different trophic feedback effects can potentially occur in detrital vs primary producer components of food webs in response to increased nutrient concentrations.

  18. Evaluating an Enrichment Program in Early Childhood: A Multi-Methods Approach

    ERIC Educational Resources Information Center

    van Aswegen, Christa; Pendergast, Donna

    2015-01-01

    This article reports on the evaluation of one topic in an enrichment program designed for children in their early years of learning. The program is responsive to an increased understanding of the benefits for very young children of programs that not only take advantage of the sensitive periods for learning but that also assist parents to a take a…

  19. Enrichment Wastes' Processing of Manganiferous Ores with the Use of Mechanochemical Methods

    ERIC Educational Resources Information Center

    Kubekova, Sholpan N.; Kapralova, Viktoria I.; Ibraimova, Gulnur T.; Batyrbayeva, Aigul A.

    2016-01-01

    The aim of the research is the study of the chemical and phase composition of enrichment wastes of manganiferous ore in Ushkatyn-III deposit and the synthesis of new materials by mechanochemical activation and subsequent heat treatment of the mechanical activation products. The use of XFA, infrared spectroscopy and electron probe microanalysis…

  20. Weighted Feature Significance: A Simple, Interpretable Model of Compound Toxicity Based on the Statistical Enrichment of Structural Features

    PubMed Central

    Huang, Ruili; Southall, Noel; Xia, Menghang; Cho, Ming-Hsuang; Jadhav, Ajit; Nguyen, Dac-Trung; Inglese, James; Tice, Raymond R.; Austin, Christopher P.

    2009-01-01

    In support of the U.S. Tox21 program, we have developed a simple and chemically intuitive model we call weighted feature significance (WFS) to predict the toxicological activity of compounds, based on the statistical enrichment of structural features in toxic compounds. We trained and tested the model on the following: (1) data from quantitative high–throughput screening cytotoxicity and caspase activation assays conducted at the National Institutes of Health Chemical Genomics Center, (2) data from Salmonella typhimurium reverse mutagenicity assays conducted by the U.S. National Toxicology Program, and (3) hepatotoxicity data published in the Registry of Toxic Effects of Chemical Substances. Enrichments of structural features in toxic compounds are evaluated for their statistical significance and compiled into a simple additive model of toxicity and then used to score new compounds for potential toxicity. The predictive power of the model for cytotoxicity was validated using an independent set of compounds from the U.S. Environmental Protection Agency tested also at the National Institutes of Health Chemical Genomics Center. We compared the performance of our WFS approach with classical classification methods such as Naive Bayesian clustering and support vector machines. In most test cases, WFS showed similar or slightly better predictive power, especially in the prediction of hepatotoxic compounds, where WFS appeared to have the best performance among the three methods. The new algorithm has the important advantages of simplicity, power, interpretability, and ease of implementation. PMID:19805409

  1. PSEA-Quant: A Protein Set Enrichment Analysis on Label-Free and Label-Based Protein Quantification Data

    PubMed Central

    2015-01-01

    The majority of large-scale proteomics quantification methods yield long lists of quantified proteins that are often difficult to interpret and poorly reproduced. Computational approaches are required to analyze such intricate quantitative proteomics data sets. We propose a statistical approach to computationally identify protein sets (e.g., Gene Ontology (GO) terms) that are significantly enriched with abundant proteins with reproducible quantification measurements across a set of replicates. To this end, we developed PSEA-Quant, a protein set enrichment analysis algorithm for label-free and label-based protein quantification data sets. It offers an alternative approach to classic GO analyses, models protein annotation biases, and allows the analysis of samples originating from a single condition, unlike analogous approaches such as GSEA and PSEA. We demonstrate that PSEA-Quant produces results complementary to GO analyses. We also show that PSEA-Quant provides valuable information about the biological processes involved in cystic fibrosis using label-free protein quantification of a cell line expressing a CFTR mutant. Finally, PSEA-Quant highlights the differences in the mechanisms taking place in the human, rat, and mouse brain frontal cortices based on tandem mass tag quantification. Our approach, which is available online, will thus improve the analysis of proteomics quantification data sets by providing meaningful biological insights. PMID:25177766

  2. An agarose gel-based neurosphere culture system leads to enrichment of neuronal lineage cells in vitro.

    PubMed

    Park, Kyuhee; Nam, Yeonju; Choi, Yongmun

    2015-05-01

    Stem cell-based therapy holds great potential especially for neurological disorders. However, clinical applications await further understanding of many aspects of stem cell differentiation and development of technology enabling manipulation of stem cells into desired cell types in the central nervous system. Here, we developed a new method that leads to enrichment of neuronal lineage cells in neural stem cell cultures. The protocol involves cultivation of primary cells derived from the forebrains of rat E18 embryos above a layer of nonadhesive hard agarose gel in the form of neurospheres. In contrast to the neurospheres that were cultured above an anti-adhesive hydrogel layer, the primary cells that were cultured above a layer of agarose gel preferentially differentiated into β-III tubulin-positive neurons when allowed to undergo differentiation in vitro.In an effort to investigate the mechanism behind this observation, we found that the gene expression of a vertebrate neuronal determination gene (neurogenin1) was enhanced in the neurospheres that proliferated above a layer of agarose gel as compared with the control, and the gene expression level of neurogenin1 was quite well correlated with the rigidity of agarose gel. These results indicate that agarose gel can contribute, at least in part, to enrich neuronal progenitors and immature postmitotic neurons during neurosphere formation and may provide additional information to establish efficient protocols for the neural stem cell-based study.

  3. Multiplex enrichment quantitative PCR (ME-qPCR): a high-throughput, highly sensitive detection method for GMO identification.

    PubMed

    Fu, Wei; Zhu, Pengyu; Wei, Shuang; Zhixin, Du; Wang, Chenguang; Wu, Xiyang; Li, Feiwu; Zhu, Shuifang

    2017-04-01

    Among all of the high-throughput detection methods, PCR-based methodologies are regarded as the most cost-efficient and feasible methodologies compared with the next-generation sequencing or ChIP-based methods. However, the PCR-based methods can only achieve multiplex detection up to 15-plex due to limitations imposed by the multiplex primer interactions. The detection throughput cannot meet the demands of high-throughput detection, such as SNP or gene expression analysis. Therefore, in our study, we have developed a new high-throughput PCR-based detection method, multiplex enrichment quantitative PCR (ME-qPCR), which is a combination of qPCR and nested PCR. The GMO content detection results in our study showed that ME-qPCR could achieve high-throughput detection up to 26-plex. Compared to the original qPCR, the Ct values of ME-qPCR were lower for the same group, which showed that ME-qPCR sensitivity is higher than the original qPCR. The absolute limit of detection for ME-qPCR could achieve levels as low as a single copy of the plant genome. Moreover, the specificity results showed that no cross-amplification occurred for irrelevant GMO events. After evaluation of all of the parameters, a practical evaluation was performed with different foods. The more stable amplification results, compared to qPCR, showed that ME-qPCR was suitable for GMO detection in foods. In conclusion, ME-qPCR achieved sensitive, high-throughput GMO detection in complex substrates, such as crops or food samples. In the future, ME-qPCR-based GMO content identification may positively impact SNP analysis or multiplex gene expression of food or agricultural samples. Graphical abstract For the first-step amplification, four primers (A, B, C, and D) have been added into the reaction volume. In this manner, four kinds of amplicons have been generated. All of these four amplicons could be regarded as the target of second-step PCR. For the second-step amplification, three parallels have been taken for

  4. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data.

    PubMed

    Cox, Juergen; Mann, Matthias

    2012-01-01

    Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated to other types of quantitative genome-wide data such as the corresponding transcriptome changes. We describe a new method, 2D annotation enrichment, which compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes. Suitable genome-wide categories are membership of proteins in biochemical pathways, their annotation with gene ontology terms, sub-cellular localization, presence of protein domains or membership in protein complexes. 2D annotation enrichment detects annotation terms whose members show consistent behavior in one or both of the data dimensions. This consistent behavior can be a correlation between the two data types, such as simultaneous up- or down-regulation in both data dimensions, or a lack thereof, such as regulation in one dimension but no change in the other. For the statistical formulation of the test we introduce a two-dimensional generalization of the nonparametric two-sample test. The false discovery rate is stringently controlled by correcting for multiple hypothesis testing. We also describe one-dimensional annotation enrichment, which can be applied to single omics data. The 1D and 2D annotation enrichment algorithms are freely available as part of the Perseus software.

  5. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

    PubMed Central

    2012-01-01

    Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated to other types of quantitative genome-wide data such as the corresponding transcriptome changes. We describe a new method, 2D annotation enrichment, which compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes. Suitable genome-wide categories are membership of proteins in biochemical pathways, their annotation with gene ontology terms, sub-cellular localization, the presence of protein domains or the membership in protein complexes. 2D annotation enrichment detects annotation terms whose members show consistent behavior in one or both of the data dimensions. This consistent behavior can be a correlation between the two data types, such as simultaneous up- or down-regulation in both data dimensions, or a lack thereof, such as regulation in one dimension but no change in the other. For the statistical formulation of the test we introduce a two-dimensional generalization of the nonparametric two-sample test. The false discovery rate is stringently controlled by correcting for multiple hypothesis testing. We also describe one-dimensional annotation enrichment, which can be applied to single omics data. The 1D and 2D annotation enrichment algorithms are freely available as part of the Perseus software. PMID:23176165

  6. Centrifuge enrichment plants. (Latest citations from the NTIS data base). Published Search

    SciTech Connect

    Not Available

    1992-09-01

    The bibliography contains citations concerning the design, control, monitoring, and safety of centrifuge enrichment plants. Power supplies, enrichment plant safeguards, facility design, cascade heater test loops to monitor the enrichment process, inspection strategies, and the socioeconomic effects of centrifuge enrichment plants are examined. Radioactive waste disposal problems are briefly considered. (Contains a minimum of 169 citations and includes a subject term index and title list.)

  7. Bead Based Proteome Enrichment Enhances Features of the Protein Elution Plate (PEP) for Functional Proteomic Profiling

    PubMed Central

    Wang, Xing; Davies, Michael; Roy, Swapan; Kuruc, Matthew

    2015-01-01

    A novel functional proteomics technology called PEP(Protein Elution Plate) was developed to separate complex proteomes from natural sources and analyze protein functions systematically. The technology takes advantage of the powerful resolution of two-dimensional gel electrophoresis (2-D Gels). The modification of electrophoretic conditions in combination with a high-resolution protein elution plate supports the recovery of functionally active proteins. As 2DE(2-Dimensional Electrophoresis) resolution can be limited by protein load, we investigated the use of bead based enrichment technologies, called AlbuVoid™ and KinaSorb™ to determine their effect on the proteomic features which can be generated from the PEP platform. Using a variety of substrates and enzyme activity assays, we report on the benefits of combining bead based enrichment to improve the signal report and the features generated for Hexokinase, Protein Kinase, Protease, and Alkaline Phosphatase activities. As a result, the PEP technology allows systematic analysis of large enzyme families and can build a comprehensive picture of protein function from a complex proteome, providing biological insights that could otherwise not be observed if only protein abundances were analyzed. PMID:28248280

  8. Selective enrichment of the degradation products of organophosphorus nerve agents by zirconia based solid-phase extraction.

    PubMed

    Kanaujia, Pankaj K; Pardasani, Deepak; Tak, Vijay; Purohit, Ajay K; Dubey, D K

    2011-09-23

    Selective extraction and enrichment of nerve agent degradation products has been achieved using zirconia based commercial solid-phase extraction cartridges. Target analytes were O-alkyl alkylphosphonic acids and alkylphosphonic acids, the environmental markers of nerve agents such as sarin, soman and VX. Critical extraction parameters such as modifier concentration, nature and volume of washing and eluting solvents were investigated. Amongst other anionic compounds, selectivity in extraction was observed for organophosphorus compounds. Recoveries of analytes were determined by GC-MS which ranged from 80% to 115%. Comparison of zirconia based solid-phase extraction method with anion-exchange solid-phase extraction revealed its selectivity towards phosphonic acids. The limits of detection (LOD) and limit of quantification (LOQ) with selected analytes were achieved down to 4.3 and 8.5 ng mL(-1), respectively, in selected ion monitoring mode.

  9. In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins.

    PubMed

    Acevedo-Pacheco, Laura; Serna-Saldívar, Sergio O

    2016-01-01

    One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. The aim was to determine and compare the essential amino acid (EAA) scores, protein digestibility corrected amino acid scores (PDCAAS), and in vivo protein quality (protein digestibility, protein efficiency ratio (PER), biological values (BV), and net protein utilization (NPU) values) of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. The proposed enrichment of cereal-based foods with soybean proteins greatly improved PDCAAS, animal growth, nitrogen retention, and PER primarily

  10. In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins

    PubMed Central

    Acevedo-Pacheco, Laura; Serna-Saldívar, Sergio O.

    2016-01-01

    Background One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. Objective The aim was to determine and compare the essential amino acid (EAA) scores, protein digestibility corrected amino acid scores (PDCAAS), and in vivo protein quality (protein digestibility, protein efficiency ratio (PER), biological values (BV), and net protein utilization (NPU) values) of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. Design To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. Results The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. Conclusions The proposed enrichment of cereal-based foods with soybean proteins greatly improved PDCAAS, animal

  11. Efficient dielectrophoretic cell enrichment using a dielectrophoresis-well based system.

    PubMed

    Abdul Razak, Mohd Azhar; Hoettges, Kai F; Fatoyinbo, Henry O; Labeed, Fatima H; Hughes, Michael P

    2013-01-01

    Whilst laboratory-on-chip cell separation systems using dielectrophoresis are increasingly reported in the literature, many systems are afflicted by factors which impede "real world" performance, chief among these being cell loss (in dead spaces, attached to glass and tubing surfaces, or sedimentation from flow), and designs with large channel height-to-width ratios (large channel widths, small channel heights) that make the systems difficult to interface with other microfluidic systems. In this paper, we present a scalable structure based on 3D wells with approximately unity height-to-width ratios (based on tubes with electrodes on the sides), which is capable of enriching yeast cell populations whilst ensuring that up to 94.3% of cells processed through the device can be collected in tubes beyond the output.

  12. [Study on the method of nanometer-size zirconium dioxide enrichment separation and inductively coupled plasma mass spectrometry determination of trace barium(II) in water].

    PubMed

    Du, Ying-Qiu; Yin, Yi-Dong; Fan, Nai-Ying; Chen, Peng-Gang; Zhang, Xiao-Bo; Ren, Hong-Bo; Chen, Guo-You; Qu, Qiu-Yao; Sun, Zhi-Bo; Chen, Yue-Xin

    2012-11-01

    Monoclinic fusiform zirconium dioxide (ZrO2) nanoparticles were synthesized by hydrothermal method, a method was established based on monoclinic fusiform nanometer-sized ZrO2 enrichment separation, and trace barium in water was determined by inductively coupled plasma mass spectrometry (ICP-MS). The detection limit for Ba(II) was 0.007 ng x mL(-1), and the relative standard deviation was 0.13% (n = 11). The optimal enrichment separation conditions of nanometer-sized ZrO2 for Ba(II) were studied in detail, it was found that the percentage of adsorbed Ba(II) was more than 99% under pH 10.0 and 2 mL 0.5 mol x L(-1) HCl was sufficient for elution of Ba(II) by more than 98%. The static adsorption capacity of ZrO2 to Ba(II) was 196.6 microg x g(-1) and enrichment factor was 250. Properties of nanometer-sized ZrO2 were discussed through regeneration experiment and effects of co-existing ions and contrast experiment to ordinary ZrO2, adsorption properties of nanometer-sized ZrO2 were applied to real samples in the analysis of Ba(II) and the determination was carried out by ICP-MS with satisfactory results.

  13. Enriching step-based product information models to support product life-cycle activities

    NASA Astrophysics Data System (ADS)

    Sarigecili, Mehmet Ilteris

    The representation and management of product information in its life-cycle requires standardized data exchange protocols. Standard for Exchange of Product Model Data (STEP) is such a standard that has been used widely by the industries. Even though STEP-based product models are well defined and syntactically correct, populating product data according to these models is not easy because they are too big and disorganized. Data exchange specifications (DEXs) and templates provide re-organized information models required in data exchange of specific activities for various businesses. DEXs show us it would be possible to organize STEP-based product models in order to support different engineering activities at various stages of product life-cycle. In this study, STEP-based models are enriched and organized to support two engineering activities: materials information declaration and tolerance analysis. Due to new environmental regulations, the substance and materials information in products have to be screened closely by manufacturing industries. This requires a fast, unambiguous and complete product information exchange between the members of a supply chain. Tolerance analysis activity, on the other hand, is used to verify the functional requirements of an assembly considering the worst case (i.e., maximum and minimum) conditions for the part/assembly dimensions. Another issue with STEP-based product models is that the semantics of product data are represented implicitly. Hence, it is difficult to interpret the semantics of data for different product life-cycle phases for various application domains. OntoSTEP, developed at NIST, provides semantically enriched product models in OWL. In this thesis, we would like to present how to interpret the GD & T specifications in STEP for tolerance analysis by utilizing OntoSTEP.

  14. Rapid Identification of Shiga Toxin-Producing Escherichia coli O Serogroups from Fresh Produce and Raw Milk Enrichment Cultures by Luminex Bead-Based Suspension Array.

    PubMed

    Kase, Julie A; Maounounen-Laasri, Anna; Lin, Andrew

    2016-09-01

    The U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM) Chapter 4a describes a Luminex microbead-based suspension array used to screen colonies for 11 clinically relevant Shiga toxin-producing Escherichia coli (STEC) serogroups: O26, O45, O91, O103, O104, O111, O113, O121, O128, O145, and O157. We evaluated the usefulness of this method to identify STEC-positive enrichment samples before agar plating. Twelve E. coli strains were added to three types of fresh produce (bagged baby spinach, alfalfa sprouts, and cilantro) at levels near the detection limit of the test. A subset of these strains (six O serogroups) was similarly evaluated in raw milk. For comparison, portions of each of the 168 enrichment cultures were analyzed for serogroup by a real-time PCR assay and a Bio-Plex 200 assay with the bead-based suspensions. No false-positive results were obtained. Of the 112 samples with a reported cycle threshold (CT) value, 101 undiluted, diluted, or extracted enrichment cultures also produced ratios above 5.0 in the Bio-Plex assay. When PCR CT values approached or were greater than 35, Bio-Plex detection became less reliable. Using undiluted or extracted enrichment cultures resulted in a significantly larger number of positive results. With the same enrichment material prepared for real-time PCR analysis as described in the BAM Chapter 4a, the STEC microbead-based suspension array can accurately screen food enrichment cultures.

  15. Imaging-based enrichment criteria using deep learning algorithms for efficient clinical trials in mild cognitive impairment.

    PubMed

    Ithapu, Vamsi K; Singh, Vikas; Okonkwo, Ozioma C; Chappell, Richard J; Dowling, N Maritza; Johnson, Sterling C

    2015-12-01

    The mild cognitive impairment (MCI) stage of Alzheimer's disease (AD) may be optimal for clinical trials to test potential treatments for preventing or delaying decline to dementia. However, MCI is heterogeneous in that not all cases progress to dementia within the time frame of a trial and some may not have underlying AD pathology. Identifying those MCIs who are most likely to decline during a trial and thus most likely to benefit from treatment will improve trial efficiency and power to detect treatment effects. To this end, using multimodal, imaging-derived, inclusion criteria may be especially beneficial. Here, we present a novel multimodal imaging marker that predicts future cognitive and neural decline from [F-18]fluorodeoxyglucose positron emission tomography (PET), amyloid florbetapir PET, and structural magnetic resonance imaging, based on a new deep learning algorithm (randomized denoising autoencoder marker, rDAm). Using ADNI2 MCI data, we show that using rDAm as a trial enrichment criterion reduces the required sample estimates by at least five times compared with the no-enrichment regime and leads to smaller trials with high statistical power, compared with existing methods.

  16. Processes involved in sweeping as sample enrichment method in cyclodextrin-modified micellar electrokinetic chromatography of hydrophobic basic analytes.

    PubMed

    El-Awady, Mohamed; Pyell, Ute

    2014-03-01

    Sweeping is an enrichment method in MEKC, which includes following steps: stacking/destacking of the micelles, sweeping of analyte by the stacked/destacked micelles, destacking/stacking of the swept analyte zone and additional focusing/defocusing due to the retention factor gradient effect (RFGE). In this study, we investigate additional processes, regarding online focusing in cyclodextrin-modified MEKC (CD-MEKC) of hydrophobic basic analytes: dynamic pH junction (sample with pH different from that of BGE) and adsorption of analyte onto the capillary wall within the sample zone. It is demonstrated that the developed method for the assessment of the sweeping efficiency is also applicable to CD-MEKC taking ethylparaben as an example of acidic analytes and desloratadine as an example of basic analytes using different types of β-cyclodextrin. Our previous results regarding RFGE as an additional focusing/defocusing effect in sweeping-MEKC are confirmed for the case that the apparent distribution coefficient differs for the sample and the BGE due to a different content of the complex-forming agent cyclodextrin and due to a pH difference between the sample and the BGE. Despite being significantly more hydrophobic than ethylparaben, desloratadine shows an unexpectedly low enrichment factor. This enrichment factor is nearly unaffected by the addition of CD to the BGE. This unexpected behavior is attributed to wall adsorption of the protonated hydrophobic basic analyte within the sample zone, which significantly counteracts the sweeping process. This assumption is corroborated by an improvement in the enrichment factor achieved via addition of a dynamic coating agent (triethylamine) to the sample solution.

  17. Inquiry-Based Science and Technology Enrichment Program: Green Earth Enhanced with Inquiry and Technology

    NASA Astrophysics Data System (ADS)

    Kim, Hanna

    2011-12-01

    This study investigated the effectiveness of a guided inquiry integrated with technology, in terms of female middle-school students' attitudes toward science/scientists and content knowledge regarding selective science concepts (e.g., Greenhouse Effect, Air/Water Quality, Alternative Energy, and Human Health). Thirty-five female students who were entering eighth grade attended an intensive, 1-week Inquiry-Based Science and Technology Enrichment Program which used a main theme, "Green Earth Enhanced with Inquiry and Technology." We used pre- and post-attitude surveys, pre- and post-science content knowledge tests, and selective interviews to collect data and measure changes in students' attitudes and content knowledge. The study results indicated that at the post-intervention measures, participants significantly improved their attitudes toward science and science-related careers and increased their content knowledge of selected science concepts ( p < .05).

  18. Synthesis and NMR of RNA with selective isotopic enrichment in the bases.

    PubMed Central

    SantaLucia, J; Shen, L X; Cai, Z; Lewis, H; Tinoco, I

    1995-01-01

    Efficient syntheses of pyrimidine and purine nucleosides and nucleotides with selective 13C enrichment in the base moieties are described. Uridine and cytidine are labeled at position C6 and adenosine and guanosine are labeled at position C8. The selectively labeled nucleosides were converted to nucleoside triphosphates and used with in vitro transcription to synthesize labeled RNA. Isotope-edited 12C and 13C sub-spectra of a omega 1-1/2-X-filtered NOESY experiment are demonstrated to be useful for making resonance assignments and for deriving structural information in large (> 20 nt) RNA molecules. The labeled RNAs also allow heteronuclear J-couplings and relaxation parameters to be measured without complications from 13C-13C J-couplings. PMID:8532537

  19. Synthesis and NMR of RNA with selective isotopic enrichment in the bases.

    PubMed

    SantaLucia, J; Shen, L X; Cai, Z; Lewis, H; Tinoco, I

    1995-12-11

    Efficient syntheses of pyrimidine and purine nucleosides and nucleotides with selective 13C enrichment in the base moieties are described. Uridine and cytidine are labeled at position C6 and adenosine and guanosine are labeled at position C8. The selectively labeled nucleosides were converted to nucleoside triphosphates and used with in vitro transcription to synthesize labeled RNA. Isotope-edited 12C and 13C sub-spectra of a omega 1-1/2-X-filtered NOESY experiment are demonstrated to be useful for making resonance assignments and for deriving structural information in large (> 20 nt) RNA molecules. The labeled RNAs also allow heteronuclear J-couplings and relaxation parameters to be measured without complications from 13C-13C J-couplings.

  20. Vital pulp therapy using calcium-enriched mixture: An evidence-based review

    PubMed Central

    Asgary, Saeed; Ahmadyar, Maryam

    2013-01-01

    Worldwide, casecontrol studies have revealed that the treatment outcomes of root canal therapy (RCT) are generally favorable; however, the overall epidemiological success rate of RCT in the general population is relatively low. On the other hand, vitality of dental pulp is a key factor in the long-term prognosis of permanent teeth; in recent years, vital pulp therapy (VPT) has received significant consideration as it has been revealed that the inflamed pulp has the potential to heal. In this review article, the current best evidence with regard to VPT using calcium-enriched mixture (CEM) cement in human permanent/primary teeth is discussed. A strategy based on a search using keywords for CEM cement as well as VPT was applied. PMID:23716958

  1. Method and apparatus for reducing cold-phase emissions by utilizing oxygen-enriched intake air

    DOEpatents

    Poola, Ramesh B.; Sekar, Ramanujam R.; Stork, Kevin C.

    1997-01-01

    An oxygen-enriched air intake control system for an internal combustion engine includes air directing apparatus to control the air flow into the intake of the engine. During normal operation of the engine, ambient air flowing from an air filter of the engine flows through the air directing apparatus into the intake of the engine. In order to decrease the amount of carbon monoxide (CO) and hydrocarbon (HC) emissions that tend to be produced by the engine during a short period of time after the engine is started, the air directing apparatus diverts for a short period of time following the start up of the engine at least a portion of the ambient air from the air filter through a secondary path. The secondary path includes a selectively permeable membrane through which the diverted portion of the ambient air flows. The selectively permeable membrane separates nitrogen and oxygen from the diverted air so that oxygen enriched air containing from about 23% to 25% oxygen by volume is supplied to the intake of the engine.

  2. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures.

    PubMed

    McMahon, Tanis C; Blais, Burton W; Wong, Alex; Carrillo, Catherine D

    2017-01-01

    Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0-2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of

  3. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures

    PubMed Central

    McMahon, Tanis C.; Blais, Burton W.; Wong, Alex; Carrillo, Catherine D.

    2017-01-01

    Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0–2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of

  4. Visual detection technique for efficient screening and isolation of Salmonella based on a novel enrichment assay using chromatography membrane.

    PubMed

    Tang, F; Xiong, Y; Zhang, H; Wu, K; Xiang, Y; Shao, J-B; Ai, H-W; Xiang, Y-P; Zheng, X-L; Lv, J-R; Sun, H; Bao, L-S; Zhang, Z; Hu, H-B; Zhang, J-Y; Chen, L; Lu, J; Liu, W-Y; Mei, H; Ma, Y; Xu, C-F; Fang, A-Y; Gu, M; Xu, C-Y; Chen, Y; Chen, Z; Sun, Z-Y

    2016-03-01

    To detect Salmonella more efficiently and isolate strains more easily, a novel and simple detection method that uses an enrichment assay and two chromogenic reactions on a chromatography membrane was developed. Grade 3 chromatography paper is used as functionalized solid phase support (SPS), which contains specially optimized medium. One reaction for screening is based on the sulfate-reducing capacity of Salmonella. Hydrogen sulfide (H2S) generated by Salmonella reacts with ammonium ferric citrate to produce black colored ferrous sulfide. Another reaction is based on Salmonella C8 esterase that is unique for Enterobacteriaceae except Serratia and interacts with 4-methylumbelliferyl caprylate (MUCAP) to produce fluorescent umbelliferone, which is visible under ultraviolet light. A very low detection limit (10(1) CFU ml(-1)) for Salmonella was achieved on the background of 10(5) CFU ml(-1) Escherichia coli. More importantly, testing with more than 1,000 anal samples indicated that our method has a high positive detection rate and is relatively low cost, compared with the traditional culture-based method. It took only 1 day for the preliminary screening and 2 days to efficiently isolate the Salmonella cells, indicating that the new assay is specific, rapid, and simple for Salmonella detection. In contrast to the traditional culture-based method, this method can be easily used to screen and isolate targeted strains with the naked eye. The results of quantitative and comparative experiments showed that the visual detection technique is an efficient alternative method for the screening of Salmonella spp. in many applications of large-sized samples related to public health surveillance.

  5. Beyond Job Enrichment to Employment Enrichment

    ERIC Educational Resources Information Center

    Werther, William B., Jr.

    1975-01-01

    Employment enrichment views the total work environment confronting employees as a system consisting of two overlapping areas: worker-job and worker-organization subsystems. Job enrichment has improved the worker-job subsystem. The focus of this article is on methods of improving the worker-organization relationship. (Author/JB)

  6. [Comparison of essential oil enriched with ultrafiltration method and extraction method respectively from essential oil-in-water emulsion of Citri Reticulatae Pericarpium Viride by GC-MS].

    PubMed

    Yin, Ailing; Han, Zhifeng; Shen, Jie; Guo, Liwei; Cao, Guiping

    2011-10-01

    To study on the separation from essential oil-in-water emulsion of Citri Reticulatae Pericarpium Viride by ultrafiltration and acetoacetate extraction methods respectively, and the comparison of the oil yields and chemical compositions. Essential oil-in-water emulsion of Citri Reticulatae Pericarpium Viride was separated by ultrafiltration and acetoacetate extraction methods respectively, and the chemical compositions were analyzed and compared by GC-MS. Ultrafiltration method could enrich essential oil more and its chemical compositions were more similar to the essential oil prepared by steam distillation method. Ultrafiltration method is a good medium to separate essential oil from essential oil-in-water emulsion of Citri Reticulatae Pericarpium Viride.

  7. Neutron source, linear-accelerator fuel enricher and regenerator and associated methods

    DOEpatents

    Steinberg, Meyer; Powell, James R.; Takahashi, Hiroshi; Grand, Pierre; Kouts, Herbert

    1982-01-01

    A device for producing fissile material inside of fabricated nuclear elements so that they can be used to produce power in nuclear power reactors. Fuel elements, for example, of a LWR are placed in pressure tubes in a vessel surrounding a liquid lead-bismuth flowing columnar target. A linear-accelerator proton beam enters the side of the vessel and impinges on the dispersed liquid lead-bismuth columns and produces neutrons which radiate through the surrounding pressure tube assembly or blanket containing the nuclear fuel elements. These neutrons are absorbed by the natural fertile uranium-238 elements and are transformed to fissile plutonium-239. The fertile fuel is thus enriched in fissile material to a concentration whereby they can be used in power reactors. After use in the power reactors, dispensed depleted fuel elements can be reinserted into the pressure tubes surrounding the target and the nuclear fuel regenerated for further burning in the power reactor.

  8. An automatic method for the enrichment of DICOM metadata using biomedical ontologies.

    PubMed

    Perez, Wilson; Tello, Andres; Saquicela, Victor; Vidal, Maria-Esther; La Cruz, Alexandra

    2015-01-01

    This work is a novel contribution for enriching medical images using semantic annotations with a strategy for unifying different ontologies and instances of DICOM medical files. We present the L-MOM library (Library for Mapping of Ontological Metadata) as a tool for making an automatic mapping between instances of DICOM medical files and different medical ontologies (e.g., FMA, RadLex, MeSH). The main contributions are: i) the domain independent L-MOM library which is able to integrate DICOM metadata with ontologies from different domains; ii) a strategy to automatically annotate DICOM data with universally accepted medical ontologies, and provide values of similarity between ontologies and DICOM metadata; and iii) a framework to traverse ontological concepts that characterized clinical studies of patients registered in the framework catalog.

  9. Abundance-based Classifier for the Prediction of Mass Spectrometric Peptide Detectability Upon Enrichment (PPA)*

    PubMed Central

    Muntel, Jan; Boswell, Sarah A.; Tang, Shaojun; Ahmed, Saima; Wapinski, Ilan; Foley, Greg; Steen, Hanno; Springer, Michael

    2015-01-01

    The function of a large percentage of proteins is modulated by post-translational modifications (PTMs). Currently, mass spectrometry (MS) is the only proteome-wide technology that can identify PTMs. Unfortunately, the inability to detect a PTM by MS is not proof that the modification is not present. The detectability of peptides varies significantly making MS potentially blind to a large fraction of peptides. Learning from published algorithms that generally focus on predicting the most detectable peptides we developed a tool that incorporates protein abundance into the peptide prediction algorithm with the aim to determine the detectability of every peptide within a protein. We tested our tool, “Peptide Prediction with Abundance” (PPA), on in-house acquired as well as published data sets from other groups acquired on different instrument platforms. Incorporation of protein abundance into the prediction allows us to assess not only the detectability of all peptides but also whether a peptide of interest is likely to become detectable upon enrichment. We validated the ability of our tool to predict changes in protein detectability with a dilution series of 31 purified proteins at several different concentrations. PPA predicted the concentration dependent peptide detectability in 78% of the cases correctly, demonstrating its utility for predicting the protein enrichment needed to observe a peptide of interest in targeted experiments. This is especially important in the analysis of PTMs. PPA is available as a web-based or executable package that can work with generally applicable defaults or retrained from a pilot MS data set. PMID:25473088

  10. Transversion-enriched sequence saturation mutagenesis (SeSaM-Tv+): a random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error-prone PCR.

    PubMed

    Wong, Tuck Seng; Roccatano, Danilo; Loakes, David; Tee, Kang Lan; Schenk, Alexander; Hauer, Bernhard; Schwaneberg, Ulrich

    2008-01-01

    The sequence saturation mutagenesis (SeSaM) method has been advanced to a random mutagenesis method with adjustable mutational biases. SeSaM offers, for example, a bias that is complementary to error-prone (ep) PCR and is enriched in transversions (SeSaM-Tv(+)). dNTP alpha S and three degenerate bases (P, K and I) are used to control mutational bias flexibly. After quantifying incorporation rates of dPTP, dKTP and dITP by terminal transferase using a luciferase-based assay and investigating the read and/or write activities of eight DNA polymerases, a transversion-enriched protocol has been developed. In a mutant library generated using dGTP alpha S and dPTP, transversion frequencies of 16.22-22.58% (G-->T) and 6.38-9.69% (G-->C) were achieved. These mutational spectra are complementary and occur twice as frequently in comparison to standard epPCR methods employing Taq DNA polymerase. For generating more complex mutant libraries, the occurrence of consecutive nucleotide exchanges was increased by 10(5)-10(6)-fold compared to epPCR. Finally, 16.7% of all sequenced mutants contained consecutive nucleotide exchanges composed mainly of a transversion followed by a transition.

  11. Attribute-Based Methods

    Treesearch

    Thomas P. Holmes; Wiktor L. Adamowicz

    2003-01-01

    Stated preference methods of environmental valuation have been used by economists for decades where behavioral data have limitations. The contingent valuation method (Chapter 5) is the oldest stated preference approach, and hundreds of contingent valuation studies have been conducted. More recently, and especially over the last decade, a class of stated preference...

  12. Literature-Based Reading: Children's Books and Activities To Enrich the K-5 Curriculum.

    ERIC Educational Resources Information Center

    Laughlin, Mildred Knight; Swisher, Claudia Lisman

    This book helps teachers and media directors to use children's literature to enrich elementary reading programs and to pursue sound educational objectives as they share the books and stories. It provides activities designed to expand and enrich the opportunities for children to become literate. It is a tool which addresses the need for children to…

  13. A "Proof-of-Concept" Demonstration of RF-Based Technologies for UF6 Cylinder Tracking at Centrifuge Enrichment Plant

    SciTech Connect

    Pickett, Chris A; Younkin, James R; Kovacic, Donald N; Dixon, E. T.; Martinez, B.

    2007-01-01

    This effort describes how radio-frequency (RF) technology can be integrated into a uranium enrichment facility's nuclear materials accounting and control program to enhance uranium hexafluoride (UF6) cylinder tracking and thus provide benefits to both domestic and international safeguards. Approved industry-standard cylinders are used to handle and store UF6 feed, product, tails, and samples at uranium enrichment plants. In the international arena, the International Atomic Energy Agency (IAEA) relies on time-consuming manual cylinder inventory and tracking techniques to verify operator declarations and to detect potential diversion of UF6. Development of a reliable, automated, and tamper-resistant process for tracking and monitoring UF6 cylinders would greatly reduce the risk of false or misreported cylinder tare weights, diversion of nuclear material, concealment of excess production, utilization of undeclared cylinders, and misrepresentation of the cylinders contents. This paper will describe a "proof-of concept" system that was designed show the feasibility of using RF based technologies to track individual UF6 cylinders throughout their entire life cycle, and thus ensure both increased domestic accountability of materials and a more effective and efficient method for application of IAEA international safeguards at the site level. The proposed system incorporates RF-based identification devices, which provide a mechanism for a reliable, automated, and tamper-resistant tracking network. We explore how securely attached RF tags can be integrated with other safeguards technologies to better detect diversion of cylinders. The tracking system could also provide a foundation for integration of other types of safeguards that would further enhance detection of undeclared activities.

  14. Development of particle induced gamma-ray emission methods for nondestructive determination of isotopic composition of boron and its total concentration in natural and enriched samples.

    PubMed

    Chhillar, Sumit; Acharya, Raghunath; Sodaye, Suparna; Pujari, Pradeep K

    2014-11-18

    We report simple particle induced gamma-ray emission (PIGE) methods using a 4 MeV proton beam for simultaneous and nondestructive determination of the isotopic composition of boron ((10)B/(11)B atom ratio) and total boron concentrations in various solid samples with natural isotopic composition and enriched with (10)B. It involves measurement of prompt gamma-rays at 429, 718, and 2125 keV from (10)B(p,αγ)(7)Be, (10)B(p, p'γ)(10)B, and (11)B(p, p'γ)(11)B reactions, respectively. The isotopic composition of boron in natural and enriched samples was determined by comparing peak area ratios corresponding to (10)B and (11)B of samples to natural boric acid standard. An in situ current normalized PIGE method, using F or Al, was standardized for total B concentration determination. The methods were validated by analyzing stoichiometric boron compounds and applied to samples such as boron carbide, boric acid, carborane, and borosilicate glass. Isotopic compositions of boron in the range of 0.247-2.0 corresponding to (10)B in the range of 19.8-67.0 atom % and total B concentrations in the range of 5-78 wt % were determined. It has been demonstrated that PIGE offers a simple and alternate method for total boron as well as isotopic composition determination in boron based solid samples, including neutron absorbers that are important in nuclear technology.

  15. Gene-Based Analysis of Regionally Enriched Cortical Genes in GWAS Data Sets of Cognitive Traits and Psychiatric Disorders

    PubMed Central

    Ersland, Kari M.; Christoforou, Andrea; Stansberg, Christine; Espeseth, Thomas; Mattheisen, Manuel; Mattingsdal, Morten; Hardarson, Gudmundur A.; Hansen, Thomas; Fernandes, Carla P. D.; Giddaluru, Sudheer; Breuer, René; Strohmaier, Jana; Djurovic, Srdjan; Nöthen, Markus M.; Rietschel, Marcella; Lundervold, Astri J.; Werge, Thomas; Cichon, Sven; Andreassen, Ole A.; Reinvang, Ivar; Steen, Vidar M.; Le Hellard, Stephanie

    2012-01-01

    Background Despite its estimated high heritability, the genetic architecture leading to differences in cognitive performance remains poorly understood. Different cortical regions play important roles in normal cognitive functioning and impairment. Recently, we reported on sets of regionally enriched genes in three different cortical areas (frontomedial, temporal and occipital cortices) of the adult rat brain. It has been suggested that genes preferentially, or specifically, expressed in one region or organ reflect functional specialisation. Employing a gene-based approach to the analysis, we used the regionally enriched cortical genes to mine a genome-wide association study (GWAS) of the Norwegian Cognitive NeuroGenetics (NCNG) sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ) (n = 3 samples) and bipolar affective disorder (BP) (n = 3 samples), to which cognitive impairment is linked. Principal Findings At the single gene level, the temporal cortex enriched gene RAR-related orphan receptor B (RORB) showed the strongest overall association, namely to a test of verbal intelligence (Vocabulary, P = 7.7E-04). We also applied gene set enrichment analysis (GSEA) to test the candidate genes, as gene sets, for enrichment of association signal in the NCNG GWAS and in GWASs of BP and of SCZ. We found that genes differentially expressed in the temporal cortex showed a significant enrichment of association signal in a test measure of non-verbal intelligence (Reasoning) in the NCNG sample. Conclusion Our gene-based approach suggests that RORB could be involved in verbal intelligence differences, while the genes enriched in the temporal cortex might be important to intellectual functions as measured by a test of reasoning in the healthy population. These findings warrant further replication in independent samples on cognitive traits. PMID

  16. Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

    PubMed Central

    Ross, Jason P.; Shaw, Jan M.; Molloy, Peter L.

    2013-01-01

    We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specific labeling (using a biotin-labeled nucleotide ligand) of methylated cytosines in bisulfite-converted DNA. This step is then followed by affinity capture, using streptavidin-coupled magnetic beads. SuBLiME is highly adaptable and can be combined with deep sequencing library generation and/or genomic complexity-reduction. In this pilot study, we enriched methylated DNA from Csp6I-cut complexity-reduced genomes of colorectal cancer cell lines (HCT-116, HT-29 and SW-480) and normal blood leukocytes with the aim of discovering colorectal cancer biomarkers. Enriched libraries were sequenced with SOLiD-3 technology. In pairwise comparisons, we scored a total of 1,769 gene loci and 33 miRNA loci as differentially methylated between the cell lines and leukocytes. Of these, 516 loci were differently methylated in at least two promoter-proximal CpG sites over two discrete Csp6I fragments. Identified methylated gene loci were associated with anatomical development, differentiation and cell signaling. The data correlated with good agreement to a number of published colorectal cancer DNA methylation biomarkers and genomic data sets. SuBLiME is effective in the enrichment of methylated nucleic acid and in the detection of known and novel biomarkers. PMID:23257838

  17. Effects of four different cooking methods on some quality characteristics of low fat Inegol meatball enriched with flaxseed flour.

    PubMed

    Turp, Gulen Yildiz

    2016-11-01

    The present study is concerned with the effects of four different cooking methods (grill, oven, pan and ohmic cooking) on physicochemical parameters (cooking yield moisture retention, fat retention, color, texture), fatty acid composition and sensory characteristics of low fat Turkish traditional Inegol meatball. Flaxseed flour was used as a fat substitute in the production of meatballs. Meatball proximate composition was affected by the cooking methods mainly as a consequence of the weight losses. The highest cooking yield was found in samples cooked in the oven. Flaxseed flour contains high amount of α-linolenic acid and ohmic cooking seems to be the best cooking method in terms of retaining this fatty acid in meatballs enriched with flaxseed flour. However ohmic cooked meatball samples had a brighter surface color and harder texture in comparison with meatball samples cooked via traditional methods. There was no significant difference between the sensory evaluation scores of meatballs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Enriching opportunities for people living with dementia: the development of a blueprint for a sustainable activity-based model.

    PubMed

    Brooker, Dawn J; Woolley, Rosemary J

    2007-07-01

    The aim of this paper is to describe the process of building a multi-level intervention called the Enriched Opportunities Programme, the objective of which is to provide a sustainable activity-based model for people with dementia living in long-term care. It is hypothesised that five key elements need to work together to bring about a sustainable activity-based model of care. These elements are specialist expertise-the staff role of Locksmith was developed as part of this programme; individualised assessment and case work; an activity and occupation programme; staff training; and management and leadership. These elements working together are known as the Enriched Opportunities Programme. This paper reports on the processes undertaken to develop Enriched Opportunities from its inception to the present, and focuses on lessons learnt from the literature, an expert working group and action research in four UK study sites. A blueprint for evaluation in other long-term care facilities is described.

  19. Frequency-selective electrokinetic enrichment of biomolecules in physiological media based on electrical double-layer polarization.

    PubMed

    Rohani, Ali; Sanghavi, Bankim J; Salahi, Armita; Liao, Kuo-Tang; Chou, Chia-Fu; Swami, Nathan S

    2017-08-24

    Proteomic biomarkers of interest to the early diagnosis of diseases and infections are present at trace levels versus interfering species. Hence, their selective enrichment is needed within bio-assays for speeding binding kinetics with receptors and for reducing signal interferences. While DC fields can separate biomolecules based on their electrokinetic mobilities, they are unable to selectively enrich biomarkers versus interfering species, which may possess like-charges. We present the utilization of AC electrokinetics to enable frequency-selective enrichment of nanocolloidal biomolecules, based on the characteristic time constant for polarization of their electrical double-layer, since surface conduction in their ion cloud depends on colloidal size, shape and surface charge. In this manner, using DC-offset AC fields, differences in frequency dispersion for negative dielectrophoresis are balanced against electrophoresis in a nanoslit channel to enable the selective enrichment of prostate specific antigen (PSA) versus anti-mouse immunoglobulin antibodies that cause signal interferences to immunoassays. Through coupling enrichment to capture by receptors on graphene-modified surfaces, we demonstrate the elimination of false positives caused by anti-mouse immunoglobulin antibodies to the PSA immunoassay.

  20. Event-Based Media Enrichment Using an Adaptive Probabilistic Hypergraph Model.

    PubMed

    Liu, Xueliang; Wang, Meng; Yin, Bao-Cai; Huet, Benoit; Li, Xuelong

    2015-11-01

    Nowadays, with the continual development of digital capture technologies and social media services, a vast number of media documents are captured and shared online to help attendees record their experience during events. In this paper, we present a method combining semantic inference and multimodal analysis for automatically finding media content to illustrate events using an adaptive probabilistic hypergraph model. In this model, media items are taken as vertices in the weighted hypergraph and the task of enriching media to illustrate events is formulated as a ranking problem. In our method, each hyperedge is constructed using the K-nearest neighbors of a given media document. We also employ a probabilistic representation, which assigns each vertex to a hyperedge in a probabilistic way, to further exploit the correlation among media data. Furthermore, we optimize the hypergraph weights in a regularization framework, which is solved as a second-order cone problem. The approach is initiated by seed media and then used to rank the media documents using a transductive inference process. The results obtained from validating the approach on an event dataset collected from EventMedia demonstrate the effectiveness of the proposed approach.

  1. Analysis methods and performance of an automated system for measuring both concentration and enrichment of uranium in solutions

    SciTech Connect

    Kelley, T.A.; Parker, J.L.; Sampson, T.E.

    1993-08-01

    For the 1992 INNM Meeting, we reported on an automated system under development for measuring both concentration and enrichment of uranium in solutions. In this paper, we report on measurement methods, ysis algorithms, and performance of the delivered system. The uranium concentration is measured by a transmission-corrected x-ray fluorescence method. Cobalt-57 is the fluorescing source and a combined {sup 153}Gd and {sup 57}Co source is used for the transmission measurements. Corrections are made for both the absorption of the exciting {sup 57}Co gamma rays and the excited uranium x-rays. The {sup 235}U concentration is measured by a transmission-corrected method, which employs the 185.7-keV gamma ray of {sup 235}U and a transmission source of {sup 75}Se to make corrections for the self-absorption of the {sup 235}U gamma rays in the solution samples. Both measurements employ high-resolution gamma-ray spectrometry and use the same 50-m{ell} sample contained in a custom-molded, flat-bottomed, polypropylene bottle. Both measurements are intended for uranium solutions with concentrations {ge}0.1 g U/{ell} although at higher enrichments the passive measurement will be even more sensitive.

  2. A Facile Method for Separating and Enriching Nano and Submicron Particles from Titanium Dioxide Found in Food and Pharmaceutical Products.

    PubMed

    Faust, James J; Doudrick, Kyle; Yang, Yu; Capco, David G; Westerhoff, Paul

    2016-01-01

    Recent studies indicate the presence of nano-scale titanium dioxide (TiO2) as an additive in human foodstuffs, but a practical protocol to isolate and separate nano-fractions from soluble foodstuffs as a source of material remains elusive. As such, we developed a method for separating the nano and submicron fractions found in commercial-grade TiO2 (E171) and E171 extracted from soluble foodstuffs and pharmaceutical products (e.g., chewing gum, pain reliever, and allergy medicine). Primary particle analysis of commercial-grade E171 indicated that 54% of particles were nano-sized (i.e., < 100 nm). Isolation and primary particle analysis of five consumer goods intended to be ingested revealed differences in the percent of nano-sized particles from 32%‒58%. Separation and enrichment of nano- and submicron-sized particles from commercial-grade E171 and E171 isolated from foodstuffs and pharmaceuticals was accomplished using rate-zonal centrifugation. Commercial-grade E171 was separated into nano- and submicron-enriched fractions consisting of a nano:submicron fraction of approximately 0.45:1 and 3.2:1, respectively. E171 extracted from gum had nano:submicron fractions of 1.4:1 and 0.19:1 for nano- and submicron-enriched, respectively. We show a difference in particle adhesion to the cell surface, which was found to be dependent on particle size and epithelial orientation. Finally, we provide evidence that E171 particles are not immediately cytotoxic to the Caco-2 human intestinal epithelium model. These data suggest that this separation method is appropriate for studies interested in isolating the nano-sized particle fraction taken directly from consumer products, in order to study separately the effects of nano and submicron particles.

  3. A Facile Method for Separating and Enriching Nano and Submicron Particles from Titanium Dioxide Found in Food and Pharmaceutical Products

    PubMed Central

    Yang, Yu; Capco, David G.; Westerhoff, Paul

    2016-01-01

    Recent studies indicate the presence of nano-scale titanium dioxide (TiO2) as an additive in human foodstuffs, but a practical protocol to isolate and separate nano-fractions from soluble foodstuffs as a source of material remains elusive. As such, we developed a method for separating the nano and submicron fractions found in commercial-grade TiO2 (E171) and E171 extracted from soluble foodstuffs and pharmaceutical products (e.g., chewing gum, pain reliever, and allergy medicine). Primary particle analysis of commercial-grade E171 indicated that 54% of particles were nano-sized (i.e., < 100 nm). Isolation and primary particle analysis of five consumer goods intended to be ingested revealed differences in the percent of nano-sized particles from 32%‒58%. Separation and enrichment of nano- and submicron-sized particles from commercial-grade E171 and E171 isolated from foodstuffs and pharmaceuticals was accomplished using rate-zonal centrifugation. Commercial-grade E171 was separated into nano- and submicron-enriched fractions consisting of a nano:submicron fraction of approximately 0.45:1 and 3.2:1, respectively. E171 extracted from gum had nano:submicron fractions of 1.4:1 and 0.19:1 for nano- and submicron-enriched, respectively. We show a difference in particle adhesion to the cell surface, which was found to be dependent on particle size and epithelial orientation. Finally, we provide evidence that E171 particles are not immediately cytotoxic to the Caco-2 human intestinal epithelium model. These data suggest that this separation method is appropriate for studies interested in isolating the nano-sized particle fraction taken directly from consumer products, in order to study separately the effects of nano and submicron particles. PMID:27798677

  4. A method and software framework for enriching private biomedical sources with data from public online repositories.

    PubMed

    Anguita, Alberto; García-Remesal, Miguel; Graf, Norbert; Maojo, Victor

    2016-04-01

    Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g. genes, compounds, pathways-that lead to interesting correlations. Normally, they must refer to additional public databases in order to enrich the information about the identified entities-e.g. scientific literature, published clinical trial results, etc. While semantic integration techniques have traditionally focused on providing homogeneous access to private datasets-thus helping automate the first part of the research, and there exist different solutions for browsing public data, there is still a need for tools that facilitate merging public repositories with private datasets. This paper presents a framework that automatically locates public data of interest to the researcher and semantically integrates it with existing private datasets. The framework has been designed as an extension of traditional data integration systems, and has been validated with an existing data integration platform from a European research project by integrating a private biological dataset with data from the National Center for Biotechnology Information (NCBI).

  5. A sensory- and consumer-based approach to optimize cheese enrichment with grape skin powders.

    PubMed

    Torri, L; Piochi, M; Marchiani, R; Zeppa, G; Dinnella, C; Monteleone, E

    2016-01-01

    The present study aimed to present a sensory- and consumer-based approach to optimize cheese enrichment with grape skin powders (GSP). The combined sensory evaluation approach, involving a descriptive and an affective test, respectively, was applied to evaluate the effect of the addition of grape skin powders from 2 grape varieties (Barbera and Chardonnay) at different levels [0.8, 1.6, and 2.4%; weight (wt) powder/wt curd] on the sensory properties and consumer acceptability of innovative soft cow milk cheeses. The experimental plan envisaged 7 products, 6 fortified prototypes (at rates of Barbera and Chardonnay of 0.8, 1.6, and 2.4%) and a control sample, with 1 wk of ripening. By means of a free choice profile, 21 cheese experts described the sensory properties of prototypes. A central location test with 90 consumers was subsequently conducted to assess the acceptability of samples. The GSP enrichment strongly affected the sensory properties of innovative products, mainly in terms of appearance and texture. Fortified samples were typically described with a marbling aspect (violet or brown as function of the grape variety) and with an increased granularity, sourness, saltiness, and astringency. The fortification also contributed certain vegetable sensations perceived at low intensity (grassy, cereal, nuts), and some potential negative sensations (earthy, animal, winy, varnish). The white color, the homogeneous dough, the compact and elastic texture, and the presence of lactic flavors resulted the positive drivers of preference. On the contrary, the marbling aspect, granularity, sandiness, sourness, saltiness, and astringency negatively affected the cheese acceptability for amounts of powder, exceeding 0.8 and 1.6% for the Barbera and Chardonnay prototypes, respectively. Therefore, the amount of powder resulted a critical parameter for liking of fortified cheeses and a discriminant between the 2 varieties. Reducing the GSP particle size and improving the GSP

  6. An efficient method to enrich for knock-out and knock-in cellular clones using the CRISPR/Cas9 system.

    PubMed

    Niccheri, Francesca; Pecori, Riccardo; Conticello, Silvestro G

    2017-09-01

    Clustered Regularly Interspaced Short Palindromic Repeats-associated protein 9 nuclease (CRISPR/Cas9) and Transcription Activator-Like Effector Nucleases (TALENs) are versatile tools for genome editing. Here we report a method to increase the frequency of Cas9-targeted cellular clones. Our method is based on a chimeric construct with a Blasticidin S Resistance gene (bsr) placed out-of-frame by a surrogate target sequence. End joining of the CRISPR/Cas9-induced double-strand break on the surrogate target can place the bsr in frame, thus providing temporary resistance to Blasticidin S: this is used to enrich for cells where Cas9 is active. By this approach, in a real experimental setting, we disrupted the Aicda gene in ~70% of clones from CH12F3 lymphoma cells (>40% biallelically). With the same approach we knocked in a single nucleotide to reconstruct the frame of Aicda in these null cells, restoring the function in ~37% of the clones (less than 10% by the standard approach). Targeting of single nucleotide changes in other genes yielded analogous results. These results support our enrichment method as an efficient tool in genome editing.

  7. Determination of plant stanols and plant sterols in phytosterol enriched foods with a gas chromatographic-flame ionization detection method: NMKL collaborative study.

    PubMed

    Laakso, Päivi H

    2014-01-01

    This collaborative study with nine participating laboratories was conducted to determine the total plant sterol and/or plant stanol contents in phytosterol fortified foods with a gas chromatographic method. Four practice and 12 test samples representing mainly commercially available foodstuffs were analyzed as known replicates. Twelve samples were enriched with phytosterols, whereas four samples contained only natural contents of phytosterols. The analytical procedure consisted of two alternative approaches: hot saponification method, and acid hydrolysis treatment prior to hot saponification. As a result, sterol/stanol compositions and contents in the samples were measured. The amounts of total plant sterols and total plant stanols varying from 0.005 to 8.04 g/100 g product were statistically evaluated after outliers were eliminated. The repeatability RSD (RSDr) varied from 1.34 to 17.13%. The reproducibility RSD (RSDR) ranged from 3.03 to 17.70%, with HorRat values ranging from 0.8 to 2.1. When only phytosterol enriched food test samples are considered, the RSDr ranged from 1.48 to 6.13%, the RSD, ranged from 3.03 to 7.74%, and HorRat values ranged from 0.8 to 2.1. Based on the results of this collaborative study, the study coordinator concludes the method is fit for its purpose.

  8. Evaluation and comparison of rapid methods for the detection of Salmonella in naturally contaminated pine nuts using different pre enrichment media.

    PubMed

    Wang, Hua; Gill, Vikas S; Cheng, Chorng-Ming; Gonzalez-Escalona, Narjol; Irvin, Kari A; Zheng, Jie; Bell, Rebecca L; Jacobson, Andrew P; Hammack, Thomas S

    2015-04-01

    Foodborne outbreaks, involving pine nuts and peanut butter, illustrate the need to rapidly detect Salmonella in low moisture foods. However, the current Bacteriological Analytical Manual (BAM) culture method for Salmonella, using lactose broth (LB) as a pre enrichment medium, has not reliably supported real-time quantitative PCR (qPCR) assays for certain foods. We evaluated two qPCR assays in LB and four other pre enrichment media: buffered peptone water (BPW), modified BPW (mBPW), Universal Pre enrichment broth (UPB), and BAX(®) MP media to detect Salmonella in naturally-contaminated pine nuts (2011 outbreak). A four-way comparison among culture method, Pathatrix(®) Auto, VIDAS(®) Easy SLM, and qPCR was conducted. Automated DNA extraction techniques were compared with manual extraction methods (boiling or InstaGene™). There were no significant differences (P > 0.05) among the five pre enrichment media for pine nuts using the culture method. While both qPCR assays produced significantly (P ≤ 0.05) higher false negatives in 24 h pre enriched LB than in the other four media, they were as sensitive as the culture method in BPW, mBPW, UPB, and BAX media. The VIDAS Easy and qPCR were equivalent; Pathatrix was the least effective method. The Automatic PrepSEQ™ DNA extraction, using 1000 μL of pre enrichment, was as effective as manual extraction methods. Published by Elsevier Ltd.

  9. Functional connectivity decreases in autism in emotion, self, and face circuits identified by Knowledge-based Enrichment Analysis.

    PubMed

    Cheng, Wei; Rolls, Edmund T; Zhang, Jie; Sheng, Wenbo; Ma, Liang; Wan, Lin; Luo, Qiang; Feng, Jianfeng

    2017-03-01

    A powerful new method is described called Knowledge based functional connectivity Enrichment Analysis (KEA) for interpreting resting state functional connectivity, using circuits that are functionally identified using search terms with the Neurosynth database. The method derives its power by focusing on neural circuits, sets of brain regions that share a common biological function, instead of trying to interpret single functional connectivity links. This provides a novel way of investigating how task- or function-related networks have resting state functional connectivity differences in different psychiatric states, provides a new way to bridge the gap between task and resting-state functional networks, and potentially helps to identify brain networks that might be treated. The method was applied to interpreting functional connectivity differences in autism. Functional connectivity decreases at the network circuit level in 394 patients with autism compared with 473 controls were found in networks involving the orbitofrontal cortex, anterior cingulate cortex, middle temporal gyrus cortex, and the precuneus, in networks that are implicated in the sense of self, face processing, and theory of mind. The decreases were correlated with symptom severity.

  10. Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials.

    PubMed

    Williams, Andrew; Halappanavar, Sabina

    2015-01-01

    The presence of diverse types of nanomaterials (NMs) in commerce is growing at an exponential pace. As a result, human exposure to these materials in the environment is inevitable, necessitating the need for rapid and reliable toxicity testing methods to accurately assess the potential hazards associated with NMs. In this study, we applied biclustering and gene set enrichment analysis methods to derive essential features of altered lung transcriptome following exposure to NMs that are associated with lung-specific diseases. Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related biclusters of genes showing similar expression profiles were identified. The identified biclusters were then used to conduct a gene set enrichment analysis on pulmonary gene expression profiles derived from mice exposed to nano-titanium dioxide (nano-TiO2), carbon black (CB) or carbon nanotubes (CNTs) to determine the disease significance of these data-driven gene sets. Biclusters representing inflammation (chemokine activity), DNA binding, cell cycle, apoptosis, reactive oxygen species (ROS) and fibrosis processes were identified. All of the NM studies were significant with respect to the bicluster related to chemokine activity (DAVID; FDR p-value = 0.032). The bicluster related to pulmonary fibrosis was enriched in studies where toxicity induced by CNT and CB studies was investigated, suggesting the potential for these materials to induce lung fibrosis. The pro-fibrogenic potential of CNTs is well established. Although CB has not been shown to induce fibrosis, it induces stronger inflammatory, oxidative stress and DNA damage responses than nano-TiO2 particles. The results of the analysis correctly identified all NMs to be inflammogenic and only CB and CNTs as potentially fibrogenic. In addition to identifying several previously defined, functionally relevant gene

  11. Enrichment, amplification, and sequence-based typing of Salmonella enterica and other foodborne pathogens

    USDA-ARS?s Scientific Manuscript database

    Detection and characterization of foodborne pathogens typically involves microbiological enrichment with subsequent isolation and identification of a pure culture; this is ideally followed by strain typing which provides information critical to outbreak and source investigations. Pulsed-field gel e...

  12. Laser and gas centrifuge enrichment

    SciTech Connect

    Heinonen, Olli

    2014-05-09

    Principles of uranium isotope enrichment using various laser and gas centrifuge techniques are briefly discussed. Examples on production of high enriched uranium are given. Concerns regarding the possibility of using low end technologies to produce weapons grade uranium are explained. Based on current assessments commercial enrichment services are able to cover the global needs of enriched uranium in the foreseeable future.

  13. Laser and gas centrifuge enrichment

    NASA Astrophysics Data System (ADS)

    Heinonen, Olli

    2014-05-01

    Principles of uranium isotope enrichment using various laser and gas centrifuge techniques are briefly discussed. Examples on production of high enriched uranium are given. Concerns regarding the possibility of using low end technologies to produce weapons grade uranium are explained. Based on current assessments commercial enrichment services are able to cover the global needs of enriched uranium in the foreseeable future.

  14. Carcass enrichment detects Salmonella from broiler carcasses found to be negative by other sampling methods

    USDA-ARS?s Scientific Manuscript database

    The most frequently used methods to recover Salmonella from processed broiler chicken carcasses involve carcass rinsing or neck skin maceration. These methods are nondestructive and practical, but have limited sensitivity. The standard carcass rinse method uses only 7.5% of the residual rinsate an...

  15. An Independent Filter for Gene Set Testing Based on Spectral Enrichment.

    PubMed

    Frost, H Robert; Li, Zhigang; Asselbergs, Folkert W; Moore, Jason H

    2015-01-01

    Gene set testing has become an indispensable tool for the analysis of high-dimensional genomic data. An important motivation for testing gene sets, rather than individual genomic variables, is to improve statistical power by reducing the number of tested hypotheses. Given the dramatic growth in common gene set collections, however, testing is often performed with nearly as many gene sets as underlying genomic variables. To address the challenge to statistical power posed by large gene set collections, we have developed spectral gene set filtering (SGSF), a novel technique for independent filtering of gene set collections prior to gene set testing. The SGSF method uses as a filter statistic the p-value measuring the statistical significance of the association between each gene set and the sample principal components (PCs), taking into account the significance of the associated eigenvalues. Because this filter statistic is independent of standard gene set test statistics under the null hypothesis but dependent under the alternative, the proportion of enriched gene sets is increased without impacting the type I error rate. As shown using simulated and real gene expression data, the SGSF algorithm accurately filters gene sets unrelated to the experimental outcome resulting in significantly increased gene set testing power.

  16. A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies.

    PubMed

    Blouin, Arnaud G; Ross, Howard A; Hobson-Peters, Jody; O'Brien, Caitlin A; Warren, Ben; MacDiarmid, Robin

    2016-09-01

    Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase-polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31-74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.

  17. Inquiry-Based Science and Technology Enrichment Program for Middle School-Aged Female Students

    NASA Astrophysics Data System (ADS)

    Kim, Hanna

    2016-04-01

    This study investigates the effects of an intensive 1-week Inquiry-Based Science and Technology Enrichment Program (InSTEP) designed for middle school-aged female students. InSTEP uses a guided/open inquiry approach that is deepened and redefined as eight sciences and engineering practices in the Next Generation Science Standards, which aimed at increasing female students' interest in science and science-related careers. This study examined the effectiveness of InSTEP on 123 female students' pre-assessment and post-assessment changes in attitudes toward science and content knowledge of selected science concepts. An attitude survey, a science content test with multiple-choice questions, written assignments, and interviews to collect data were all used to measure students' attitudes and content knowledge. A within-group, repeated measure design was conducted, and the results indicated that at the post-intervention level, InSTEP increased the participants' positive attitudes toward science, science-related careers, and content knowledge of selected science concepts.

  18. Zein based oil-in-glycerol emulgels enriched with β-carotene as margarine alternatives.

    PubMed

    Chen, Xiao-Wei; Fu, Shi-Yao; Hou, Jun-Jie; Guo, Jian; Wang, Jin-Mei; Yang, Xiao-Quan

    2016-11-15

    Structuring edible oils into solid lipids without saturated and trans fats has attracted increasing interest due to the benefits for human health and promises potential as novel delivery systems for lipophilic bioactive ingredients. The study shows that a zein stabilized high (ϕ=0.6) oil-in-glycerol (O/G) emulgels enriched with β-carotene was performed, by a facile one-step homogenization. Rheological measurements and morphologies observations indicated that increasing β-carotene resulted in a progressive strengthening of gel-like network and improving their spreadability in the O/G emulgels stabilized by zein, which was closely related to the hydrophobic interaction of zein and β-carotene. The formation of emulgels significantly enhanced the UV photo-stability of β-carotene, and more than 88% of β-carotene was retained in 64h storage under UV exposure, and consequently retarded oil oxidation while storage. Further, cakes prepared using zein-based O/G emulgels as a margarine alternative showed comparable functionalities (texture and sensory attributes) to the standard cake.

  19. A lectin-based isolation/enrichment strategy for improved coverage of N-glycan analysis.

    PubMed

    Guan, Feng; Tan, Zengqi; Li, Xiang; Pang, Xingchen; Zhu, Yunlin; Li, Dongliang; Yang, Ganglong

    2015-10-30

    Glycomics provides an increasingly useful research tool as the genomes and proteomes of more and more animal species are elucidated. In view of the general complexity and heterogeneity of glycans, improved depth-of-coverage and sensitivity are required for glycosylation analysis. In this study, we established the lectin-based isolation/enrichment strategy for total glycomic information. Specific lectins are added onto the filter to capture corresponding glycans prior to release of N-glycans by peptide N-glycosidase F (PNGase F). Non-bound glycans and bound glycans are released and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), respectively. Application of the strategy to chicken ovalbumin, normal mouse mammary epithelial cells (NMuMG), and human serum resulted in detection of 5, 6, and 11 additional N-glycan structures, respectively. The strategy facilitates identification of intact N-glycans in biological samples, and can be extended to detailed analysis of O-glycome or glycoproteome.

  20. Combining auctions and performance-based payments in a forest enrichment field trial in Western Kenya.

    PubMed

    Khalumba, Mercelyne; Wünscher, Tobias; Wunder, Sven; Büdenbender, Mirjam; Holm-Müller, Karin

    2014-06-01

    Cost-effectiveness is an important aspect in the assessment of payments for environmental services (PES) initiatives. In participatory field trials with communities in Western Kenya, we combined procurement auctions for forest enrichment contracts with performance-based payments and compared the outcomes with a baseline scenario currently used by the Kenyan Forest Service. Procurement auctions were the most cost-effective. The competitive nature of the auction reduced contracting expenses (provision costs), and the result-oriented payments provided additional incentives to care for the planted seedlings, resulting in their improved survival rates (service quantity). These gains clearly exceeded increases in transaction costs associated with conducting an auction. The number of income-poor auction participants and winners was disproportionately high and local institutional buy-in was remarkably strong. Our participatory approach may, however, require adaptations when conducted at a larger scale. Although the number of contracts we monitored was limited and prohibited the use of statistical tests, our study is one of the first to reveal the benefits of using auctions for PES in developing countries. © 2014 Society for Conservation Biology.

  1. Starch-based extruded cereals enriched in fibers: a behavior of composite solid foams.

    PubMed

    Chanvrier, Hélène; Desbois, Fabrice; Perotti, Fabienne; Salzmann, Claire; Chassagne, Sophie; Gumy, Jean-Claude; Blank, Imre

    2013-10-15

    Extruded cereals mainly composed of starch and enriched in fibers were produced with two types of base recipes: (i) one recipe mainly composed of wheat flour and (ii) one recipe mainly composed of corn and soya flours. The addition of fibers was performed through the use of oat bran concentrate or wheat bran, up to 32% of the recipe. The structure of the extrudates, assessed by X-ray tomography, pointed out the decrease of porosity and of mean cells size with the increase of the total dietary fibers content of the recipe. The hardness of the products, i.e. the maximum stress determined by a compression test, was linked to their porosity. The Gibson-Ashby relationship could be applied and the fit was even improved when considering the walls of the solid foam as composite materials. Fibers and proteins can be indeed considered as particles dispersed in the starchy phase. This work thus shows the impact of the structure of the extrudates on their mechanical properties. The structure is taken into account at different length scales; at the level of the porous structure and at the level of the phase of the main biopolymers present in the recipe (starch, proteins and fibers). The mechanical behavior of these products is then discussed according to their characteristics of composite solid foams. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Improved accountability method for measuring enriched uranium in H-Canyon dissolver solution at the Savannah River Site

    SciTech Connect

    Maxwell, S.L. III; Satkowski, J.; Mahannah, R.N.

    1992-08-01

    At the Savannah River Site (SRS), accountability measurement of enriched uranium dissolved in H-Canyon is performed using isotope dilution mass spectrometry (IDMS). In the IDMS analytical method, a known quantity of uranium{sup 233} is added to the sample solution containing enriched uranium and fission products. The resulting uranium mixture must first be purified using a separation technique in the shielded analytical(``hot``) cells to lower radioactivity levels by removing fission products. Following this purification, the sample is analyzed by mass spectrometry to determine the total uranium content and isotopic abundance. The magnitude of the response of each uranium isotope in the sample solution and the response of the U{sup 233} spike is measured. By ratioing these responses, relative to the known quantity of the U{sup 233} spike, the uranium content can be determined. A hexane solvent extraction technique, used for years at SRS to remove fission products prior to the mass spectrometry analysis of uranium, has several problems. The hexone method is tedious, requires additional sample clean-up after the purified sample is removed from the shielded cells and requires the use of Resource Conservation and Recovery Act (RCRA)-listed hazardous materials (hexone and chromium compounds). A new high speed separation method that enables a rapid removal of fission products in a shielded cells environment has been developed by the SRS Central Laboratory to replace the hexone method. The new high speed column extraction chromatography technique employs applied vacuum and columns containing tri (2-ethyl-hexyl) phosphate (TEHP) solvent coated on a small particle inert support (SM-7 Bio Beads). The new separation is rapid, user friendly, eliminates the use of the RCA-listed hazardous chemicals and reduces the amount of solid waste generated by the separation method. 2 tabs. 4 figs.

  3. Improved accountability method for measuring enriched uranium in H-Canyon dissolver solution at the Savannah River Site

    SciTech Connect

    Maxwell, S.L. III; Satkowski, J.; Mahannah, R.N.

    1992-01-01

    At the Savannah River Site (SRS), accountability measurement of enriched uranium dissolved in H-Canyon is performed using isotope dilution mass spectrometry (IDMS). In the IDMS analytical method, a known quantity of uranium{sup 233} is added to the sample solution containing enriched uranium and fission products. The resulting uranium mixture must first be purified using a separation technique in the shielded analytical( hot'') cells to lower radioactivity levels by removing fission products. Following this purification, the sample is analyzed by mass spectrometry to determine the total uranium content and isotopic abundance. The magnitude of the response of each uranium isotope in the sample solution and the response of the U{sup 233} spike is measured. By ratioing these responses, relative to the known quantity of the U{sup 233} spike, the uranium content can be determined. A hexane solvent extraction technique, used for years at SRS to remove fission products prior to the mass spectrometry analysis of uranium, has several problems. The hexone method is tedious, requires additional sample clean-up after the purified sample is removed from the shielded cells and requires the use of Resource Conservation and Recovery Act (RCRA)-listed hazardous materials (hexone and chromium compounds). A new high speed separation method that enables a rapid removal of fission products in a shielded cells environment has been developed by the SRS Central Laboratory to replace the hexone method. The new high speed column extraction chromatography technique employs applied vacuum and columns containing tri (2-ethyl-hexyl) phosphate (TEHP) solvent coated on a small particle inert support (SM-7 Bio Beads). The new separation is rapid, user friendly, eliminates the use of the RCA-listed hazardous chemicals and reduces the amount of solid waste generated by the separation method. 2 tabs. 4 figs.

  4. RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans

    PubMed Central

    Amorim-Vaz, Sara; Tran, Van Du T.; Pradervand, Sylvain; Pagni, Marco; Coste, Alix T.

    2015-01-01

    ABSTRACT In vivo transcriptional analyses of microbial pathogens are often hampered by low proportions of pathogen biomass in host organs, hindering the coverage of full pathogen transcriptome. We aimed to address the transcriptome profiles of Candida albicans, the most prevalent fungal pathogen in systemically infected immunocompromised patients, during systemic infection in different hosts. We developed a strategy for high-resolution quantitative analysis of the C. albicans transcriptome directly from early and late stages of systemic infection in two different host models, mouse and the insect Galleria mellonella. Our results show that transcriptome sequencing (RNA-seq) libraries were enriched for fungal transcripts up to 1,600-fold using biotinylated bait probes to capture C. albicans sequences. This enrichment biased the read counts of only ~3% of the genes, which can be identified and removed based on a priori criteria. This allowed an unprecedented resolution of C. albicans transcriptome in vivo, with detection of over 86% of its genes. The transcriptional response of the fungus was surprisingly similar during infection of the two hosts and at the two time points, although some host- and time point-specific genes could be identified. Genes that were highly induced during infection were involved, for instance, in stress response, adhesion, iron acquisition, and biofilm formation. Of the in vivo-regulated genes, 10% are still of unknown function, and their future study will be of great interest. The fungal RNA enrichment procedure used here will help a better characterization of the C. albicans response in infected hosts and may be applied to other microbial pathogens. PMID:26396240

  5. Assessment of adrenocortical activity and behavior of the collared anteater (Tamandua tetradactyla) in response to food-based environmental enrichment.

    PubMed

    Eguizábal, Gabina V; Palme, Rupert; Villarreal, Daniel; Dal Borgo, Carla; Di Rienzo, Julio A; Busso, Juan M

    2013-01-01

    One of the current standard approaches to the study of animal welfare is measuring hypothalamic-pituitary-adrenal activity, frequently in association with behavioral assessment. We studied the effects of food-based environmental enrichment on adrenocortical activity and behavior in zoo-housed collared anteaters (Tamandua tetradactyla; n = 5). We successfully validated measurements of fecal cortisol metabolites (FCMs) using an 11-oxoetiocholanolone enzyme immunoassay by stimulating (ACTH injection) and suppressing (dexamethasone administration) adrenocortical activity. Three months later, we subjected animals to an ABA-type experiment (three 6-week periods): pre-enrichment (routine diet: A), enrichment (modified diet: B), and post-enrichment (routine diet: A) periods. We assessed adrenocortical activity by collecting individual feces three times a week (total number of samples: 228), and evaluated behavior by performing 3 days of behavioral observations per period (with a total of 3,600 behavioral data points for the individuals studied). Statistical analysis revealed changes in FCM concentrations (µg/g) over the periods (3.04 ± 0.68, 2.98 ± 0.66, and 4.04 ± 0.90, respectively). Additionally, it showed that the number of FCM peaks was highly reduced during enrichment; meanwhile active natural behaviors were significantly increased. We consider that these changes in response to food-based environmental enrichment improved the welfare of individual zoo-housed collared anteaters. This research might contribute to in situ and ex situ studies on the physiology and behavior of this endemic South American species.

  6. Comparative and multilaboratory studies of two immunodiffusion method enrichment protocols and the AOAC/Bacteriological Analytical Manual culture method for detection of Salmonella in all foods.

    PubMed

    Feldsine, P T; Falbo-Nelson, M T; Hustead, D L; Flowers, R S; Flowers, M J

    1995-01-01

    The single enrichment immunodiffusion (1-step), the preenrichment and selective enrichment immunodiffusion (2-step), and the AOAC/Bacteriological Analytical Manual culture methods for Salmonella were evaluated for equivalence in 2 separate studies, a comparative evaluation and a multilaboratory dilution study. In the comparative study, all 3 methods were performed on 10 food types. For 550 samples, analyses resulted in 99.3 and 99.6% agreement between the culture method and the 1-step and 2-step methods, respectively. False negative rates were 0.9 and 0.3% for 1-step and culture, and 0.0% and 0.6% for the 2-step and culture, respectively. Subsequently, 6 food types were included in a multilaboratory dilution-to-extinction study. A sequential dilution series of Salmonella in foods was analyzed by the 3 methods to determine their lower limits of detection for Salmonella. A total of 1185 samples analyzed resulted in 98.9% agreement between 1-step and culture, and 99.7% agreement between 2-step and culture. False negative rates were 1.8 and 0.1% for 1-step and culture, and 0.4 and 0.1% for 2-step and culture, respectively. During these evaluations, 1735 samples and controls representing 10 different naturally contaminated and inoculated foods were tested. The data indicate statistical equivalence of all 3 methods when analyzing all food types.

  7. Qualitative Methods Can Enrich Quantitative Research on Occupational Stress: An Example from One Occupational Group

    ERIC Educational Resources Information Center

    Schonfeld, Irvin Sam; Farrell, Edwin

    2010-01-01

    The chapter examines the ways in which qualitative and quantitative methods support each other in research on occupational stress. Qualitative methods include eliciting from workers unconstrained descriptions of work experiences, careful first-hand observations of the workplace, and participant-observers describing "from the inside" a…

  8. Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

    PubMed Central

    Novais, Sara C.; Arrais, Joel; Lopes, Pedro; Vandenbrouck, Tine; De Coen, Wim; Roelofs, Dick; Soares, Amadeu M. V. M.; Amorim, Mónica J. B.

    2012-01-01

    Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value≤10-5) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies. PMID:22558086

  9. Method of controlling the mercury vapor pressure in a photo-chemical lamp or vapor filter used for Hg.sup.196 enrichment

    DOEpatents

    Grossman, Mark W.

    1993-01-01

    The present invention is directed to a method of eliminating the cold spot zones presently used on Hg.sup.196 isotope separation lamps and filters by the use of a mercury amalgams, preferably mercury - indium amalgams. The use of an amalgam affords optimization of the mercury density in the lamp and filter of a mercury enrichment reactor, particularly multilamp enrichment reactors. Moreover, the use of an amalgam in such lamps and/or filters affords the ability to control the spectral line width of radiation emitted from lamps, a requirement for mercury enrichment.

  10. Method of controlling the mercury vapor pressure in a photo-chemical lamp or vapor filter used for Hg[sup 196] enrichment

    DOEpatents

    Grossman, M.W.

    1993-02-16

    The present invention is directed to a method of eliminating the cold spot zones presently used on Hg[sup 196] isotope separation lamps and filters by the use of a mercury amalgams, preferably mercury - indium amalgams. The use of an amalgam affords optimization of the mercury density in the lamp and filter of a mercury enrichment reactor, particularly multilamp enrichment reactors. Moreover, the use of an amalgam in such lamps and/or filters affords the ability to control the spectral line width of radiation emitted from lamps, a requirement for mercury enrichment.

  11. Solid-phase extraction disk based on multiwalled carbon nanotubes for the enrichment of targeted pesticides from aqueous samples.

    PubMed

    Zdolšek, Nikola; Kumrić, Ksenija; Kalijadis, Ana; Trtić-Petrović, Tatjana

    2017-04-01

    A sensitive method for the determination of six varying polarity pesticides (imidacloprid, acetamiprid, carbendazim, simazine, linuron, and tebufenozide) based on a solid-phase extraction disk with multiwalled nanotubes is proposed.A dispersion of multiwalled nanotubes in a surfactant aqueous solution (Triton X-100) was used for the preparation of the solid-phase extraction disk. The effect of surfactant on the functional groups of multiwalled nanotubes was examined by applying temperature-programmed desorption. It was found that this treatment increased the amount of oxygen groups of treated multiwalled nanotubes comparing with untreated ones. The factors that may influence the adsorption and recovery such as the kind and volume of eluent, volume, flow rate and pH of sample were investigated and optimized. Under the optimized conditions, the maximal enrichment factors for low polar pesticides are ranging from 4000 to 4985 and for more polar are 2250 and 2750. The linear range of calibration curves was 10-500 ng/L with correlation coefficient higher than 0.9960, and the detection limit was 6.2-23.7 ng/L. Finally optimized method was applied for determination trace level of five out of six pesticides in tap and river water samples with good recovery.

  12. A Novel Method for Molybdenum-99/Technetium-99m Recovery via Anodic Carbonate Dissolution of Irradiated Low-Enriched Uranium Metal Foil

    SciTech Connect

    Brown, Michael A.

    2015-01-21

    A new method is presented here for digesting irradiated low-enriched uranium foil targets in alkaline carbonate media to recover 99Mo. This method consists of the electrolytic dissolution of uranium foil in a sodium bicarbonate solution, followed by the precipitation of carbonate, base-insoluble fission products, activation products, and actinides with calcium oxide; most of the molybdenum, technetium, and iodine remain in solution. An electrochemical dissolver and mixing vessel were designed, fabricated, and tested for the processing of a full-sized irradiated foil under ambient pressure and elevated temperature. Over 92% of the fission-induced Mo-99 was recovered in a product solution that was compatible with an anion-exchange column for retaining molybdenum and iodine.

  13. Reliability-targeted HPLC-UV method validation--a protocol enrichment perspective.

    PubMed

    Dharuman, Joghee Gowder; Vasudevan, Mahalingam

    2014-02-01

    Method validation is important in analytical chemistry to obtain the reliability of an analytical method. Guidelines provided by the regulatory bodies can be used as a general framework to assess the validity of a method. Since these guidelines do not focus on the reliability of analytical results exclusively, this study was aimed to combine a few recently evolved strategies that may render analytical method validation more reliable and trustworthy. In this research, the analytical error function was determined by appropriate polynomial regression statistics that determine the range of analyte concentration that may lead to more accurate measurements by producing the least possible total error in the assay and can be regarded as a reliable weighting method. The reliability of the analytical results over a particular concentration range has been proposed by a Bayesian probability study. In order to ensure the applicability of this approach, it was applied for the validation of an HPLC-UV assay method dedicated to the quantification of cefepime and tazobactam in human plasma. A comparison between the newer approach and the usual method validation revealed that the application of analytical error function and Bayesian analysis at the end of the validation process can produce significant improvements in the analytical results.

  14. A molecular enrichment strategy based on cpn60 for detection of epsilon-proteobacteria in the dog fecal microbiome.

    PubMed

    Chaban, Bonnie; Links, Matthew G; Hill, Janet E

    2012-02-01

    Members of the rare microbiome can be important components of complex microbial communities. For example, pet dog ownership is a known risk factor for human campylobacteriosis, and Campylobacter is commonly detected in dog feces by targeted assays. However, these organisms have not been detected by metagenomic methods. The goal of this study was to characterize fecal microbiota from healthy and diarrheic pet dogs using two different levels of molecular detection. PCR amplification and pyrosequencing of the universal cpn60 gene target was used to obtain microbial profiles from each dog. To investigate the relatively rare epsilon-proteobacteria component of the microbiome, a molecular enrichment was carried out using a PCR that first amplified the cpn10-cpn60 region from epsilon-proteobacteria, followed by universal cpn60 target amplification and pyrosequencing. From the non-enriched survey, the major finding was a significantly higher proportion of Bacteroidetes, notably Bacteroides vulgatus, in healthy dogs compared to diarrheic dogs. Epsilon-proteobacteria from the genera Helicobacter and Campylobacter were also detected at a low level in the non-enriched profiles of some dogs. Molecular enrichment increased the proportion of epsilon-proteobacteria sequences detected from each dog, as well as identified novel, presumably rare sequences not seen in the non-enriched profiles. Enriched profiles contained known species of Arcobacter, Campylobacter, Flexispira, and Helicobacter and identified two possibly novel species. These findings add to our understanding of the canine fecal microbiome in general, the epsilon-proteobacteria component specifically, and present a novel modification to traditional metagenomic approaches for study of the rare microbiome.

  15. Circulating tumour cells: the evolving concept and the inadequacy of their enrichment by EpCAM-based methodology for basic and clinical cancer research.

    PubMed

    Grover, P K; Cummins, A G; Price, T J; Roberts-Thomson, I C; Hardingham, J E

    2014-08-01

    Increasing evidence suggests that circulating tumour cells (CTCs) are responsible for metastatic relapse and this has fuelled interest in their detection and quantification. Although numerous methods have been developed for the enrichment and detection of CTCs, none has yet reached the 'gold' standard. Since epithelial cell adhesion molecule (EpCAM)-based enrichment of CTCs offers several advantages, it is one of the most commonly used and has been adapted for high-throughput technology. However, emerging evidence suggests that CTCs are highly heterogeneous: they consist of epithelial tumour cells, epithelial-to-mesenchymal transition (EMT) cells, hybrid (epithelial/EMT(+)) tumour cells, irreversible EMT(+) tumour cells, and circulating tumour stem cells (CTSCs). The EpCAM-based approach does not detect CTCs expressing low levels of EpCAM and non-epithelial phenotypes such as CTSCs and those that have undergone EMT and no longer express EpCAM. Thus, the approach may lead to underestimation of the significance of CTCs, in general, and CTSCs and EMT(+) tumour cells, in particular, in cancer dissemination. Here, we provide a critical review of research literature on the evolving concept of CTCs and the inadequacy of their enrichment by EpCAM-based technology for basic and clinical cancer research. The review also outlines future perspectives in the field. © The Author 2014. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  16. Click Synthesis of Hydrophilic Maltose-Functionalized Iron Oxide Magnetic Nanoparticles Based on Dopamine Anchors for Highly Selective Enrichment of Glycopeptides.

    PubMed

    Bi, Changfen; Zhao, Yingran; Shen, Lijin; Zhang, Kai; He, Xiwen; Chen, Langxing; Zhang, Yukui

    2015-11-11

    The development of methods to isolate and enrich low-abundance glycopeptides from biological samples is crucial to glycoproteomics. Herein, we present an easy and one-step surface modification strategy to prepare hydrophilic maltose functionalized Fe3O4 nanoparticles (NPs). First, based on the chelation of the catechol ligand with iron atoms, azido-terminated dopamine (DA) derivative was assembled on the surface of magnetic Fe3O4 nanoparticles by sonication. Second, the hydrophilic maltose-functionalized Fe3O4 (Fe3O4-DA-Maltose) NPs were obtained via copper(I)-catalyzed azide-alkyne cycloaddition (click chemistry). The morphology, structure, and composition of Fe3O4-DA-Maltose NPs were investigated by Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM), X-ray powder diffraction (XRD), X-ray photoelectron spectrometer (XPS), and vibrating sample magnetometer (VSM). Meanwhile, hydrophilicity of the obtained NPs was evaluated by water contact angle measurement. The hydrophilic Fe3O4-DA-Maltose NPs were applied in isolation and enrichment of glycopeptides from horseradish peroxidase (HRP), immunoglobulin (IgG) digests. The MALDI-TOF mass spectrometric analysis indicated that the novel NPs exhibited high detection sensitivity in enrichment from HRP digests at concentration as low as 0.05 ng μL(-1), a large binding capacity up to 43 mg g(-1), and good recovery for glycopeptides enrichment (85-110%). Moreover, the Fe3O4-DA-Maltose NPs were applied to enrich glycopeptides from human renal mesangial cells (HRMC) for identification of N-glycosylation sites. Finally, we identified 115 different N-linked glycopeptides, representing 93 gene products and 124 glycosylation sites in HRMC.

  17. A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits.

    PubMed

    Karamitros, Timokratis; Magiorkinis, Gkikas

    2015-12-15

    The enrichment of targeted regions within complex next generation sequencing libraries commonly uses biotinylated baits to capture the desired sequences. This method results in high read coverage over the targets and their flanking regions. Oxford Nanopore Technologies recently released an USB3.0-interfaced sequencer, the MinION. To date no particular method for enriching MinION libraries has been standardized. Here, using biotinylated PCR-generated baits in a novel approach, we describe a simple and efficient way for multiplexed enrichment of MinION libraries, overcoming technical limitations related with the chemistry of the sequencing-adapters and the length of the DNA fragments. Using Phage Lambda and Escherichia coli as models we selectively enrich for specific targets, significantly increasing the corresponding read-coverage, eliminating unwanted regions. We show that by capturing genomic fragments, which contain the target sequences, we recover reads extending targeted regions and thus can be used for the determination of potentially unknown flanking sequences. By pooling enriched libraries derived from two distinct E. coli strains and analyzing them in parallel, we demonstrate the efficiency of this method in multiplexed format. Crucially we evaluated the optimal bait size for large fragment libraries and we describe for the first time a standardized method for target enrichment in MinION platform.

  18. Test methods for determining the suitability of metal alloys for use in oxygen-enriched environments

    NASA Technical Reports Server (NTRS)

    Stoltzfus, Joel M.; Gunaji, Mohan V.

    1991-01-01

    Materials are more flammable in oxygen rich environments than in air. When the structural elements of a system containing oxygen ignite and burn, the results are often catastrophic, causing loss of equipment and perhaps even human lives. Therefore, selection of the proper metallic and non-metallic materials for use in oxygen systems is extremely important. While test methods for the selection of non-metallic materials have been available for years, test methods for the selection of alloys have not been available until recently. Presented here are several test methods that were developed recently at NASA's White Sands Test Facility (WSTF) to study the ignition and combustion of alloys, including the supersonic and subsonic speed particle impact tests, the frictional heating and coefficient of friction tests, and the promoted combustion test. These test methods are available for commercial use.

  19. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

    USDA-ARS?s Scientific Manuscript database

    Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylat...

  20. An Easy and Fast Protocol for Affinity Bead-Based Protein Enrichment and Storage of Proteome Samples.

    PubMed

    Otto, A; Maaß, S; Bonn, F; Büttner, K; Becher, D

    2017-01-01

    Analysis of dilute protein samples is a challenging task for scientific and industrial labs all over the world. Although there are different methods available that allow for protein enrichment from various biological sources, all of them have serious limitations apart from their advantages. In order to perform highly reproducible and sensitive protein analysis of lowest concentrated samples, we optimized a method to enrich proteins on affinity beads (StrataClean) recently. This chapter describes the general protocol of this strategy, thereby discussing the power as well as the limits of this technique for qualitative and quantitative proteomic studies. Moreover, additional application and protocol variants will be discussed, expanding the number of compatible up- and downstream processing techniques compared to the originally published method. Hence, we evaluated the reduction of time for sample preparation by use of preprimed affinity beads and shorter incubation durations as well as the influence of high concentration of salts or urea in the sample buffer.

  1. The Impact of a Cryogenics-Based Enrichment Programme on Attitude Towards Science and the Learning of Science Concepts. Research Report

    ERIC Educational Resources Information Center

    Caleon, Imelda; Subramaniam, R.

    2005-01-01

    This study explores the impact of a cryogenics-based enrichment programme, which involves demonstrations that use liquid nitrogen, on attitudes towards science and the learning of science concepts. The findings presented in this paper are based on a sample of 214 fifth-grade students from two schools in Singapore who had their enrichment lesson in…

  2. The Impact of a Cryogenics-Based Enrichment Programme on Attitude Towards Science and the Learning of Science Concepts. Research Report

    ERIC Educational Resources Information Center

    Caleon, Imelda; Subramaniam, R.

    2005-01-01

    This study explores the impact of a cryogenics-based enrichment programme, which involves demonstrations that use liquid nitrogen, on attitudes towards science and the learning of science concepts. The findings presented in this paper are based on a sample of 214 fifth-grade students from two schools in Singapore who had their enrichment lesson in…

  3. Method of synthesizing enriched decaborane for use in generating boron neutron capture therapy pharmaceuticals

    DOEpatents

    Cowan, Robert L.; Ginosar, Daniel M.; Dunks, Gary B.

    2000-01-01

    A method is described for synthesizing decaborane wherein at least about 90% of the boron atoms in the decaborane are the .sup.10 B isotope, comprising the steps of: (a) reacting boric acid with a C.sub.1 to C.sub.10 alkanol to form a .sup.10 B-alkyl borate wherein at least about 90% of the boron atoms in the boric acid are the .sup.10 B isotope; (b) reducing the .sup.10 B-alkyl borate to form an alkali metal .sup.10 B-borohydride; (c) converting the alkali metal .sup.10 B-borohydride to a .sup.10 B-tetradecahydroundecaborate ion; and (d) converting the .sup.10 B-tetradecahydroundecaborate ion to .sup.10 B-decaborane. Methods of preparing tetradecahydroundecaborate ions and decaborane from alkali metal borohydrides are also described.

  4. Isotopic enrichment of Zn particles by laser ablation

    NASA Astrophysics Data System (ADS)

    Felix Pozzi, Marcelo N.; Guidali, Gonzalo; Fernández, Mauricio; Zubillaga, Erica; Rinaldi, Carlos A.

    2017-07-01

    The use of Zn in nuclear reactors reduces the amount of 60Co generated as a consequence of the natural activation of Co. On the other hand, isotopically enriched Zn can be used as a tracer in biological systems. At the present, the enrichment of Zn is obtained using gaseous compounds of the metal by centrifugal force. In this paper, we present a method based on laser ablation of metallic targets of Zn with a Nd-YAG nanosecond laser to produce isotopically enriched Zn particles. Also, the effect of the wavelength irradiation laser on the enrichment factor was studied and a procedure is proposed to collect the different enrichment fractions yield.

  5. Comparison of nutritional qualities and antioxidant properties of ready-to-eat fruit-enriched corn based breakfast cereals.

    PubMed

    Bhavya, S N; Prakash, J

    2012-12-01

    The study aimed to analyse the nutritional quality, antioxidant components and activity of three varieties of corn based ready-to- eat (RTE) breakfast cereals (BFC) enriched with strawberry, banana and mango. Fruit-enriched corn based breakfast cereals manufactured in India were purchased and ground to obtain homogeneous samples for analysis. The contents of moisture, protein, total fat, dietary fibre, iron, phosphorous, calcium, vitamin C, total carotene, thiamine, riboflavin, in vitro digestible protein, bioaccessible calcium and iron, and digestible starch fractions were determined. The antioxidant components namely, polyphenols, flavonoids and antioxidant activity in different extracts were also determined using total antioxidant, free radical scavenging (2,2-diphenyl-1-picrylhydrazyl) and reducing power assays. The protein and dietary fibre contents in all samples ranged between 4.0-4.6 and 6.4-7.6 g/ 100g respectively. Total iron and vitamin C ranged between 10.7-13.3 mg and 33.2-43.6 mg/100g respectively. Cereals with mango had high total carotene in comparison with other samples. In vitro digestible protein of the processed cereals was low, while bioaccessible calcium (50.2-59.5%) and iron (8.5-15.1%) levels were high due to low oxalates and phytic acid contents. The starch profiles of the breakfast cereals showed high rapidly available glucose and starch digestibility index. Fruit-enriched breakfast cereals showed high polyphenol content in methanol extract (48.6-71.3 mg/100g) and high total antioxidant activity in aqueous extracts. Free radical scavenging and reducing power assay showed high activity in 80% methanol extract. Fruit-enriched breakfast cereals have the potential to be a good source of iron, dietary fibre, vitamin C and total carotene. The fruit-enriched cereals also had high bioaccessible iron and antioxidant activity.

  6. Accelerator-based method of producing isotopes

    DOEpatents

    Nolen, Jr., Jerry A.; Gomes, Itacil C.

    2015-11-03

    The invention provides a method using accelerators to produce radio-isotopes in high quantities. The method comprises: supplying a "core" of low-enrichment fissile material arranged in a spherical array of LEU combined with water moderator. The array is surrounded by substrates which serve as multipliers and moderators as well as neutron shielding substrates. A flux of neutrons enters the low-enrichment fissile material and causes fissions therein for a time sufficient to generate desired quantities of isotopes from the fissile material. The radio-isotopes are extracted from said fissile material by chemical processing or other means.

  7. Oxidized dextran facilitated synthesis of a silica-based concanavalin a material for lectin affinity enrichment of glycoproteins/glycopeptides.

    PubMed

    Liu, Yujie; Fu, Dongmei; Yu, Long; Xiao, Yuansheng; Peng, Xiaojun; Liang, Xinmiao

    2016-07-15

    Lectin affinity chromatography (LAC) is an important enrichment technique in glycoproteomics analysis. In order to improve the effectiveness of enrichment, it is necessary to develop LAC materials with high specificity and efficiency. Herein, using oxidized dextran as the spacer, a silica-based concanavalin A material (SiO2-ODex Con A) was synthesized to enrich glycoproteins/glycopeptides. For comparison, the SiO2-Ald Con A material was synthesized using conventional (3-glycidoxypropyl) triethoxysilane (GPMS) as the initial spacer arm. The analytical merits of both Con A materials, such as non-specific adsorption, binding capacity and trapping efficiency, have been evaluated using ovalbumin. Under high performance liquid affinity chromatography (HPLAC) mode, the SiO2-ODex Con A material was highly effective in the enrichment of glycoproteins/glycopeptides attached to high-mannose-type and bi-antennary complex-type glycans. The promising potential of the SiO2-ODex Con A material was demonstrated by selective fractionation of glycoproteins from complex biological samples for glycosylation analysis.

  8. Nutrient enrichment affects immature mosquito abundance and species composition in field-based mesocosms in the coastal plain of Georgia.

    PubMed

    Young, Gina Botello; Golladay, Stephen; Covich, Alan; Blackmore, Mark

    2014-02-01

    This study is the first to examine the relationship between nutrient enrichment and oviposition preference as measured by larval mosquito abundance using field-based mesocosms adjacent to wetlands in the Gulf Coastal Plain of Georgia. Agricultural wetlands in this region are known to have higher levels of nutrients and suspended sediments compared with forested wetlands, and previous studies have shown differences in mosquito communities in agricultural and forested wetlands. The purpose of this study was to determine whether nutrient enrichment contributes to the differences in mosquito oviposition preferences as reflected by larval mosquito presence and abundance in wetlands. We predicted that adding nutrients to mesocosms similar to concentrations in agricultural wetlands would favor responses of mosquito species often associated with nutrient-rich agricultural wetlands. Results indicated vegetation height, vegetation stem density, and phosphate levels were greater in fertilized mesocosms compared with nonfertilized mesocosms. The abundance of Aedes albopictus (Skuse) and Culex restuans Theobald was greater in mesocosms treated with fertilizer compared with nonfertilized mesocosms. Nutrient enrichment influenced oviposition and larval abundance of some mosquitoes of medical concern. This study provides evidence that can be used to predict the influence of nutrient enrichment on distribution and abundance of disease vectors and other nuisance mosquito species within an agricultural landscape.

  9. Replacements of Rare Herbs and Simplifications of Traditional Chinese Medicine Formulae Based on Attribute Similarities and Pathway Enrichment Analysis

    PubMed Central

    Fang, Zhao; Zhang, Meixia; Yi, Zhenghui; Wen, Chengping; Qian, Min; Shi, Tieliu

    2013-01-01

    A Traditional Chinese Medicine (TCM) formula is a collection of several herbs. TCM formulae have been used to treat various diseases for several thousand years. However, wide usage of TCM formulae has results in rapid decline of some rare herbs. So it is urgent to find common available replacements for those rare herbs with the similar effects. In addition, a formula can be simplified by reducing herbs with unchanged effects. Based on this consideration, we propose a method, called “formula pair,” to replace the rare herbs and simplify TCM formulae. We show its reasonableness from a perspective of pathway enrichment analysis. Both the replacements of rare herbs and simplifications of formulae provide new approaches for a new formula discovery. We demonstrate our approach by replacing a rare herb “Forsythia suspensa” in the formula “the seventh of Sang Ju Yin plus/minus herbs (SSJY)” with a common herb “Thunberg Fritillary Bulb” and simplifying two formulae, “the fifth of Du Huo Ji Sheng Tang plus/minus herbs (FDHJST)” and “Fang Feng Tang” (FFT) to a new formula “Fang Feng Du Huo Tang” (FFDHT). PMID:23533462

  10. Replacements of rare herbs and simplifications of traditional chinese medicine formulae based on attribute similarities and pathway enrichment analysis.

    PubMed

    Fang, Zhao; Zhang, Meixia; Yi, Zhenghui; Wen, Chengping; Qian, Min; Shi, Tieliu

    2013-01-01

    A Traditional Chinese Medicine (TCM) formula is a collection of several herbs. TCM formulae have been used to treat various diseases for several thousand years. However, wide usage of TCM formulae has results in rapid decline of some rare herbs. So it is urgent to find common available replacements for those rare herbs with the similar effects. In addition, a formula can be simplified by reducing herbs with unchanged effects. Based on this consideration, we propose a method, called "formula pair," to replace the rare herbs and simplify TCM formulae. We show its reasonableness from a perspective of pathway enrichment analysis. Both the replacements of rare herbs and simplifications of formulae provide new approaches for a new formula discovery. We demonstrate our approach by replacing a rare herb "Forsythia suspensa" in the formula "the seventh of Sang Ju Yin plus/minus herbs (SSJY)" with a common herb "Thunberg Fritillary Bulb" and simplifying two formulae, "the fifth of Du Huo Ji Sheng Tang plus/minus herbs (FDHJST)" and "Fang Feng Tang" (FFT) to a new formula "Fang Feng Du Huo Tang" (FFDHT).

  11. An enrichment, amplification, and sequence-based typing (EAST) approach for foodborne pathogen detection and surveillance

    USDA-ARS?s Scientific Manuscript database

    Introduction: Detection of foodborne pathogens typically involves microbiological enrichment with subsequent isolation and identification of a pure culture. This is typically followed by strain typing, which provides information critical to outbreak and source investigations. In the early 1990’s pul...

  12. twzPEA: A Topology and Working Zone Based Pathway Enrichment Analysis Framework

    USDA-ARS?s Scientific Manuscript database

    Sensitive detection of involvement and adaptation of key signaling, regulatory, and metabolic pathways holds the key to deciphering molecular mechanisms such as those in the biomass-to-biofuel conversion process in yeast. Typical gene set enrichment analyses often do not use topology information in...

  13. Nutrient enrichment reduces constraints on material flows in a detritus-based food web

    Treesearch

    Wyatt F. Cross; Bruce Wallace; Amy D. Rosemond

    2007-01-01

    Most aquatic and terrestrial ecosystems are experiencing increased nutrient availability, which is affecting their structure and function. By altering community composition and productivity of consumers, enrichment can indirectly cause changes in the pathways and magnitude of material flows in food webs. These changes, in turn, have major consequences for material...

  14. A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples.

    PubMed

    Johansen, Eric; Schilling, Birgit; Lerch, Michael; Niles, Richard K; Liu, Haichuan; Li, Bensheng; Allen, Simon; Hall, Steven C; Witkowska, H Ewa; Regnier, Fred E; Gibson, Bradford W; Fisher, Susan J; Drake, Penelope M

    2009-10-01

    Glycans are an important class of post-translational modifications. Typically found on secreted and extracellular molecules, glycan structures signal the internal status of the cell. Glycans on tumor cells tend to have abundant sialic acid and fucose moieties. We propose that these cancer-associated glycan variants be exploited for biomarker development aimed at diagnosing early-stage disease. Accordingly, we developed a mass spectrometry-based workflow that incorporates chromatography on affinity matrices formed from lectins, proteins that bind specific glycan structures. The lectins Sambucus nigra (SNA) and Aleuria aurantia (AAL), which bind sialic acid and fucose, respectively, were covalently coupled to POROS beads (Applied Biosystems) and packed into PEEK columns for high pressure liquid chromatography (HPLC). Briefly, plasma was depleted of the fourteen most abundant proteins using a multiple affinity removal system (MARS-14; Agilent). Depleted plasma was trypsin-digested and separated into flow-through and bound fractions by SNA or AAL HPLC. The fractions were treated with PNGaseF to remove N-linked glycans, and analyzed by LC-MS/MS on a QStar Elite. Data were analyzed using Mascot software. The experimental design included positive controls-fucosylated and sialylated human lactoferrin glycopeptides-and negative controls-high mannose glycopeptides from Saccharomyces cerevisiae-that were used to monitor the specificity of lectin capture. Key features of this workflow include the reproducibility derived from the HPLC format, the positive identification of the captured and PNGaseF-treated glycopeptides from their deamidated Asn-Xxx-Ser/Thr motifs, and quality assessment using glycoprotein standards. Protocol optimization also included determining the appropriate ratio of starting material to column capacity, identifying the most efficient capture and elution buffers, and monitoring the PNGaseF-treatment to ensure full deglycosylation. Future directions include

  15. Compton DIV: Using a Compton-Based Gamma-Ray Imager for Design Information Verification of Uranium Enrichment Plants

    SciTech Connect

    Burks, M; Verbeke, J; Dougan, A; Wang, T; Decman, D

    2009-07-04

    A feasibility study has been performed to determine the potential usefulness of Compton imaging as a tool for design information verification (DIV) of uranium enrichment plants. Compton imaging is a method of gamma-ray imaging capable of imaging with a 360-degree field of view over a broad range of energies. These systems can image a room (with a time span on the order of one hour) and return a picture of the distribution and composition of radioactive material in that room. The effectiveness of Compton imaging depends on the sensitivity and resolution of the instrument as well the strength and energy of the radioactive material to be imaged. This study combined measurements and simulations to examine the specific issue of UF{sub 6} gas flow in pipes, at various enrichment levels, as well as hold-up resulting from the accumulation of enriched material in those pipes. It was found that current generation imagers could image pipes carrying UF{sub 6} in less than one hour at moderate to high enrichment. Pipes with low enriched gas would require more time. It was also found that hold-up was more amenable to this technique and could be imaged in gram quantities in a fraction of an hour. another questions arises regarding the ability to separately image two pipes spaced closely together. This depends on the capabilities of the instrument in question. These results are described in detail. In addition, suggestions are given as to how to develop Compton imaging as a tool for DIV.

  16. Selection based on indirect genetic effects for growth, environmental enrichment and coping style affect the immune status of pigs.

    PubMed

    Reimert, Inonge; Rodenburg, T Bas; Ursinus, Winanda W; Kemp, Bas; Bolhuis, J Elizabeth

    2014-01-01

    Pigs living in intensive husbandry systems may experience both acute and chronic stress through standard management procedures and limitations in their physical and social environment, which may have implications for their immune status. Here, the effect of a new breeding method where pigs were selected on their heritable influence on their pen mates' growth, and environmental enrichment on the immune status of pigs was investigated. Hereto, 240 pigs with a relatively positive genetic effect on the growth of their pen mates (+SBV) and 240 pigs with a relatively negative genetic effect on the growth of their pen mates (-SBV) were housed in barren or straw-enriched pens from 4 to 23 weeks of age (n  =  80 pens in total). A blood sample was taken from the pigs before, three days after a 24 h regrouping test, and at week 22. In addition, effects of coping style, as assessed in a backtest, and gender were also investigated. Mainly, +SBV were found to have lower leukocyte, lymphocyte and haptoglobin concentrations than -SBV pigs. Enriched housed pigs had a lower neutrophil to lymphocyte (N:L) ratio and lower haptoglobin concentrations, but had higher antibody titers specific for Keyhole Limpet Hemocyanin (KLH) than barren housed pigs. No interactions were found between SBV class and housing. Furthermore, pigs with a proactive coping style had higher alternative complement activity and, in the enriched pens, higher antibody titers specific for KLH than pigs with a reactive coping style. Lastly, females tended to have lower leukocyte, but higher haptoglobin concentrations than castrated males. Overall, these results suggest that +SBV pigs and enriched housed pigs were less affected by stress than -SBV and barren housed pigs, respectively. Moreover, immune activation might be differently organized in individuals with different coping styles and to a lesser extent in individuals of opposite genders.

  17. MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes.

    PubMed

    Ma, Wei; Huang, Chuanbo; Zhou, Yuan; Li, Jianwei; Cui, Qinghua

    2017-01-10

    The microbiota colonized on human body is renowned as "a forgotten organ" due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes. In addition, MicroPattern implemented and integrated an algorithm we previously presented for the calculation of disease similarity based on disease-microbe association data. MicroPattern first grouped microbes into different sets based on the associated diseases and the colonized positions. Then, for a given list of microbes, MicroPattern performed enrichment analysis of the given microbes on all of the microbe sets. Moreover, using MicroPattern, we can also calculate disease similarity based on the shared microbe associations. Finally, we confirmed the accuracy and usefulness of MicroPattern by applying it to the changed microbes under the animal-based diet condition. MicroPattern is freely available at http://www.cuilab.cn/micropattern.

  18. MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes

    PubMed Central

    Ma, Wei; Huang, Chuanbo; Zhou, Yuan; Li, Jianwei; Cui, Qinghua

    2017-01-01

    The microbiota colonized on human body is renowned as “a forgotten organ” due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes. In addition, MicroPattern implemented and integrated an algorithm we previously presented for the calculation of disease similarity based on disease-microbe association data. MicroPattern first grouped microbes into different sets based on the associated diseases and the colonized positions. Then, for a given list of microbes, MicroPattern performed enrichment analysis of the given microbes on all of the microbe sets. Moreover, using MicroPattern, we can also calculate disease similarity based on the shared microbe associations. Finally, we confirmed the accuracy and usefulness of MicroPattern by applying it to the changed microbes under the animal-based diet condition. MicroPattern is freely available at http://www.cuilab.cn/micropattern. PMID:28071710

  19. Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes

    PubMed Central

    2014-01-01

    Background The use of whole-genome sequencing in microbiology at a diagnostic level, although feasible, is still limited by the expenses associated and by the complex bioinformatics pipelines in data analyses. We describe the use of target enrichment-based next-generation sequencing for pneumococcal identification and serotyping as applied to the polysaccharide 23 valent vaccine serotypes as an affordable alternative to whole genome sequencing. Results Correct identification of Streptococcus pneumoniae and prediction of common vaccine serotypes: 12 to serotype level and the rest to serogroup levels were achieved for all serotypes with >500 reads mapped against serotypes sequences. A proportion-based criterion also enabled the identification of two serotypes present in the same sample, thus indicating the possibility of using this method in detecting co-colonizing serotypes. The results obtained were comparable to or an improvement on the currently existing molecular serotyping methods for S. pneumoniae in relation to the polysaccharide vaccine serotypes. Conclusion We propose that this method has the potential to become an affordable and adaptable alternative to whole-genome sequencing for pneumococcal identification and serotyping. PMID:24612771

  20. Direct PCR - A rapid method for multiplexed detection of different serotypes of Salmonella in enriched pork meat samples.

    PubMed

    Chin, Wai Hoe; Sun, Yi; Høgberg, Jonas; Quyen, Than Linh; Engelsmann, Pia; Wolff, Anders; Bang, Dang Duong

    2017-04-01

    Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture method is time consuming. In response to the demand for rapid on line or at site detection of pathogens, in this study, we developed a multiplex Direct PCR method for rapid detection of different Salmonella serotypes directly from pork meat samples without any DNA purification steps. An inhibitor-resistant Phusion Pfu DNA polymerase was used to overcome PCR inhibition. Four pairs of primers including a pair of newly designed primers targeting Salmonella spp. at subtype level were incorporated in the multiplex Direct PCR. To maximize the efficiency of the Direct PCR, the ratio between sample and dilution buffer was optimized. The sensitivity and specificity of the multiplex Direct PCR were tested using naturally contaminated pork meat samples for detecting and subtyping of Salmonella spp. Conventional bacterial culture methods were used as reference to evaluate the performance of the multiplex Direct PCR. Relative accuracy, sensitivity and specificity of 98.8%; 97.6% and 100%, respectively, were achieved by the method. Application of the multiplex Direct PCR to detect Salmonella in pork meat at slaughter reduces the time of detection from 5 to 6 days by conventional bacterial culture and serotyping methods to 14 h (including 12 h enrichment time). Furthermore, the method poses a possibility of miniaturization and integration into a point-of-need Lab-on-a-chip system for rapid online pathogen detection. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Multilevel correlations in the biological phosphorus removal process: From bacterial enrichment to conductivity-based metabolic batch tests and polyphosphatase assays.

    PubMed

    Weissbrodt, David G; Maillard, Julien; Brovelli, Alessandro; Chabrelie, Alexandre; May, Jonathan; Holliger, Christof

    2014-12-01

    Enhanced biological phosphorus removal (EBPR) from wastewater relies on the preferential selection of active polyphosphate-accumulating organisms (PAO) in the underlying bacterial community continuum. Efficient management of the bacterial resource requires understanding of population dynamics as well as availability of bioanalytical methods for rapid and regular assessment of relative abundances of active PAOs and their glycogen-accumulating competitors (GAO). A systems approach was adopted here toward the investigation of multilevel correlations from the EBPR bioprocess to the bacterial community, metabolic, and enzymatic levels. Two anaerobic-aerobic sequencing-batch reactors were operated to enrich activated sludge in PAOs and GAOs affiliating with "Candidati Accumulibacter and Competibacter phosphates", respectively. Bacterial selection was optimized by dynamic control of the organic loading rate and the anaerobic contact time. The distinct core bacteriomes mainly comprised populations related to the classes Betaproteobacteria, Cytophagia, and Chloroflexi in the PAO enrichment and of Gammaproteobacteria, Alphaproteobacteria, Acidobacteria, and Sphingobacteria in the GAO enrichment. An anaerobic metabolic batch test based on electrical conductivity evolution and a polyphosphatase enzymatic assay were developed for rapid and low-cost assessment of the active PAO fraction and dephosphatation potential of activated sludge. Linear correlations were obtained between the PAO fraction, biomass specific rate of conductivity increase under anaerobic conditions, and polyphosphate-hydrolyzing activity of PAO/GAO mixtures. The correlations between PAO/GAO ratios, metabolic activities, and conductivity profiles were confirmed by simulations with a mathematical model developed in the aqueous geochemistry software PHREEQC. © 2014 Wiley Periodicals, Inc.

  2. Hydrogels Based on Ag+-Modulated-Assembly of 5'-Adenosine Monophosphate for Enriching Biomolecules.

    PubMed

    Hao, Jingcheng; Hu, Yuanyuan; Dong, Xie; Wu, Yang; Lin, Nangui; Song, Aixin

    2017-08-22

    The supramolecular hydrogels by combining 5'-adenosine monophosphate (AMP) with Ag+ were fabricated in this work. Their gelation capability was enhanced with the increase in the concentration of Ag+ or decrease in pH. The gels were found to be very sensitive to light which endows the hydrogels potential applications in visible photosensitive materials. The coordination between nucleobase of AMP and Ag+ and stacking of nucleobases are considered to be the main driving force for self-assembly. The hydrogels successfully achieved the encapsulation and enrichment of biomolecules. The hydrogen bonding between the amino group of guest molecules and silver-nanoparticles (Ag-NPs) along the nanofibers which drives the enrichment is considered the crucial interaction. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. The occurrence of salmonellas and lactose-negative Arizonas in reptiles in The Netherlands, and a comparison of three enrichment methods used in their isolation

    PubMed Central

    Koopman, J. P.; Janssen, F. G. J.

    1973-01-01

    A survey was conducted in 1971 in healthy reptiles supplied to the Central Animal Laboratory of Nijmegen for experimental animal research. In order to determine which salmonella serotypes occur, and whether there are several serotypes per animal, several strains of each positive sample were typed. It was found that 160 of 169 samples contained salmonellas or lactose-negative Arizonas or both, and 95 different serotypes were isolated. Of 127 animals examined individually, 67 were carriers of more than one serotype, 42 animals having two types, 21 three types and 4 animals four types. Three enrichment methods were compared. These were tetrathionate broth incubated at 37° C. (T37) and at 43° C. (T43), and selenite broth incubated at 37° C. (SB). All were incubated for 48 hr. before subculture on brilliant-green agar plates. The enrichment methods T37, T43 and SB produced 99, 125 and 123 positive samples respectively, when taken separately. The combinations of T37 and T43, T37 and SB, and T43 and SB produced 145, 142 and 150 positive samples respectively. The yield of serotypes in comparable samples showed no difference between the three enrichment methods. With the use of two methods the yield increased by about 38% compared with one method, and the combination of three methods showed an increase in serotype yield of about 64% compared with one method. A distinct preference by serotypes for definite enrichment methods was not proved. PMID:4578303

  4. A more accurate and penetrating method to measure the enrichment and mass of UF6 storage containers using passive neutron self-interrogation

    SciTech Connect

    Menlove, Howard O; Swinhoe, Martyn T; Miller, Karen A

    2010-01-01

    This paper describes an unattended mode neutron measurement that can provide the enrichment of the uranium in UF{sub 6} cylinders. The new passive neutron measurement provides better penetration into the uranium mass than prior gamma-ray enrichment measurement methods. The Passive Neutron Enrichment Monitor (PNEM) provides a new measurement technique that uses passive neutron totals and coincidence counting together with neutron self-interrogation to measure the enrichment in the cylinders. The measurement uses the neutron rates from two detector pods. One of the pods has a bare polyethylene surface next to the cylinder and the other polyethylene surface is covered with Cd to prevent thermal neutrons from returning to the cylinder. The primary neutron source from the enriched UF{sub 6} is the alpha-particle decay from the {sub 234}U that interacts with the fluorine to produce random neutrons. The singles neutron counting rate is dominated by the {sub 234}U neutrons with a minor contribution from the induced fissions in the {sub 235}U. However, the doubles counting rate comes primarily from the induced fissions (i.e., multiplication) in the {sub 235}U in enriched uranium. The PNEM concept makes use of the passive neutrons that are initially produced from the {sub 234}U reactions that track the {sub 235}U enrichment during the enrichment process. The induced fission reactions from the thermal-neutron albedo are all from the {sub 235}U and provide a measurement of the {sub 235}U. The Cd ratio has the desirable feature that all of the thermal-neutron-induced fissions in {sub 235}U are independent of the original neutron source. Thus, the ratio is independent of the uranium age, purity, and prior reactor history.

  5. Isotope Enrichment Detection by Laser Ablation - Laser Absorption Spectrometry: Automated Environmental Sampling and Laser-Based Analysis for HEU Detection

    SciTech Connect

    Anheier, Norman C.; Bushaw, Bruce A.

    2010-01-01

    The global expansion of nuclear power, and consequently the uranium enrichment industry, requires the development of new safeguards technology to mitigate proliferation risks. Current enrichment monitoring instruments exist that provide only yes/no detection of highly enriched uranium (HEU) production. More accurate accountancy measurements are typically restricted to gamma-ray and weight measurements taken in cylinder storage yards. Analysis of environmental and cylinder content samples have much higher effectiveness, but this approach requires onsite sampling, shipping, and time-consuming laboratory analysis and reporting. Given that large modern gaseous centrifuge enrichment plants (GCEPs) can quickly produce a significant quantity (SQ ) of HEU, these limitations in verification suggest the need for more timely detection of potential facility misuse. The Pacific Northwest National Laboratory (PNNL) is developing an unattended safeguards instrument concept, combining continuous aerosol particulate collection with uranium isotope assay, to provide timely analysis of enrichment levels within low enriched uranium facilities. This approach is based on laser vaporization of aerosol particulate samples, followed by wavelength tuned laser diode spectroscopy to characterize the uranium isotopic ratio through subtle differences in atomic absorption wavelengths. Environmental sampling (ES) media from an integrated aerosol collector is introduced into a small, reduced pressure chamber, where a focused pulsed laser vaporizes material from a 10 to 20-µm diameter spot of the surface of the sampling media. The plume of ejected material begins as high-temperature plasma that yields ions and atoms, as well as molecules and molecular ions. We concentrate on the plume of atomic vapor that remains after the plasma has expanded and then cooled by the surrounding cover gas. Tunable diode lasers are directed through this plume and each isotope is detected by monitoring absorbance

  6. Uncovering Arabidopsis Membrane Protein Interactome Enriched in Transporters Using Mating-Based Split Ubiquitin Assays and Classification Models

    PubMed Central

    Chen, Jin; Lalonde, Sylvie; Obrdlik, Petr; Noorani Vatani, Azam; Parsa, Saman A.; Vilarino, Cristina; Revuelta, Jose Luis; Frommer, Wolf B.; Rhee, Seung Y.

    2012-01-01

    High-throughput data are a double-edged sword; for the benefit of large amount of data, there is an associated cost of noise. To increase reliability and scalability of high-throughput protein interaction data generation, we tested the efficacy of classification to enrich potential protein–protein interactions. We applied this method to identify interactions among Arabidopsis membrane proteins enriched in transporters. We validated our method with multiple retests. Classification improved the quality of the ensuing interaction network and was effective in reducing the search space and increasing true positive rate. The final network of 541 interactions among 239 proteins (of which 179 are transporters) is the first protein interaction network enriched in membrane transporters reported for any organism. This network has similar topological attributes to other published protein interaction networks. It also extends and fills gaps in currently available biological networks in plants and allows building a number of hypotheses about processes and mechanisms involving signal-transduction and transport systems. PMID:22737156

  7. Pruned-enriched Rosenbluth method: Simulations of θ polymers of chain length up to 1 000 000

    NASA Astrophysics Data System (ADS)

    Grassberger, Peter

    1997-09-01

    We present an algorithm for simulating flexible chain polymers. It combines the Rosenbluth-Rosenbluth method with recursive enrichment. Although it can be applied also in more general situations, it is most efficient for three-dimensional θ polymers on the simple-cubic lattice. There it allows high statistics simulations of chains of length up to N=106. For storage reasons, this is feasable only for polymers in a finite volume. For free θ polymers in infinite volume, we present very high statistics runs with N=10 000. These simulations fully agree with previous simulations made by Hegger and Grassberger [J. Chem. Phys. 102, 6681 (1995)] with a similar but less efficient algorithm, showing that logarithmic corrections to mean field behavior are much stronger than predicted by field theory. But the finite volume simulations show that the density inside a collapsed globule scales with the distance from the θ point as predicted by mean field theory, in contrast to claims in the work mentioned above. In addition to the simple-cubic lattice, we also studied two versions of the bond fluctuation model, but with much shorter chains. Finally, we show that our method can be applied also to off-lattice models, and illustrate this with simulations of a model studied in detail by Freire et al. [Macromolecules 19, 452 (1986) and later work].

  8. Halogen-enriched fragment libraries as chemical probes for harnessing halogen bonding in fragment-based lead discovery.

    PubMed

    Zimmermann, Markus O; Lange, Andreas; Wilcken, Rainer; Cieslik, Markus B; Exner, Thomas E; Joerger, Andreas C; Koch, Pierre; Boeckler, Frank M

    2014-04-01

    Halogen bonding has recently experienced a renaissance, gaining increased recognition as a useful molecular interaction in the life sciences. Halogen bonds are favorable, fairly directional interactions between an electropositive region on the halogen (the σ-hole) and a number of different nucleophilic interaction partners. Some aspects of halogen bonding are not yet understood well enough to take full advantage of its potential in drug discovery. We describe and present the concept of halogen-enriched fragment libraries. These libraries consist of unique chemical probes, facilitating the identification of favorable halogen bonds by sharing the advantages of classical fragment-based screening. Besides providing insights into the nature and applicability of halogen bonding, halogen-enriched fragment libraries provide smart starting points for hit-to-lead evolution.

  9. Enrichment of low molecular weight serum proteins using acetonitrile precipitation for mass spectrometry based proteomic analysis.

    PubMed

    Kay, Richard; Barton, Chris; Ratcliffe, Lucy; Matharoo-Ball, Balwir; Brown, Pamela; Roberts, Jane; Teale, Phil; Creaser, Colin

    2008-10-01

    A rapid acetonitrile (ACN)-based extraction method has been developed that reproducibly depletes high abundance and high molecular weight proteins from serum prior to mass spectrometric analysis. A nanoflow liquid chromatography/tandem mass spectrometry (nano-LC/MS/MS) multiple reaction monitoring (MRM) method for 57 high to medium abundance serum proteins was used to characterise the ACN-depleted fraction after tryptic digestion. Of the 57 targeted proteins 29 were detected and albumin, the most abundant protein in serum and plasma, was identified as the 20th most abundant protein in the extract. The combination of ACN depletion and one-dimensional nano-LC/MS/MS enabled the detection of the low abundance serum protein, insulin-like growth factor-I (IGF-I), which has a serum concentration in the region of 100 ng/mL. One-dimensional sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the depleted serum showed no bands corresponding to proteins of molecular mass over 75 kDa after extraction, demonstrating the efficiency of the method for the depletion of high molecular weight proteins. Total protein analysis of the ACN extracts showed that approximately 99.6% of all protein is removed from the serum. The ACN-depletion strategy offers a viable alternative to the immunochemistry-based protein-depletion techniques commonly used for removing high abundance proteins from serum prior to MS-based proteomic analyses.

  10. Direct analysis of δ2H and δ18O in natural and enriched human urine using laser-based, Off-Axis Integrated Cavity Output Spectroscopy

    PubMed Central

    Berman, Elena S.F.; Fortsona, Susan L.; Snaith, Steven P.; Gupta, Manish; Baer, Douglas S.; Chery, Isabelle; Blanc, Stephane; Melanson, Edward L.; Thomson, Peter J; Speakman, John R.

    2012-01-01

    The stable isotopes of hydrogen (δ2H) and oxygen (δ18O) in human urine are measured during studies of total energy expenditure by the doubly labeled water method, measurement of total body water, and measurement of insulin resistance by glucose disposal among other applications. An ultrasensitive laser absorption spectrometer based on off-axis integrated cavity output spectroscopy was demonstrated for simple and inexpensive measurement of stable isotopes in natural isotopic abundance and isotopically enriched human urine. Preparation of urine for analysis was simple and rapid (approx. 25 samples per hour), requiring no decolorizing or distillation steps. Analysis schemes were demonstrated to address sample-to-sample memory while still allowing analysis of 45 natural or 30 enriched urine samples per day. The instrument was linear over a wide range of water isotopes (δ2H = −454 to +1702 ‰ and δ18O= −58.3 to +265 ‰). Measurements of human urine were precise to better than 0.65 ‰ 1σ for δ2H and 0.09 ‰ 1σ for δ18O for natural urines, 1.1 ‰ 1σ for δ2H and 0.13 ‰ 1σ for δ18O for low enriched urines, and 1.0 ‰ 1σ for δ2H and 0.08 ‰ 1σ for δ18O for high enriched urines. Furthermore, the accuracy of the isotope measurements of human urines was verified to better than ±0.81 ‰ in δ2H and ±0.13 ‰ in δ18O (average deviation) against three independent IRMS laboratories. The ability to immediately and inexpensively measure the stable isotopes of water in human urine is expected to increase the number and variety of experiments which can be undertaken. PMID:23075099

  11. Validation of a novel cognitive bias task based on difference in quantity of reinforcement for assessing environmental enrichment.

    PubMed

    Keen, Heidi A; Nelson, O Lynne; Robbins, Charles T; Evans, Marc; Shepherdson, David J; Newberry, Ruth C

    2014-05-01

    Cognitive bias tasks purport to assess affective states via responses to ambiguous stimuli. We hypothesized that a novel cognitive bias task based on positive reinforcement using quantity differences would detect changes in affect in captive grizzly bears (Ursus arctos horribilis). We trained bears (n = 8) to respond differently (nose or paw touch) to two stimuli (light or dark gray cue cards), with responses counterbalanced across bears. The two cues signaled a small or large food reward, respectively. Responses to ambiguous probe stimuli (i.e., shades of gray) intermediate to the trained stimuli were classified as either 'optimistic,' appropriate for the larger reward, or 'pessimistic,' appropriate for the smaller reward. In Experiment 1, we explored the contrast in reward size necessary to detect a change in response across probe stimuli (large reward, 3 or 6 apple slices: small reward, 1 slice). We observed a change in response across probe stimuli, with no difference in response between reward-value groups, indicating that a contrast of 3:1 apple slices was sufficient to affect responses. In Experiment 2, we investigated cognitive bias after 2.1 h of exposure to enrichment items varying in attractiveness. Results were unaffected by enrichment type or time spent interacting with enrichments, indicating that the task failed to demonstrate criterion validity for comparing mood following exposure to different enrichment items. However, greater time spent pacing prior to testing was associated with 'optimistic' judgments. The data provide some support for use of cognitive bias tasks based on quantity differences in animal welfare assessments involving captive wildlife.

  12. L-Lactate-selective microbial sensor based on flavocytochrome b2-enriched yeast cells using recombinant and nanotechnology approaches.

    PubMed

    Karkovska, Maria; Smutok, Oleh; Stasyuk, Nataliya; Gonchar, Mykhailo

    2015-11-01

    In the recent years, nanotechnology is the most developing branch due to a wide variety of potential applications in biomedical, biotechnological and agriculture fields. The binding nanoparticles with various biological molecules makes them attractive candidates for using in sensor technologies. The particularly actual is obtaining the bionanomembranes based on biocatalytic elements with improved sensing characteristics. The aim of this investigation is to study the properties of microbial L-lactate-selective sensor based on using the recombinant Hansenula polymorpha yeast cells overproducing flavocytochrome b2 (FC b2), as well as additionally enriched by the enzyme bound with gold nanoparticles (FC b2-nAu). Although, the high permeability of the living cells to nanoparticles is being intensively studied (mostly for delivery of drugs), the idea of using both recombinant technology and nanotechnology to increase the amount of the target enzyme in the biosensing layer is really novel. The FC b2-nAu-enriched living and permeabilized yeast cells were used for construction of a bioselective membrane of microbial L-lactate-selective amperometric biosensor. Phenazine methosulphate was served as a free defusing electron transfer mediator which provides effective electron transfer from the reduced enzyme to the electrode surface. It was shown that the output to L-lactate of FC b2-nAu-enriched permeabilized yeast cells is 2.5-fold higher when compared to the control cells. The obtained results confirm that additional enrichment of the recombinant yeast cell by the enzyme bound with nanoparticles improves the analytical parameters of microbial sensor.

  13. A liquid chromatography - mass spectrometry method to measure ¹³C-isotope enrichment for DNA stable-isotope probing.

    PubMed

    Auclair, Julie; Lépine, François; Villemur, Richard

    2012-03-01

    DNA stable-isotope probing (DNA-SIP) is a cultivation-independent technique that makes it possible to associate metabolic function and taxonomic identity in a wide range of terrestrial and aquatic environments. In DNA-SIP, DNA is labeled via the assimilation of a labeled growth substrate that is subsequently used to identify microorganisms involved in assimilation of the substrate. However, the labeling time has to be sufficient to obtain labeled DNA but not so long such that cross-feeding of ¹³C-labeled metabolites from the primary consumers to nontarget species can occur. Confirmation that the DNA is isotopically labeled in DNA-SIP assays can be achieved using an isotope ratio mass spectrometer. In this study, we describe the development of a method using liquid chromatography (HPLC) coupled to a quadrupole mass spectrometer (QMS) to measure the ¹³C enrichment of thymine incorporated into DNA in Escherichia coli cultures fed with [¹³C]acetate. The method involved the hydrolysis of DNA extracted from the cultures that released the nucleotides, followed by the separation of the thymine by HPLC on a reverse-phase C₈ column in isocratic elution mode and the detection and quantification of ¹³C-labeled thymine by QMS. To mimic a DNA-SIP assay, a DNA mixture was made using ¹³C-labeled E. coli DNA with DNA extracted from five bacterial species. The HPLC-MS method was able to measure the correct proportion of ¹³C-DNA in the mix. This method can then be used as an alternative to the use of isotope ratio mass spectrometry in DNA-SIP assays.

  14. Centrifuge enrichment plants. January 1970-October 1988 (Citations from the NTIS data base). Report for January 1970-October 1988

    SciTech Connect

    Not Available

    1988-11-01

    This bibliography contains citations concerning the design, control, monitoring, and safety of centrifuge enrichment plants. Power supplies, enrichment plant safeguards, facility design, cascade heater test loops to monitor the enrichment process, inspection strategies, and the socio-economic effects of centrifuge enrichment plants are examined. Radioactive waste disposal problems are briefly considered. (Contains 151 citations fully indexed and including a title list.)

  15. Universal method for online enrichment of target compounds in capillary gas chromatography using in-oven cryotrapping.

    PubMed

    Chin, Sung-Tong; Maikhunthod, Bussayarat; Marriott, Philip J

    2011-09-01

    A method is described that permits automated online enrichment of injected compounds in multidimensional gas chromatography by using a microfluidic heart-cut (H-C) device to direct target compounds into a cryogenically cooled internal trap (cryotrap, CT). By performing multiple injections of a sample, selected compounds or regions of a primary column separation can be collected in the CT. Remobilizing the trapped species allows elution and further resolution on the second column. Using a well-balanced H-C device, compounds can be fully excluded from the collection step or quantitatively transferred to the CT. Peak areas of the remobilized compound correlate well with the number of sample injections. Trapping on various column phases shows the method is suited to quantitative trapping of alkanes of mass greater than about dodecane and fatty acid methyl esters greater than the C8 homologue. Caffeine and menthol standards of concentration 100 μg mL(-1) gave peak area correlation coefficients for 1-10 and 1-50 replicate split injections of 1 μL volume of 0.999 and 0.996, respectively. Peak height correlations were less favorable as a result of peak broadening on the second column, presumably due to overloading at greater collected mass. The method was applied to 0.2% solutions of peppermint oil (menthol; a major component; 44%) and 1.0% lavender oil (α-terpineol and neryl acetate; minor components of 1.05 and 0.42% abundance). The minor components gave good area and height correlations, and good recovery around 90% was observed for menthol compounds recovered from 15 accumulations. Response amplification was further demonstrated for menthol from mint oil headspace sampling using solid phase microextraction. This approach should be a valuable adjunct for improved detection specificity, for detectors of low sensitivity, and when prior sample concentration provides insufficient response of selected target analytes.

  16. Rapid enrichment of leucocytes and genomic DNA from blood based on bifunctional core shell magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Xie, Xin; Nie, Xiaorong; Yu, Bingbin; Zhang, Xu

    2007-04-01

    A series of protocols are proposed to extract genomic DNA from whole blood at different scales using carboxyl-functionalized magnetic nanoparticles as solid-phase absorbents. The enrichment of leucocytes and the adsorption of genomic DNA can be achieved with the same carboxyl-functionalized magnetic nanoparticles. The DNA bound to the bead surfaces can be used directly as PCR templates. By coupling cell separation and DNA purification, the whole operation can be accomplished in a few minutes. Our simplified protocols proved to be rapid, low cost, and biologically and chemically non-hazardous, and are therefore promising for microfabrication of a DNA-preparation chip and routine laboratory use.

  17. Decay chains and photofission investigation based on nuclear spectroscopy of highly enriched uranium sample.

    PubMed

    Sibczynski, P; Kownacki, J; Syntfeld-Kazuch, A; Moszynski, M; Kisielinski, M; Czarnacki, W; Kosinski, K; Matusiak, M; Klimasz, M; Kowalczyk, M; Abraham, T; Mierzejewski, J; Srebrny, J

    2013-12-01

    Nuclear spectroscopy experiments were performed for 100g metallic uranium rod enriched to 93% (235)U, in order to establish and characterize the most prominent γ-rays in the natural decay series and photofission reaction. Single γ-ray spectra and γ-γ coincidences measurements were conducted before irradiation. The uranium sample was subsequently irradiated with 15 MeV bremsstrahlung photons. Relative intensities of γ-lines and several values of half-lives of the fission fragments decays were determined. The obtained information can be utilized in detection of smuggled nuclear materials and characterization of bulky nuclear waste packages. © 2013 Elsevier Ltd. All rights reserved.

  18. Enriching healthcare applications with cryptographic mechanisms and XML- based security services.

    PubMed

    Bourka, A; Kaliontzoglou, A; Polemi, D; Georgoulas, A; Sklavos, P

    2003-01-01

    The paper presents the enrichment of an existing e-referral / e-prescription application within a Regional Healthcare Information Network with security functionality, solving current authentication, integrity, non-repudiation and confidentiality issues and thus significantly enhancing the overall system security, operability, applicability and user acceptance. The application makes use of an underlying PKI framework, in order to provide strong authentication, digital signature, encryption and time-stamping services. XML is used for the representation of the healthcare data itself, the encrypted form of this data, as well as the relevant data security information, following W3C standards.

  19. Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications

    SciTech Connect

    Guo, Jia; Gaffrey, Matthew J.; Su, Dian; Liu, Tao; Camp, David G.; Smith, Richard D.; Qian, Weijun

    2013-12-12

    Reversible modifications on cysteine thiols play a significant role in redox signaling and regulation. A number of reversible redox modifications, including disulfide formation, S-nitrosylation, and S-glutathionylation, have been recognized for their significance in various physiological and pathological processes. Here we describe in detail a resin-assisted thiol-affinity enrichment protocol for both biochemical and proteomics applications. This protocol serves as a general approach for specific isolation of thiol-containing proteins or peptides derived from reversible redox-modified proteins. This approach utilizes thiol-affinity resins to directly capture thiol-containing proteins or peptides through a disulfide exchange reaction followed by on-resin protein digestion and on-resin multiplexed isobaric labeling to facilitate LC-MS/MS based quantitative site-specific analysis of redox modifications. The overall approach requires a much simpler workflow with increased specificity compared to the commonly used biotin switch technique. By coupling different selective reduction strategies, the resin-assisted approach provides the researcher with a useful tool capable of enriching different types of reversible modifications on protein thiols. Procedures for selective enrichment and analyses of S-nitrosylation and total reversible cysteine oxidation are presented to demonstrate the utility of this general strategy.

  20. Methods applied in the large littoral mesocosms study of nutrient enrichment in rocky shore ecosystems—EULIT

    NASA Astrophysics Data System (ADS)

    Bokn, T. L.; Hoell, E. E.; Kersting, K.; Moy, F. E.; Sørensen, K.

    2001-12-01

    Eight concrete land-based mesocosms have been set up for a study of the effect of nutrient enrichment on littoral hard bottom ecosystems. The construction of the mesocosms and the community establishment were initiated 2 yr ahead of the MAST-III project. The littoral communities were established by transplanting rocks with attached macroalgae and associated animals from the Oslofjord, followed by a period of natural community development which has resulted in a highly diverse flora and fauna. During this 2-yr pilot project, the efficiency of relevant techniques and statistical design for the EULIT experiments in the mesocosms have been tested, as well as the performance of the mesocosms ahead of the nutrient manipulation. The pilot project has thus extended the total experimental period. The mesocosms are fed with water from 1 m depth in the Oslofjord—residence time about 2 h—which also acts as a source for spores, zygotes and larvae. A tidal regime with a 36 cm amplitude is maintained and waves are regularly generated. Oxygen concentration, temperature and salinity are measured continuously by probes. Nutrient addition started in May 1998. Nutrient and carbon input and outflow are measured on an average weekly basis. Community analyses, species compositions, biomass, growth and grazing of the different components of the mesocosms are studied during 3-week periods (spring, summer and autumn) each year.

  1. Culture enrichment assists the diagnosis of cattle botulism by a monoclonal antibody based sandwich ELISA.

    PubMed

    Brooks, C E; Clarke, H J; Finlay, D A; McConnell, W; Graham, D A; Ball, H J

    2010-07-29

    Monoclonal antibodies (MAbs) obtained from a mouse immunised with Clostridium botulinum type D toxoid were developed into a sandwich ELISA (sELISA) format that was able to detect type D toxin and types C and D toxin complexes. The sELISA was examined for its potential to replace the mouse bioassay as an alternative in vitro assay for the diagnosis of cattle botulism. Its application directly to intestinal samples collected from suspect cattle botulism cases and prepared for testing for the standard mouse bioassay showed poor correlation and sensitivity with the mouse bioassay results. However, anaerobic pre-enrichment of the samples after heat treatment at 80 degrees C for 10 min to activate any residual C. botulinum spores greatly improved the sELISA detection rate of the toxin by increasing the sample toxin levels. All of the mouse bioassay positive cattle cases tested were detected by the sELISA from the heated and pre-enriched samples tested after 24h incubation. Toxin was detected by sELISA and subsequently confirmed by mouse bioassay in samples from an additional 3 cases that had been originally mouse bioassay negative. The results indicate that the application of this procedure for screening intestinal samples for C. botulinum strains that produce types C and D toxins from suspect cattle botulism cases would improve the diagnostic rate as well as significantly reduce the number of mice involved in diagnosis.

  2. Conversion and enrichment in the Soviet Union

    SciTech Connect

    1991-04-01

    In the Soviet Union, just as in the West, the civilian nuclear industry emerged from research work undertaken for nuclear weapons development. At first, researchers tried various techniques for physical separation of uranium isotopes: electromagnetic and molecular-kinetic thermo-diffusion methods; gaseous diffusion; and centrifuge methods. All of those methods, which are based primarily on differences in the atomic mass of uranium isotopes, called for extensive research and the development of new, technically unprecedented equipment. Gradually gaseous diffusion and gas centrifuge technology became recognized as most feasible for industrial use, so research on other methods was terminated. Industrial-scale uranium enrichment in the Soviet Union began in 1949 using the gaseous diffusion method; by the early 1960s, centrifuge technology was in use on an industrial scale. All Soviet production of highly-enriched, weapons-grade uranium was halted in 1987. The Soviet Union now has four enrichment plants in operation (at classified locations), solely for civilian nuclear power needs. All four enrichment plants have centrifuge modules, and enrichment provided by gaseous diffusion accounts for less than 5% of their total output. Two of the four enrichment plants also incorporate facilities for conversion to uranium hexafluoride (UF{sub 6}).

  3. Spectral gene set enrichment (SGSE).

    PubMed

    Frost, H Robert; Li, Zhigang; Moore, Jason H

    2015-03-03

    Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in the absence of a phenotype variable. Although methods exist for unsupervised gene set testing, they predominantly compute enrichment relative to clusters of the genomic variables with performance strongly dependent on the clustering algorithm and number of clusters. We propose a novel method, spectral gene set enrichment (SGSE), for unsupervised competitive testing of the association between gene sets and empirical data sources. SGSE first computes the statistical association between gene sets and principal components (PCs) using our principal component gene set enrichment (PCGSE) method. The overall statistical association between each gene set and the spectral structure of the data is then computed by combining the PC-level p-values using the weighted Z-method with weights set to the PC variance scaled by Tracy-Widom test p-values. Using simulated data, we show that the SGSE algorithm can accurately recover spectral features from noisy data. To illustrate the utility of our method on real data, we demonstrate the superior performance of the SGSE method relative to standard cluster-based techniques for testing the association between MSigDB gene sets and the variance structure of microarray gene expression data. Unsupervised gene set testing can provide important information about the biological signal held in high-dimensional genomic data sets. Because it uses the association between gene sets and samples PCs to generate a measure of unsupervised enrichment, the SGSE method is independent of cluster or network creation algorithms and, most importantly, is able to utilize the statistical significance of PC eigenvalues to ignore elements of the data most likely to represent noise.

  4. Application of an efficient strategy based on liquid-liquid extraction, high-speed counter-current chromatography, and preparative HPLC for the rapid enrichment, separation, and purification of four anthraquinones from Rheum tanguticum.

    PubMed

    Chen, Tao; Liu, Yongling; Zou, Denglang; Chen, Chen; You, Jinmao; Zhou, Guoying; Sun, Jing; Li, Yulin

    2014-01-01

    This study presents an efficient strategy based on liquid-liquid extraction, high-speed counter-current chromatography, and preparative HPLC for the rapid enrichment, separation, and purification of four anthraquinones from Rheum tanguticum. A new solvent system composed of petroleum ether/ethyl acetate/water (4:2:1, v/v/v) was developed for the liquid-liquid extraction of the crude extract from R. tanguticum. As a result, emodin, aloe-emodin, physcion, and chrysophanol were greatly enriched in the organic layer. In addition, an efficient method was successfully established to separate and purify the above anthraquinones by high-speed counter-current chromatography and preparative HPLC. This study supplies a new alternative method for the rapid enrichment, separation, and purification of emodin, aloe-emodin, physcione, and chrysophanol.

  5. Evaluation of PCR inhibitory effect of enrichment broths and comparison of DNA extraction methods for detection of Salmonella Enteritidis using real-time PCR assay.

    PubMed

    Hyeon, Ji Yeon; Hwang, In Gyun; Kwak, Hyo Sun; Park, Chankyu; Choi, In Soo; Seo, Kun Ho

    2010-06-01

    The best enrichment broth and DNA extraction scheme was determined for rapid and sensitive detection of Salmonella Enteritidis in steamed pork using real-time PCR. The inhibitory effect of commonly used Salmonella enrichment broths, Rappaport-Vassiliadis (RV) and Muller-Kauffmann tetrathionate with novobiocin (MKTTn), on real-time PCR was confirmed. The inhibition of PCR was statistically significant (p < 0.05) in RV and MKTTn, as compared with buffered peptone water (BPW) or phosphate-buffered saline. The inhibitory effect of the selective enrichment media was successfully removed by using a modified DNA extraction, PrepMan Ultra Reagent with an additional washing step or the DNeasy Tissue Kit. In three experiments, when applied to detection of Salmonella Enteritidis in steamed pork, the real-time PCR coupled with single 24 h enrichment with BPW performed better than double 48 h enrichment with BPW plus RV or MKTTn. The simple real-time PCR assay using BPW proved to be a rapid and sensitive test for detection of low concentrations of Salmonella Enteritidis in steamed pork samples as compared with the conventional culture method.

  6. Evaluation of PCR inhibitory effect of enrichment broths and comparison of DNA extraction methods for detection of Salmonella Enteritidis using real-time PCR assay

    PubMed Central

    Hyeon, Ji-Yeon; Hwang, In-Gyun; Kwak, Hyo-Sun; Park, Chankyu; Choi, In-Soo

    2010-01-01

    The best enrichment broth and DNA extraction scheme was determined for rapid and sensitive detection of Salmonella Enteritidis in steamed pork using real-time PCR. The inhibitory effect of commonly used Salmonella enrichment broths, Rappaport-Vassiliadis (RV) and Muller-Kauffmann tetrathionate with novobiocin (MKTTn), on real-time PCR was confirmed. The inhibition of PCR was statistically significant (p < 0.05) in RV and MKTTn, as compared with buffered peptone water (BPW) or phosphate-buffered saline. The inhibitory effect of the selective enrichment media was successfully removed by using a modified DNA extraction, PrepMan Ultra Reagent with an additional washing step or the DNeasy Tissue Kit. In three experiments, when applied to detection of Salmonella Enteritidis in steamed pork, the real-time PCR coupled with single 24 h enrichment with BPW performed better than double 48 h enrichment with BPW plus RV or MKTTn. The simple real-time PCR assay using BPW proved to be a rapid and sensitive test for detection of low concentrations of Salmonella Enteritidis in steamed pork samples as compared with the conventional culture method. PMID:20458155

  7. Method for fabricating .sup.99 Mo production targets using low enriched uranium, .sup.99 Mo production targets comprising low enriched uranium

    DOEpatents

    Wiencek, Thomas C.; Matos, James E.; Hofman, Gerard L.

    2000-12-12

    A radioisotope production target and a method for fabricating a radioisotope production target is provided, wherein the target comprises an inner cylinder, a foil of fissionable material circumferentially contacting the outer surface of the inner cylinder, and an outer hollow cylinder adapted to receive the substantially foil-covered inner cylinder and compress tightly against the foil to provide good mechanical contact therewith. The method for fabricating a primary target for the production of fission products comprises preparing a first substrate to receive a foil of fissionable material so as to allow for later removal of the foil from the first substrate, preparing a second substrate to receive the foil so as to allow for later removal of the foil from the second substrate; attaching the first substrate to the second substrate such that the foil is sandwiched between the first substrate and second substrate to prevent foil exposure to ambient atmosphere, and compressing the exposed surfaces of the first and second substrate to assure snug mechanical contact between the foil, the first substrate and the second substrate.

  8. Method for fabricating {sup 99}Mo production targets using low enriched uranium, {sup 99}Mo production targets comprising low enriched uranium

    DOEpatents

    Wiencek, T.C.; Matos, J.E.; Hofman, G.L.

    1997-03-25

    A radioisotope production target and a method for fabricating a radioisotope production target is provided, wherein the target comprises an inner cylinder, a foil of fissionable material circumferentially contacting the outer surface of the inner cylinder, and an outer hollow cylinder adapted to receive the substantially foil-covered inner cylinder and compress tightly against the foil to provide good mechanical contact therewith. The method for fabricating a primary target for the production of fission products comprises preparing a first substrate to receive a foil of fissionable material so as to allow for later removal of the foil from the first substrate, preparing a second substrate to receive the foil so as to allow for later removal of the foil from the second substrate; attaching the first substrate to the second substrate such that the foil is sandwiched between the first substrate and second substrate to prevent foil exposure to ambient atmosphere, and compressing the exposed surfaces of the first and second substrate to assure snug mechanical contact between the foil, the first substrate and the second substrate. 3 figs.

  9. Method for fabricating .sup.99 Mo production targets using low enriched uranium, .sup.99 Mo production targets comprising low enriched uranium

    DOEpatents

    Wiencek, Thomas C.; Matos, James E.; Hofman, Gerard L.

    1997-01-01

    A radioisotope production target and a method for fabricating a radioisotope production target is provided, wherein the target comprises an inner cylinder, a foil of fissionable material circumferentially contacting the outer surface of the inner cylinder, and an outer hollow cylinder adapted to receive the substantially foil-covered inner cylinder and compress tightly against the foil to provide good mechanical contact therewith. The method for fabricating a primary target for the production of fission products comprises preparing a first substrate to receive a foil of fissionable material so as to allow for later removal of the foil from the first substrate, preparing a second substrate to receive the foil so as to allow for later removal of the foil from the second substrate; attaching the first substrate to the second substrate such that the foil is sandwiched between the first substrate and second substrate to prevent foil exposure to ambient atmosphere, and compressing the exposed surfaces of the first and second substrate to assure snug mechanical contact between the foil, the first substrate and the second substrate.

  10. Simple procedures for enrichment of chlorinated aromatic pollutants from fat, water and milk for subsequent analysis by high-resolution methods

    SciTech Connect

    Egestad, B.; Curstedt, T.; Sjoevall, J.

    1982-01-01

    Procedures for enrichment of non-volatile chlorinated aromatic pollutants from fat, water and milk are described. /sup 14/C-DDT was used as a model compound in recovery experiments. A several thousand-fold enrichment of DDT added to butter was achieved by two consecutive straight-phase chromatographies on Lipidex 5000. Trace amounts of DDT in liter volumes of water could be quantitatively extracted by rapid filtration through 2 ml beds of Lipidex 1000. A batch extraction procedure permitted enrichment of DDT from milk after addition of n-pentylamine, methanol and water. DDT could then be eluted from the gel with retention of more than 90% of the lipids. A reversed-phase system with Lipidex 5000 could be used for separation of TCDD from DDT and PCBs. The liquid-gel chromatographic procedures are simple and suitable for clean-up of samples prior to application of high-resolution methods. 5 tables.

  11. Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach

    PubMed Central

    Razi, Abolfazl; Afghah, Fatemeh; Singh, Salendra; Varadan, Vinay

    2016-01-01

    Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear. Recently, integrative data-driven models have been developed to integrate multiomics data with signaling pathway networks in order to identify pathways associated with clinical or biological phenotypes. However, these approaches suffer from an important drawback of being restricted to previously discovered pathway structures and miss novel genomic interactions as well as potential crosstalk among the pathways. In this article, we propose a novel coalition-based game-theoretic approach to overcome the challenge of identifying biologically relevant gene subnetworks associated with disease phenotypes. The algorithm starts from a set of seed genes and traverses a protein–protein interaction network to identify modulated subnetworks. The optimal set of modulated subnetworks is identified using Shapley value that accounts for both individual and collective utility of the subnetwork of genes. The algorithm is applied to two illustrative applications, including the identification of subnetworks associated with (i) disease progression risk in response to platinum-based therapy in ovarian cancer and (ii) immune infiltration in triple-negative breast cancer. The results demonstrate an improved predictive power of the proposed method when compared with state-of-the-art feature selection methods, with the added advantage of identifying novel potentially functional gene subnetworks

  12. Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach.

    PubMed

    Razi, Abolfazl; Afghah, Fatemeh; Singh, Salendra; Varadan, Vinay

    2016-01-01

    Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear. Recently, integrative data-driven models have been developed to integrate multiomics data with signaling pathway networks in order to identify pathways associated with clinical or biological phenotypes. However, these approaches suffer from an important drawback of being restricted to previously discovered pathway structures and miss novel genomic interactions as well as potential crosstalk among the pathways. In this article, we propose a novel coalition-based game-theoretic approach to overcome the challenge of identifying biologically relevant gene subnetworks associated with disease phenotypes. The algorithm starts from a set of seed genes and traverses a protein-protein interaction network to identify modulated subnetworks. The optimal set of modulated subnetworks is identified using Shapley value that accounts for both individual and collective utility of the subnetwork of genes. The algorithm is applied to two illustrative applications, including the identification of subnetworks associated with (i) disease progression risk in response to platinum-based therapy in ovarian cancer and (ii) immune infiltration in triple-negative breast cancer. The results demonstrate an improved predictive power of the proposed method when compared with state-of-the-art feature selection methods, with the added advantage of identifying novel potentially functional gene subnetworks

  13. Effects of citrate-enriched bicarbonate based dialysate on anticoagulation and dialyzer reuse in maintenance hemodialysis patients.

    PubMed

    Rocha, Amanda D; Padua, Vanessa C; Oliveira, Esther; Guimaraes, Márcia M; Lugon, Jocemir R; Strogoff de Matos, Jorge P

    2014-04-01

    Systemic anticoagulation with unfractionated heparin is commonly used in maintenance hemodialysis (HD), but it increases the risk of bleeding complications. We investigated whether the use of citrate-enriched bicarbonate based dialysate (CD) would reduce systemic anticoagulation without compromising the efficacy of reprocessed dialyzers. This is a crossover study in which half of a total of 30 patients initially underwent HD with acetate-enriched bicarbonate based dialysate and a standard heparin dose of ∼ 100 IU/kg (Treatment A), whereas the remaining patients were treated with CD and a 30% reduced heparin dose (Treatment B). After 12 consecutive HD sessions in each treatment, the dialysate and heparin doses were reversed, then followed for another period of 12 HD sessions. The two treatment phases were split by a washout period of six HD sessions using acetate-enriched bicarbonate based dialysate and standard heparin dose. Systemic anticoagulation was higher in Treatment A. The activated partial thromboplastin time at the end of HD session was 68 ± 36 seconds in Treatment A and 47 ± 16 seconds in Treatment B (P = 0.005). Sixty-eight percent of the dialyzers remained adequate until the 12th use in Treatment A and 61% did so in Treatment B (P = 0.63). Patients had three and 24 cramps episodes during Treatment A and B, respectively (P < 0.001). Nine and 26 symptomatic intradialytic hypotension episodes were seen in Treatment A and B, respectively, (P = 0.003). In conclusion, the use of CD had a favorable effect on anticoagulation in the extracorporeal circuit in patients on maintenance HD, but it was also associated with more hypotension and cramps.

  14. Application of Condition-Based Monitoring Techniques for Remote Monitoring of a Simulated Gas Centrifuge Enrichment Plant

    SciTech Connect

    Hooper, David A; Henkel, James J; Whitaker, Michael

    2012-01-01

    This paper presents research into the adaptation of monitoring techniques from maintainability and reliability (M&R) engineering for remote unattended monitoring of gas centrifuge enrichment plants (GCEPs) for international safeguards. Two categories of techniques are discussed: the sequential probability ratio test (SPRT) for diagnostic monitoring, and sequential Monte Carlo (SMC or, more commonly, particle filtering ) for prognostic monitoring. Development and testing of the application of condition-based monitoring (CBM) techniques was performed on the Oak Ridge Mock Feed and Withdrawal (F&W) facility as a proof of principle. CBM techniques have been extensively developed for M&R assessment of physical processes, such as manufacturing and power plants. These techniques are normally used to locate and diagnose the effects of mechanical degradation of equipment to aid in planning of maintenance and repair cycles. In a safeguards environment, however, the goal is not to identify mechanical deterioration, but to detect and diagnose (and potentially predict) attempts to circumvent normal, declared facility operations, such as through protracted diversion of enriched material. The CBM techniques are first explained from the traditional perspective of maintenance and reliability engineering. The adaptation of CBM techniques to inspector monitoring is then discussed, focusing on the unique challenges of decision-based effects rather than equipment degradation effects. These techniques are then applied to the Oak Ridge Mock F&W facility a water-based physical simulation of a material feed and withdrawal process used at enrichment plants that is used to develop and test online monitoring techniques for fully information-driven safeguards of GCEPs. Advantages and limitations of the CBM approach to online monitoring are discussed, as well as the potential challenges of adapting CBM concepts to safeguards applications.

  15. Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications.

    PubMed

    Guo, Jia; Gaffrey, Matthew J; Su, Dian; Liu, Tao; Camp, David G; Smith, Richard D; Qian, Wei-Jun

    2014-01-01

    Reversible modifications of cysteine thiols have a key role in redox signaling and regulation. A number of reversible redox modifications, including disulfide formation, S-nitrosylation (SNO) and S-glutathionylation (SSG), have been recognized for their significance in various physiological and pathological processes. Here we describe a procedure for the enrichment of peptides containing reversible cysteine modifications. Starting with tissue or cell lysate samples, all of the unmodified free thiols are blocked using N-ethylmaleimide (NEM). This is followed by the selective reduction of those cysteines bearing the reversible modification(s) of interest. The reduction is achieved by using different reducing reagents that react specifically with each type of cysteine modification (e.g., ascorbate for SNO). This protocol serves as a general approach for enrichment of thiol-containing proteins or peptides derived from reversibly modified proteins. The approach uses a commercially available thiol-affinity resin (thiopropyl Sepharose 6B) to directly capture free thiol-containing proteins through a disulfide exchange reaction, followed by on-resin protein digestion and multiplexed isobaric labeling to facilitate liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based quantitative site-specific analysis of cysteine-based reversible modifications. The overall approach requires a simpler workflow with increased specificity compared with the commonly used biotinylation-based assays. The procedure for selective enrichment and analyses of SNO and the level of total reversible cysteine modifications (or total oxidation) is presented to demonstrate the utility of this general strategy. The entire protocol requires ∼3 d for sample processing with an additional day for LC-MS/MS and data analysis.

  16. Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications

    PubMed Central

    Guo, Jia; Gaffrey, Matthew J.; Su, Dian; Liu, Tao; Camp, David G.; Smith, Richard D.; Qian, Wei-Jun

    2014-01-01

    Reversible modifications of cysteine thiols play a significant role in redox signaling and regulation. A number of reversible redox modifications, including disulfide formation, S-nitrosylation, and S-glutathionylation, have been recognized for their significance in various physiological and pathological processes. Here we describe a procedure for the enrichment of peptides containing reversible cysteine modifications. Starting with tissue or cell lysate samples, all of the unmodified free thiols are blocked using N-ethylmaleimide (NEM). This is followed by the selective reduction of those cysteines bearing the reversible modification(s) of interest. The reduction is achieved by using different reducing reagents that react specifically with each type of cysteine modification (e.g., ascorbate for S-nitrosylation). This protocol serves as a general approach for enrichment of thiol-containing proteins or peptides derived from reversibly modified proteins. The approach utilizes a commercially available thiol-affinity resin (Thiopropyl Sepharose 6B) to directly capture free thiol-containing proteins through a disulfide exchange reaction followed by on-resin protein digestion and multiplexed isobaric labeling to facilitate LC–MS/MS based quantitative site-specific analysis of cysteine-based reversible modifications. The overall approach requires a simpler workflow with increased specificity compared to the commonly used biotinylation-based assays. The procedure for selective enrichment and analyses of S-nitrosylation and the level of total reversible cysteine modifications (or total oxidation) is presented to demonstrate the utility of this general strategy. The entire protocol requires approximately 3 days for sample processing with an additional day for LC-MS/MS and data analysis. PMID:24336471

  17. Enrichment of human osteosarcoma stem cells based on hTERT transcriptional activity

    PubMed Central

    Yu, Ling; Liu, Shiqing; Zhang, Chun; Zhang, Bo; Simões, Bruno M.; Eyre, Rachel; Liang, Yi; Yan, Huichao; Wu, Zheng; Guo, Weichun; Clarke, Robert B.

    2013-01-01

    Telomerase is crucial for the maintenance of stem/progenitor cells in adult tissues and is detected in most malignant cancers, including osteosarcoma. However, the relationship between telomerase expression and cancer stem cells remains unknown. We observed that sphere-derived osteosarcoma cells had higher telomerase activity, indicating that telomerase activity might be enriched in osteosarcoma stem cells. We sorted subpopulations with high or low telomerase activity (TEL) using hTERT transcriptional promoter-induced green fluorescent protein (GFP). The TELpos cells showed an increased sphere and tumor propagating capacity compared to TELneg cells, and enhanced stem cell-like properties such as invasiveness, metastatic activity and resistance to chemotherapeutic agents both in vitro and in vivo. Furthermore, the telomerase inhibitor MST312 prevented tumorigenic potential both in vitro and in vivo, preferentially targeting the TELpos cells. These data support telomerase inhibition as a potential targeted therapy for osteosarcoma stem-like cells. PMID:24334332

  18. Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation.

    PubMed

    Junker, Astrid; Rohn, Hendrik; Czauderna, Tobias; Klukas, Christian; Hartmann, Anja; Schreiber, Falk

    2012-03-01

    The Systems Biology Graphical Notation (SBGN) is an emerging standard for the uniform representation of biological processes and networks. By using examples from gene regulation and metabolism, this protocol shows the construction of SBGN maps by either manual drawing or automatic translation using the tool SBGN-ED. In addition, it discusses the enrichment of SBGN maps with different kinds of -omics data to bring numerical data into the context of these networks in order to facilitate the interpretation of experimental data. Finally, the export of such maps to public websites, including clickable images, supports the communication of results within the scientific community. With regard to the described functionalities, other tools partially overlap with SBGN-ED. However, currently, SBGN-ED is the only tool that combines all of these functions, including the representation in SBGN, data mapping and website export. This protocol aims to assist scientists with the step-by-step procedure, which altogether takes ∼90 min.

  19. Impact of oxygen limitation on glycerol-based biopolymer production by bacterial enrichments.

    PubMed

    Moralejo-Gárate, Helena; Kleerebezem, Robbert; Mosquera-Corral, Anuska; van Loosdrecht, Mark C M

    2013-03-01

    The increasing production of bioethanol and biodiesel has resulted in the generation of a massive amount of crude glycerol, inducing the need for effective valorization of these waste streams. One of the valorization options could be through conversion of crude glycerol into a biopolymer using microbial community engineering in a feast-famine process. A complicating factor in the production of biopolymers from glycerol encountered in previous works is that two different types of polymers can be formed; polyhydroxyalkanoate (PHA) and polyglucose. Here we describe the effect of limiting the oxygen supply rate on the polymer distribution with the aim of defining the conditions that favour the conversion of glycerol in one single polymer. The decrease of oxygen supply rate during the biopolymer maximization step did not influence glycerol partitioning among PHA and polyglucose, but oxygen limitation during the community enrichment step favoured polyglucose storage over PHA. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Enrichment for murine keratinocyte stem cells based on cell surface phenotype

    PubMed Central

    Tani, Hiroaki; Morris, Rebecca J.; Kaur, Pritinder

    2000-01-01

    The identification and physical isolation of epithelial stem cells is critical to our understanding of their growth regulation during homeostasis, wound healing, and carcinogenesis. These stem cells remain poorly characterized because of the absence of specific molecular markers that permit us to distinguish them from their progeny, the transit amplifying (TA) cells, which have a more restricted proliferative potential. Cell kinetic analyses have permitted the identification of murine keratinocyte stem cells (KSCs) as slowly cycling cells that retain [3H]thymidine ([3H]Tdr) label, termed label-retaining cells (LRCs), whereas TA cells are visualized as rapidly cycling cells after a single pulse of [3H]Tdr, termed pulse-labeled cells (PLCs). Here, we report on the successful separation of KSCs from TA cells through the combined use of in vivo cell kinetic analysis and fluorescence-activated cell sorting. Specifically, we demonstrate that murine dorsal keratinocytes characterized by their high levels of α6 integrin and low to undetectable expression of the transferrin receptor (CD71) termed α6briCD71dim cells, are enriched for epithelial stem cells because they represent a minor (≈8%) and quiescent subpopulation of small blast-like cells, with a high nuclear:cytoplasmic ratio, containing ≈70% of label-retaining cells, the latter being a well documented characteristic of stem cells. Conversely, TA cells could be enriched in a phenotypically distinct subpopulation termed α6briCD71bri, representing the majority (≈60%) of basal keratinocytes that are actively cycling, and importantly contain ≈70% of [3H]Tdr pulse-labeled cells. Importantly, immunostaining of dorsal skin revealed the presence of CD71dim cells in the hair follicle bulge region, a well documented location for KSCs. PMID:11005869

  1. Enriching a cellulose hydrogel with a biologically active marine exopolysaccharide for cell-based cartilage engineering.

    PubMed

    Rederstorff, E; Rethore, G; Weiss, P; Sourice, S; Beck-Cormier, S; Mathieu, E; Maillasson, M; Jacques, Y; Colliec-Jouault, S; Fellah, B H; Guicheux, J; Vinatier, C

    2017-04-01

    The development of biologically and mechanically competent hydrogels is a prerequisite in cartilage engineering. We recently demonstrated that a marine exopolysaccharide, GY785, stimulates the in vitro chondrogenesis of adipose stromal cells. In the present study, we thus hypothesized that enriching our silated hydroxypropyl methylcellulose hydrogel (Si-HPMC) with GY785 might offer new prospects in the development of scaffolds for cartilage regeneration. The interaction properties of GY785 with growth factors was tested by surface plasmon resonance (SPR). The biocompatibility of Si-HPMC/GY785 towards rabbit articular chondrocytes (RACs) and its ability to maintain and recover a chondrocytic phenotype were then evaluated in vitro by MTS assay, cell counting and qRT-PCR. Finally, we evaluated the potential of Si-HPMC/GY785 associated with RACs to form cartilaginous tissue in vivo by transplantation into the subcutis of nude mice for 3 weeks. Our SPR data indicated that GY785 was able to physically interact with BMP-2 and TGFβ. Our analyses also showed that three-dimensionally (3D)-cultured RACs into Si-HPMC/GY785 strongly expressed type II collagen (COL2) and aggrecan transcripts when compared to Si-HPMC alone. In addition, RACs also produced large amounts of extracellular matrix (ECM) containing glycosaminoglycans (GAG) and COL2. When dedifferentiated RACs were replaced in 3D in Si-HPMC/GY785, the expressions of COL2 and aggrecan transcripts were recovered and that of type I collagen decreased. Immunohistological analyses of Si-HPMC/GY785 constructs transplanted into nude mice revealed the production of a cartilage-like extracellular matrix (ECM) containing high amounts of GAG and COL2. These results indicate that GY785-enriched Si-HPMC appears to be a promising hydrogel for cartilage tissue engineering. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  2. New method for GC/FID and GC-C-IRMS analysis of plasma free fatty acid concentration and isotopic enrichment.

    PubMed

    Kangani, Cyrous O; Kelley, David E; Delany, James P

    2008-09-15

    A simple, direct and accurate method for the determination of concentration and enrichment of free fatty acids (FFAs) in human plasma was developed. The validation and comparison to a conventional method are reported. Three amide derivatives, dimethyl, diethyl and pyrrolidide, were investigated in order to achieve optimal resolution of the individual fatty acids. This method involves the use of dimethylamine/Deoxo-Fluor to derivatize plasma free fatty acids to their dimethylamides. This derivatization method is very mild and efficient, and is selective only towards FFAs so that no separation from a total lipid extract is required. The direct method gave lower concentrations for palmitic acid and stearic acid and increased concentrations for oleic acid and linoleic acid in plasma as compared to methyl ester derivative after thin-layer chromatography. The [(13)C]palmitate isotope enrichment measured using direct method was significantly higher than that observed with the BF(3)/MeOH-TLC method. The present method provided accurate and precise measures of concentration as well as enrichment when analyzed with gas chromatography combustion-isotope ratio-mass spectrometry.

  3. New method for GC/FID and GC-C-IRMS Analysis of plasma free fatty acid concentration and isotopic enrichment

    PubMed Central

    Kangani, Cyrous O.; Kelley, David E.; DeLany, James P.

    2008-01-01

    A simple, direct and accurate method for the determination of concentration and enrichment of free fatty acids in human plasma was developed. The validation and comparison to a conventional method are reported. Three amide derivatives, dimethyl, diethyl and pyrrolidide, were investigated in order to achieve optimal resolution of the individual fatty acids. This method involves the use of dimethylamine/Deoxo-Fluor to derivatize plasma free fatty acids to their dimethylamides. This derivatization method is very mild and efficient, and is selective only towards free fatty acids so that no separation from a total lipid extract is required. The direct method gave lower concentrations for palmitic acid and stearic acid and increased concentrations for oleic acid and linoleic acid in plasma as compared to methylester derivative after thin-layer chromatography. The [13C]palmitate isotope enrichment measured using direct method was significantly higher than that observed with the BF3/MeOH-TLC method. The present method provided accurate and precise measures of concentration as well as enrichment when analyzed with gas chromatography combustion-isotope ratio-mass spectrometry. PMID:18757250

  4. Project ENRICH.

    ERIC Educational Resources Information Center

    Gwaley, Elizabeth; And Others

    Project ENRICH was conceived in Beaver County, Pennsylvania, to: (1) identify preschool children with learning disabilities, and (2) to develop a program geared to the remediation of the learning disabilities within a school year, while allowing the child to be enrolled in a regular class situation for the following school year. Through…

  5. Job Enrichment

    ERIC Educational Resources Information Center

    Sanders, Rick

    1970-01-01

    Job enrichment means giving people more decision-making power, more responsibility, more grasp of the totality of the job, and a sense of their own importance in the company. This article presents evidence of the successful working of this approach (Donnelly Mirrors), and the lack of success with an opposing approach (General Motors). (NL)

  6. Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens.

    PubMed

    Margot, Heike; Stephan, Roger; Tasara, Taurai

    2016-09-06

    Fresh sprouted seeds have been associated with a number of large outbreaks caused by Salmonella and Shiga toxin-producing E. coli. However, the high number of commensal bacteria found on sprouted seeds hampers the detection of these pathogens. Knowledge about the composition of the sprout microbiome is limited. In this study, the microbiome of mungo bean sprouts and the impact of buffered peptone water (BPW) and Enterobacteriaceae enrichment broth (EE-broth)-based enrichment protocols on this microbiome were investigated. Assessments based on aerobic mesophilic colony counts showed similar increases in mungo bean sprout background flora levels independent of the enrichment protocol used. 16S rRNA sequencing revealed a mungo bean sprout microbiome dominated by Proteobacteria and Bacteroidetes. EE-broth enrichment of such samples preserved and increased Proteobacteria dominance while reducing Bacteroidetes and Firmicutes relative abundances. BPW enrichment, however, increased Firmicutes relative abundance while decreasing Proteobacteria and Bacteroidetes levels. Both enrichments also lead to various genus level changes within the Protobacteria and Firmicutes phyla. New insights into the microbiome associated with mungo bean sprout and how it is influenced through BPW and EE-broth-based enrichment strategies used for detecting Gram-negative pathogens were generated. BPW enrichment leads to Firmicutes and Proteobacteria dominance, whereas EE-broth enrichment preserves Proteobacteria dominance in the mungo bean sprout samples. By increasing the relative abundance of Firmicutes, BPW also increases the abundance of Gram-positive organisms including some that might inhibit recovery of Gram-negative pathogens. The use of EE-broth, although preserving and increasing the dominance of Proteobacteria, can also hamper the detection of lowly abundant Gram-negative target pathogens due to outgrowth of such organisms by the highly abundant non-target Proteobacteria genera

  7. Development of a method to measure preβHDL and αHDL apoA-I enrichment for stable isotopic studies of HDL kinetics.

    PubMed

    Li, Xuefei; Stolinski, Michael; Umpleby, A Margot

    2012-10-01

    Our understanding of HDL metabolism would be enhanced by the measurement of the kinetics of preβHDL, the nascent form of HDL, since elevated levels have been reported in patients with coronary artery disease. Stable isotope methodology is an established technique that has enabled the determination of the kinetics (production and catabolism) of total HDL apoA-I in vivo. The development of separation procedures to obtain a preβHDL fraction, the isotopic enrichment of which could then be measured, would enable further understanding of the pathways in vivo for determining the fate of preβHDL and the formation of αHDL. A method was developed and optimised to separate and measure preβHDL and αHDL apoA-I enrichment. Agarose gel electrophoresis was first used to separate lipoprotein subclasses, and then a 4-10 % discontinuous SDS-PAGE used to isolate apoA-I. Measures of preβHDL enrichment in six healthy subjects were undertaken following an infusion of L-[1-¹³C-leucine]. After isolation of preβ and αHDL, the isotopic enrichment of apoA-I for each fraction was measured by gas chromatography-mass spectrometry. PreβHDL apoA-I enrichment was measured with a CV of 0.51 % and αHDL apoA-I with a CV of 0.34 %. The fractional catabolic rate (FCR) of preβHDL apoA-I was significantly higher than the FCR of αHDL apoA-I (p < 0.005). This methodology can be used to selectively isolate preβ and αHDL apoA-I for the measurement of apoA-I isotopic enrichment for kinetics studies of HDL subclass metabolism in a research setting.

  8. In Vitro Amphotericin B Susceptibility of Malassezia pachydermatis Determined by the CLSI Broth Microdilution Method and Etest Using Lipid-Enriched Media

    PubMed Central

    Álvarez-Pérez, Sergio; Peláez, Teresa; Cutuli, Maite; García, Marta E.

    2014-01-01

    We determined the in vitro amphotericin B susceptibility of 60 Malassezia pachydermatis isolates by the CLSI broth microdilution method and the Etest using lipid-enriched media. All isolates were susceptible at MICs of ≤1 μg/ml, confirming the high activity of amphotericin B against this yeast species. Overall, the essential agreement between the tested methods was high (80% and 96.7% after 48 h and 72 h, respectively), and all discrepancies were regarded as nonsubstantial. PMID:24752258

  9. Edge-enriched, porous carbon-based, high energy density supercapacitors for hybrid electric vehicles.

    PubMed

    Kim, Yong Jung; Yang, Cheol-Min; Park, Ki Chul; Kaneko, Katsumi; Kim, Yoong Ahm; Noguchi, Minoru; Fujino, Takeshi; Oyama, Shigeki; Endo, Morinobu

    2012-03-12

    Supercapacitors can store and deliver energy by a simple charge separation, and thus they could be an attractive option to meet transient high energy density in operating fuel cells and in electric and hybrid electric vehicles. To achieve such requirements, intensive studies have been carried out to improve the volumetric capacitance in supercapacitors using various types and forms of carbons including carbon nanotubes and graphenes. However, conventional porous carbons are not suitable for use as electrode material in supercapacitors for such high energy density applications. Here, we show that edge-enriched porous carbons are the best electrode material for high energy density supercapacitors to be used in vehicles as an auxiliary powertrain. Molten potassium hydroxide penetrates well-aligned graphene layers vertically and consequently generates both suitable pores that are easily accessible to the electrolyte and a large fraction of electrochemically active edge sites. We expect that our findings will motivate further research related to energy storage devices and also environmentally friendly electric vehicles. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Thermal reversibility of vitamin E-enriched emulsion-based delivery systems produced using spontaneous emulsification.

    PubMed

    Saberi, Amir Hossein; Fang, Yuan; McClements, David Julian

    2015-10-15

    The influence of temperature scanning and isothermal storage conditions on turbidity, particle size, and thermal reversibility of vitamin E-enriched emulsions produced by spontaneous emulsification was examined. Initially, the mini-emulsions formed were optically transparent and contained small droplets (d ≈ 44 nm). When heated (20-90 °C), emulsions exhibited a complex turbidity-temperature profile with a phase inversion temperature (PIT) at ≈ 75-80 °C. Temperature scanning rate had a major influence on emulsion thermal reversibility. Slow heating (0.5 °C/min) above the PIT followed by quench cooling (≈ 67 °C min(-1)) to 30 °C did not appreciably increase turbidity or droplet diameter (d ≈ 50 nm), suggesting these systems were thermo-reversible. However, slow heating to temperatures below the PIT followed by rapid cooling appreciably increased droplet size and turbidity (thermo-irreversible). Cooling rate also affected emulsion thermo-reversibility: the turbidity and droplet size after heating above the PIT decreased with increasing cooling rate. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Development of functional milk desserts enriched with resistant starch based on consumers' perception.

    PubMed

    Ares, Florencia; Arrarte, Eloísa; De León, Tania; Ares, Gastón; Gámbaro, Adriana

    2012-10-01

    Sensory characteristics play a key role in determining consumers' acceptance of functional foods. In this context, the aim of the present work was to apply a combination of sensory and consumer methodologies to the development of chocolate milk desserts enriched with resistant starch. Chocolate milk desserts containing modified waxy maize starch were formulated with six different concentrations of two types of resistant starch (which are part of insoluble dietary fiber). The desserts were evaluated by trained assessors using Quantitative Descriptive Analysis. Moreover, consumers scored their overall liking and willingness to purchase and answered an open-ended question. Resistant starch caused significant changes in the sensory characteristics of the desserts and a significant decrease in consumers' overall liking and willingness to purchase. Consumer data was analyzed applying survival analysis on overall liking scores, considering the risk on consumers liking and willing to purchase the functional products less than their regular counterparts. The proposed methodologies proved to be useful to develop functional foods taking into account consumers' perception, which could increase their success in the market.

  12. Evaluation of an automated high-volume extraction method for viral nucleic acids in comparison to a manual procedure with preceding enrichment.

    PubMed

    Hourfar, M K; Schmidt, M; Seifried, E; Roth, W K

    2005-08-01

    Nucleic acid extraction still harbours the potential for improvements in automation and sensitivity of nucleic acid amplification technology (NAT) testing. This study evaluates the feasibility of a novel automated high-volume extraction protocol for NAT minipool testing in a blood bank setting. The chemagic Viral DNA/RNA Kit special for automated purification of viral nucleic acids from 9.6 ml of plasma by using the chemagic Magnetic Separation Module I was investigated. Analytical sensitivity for hepatitis C virus (HCV), human immunodeficiency virus-1 (HIV-1), hepatitis B virus (HBV), hepatitis A virus (HAV) and parvovirus B19 (B19) was compared to our present manual procedure that involves virus enrichment by centrifugation. Chemagic technology allows automation of the viral DNA/RNA extraction process. Viral nucleic acids were bound directly to magnetic beads from 9.6-ml minipools. By combining the automated magnetic beads-based extraction technology with our in-house TaqMan polymerase chain reaction (PCR) assays, 95% detection limits were 280 IU/ml for HCV, 4955 IU/ml for HIV-1, 249 IU/ml for HBV, 462 IU/ml for HAV and 460 IU/ml for B19, calculated for an individual donation in a pool of 96 donors. The detection limits of our present method were 460 IU/ml for HCV, 879 IU/ml for HIV-1, 90 IU/ml for HBV, 203 IU/ml for HAV and 314 IU/ml for B19. The 95% detection limits obtained by using the chemagic method were within the regulatory requirements for blood donor screening. The sensitivities detected for HCV, HBV, HAV and B19 were found to be in a range similar to that of the manual purification method. Sensitivity for HIV-1, however, was found to be inferior for the chemagic method in this study.

  13. Selective extraction and enrichment of glycoproteins based on boronate affinity SPME and determination by CIEF-WCID.

    PubMed

    Li, Lixian; Xia, Zhining; Pawliszyn, Janusz

    2015-07-30

    In this study, a new thin-film boronic acid coating was developed for solid-phase microextraction (SPME) followed by capillary isoelectric focusing with whole-column imaging detection (CIEF-WCID). Boronate functionalized particles of phenylboronic acid (PBA) and 3-aminophenylboronic acid (3-aPBA) were utilized as boronate affinity solid phase coating on thin-film stainless steel blades for selective extraction and enrichment of glycoproteins. The process of extraction and elution could be easily controlled by adjusting pH. To test specificity, asialofetuin and lactoferrin were selected as glycoproteins test molecules, while BSA and myoglobin were used as control non-glycoproteins in this study. The boronate affinity coating was characterized. The effect of buffer, pH, extraction profiles and elution profiles were investigated. The developed method was successfully applied to extract glycoproteins from standard buffer, PBS, human plasma and 10-fold diluted human blood using two kinds of boronate affinity blades. Boronate affinity SPME could be a promising tool for selective extraction and enrichment of low-abundance glycoproteins in real biological samples.

  14. Refining environmental enrichment to advance rehabilitation based research after experimental traumatic brain injury.

    PubMed

    Radabaugh, Hannah L; LaPorte, Megan J; Greene, Anna M; Bondi, Corina O; Lajud, Naima; Kline, Anthony E

    2017-08-01

    The typical environmental enrichment (EE) paradigm, which consists of continuous exposure after experimental traumatic brain injury (TBI), promotes behavioral and histological benefits. However, rehabilitation is often abbreviated in the clinic and administered in multiple daily sessions. While recent studies have demonstrated that a once daily 6-hr bout of EE confers benefits comparable to continuous EE, breaking the therapy into two shorter sessions may increase novelty and ultimately enhance recovery. Hence, the aim of the study was to test the hypothesis that functional and histological outcomes will be significantly improved by daily preclinical neurorehabilitation consisting of two 3-hr periods of EE vs. a single 6-hr session. Anesthetized adult male rats received a controlled cortical impact of moderate-to-severe injury (2.8mm tissue deformation at 4m/s) or sham surgery and were then randomly assigned to groups receiving standard (STD) housing, a single 6-hr session of EE, or two 3-hr sessions of EE daily for 3weeks. Motor function (beam-balance/traversal) and acquisition of spatial learning/memory retention (Morris water maze) were assessed on post-operative days 1-5 and 14-19, respectively. Cortical lesion volume was quantified on day 21. Both EE conditions improved motor function and acquisition of spatial learning, and reduced cortical lesion volume relative to STD housing (p<0.05), but did not differ from one another in any endpoint (p>0.05). The findings replicate previous work showing that 6-hr of EE daily is sufficient to confer behavioral and histological benefits after TBI and extend the findings by demonstrating that the benefits are comparable regardless of how the 6-hrs of EE are accrued. The relevance of the finding is that it can be extrapolated to the clinic and may benefit patients who cannot endure a single extended period of neurorehabilitation. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Development of a novel stirrerliquid/solid microextraction method for the separation and enrichment of trace levels of active compounds in traditional Chinese medicine.

    PubMed

    Wang, Caiyun; Chen, Xuan; Hu, Shuang; Bai, Xiaohong

    2016-11-01

    A novel stirrer-liquid/solid microextraction method was developed for the separation and enrichment of trace levels of curcumin, bisdemethoxycurcumin, and demethoxycurcumin in Rhizoma Curcumae Longae, Radix Curcumae, and Rhizoma Curcumae before their analysis by high-performance liquid chromatography with ultraviolet detection. In the proposed approach, a magnetic stirrer was immersed in decanol to coat its surface completely with decanol, which was used as an extraction platform. The stirrer coated with decanol is not only a power to agitate the sample solution to constantly update the sample on the stirrer surface but also it can adsorb and extract the target analytes. Some effective parameters, including suitable superficial area of stirrer, extraction solvent, sample phase pH, NaCl concentration, stirring rate, extraction time, sample phase volume, were analyzed and selected. Under the optimal conditions, the linearities are 0.0044-2.20 μg/mL, detection limits are 0.3-0.6 ng/mL, and the extraction content per unit length and enrichment factors of the target analytes are 6.24-9.71/mm and 589-917, respectively. Also, the stirrer-liquid/solid microextraction mechanism for the extraction and enrichment of the target analytes was analyzed and expounded. The results showed that stirrer-liquid/solid microextraction is a simple, rapid sample pretreatment approach with a high enrichment factor.

  16. Synthesis and Oxidation Behavior of Platinum-Enriched γ+γ' Bond Coatings on Ni-Based Superalloys

    SciTech Connect

    Zhang, Ying; Ballard, D A; Stacy, J P; Pint, Bruce A; Haynes, James A

    2006-01-01

    Simple Pt-enriched {gamma}+{gamma}{prime} coatings were synthesized on Rene 142 and Rene N5 Ni-based superalloys by electroplating a thin layer of Pt followed by a diffusion treatment at 1150-1175 C. The Al content in the resulting {gamma}+{gamma}{prime} coating was in the range of 16-19 at.% on superalloys with 13-14 at.% Al. After oxidation testing, alumina scale adherence to these {gamma}+{gamma}{prime} coatings was not as uniform as to the {beta}-(Ni,Pt)Al coatings on the same superalloy substrates. To better understand the effect of Al, Pt and Hf concentrations on coating oxidation resistance, a number of Ni-Pt-Al cast alloys with {gamma}+{gamma}{prime} or {beta} phase were cyclically oxidized at 1100 C. The Hf-containing {gamma}+{gamma}{prime} alloys with 22 at.% Al and 10-30 at.% Pt exhibited similar oxidation resistance to the {beta} alloys with 50 at.% Al. An initial effort was made to increase the Al content in the Pt-enriched {gamma}+{gamma}{prime} coatings by introducing a short-term aluminizing process via chemical vapor deposition or pack cementation. However, too much Al was deposited, leading to the formation of {beta} or martensitic phase on the coating surface.

  17. Formulation Optimization of Gluten-Free Functional Spaghetti Based on Maize Flour and Oat Bran Enriched in β-Glucans

    PubMed Central

    Padalino, Lucia; Mastromatteo, Marcella; Sepielli, Grazia; Del Nobile, Matteo Alessandro

    2011-01-01

    The aim of this work concerns the manufacturing process of gluten-free functional spaghetti based on maize flour and oat bran, enriched with β-glucans (22%). More specifically, the goal of the study was to obtain oat bran-loaded maize spaghetti with sensory properties close to unloaded pasta. To this aim, the study has been organized in two subsequent trials. In the first one, the oat bran amount added to spaghetti was continuously increased until the overall sensory quality of pasta reached the set sensory threshold (oat bran concentration = 20%). The second experimental step was aimed to improve the overall sensory quality of oat bran loaded maize spaghetti. In particular, an attempt was made to increase the sensory quality of spaghetti added with 20% oat bran by means of structuring agents. To this aim, the effects of different kinds of some hydrocolloids and egg white powder on the rheological properties of dough, as well as on quality attributes of pasta were examined. The rheological analysis showed that the addition of hydrocolloids and white egg to the dough enriched with 20% oat bran did not cause any substantial difference in the viscoelastic properties, compared to samples without any structuring agents. The best overall quality for both fresh and dry spaghetti was obtained by the addition of carboxymethylcellulose and chitosan at a concentration of 2%. PMID:28824128

  18. Ion Enrichment on the Hydrophobic Carbon-based Surface in Aqueous Salt Solutions due to Cation-π Interactions

    PubMed Central

    Shi, Guosheng; Liu, Jian; Wang, Chunlei; Song, Bo; Tu, Yusong; Hu, Jun; Fang, Haiping

    2013-01-01

    By incorporating cation-π interactions to classic all-atoms force fields, we show that there is a clear enrichment of Na+ on a carbon-based π electron-rich surface in NaCl solutions using molecular dynamics simulations. Interestingly, Cl− is also enriched to some extend on the surface due to the electrostatic interaction between Na+ and Cl−, although the hydrated Cl−-π interaction is weak. The difference of the numbers of Na+ and Cl− accumulated at the interface leads to a significant negatively charged behavior in the solution, especially in nanoscale systems. Moreover, we find that the accumulation of the cations at the interfaces is universal since other cations (Li+, K+, Mg2+, Ca2+, Fe2+, Co2+, Cu2+, Cd2+, Cr2+, and Pb2+) have similar adsorption behaviors. For comparison, as in usual force field without the proper consideration of cation-π interactions, the ions near the surfaces have a similar density of ions in the solution. PMID:24310448

  19. A Platinum-Enriched gamma+gamma' Two-Phase Bond Coat on Ni-Base Superalloys

    SciTech Connect

    Zhang, Ying; Pint, Bruce A; Haynes, James A; Wright, Ian G

    2005-01-01

    Pt-enriched {gamma} + {gamma}{prime} two-phase coating was applied to directionally-solidified Ni-based superalloy Ren{acute e} 142 substrates with three different Hf levels (0.02, 0.76, and 1.37 wt.%). The coating was prepared by electroplating a thin layer of Pt on the superalloy followed by a diffusion treatment. The as-deposited coating exhibited a {gamma} + {gamma}{prime} two-phase microstructure with a major composition of Ni-16Al-18Pt-7Cr-9Co (in at.%) along with some incorporation of refractory elements from the substrates. Cyclic oxidation testing at 1100 C in air indicated improved oxidation resistance of the Ren{acute e} 142 alloys with the Pt-enriched {gamma} + {gamma}{prime} coatings. In addition, the oxidation resistance of both uncoated and coated alloys was proportional to the Hf content in the substrate. Compared with the single-phase {beta}-(Ni,Pt)Al coating, slightly higher mass gains and localized spallation were observed on the {gamma} + {gamma}{prime} two-phase coating, which might be due to the segregation of refractory elements and high sulfur levels in these superalloy substrates.

  20. Rapid enrichment of rare-earth metals by carboxymethyl cellulose-based open-cellular hydrogel adsorbent from HIPEs template.

    PubMed

    Zhu, Yongfeng; Wang, Wenbo; Zheng, Yian; Wang, Feng; Wang, Aiqin

    2016-04-20

    A series of monolithic open-cellular hydrogel adsorbents based on carboxymethylcellulose (CMC) were prepared through high internal phase emulsions (HIPEs) and used to enrich the rare-earth metals La(3+) and Ce(3+). The changes of pore structure, and the effects of pH, contact time, initial concentration on the adsorption performance were systematically studied. The results show that the as-prepared monolithic hydrogel adsorbents possess good open-cellular framework structure and have fast adsorption kinetics and high adsorption capacity for La(3+) and Ce(3+). The involved adsorption system can reach equilibrium within 30min and the maximal adsorption capacity is determined to be 384.62mg/g for La(3+) and 333.33mg/g for Ce(3+). Moreover, these porous hydrogel adsorbents show an excellent adsorptive reusability for La(3+) and Ce(3+) through five adsorption-desorption cycles. Such a pore hierarchy structure makes this monolithic open-cellular hydrogel adsorbent be an effective adsorbent for effective enrichment of La(3+) and Ce(3+) from aqueous solution.

  1. Formulation Optimization of Gluten-Free Functional Spaghetti Based on Maize Flour and Oat Bran Enriched in b-Glucans.

    PubMed

    Padalino, Lucia; Mastromatteo, Marcella; Sepielli, Grazia; Nobile, Matteo Alessandro Del

    2011-12-08

    The aim of this work concerns the manufacturing process of gluten-free functional spaghetti based on maize flour and oat bran, enriched with b-glucans (22%). More specifically, the goal of the study was to obtain oat bran-loaded maize spaghetti with sensory properties close to unloaded pasta. To this aim, the study has been organized in two subsequent trials. In the first one, the oat bran amount added to spaghetti was continuously increased until the overall sensory quality of pasta reached the set sensory threshold (oat bran concentration = 20%). The second experimental step was aimed to improve the overall sensory quality of oat bran loaded maize spaghetti. In particular, an attempt was made to increase the sensory quality of spaghetti added with 20% oat bran by means of structuring agents. To this aim, the effects of different kinds of some hydrocolloids and egg white powder on the rheological properties of dough, as well as on quality attributes of pasta were examined. The rheological analysis showed that the addition of hydrocolloids and white egg to the dough enriched with 20% oat bran did not cause any substantial difference in the viscoelastic properties, compared to samples without any structuring agents. The best overall quality for both fresh and dry spaghetti was obtained by the addition of carboxymethylcellulose and chitosan at a concentration of 2%.

  2. A method to assess relative preference for training and environmental enrichment in captive wolves (Canis lupus and Canis lupus arctos).

    PubMed

    Dorey, Nicole R; Mehrkam, Lindsay R; Tacey, Jay

    2015-11-01

    It is currently debated as to whether or not positive reinforcement training is enriching to captive animals. Although both husbandry training and environmental enrichment (EE) have been found to benefit animal welfare in captivity, to date, no systematic investigation has compared an animal's preference for performing a trained behavior to engaging freely with a stimuli provided as EE. In the current paper, we used four captive wolves to (1) test the efficacy of a paired-stimulus preference assessment to determine preference for engaging in a trained behavior as a choice; and to (2) use a paired-stimulus preference assessment to determine whether or not individuals prefer to engage in a previously trained behavior versus a previously encountered EE stimuli. Of the four subjects tested, visual inspection of the graphs revealed that two of the subjects preferred trained behavior stimuli and two of the subjects preferred EE stimuli; only one of the wolves had a statically higher preference for an EE stimulus over a trained behavior. We believe that letting the animals choose between these two events is the first step in answering the question of whether or not is training enriching, however more research needs to be done and suggestions for future research is discussed. © 2015 Wiley Periodicals, Inc.

  3. Alternative anaerobic enrichments to the bacteriological analytical manual culture method for isolation of Shigella sonnei from selected types of fresh produce.

    PubMed

    Jacobson, Andrew P; Thunberg, Richard L; Johnson, Mildred L; Hammack, Thomas S; Andrews, Wallace H

    2004-01-01

    Alternative methods of reducing oxygen during anaerobic enrichment in the Bacteriological Analytical Manual (BAM) Shigella culture method were evaluated and compared to the current and less practical GasPak method. The alternative anaerobic methods included the use of reducing agents in Shigella broth and reducing culture container headspace volume to minimize atmospheric effects on oxygen concentration in Shigella broth during enrichment. The reducing agents evaluated were sodium thioglycollate, L-cystine, L-cysteine, titanium(III) citrate, and dithiothreitol, each at concentrations of 0.1, 0.05, and 0.01%. The use of Oxyrase for Broth with the enrichment medium (Shigella broth) was evaluated at concentrations of 10, 20 and 30 microL/mL. Recoveries of chill- and freeze-stressed S. sonnei strains 357 and 20143 were determined with each anaerobic method, including the GasPak method, using inoculation levels ranging from 10(0)to 10(3) cells. For each anaerobic method, strain, inoculation level, and stress type, 5 replicate enrichments were evaluated by streaking to MacConkey agar for isolation. The numbers of cultures with each method from which S. sonnei was isolated were used to compare the alternative anaerobic methods to the GasPak method. The alternative anaerobic method with which chill- and freeze-stressed S. sonnei strains 357 and 20143 were isolated most consistently was the use of Oxyrase for Broth in Shigella broth at a concentration of 20 microL/mL. This method was compared to the GasPak anaerobic method in evaluations on the recovery of S. sonnei strains 357 and 20143 from artificially contaminated test portions of parsley, cilantro, green onions, strawberries, carrots, and celery. A third anaerobic method included the use of 0.5 cm mineral oil overlay on cultures containing Oxyrase for Broth at concentrations of 20 microL/mL. Recovery rates of strain 357 were significantly greater (p < 0.05) with the GasPak method than with Oxyrase for Broth, with and

  4. Tissue enrichment analysis for C. elegans genomics.

    PubMed

    Angeles-Albores, David; N Lee, Raymond Y; Chan, Juancarlos; Sternberg, Paul W

    2016-09-13

    Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available for Caenorhabditis elegans, it does not include anatomical information. We have developed a tool for identifying enrichment of C. elegans tissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection in C. elegans. Our Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python's standard pip installer. It tests a slimmed-down C. elegans tissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results.

  5. Enriching Project-Based Learning Environments with Virtual Manipulatives: A Comparative Study

    ERIC Educational Resources Information Center

    Çakiroglu, Ünal

    2014-01-01

    Problem statement: Although there is agreement on the potential of project based learning (PBL) and virtual manipulatives (VMs), their positive impact depends on how they are used. This study was based on supporting the use of online PBL environments and improving the efficacy of the instructional practices in PBL by combining the potentials of…

  6. Synchrotron based infrared imaging and spectroscopy via focal plane array on live fibroblasts in D2O enriched medium

    SciTech Connect

    Quaroni, Luca; Zlateva, Theodora; Sarafimov, Blagoj; Kreuzer, Helen W.; Wehbe, Katia; Hegg, Eric L.; Cinque, Gianfelice

    2014-03-26

    We tested the viability of using synchrotron based infrared imaging to study biochemical processes inside living cells. As a model system, we studied fibroblast cells exposed to a medium highly enriched with D2O. We could show that the experimental technique allows us to reproduce at the cellular level measurements that are normally performed on purified biological molecules. We can obtain information about lipid conformation and distribution, kinetics of hydrogen/deuterium exchange, and the formation of concentration gradients of H and O isotopes in water that are associated with cell metabolism. The implementation of the full field technique in a sequential imaging format gives a description of cellular biochemistry and biophysics that contains both spatial and temporal information.

  7. Universal screening test based on analysis of circulating organ-enriched microRNAs: a novel approach to diagnostic screening.

    PubMed

    Sheinerman, Kira S; Umansky, Samuil

    2015-03-01

    Early disease detection leads to more effective and cost-efficient treatment. It is especially important for cancer and neurodegenerative diseases, because progression of these pathologies leads to significant and frequently irreversible changes in underlying pathophysiological processes. At the same time, the development of specific screening tests for detection of each of the hundreds of human pathologies in asymptomatic stage may be impractical. Here, we discuss a recently proposed concept: the development of minimally invasive Universal Screening Test (UST) based on analysis of organ-enriched microRNAs in plasma and other bodily fluids. The UST is designed to detect the presence of a pathology in particular organ systems, organs, tissues or cell types without diagnosing a specific disease. Once the pathology is detected, more specific, and if necessary invasive and expensive, tests can be administered to precisely define the nature of the disease. Here, we discuss recent studies and analyze the data supporting the UST approach.

  8. An efficient and rapid method for enrichment of lipophilic proteins from Mycobacterium tuberculosis H37Rv for two-dimensional gel electrophoresis.

    PubMed

    Sharma, Divakar; Bisht, Deepa

    2016-05-01

    Lipophilic proteome profiling is crucial because they have an anticipated role in biological processes and pathogenesis of Mycobacterium tuberculosis. These lipophilic proteins might be used as potential targets for the development of newer diagnostic markers and drug targets due to their association with membranes and drugs. We developed an efficient and rapid method to enrich the lipophilic proteins extraction from M. tuberculosis H37Rv for 2DE. In the extraction of lipophilic proteins, nonionic detergent (Triton X-100) was added in sonication buffer that augmented the solubilization of the proteins at the time of sonication. Enriched whole cell lysate was subjected to direct phase separation using Triton X-114, without the need for preisolation of membranes. In this study, we report that our optimized extraction buffer increased the lipophilic proteins extraction and their improved resolution on 2D gel up to two- to threefolds (quantitatively and qualitatively) as compared to standard extraction buffer. Some proteins were identified by MALDI-TOF/MS.

  9. A history-based method to estimate animal preference

    PubMed Central

    Maia, Caroline Marques; Volpato, Gilson Luiz

    2016-01-01

    Giving animals their preferred items (e.g., environmental enrichment) has been suggested as a method to improve animal welfare, thus raising the question of how to determine what animals want. Most studies have employed choice tests for detecting animal preferences. However, whether choice tests represent animal preferences remains a matter of controversy. Here, we present a history-based method to analyse data from individual choice tests to discriminate between preferred and non-preferred items. This method differentially weighs choices from older and recent tests performed over time. Accordingly, we provide both a preference index that identifies preferred items contrasted with non-preferred items in successive multiple-choice tests and methods to detect the strength of animal preferences for each item. We achieved this goal by investigating colour choices in the Nile tilapia fish species. PMID:27350213

  10. Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

    SciTech Connect

    Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.; Lindemann, Stephen R.; Ewing, Timothy; Call, Douglas R.; Fredrickson, James K.; Beyenal, Haluk

    2014-01-01

    Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode- associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

  11. Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

    PubMed Central

    Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.; Lindemann, Stephen R.; Ewing, Timothy; Call, Douglas R.; Fredrickson, James K.; Beyenal, Haluk

    2014-01-01

    Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1–V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community. PMID:24478768

  12. Growing Gifted Students in the Desert: Using Alternative, Community-Based Assessment and an Enriched Curriculum.

    ERIC Educational Resources Information Center

    Belcher, Rebecca Newcom; Fletcher-Carter, R.

    1999-01-01

    Describes a federally funded Javits project that involved two rural elementary schools with a primarily Hispanic population. The project was designed to develop an alternative community-based assessment procedure for identifying gifted minority students. Identified students were taught using a developed science curriculum that focused on problem…

  13. Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

    PubMed Central

    Anwar, Nadia; Hunt, Ela

    2009-01-01

    Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

  14. The Perspectives of Major Stakeholders on Video Enriched Problem-Based Learning for Chinese Teacher Education

    ERIC Educational Resources Information Center

    Ma, Angela Kit Fong; O'Toole, John Mitchell

    2013-01-01

    The study described in this paper investigated how the major stakeholders of a teacher education institution responded to a particular suite of educational products that involved video-based educational learning objects. It aims to look into stakeholder attitudes to potential technological development in fostering student-centred learning in…

  15. About Prospects of Enrichment of Mineral Raw Materials and Chemical Activation of Water Suspensions by Electroexplosive Method

    NASA Astrophysics Data System (ADS)

    Bordunov, S. V.; Galtseva, O. V.

    2016-01-01

    A series of experiments is conducted on laboratory and pilot-production installation for the application of high-voltage pulsed discharge in the processes of enrichment of goldbearing mineral raw materials with a relatively low energy electrical discharge in the pulse of 120 J. At the same time the conglomerates of clay components are breaking down to micron and submicron sizes completely. Solid minerals such as quartz are simultaneously destroyed by defects and grains and withdrawn from the installation with water, thus increasing degree of enrichment of concentrate. The results of the processing by high-voltage pulsed discharges of building sand from the Ob riverbed are given. Discharge energy is 45 J. Relations of fractions in the original sand and in the sand after electroexplosive process show the uniform crushing of sand particles with splitting off particles with size of less than 0.045 mm. A content of chipped particles is 18%. The results of particle-size and X-ray structural analyses are shown.

  16. Backward Mathematics for Enrichment.

    ERIC Educational Resources Information Center

    Westcott, Alvin M.; Shuler, Nancy L.

    1982-01-01

    The use of backward mathematics is promoted as an enrichment strategy which gives pupils the opportunity to generate creative responses that explore many possibilities. It is felt that teachers will find the instructional method a worthwhile innovation, and a technique useful in any curricular area. (MP)

  17. Coffee-ring effect-based simultaneous SERS substrate fabrication and analyte enrichment for trace analysis

    NASA Astrophysics Data System (ADS)

    Wang, Weidong; Yin, Yongguang; Tan, Zhiqiang; Liu, Jingfu

    2014-07-01

    Based on the ``coffee-ring effect'', we developed a highly efficient SERS platform which integrates the fabrication of SERS-active substrates and the preconcentration of analytes into one step. The high sensitivity, robustness, reproducibility and simplicity make this platform ideal for on-site analysis of small volume samples at low concentrations in complex matrices.Based on the ``coffee-ring effect'', we developed a highly efficient SERS platform which integrates the fabrication of SERS-active substrates and the preconcentration of analytes into one step. The high sensitivity, robustness, reproducibility and simplicity make this platform ideal for on-site analysis of small volume samples at low concentrations in complex matrices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03198a

  18. Comparison of cold enrichment and U.S. Department of Agriculture methods for isolating Listeria monocytogenes from naturally contaminated foods. The Listeria Study Group.

    PubMed Central

    Hayes, P S; Graves, L M; Ajello, G W; Swaminathan, B; Weaver, R E; Wenger, J D; Schuchat, A; Broome, C V

    1991-01-01

    We compared the cold enrichment (CE) and U.S. Department of Agriculture (USDA) methods for isolating Listeria monocytogenes by examining 402 food samples. The food samples were collected from refrigerators of listeriosis patients as part of a multistate active surveillance project to determine the role of foods in sporadic listeriosis in the United States. L. monocytogenes was isolated from 51 food samples (13%). The USDA method was significantly better (P less than 0.001) than the CE method. The isolation efficiencies of the USDA and CE methods were 96 and 59%, respectively. Quantitation of L. monocytogenes in the food samples revealed that many food samples containing less than 0.3 CFU/g were negative as determined by the CE method but positive as determined by the USDA method. PMID:1768082

  19. Thermal breeder fuel enrichment zoning

    DOEpatents

    Capossela, Harry J.; Dwyer, Joseph R.; Luce, Robert G.; McCoy, Daniel F.; Merriman, Floyd C.

    1992-01-01

    A method and apparatus for improving the performance of a thermal breeder reactor having regions of higher than average moderator concentration are disclosed. The fuel modules of the reactor core contain at least two different types of fuel elements, a high enrichment fuel element and a low enrichment fuel element. The two types of fuel elements are arranged in the fuel module with the low enrichment fuel elements located between the high moderator regions and the high enrichment fuel elements. Preferably, shim rods made of a fertile material are provided in selective regions for controlling the reactivity of the reactor by movement of the shim rods into and out of the reactor core. The moderation of neutrons adjacent the high enrichment fuel elements is preferably minimized as by reducing the spacing of the high enrichment fuel elements and/or using a moderator having a reduced moderating effect.

  20. Comparison of direct and enrichment methods for the selective isolation of vancomycin-resistant enterococci from feces of pigs and poultry.

    PubMed

    Butaye, P; Devriese, L A; Haesebrouck, F

    1999-01-01

    Isolation results of vancomycin-resistant enterococci (VRE) of fecal samples from pigs and broiler and layer chickens obtained with two vancomycin-supplemented enrichment media, kanamycin aesculin azide (KAA) broth and Enterococcosel (ECC) broth, and three isolation media, KAA agar, ECC agar, and Slanetz and Bartley (SL) agar, were compared. Direct isolation on vancomycin-containing agar plates was not efficient in swine and layer chickens, which had only low numbers of VRE. In broilers chickens, the VRE content of the samples was high, and SL as well as ECC were found to perform better than KAA agar. The same three agar media were used as selective plating media after 1 and 2 days incubation of the samples in KAA and ECC enrichment broths. Sensitivities of the 12 different enrichment-plate combinations tested ranged from 0 to 81% in layer chickens and from 5 to 44% in samples from pigs. In the high prevalence type of samples from broilers, sensitivities still varied substantially from 52 to 78%. Incubating vancomycin-containing enrichment broths for 2 days compared with 1 day was favorable for the isolation of vancomycin-resistant Enterococcus faecalis, E. gallinarum, and E. casseliflavus but not for E. faecium and E. hirae/E. durans. ECC broth and ECC plates yielded the highest number of E. gallinarum and E. casseliflavus. In layer as well as in broiler chickens, ECC broth incubated for 2 days and plated on ECC agar was the most sensitive method. In pigs, however, KAA broth incubated for 2 days and plated on ECC medium yielded the highest number of VRE.

  1. Comparison of Ti-Based Coatings on Silicon Nanowires for Phosphopeptide Enrichment and Their Laser Assisted Desorption/Ionization Mass Spectrometry Detection.

    PubMed

    Kurylo, Ievgen; Hamdi, Abderrahmane; Addad, Ahmed; Boukherroub, Rabah; Coffinier, Yannick

    2017-09-15

    We created different TiO₂-based coatings on silicon nanowires (SiNWs) by using either thermal metallization or atomic layer deposition (ALD). The fabricated surfaces were characterized by X-ray photoelectron spectroscopy (XPS), energy dispersive X-ray spectroscopy (EDX), and reflectivity measurements. Surfaces with different TiO₂ based coating thicknesses were then used for phosphopeptide enrichment and subsequent detection by laser desorption/ionization mass spectrometry (LDI-MS). Results showed that the best enrichment and LDI-MS detection were obtained using the silicon nanowires covered with 10 nm of oxidized Ti deposited by means of thermal evaporation. This sample was also able to perform phosphopeptide enrichment and MS detection from serum.

  2. Faith-Based Organizations and Veteran Reintegration: Enriching the Web of Support.

    PubMed

    Werber, Laura; Derose, Kathryn Pitkin; Rudnick, Mollie; Harrell, Margaret C; Naranjo, Diana

    2015-11-30

    Faith-based organizations (FBOs) are an important community-based resource for veterans as they readjust to civilian life. Through interviews with both national-level and smaller, local FBOs, the authors sought to understand better the current and potential roles for FBOs in veteran reintegration. Interviewees suggested that veterans may look to FBOs for support because they offer privacy and confidentiality, two features that may be especially critical when a potential stigma is involved. Some FBOs have also developed a reputation as safe places for veterans, providing supportive, judgment-free environments. FBOs not only help veterans with spiritual matters but address diverse areas of veteran health and wellness, including vocation, education, financial and legal stability, shelter, access to goods and services, mental health, access to health care, physical health, family, and social networks. In some cases, the support is offered to veterans directly; in other instances, the support is indirect, via training individuals to help veterans or educating the public about them. In the process of providing support, FBOs interact with varied organizations, including government entities, private nonprofits, and one another, for training, outreach, referrals, information exchange, obtaining donations, and collaboration. Yet challenges exist, including insufficient connections with chaplains working in different settings and others in the web of support, resource and capacity constraints, lack of awareness of experience with veterans, issues related to religious philosophy or orientation, and characteristics of veterans themselves. To move forward, the authors offer recommendations for policymakers, organizations that interact with FBOs, and FBOs themselves to help FBOs engage fully in the web of reintegration support.

  3. A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae).

    PubMed

    Fragoso-Martínez, Itzi; Salazar, Gerardo A; Martínez-Gordillo, Martha; Magallón, Susana; Sánchez-Reyes, Luna; Moriarty Lemmon, Emily; Lemmon, Alan R; Sazatornil, Federico; Granados Mendoza, Carolina

    2017-02-09

    We conducted a pilot study using Anchored Hybrid Enrichment to resolve relationships among a mostly Neotropical sage lineage that may have undergone a recent evolutionary radiation. Conventional markers (ITS, trnL-trnF and trnH-psbA) have not been able to resolve the relationships among species nor within portions of the backbone of the lineage. We sampled 12 representative species of subgenus Calosphace and included one species of Salvia's s.l. closest relative, Lepechinia, as outgroup. Hybrid enrichment and sequencing were successful, yielding 448 alignments of individual loci with an average length of 704bp. The performance of the phylogenomic data in phylogenetic reconstruction was superior to that of conventional markers, increasing both support and resolution. Because the captured loci vary in the amount of net phylogenetic informativeness at different phylogenetic depths, these data are promising in phylogenetic reconstruction of this group and likely other lineages within Lamiales. However, special attention should be placed on the amount of phylogenetic noise that the data could potentially contain. A prior exploration step using phylogenetic informativeness profiles to detect loci with sites with disproportionately high substitution rates (showing "phantom" spikes) and, if required, the ensuing filtering of the problematic data is recommended. In our dataset, filtering resulted in increased support and resolution for the shallow nodes in maximum likelihood phylogenetic trees resulting from concatenated analyses of all the loci. Additionally, it is expected that an increase in sampling (loci and taxa) will aid in resolving weakly supported, short deep internal branches. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules

    PubMed Central

    Bersanelli, Matteo; Mosca, Ettore; Remondini, Daniel; Castellani, Gastone; Milanesi, Luciano

    2016-01-01

    A relation exists between network proximity of molecular entities in interaction networks, functional similarity and association with diseases. The identification of network regions associated with biological functions and pathologies is a major goal in systems biology. We describe a network diffusion-based pipeline for the interpretation of different types of omics in the context of molecular interaction networks. We introduce the network smoothing index, a network-based quantity that allows to jointly quantify the amount of omics information in genes and in their network neighbourhood, using network diffusion to define network proximity. The approach is applicable to both descriptive and inferential statistics calculated on omics data. We also show that network resampling, applied to gene lists ranked by quantities derived from the network smoothing index, indicates the presence of significantly connected genes. As a proof of principle, we identified gene modules enriched in somatic mutations and transcriptional variations observed in samples of prostate adenocarcinoma (PRAD). In line with the local hypothesis, network smoothing index and network resampling underlined the existence of a connected component of genes harbouring molecular alterations in PRAD. PMID:27731320

  5. Status of gadolinium enrichment technology at LLNL

    SciTech Connect

    Haynam, C.; Comaskey, B.; Conway, J.; Eggert, J.; Glaser, J.; Ng, E.; Paisner, J.; Solarz, R.; Worden, E.

    1993-01-01

    A method based on,polarization selectivity and three step laser photoionization is presented for separation of the odd isotopes of gadolinium. Measurements of the spectroscopic parameters needed to quantify the excitation pathway are discussed. Model results are presented for the efficiency of photoionization. The vapor properties of electron beam vaporized gadolinium are presented which show dramatic cooling during the expansion of the hot dense vapor into a vacuum. This results in a significant increase in the efficiency of conversion of natural feed into enriched product in the AVLIS process. Production of enriched gadolinium for use in commercial power reactors appears to be economically viable using technology in use at LLNL.

  6. Fire extinguishment in oxygen enriched atmospheres

    NASA Technical Reports Server (NTRS)

    Robertson, A. F.; Rappaport, M. W.

    1973-01-01

    Current state-of-the-art of fire suppression and extinguishment techniques in oxygen enriched atmosphere is reviewed. Four classes of extinguishment action are considered: cooling, separation of reactants, dilution or removal of fuel, and use of chemically reactive agents. Current practice seems to show preference for very fast acting water spray applications to all interior surfaces of earth-based chambers. In space, reliance has been placed on fire prevention methods through the removal of ignition sources and use of nonflammable materials. Recommendations are made for further work related to fire suppression and extinguishment in oxygen enriched atmospheres, and an extensive bibliography is appended.

  7. Applications and theory of electrokinetic enrichment in micro-nanofluidic chips.

    PubMed

    Chen, Xueye; Zhang, Shuai; Zhang, Lei; Yao, Zhen; Chen, Xiaodong; Zheng, Yue; Liu, Yanlin

    2017-09-01

    This review reports the progress on the recent development of electrokinetic enrichment in micro-nanofluidic chips. The governing equations of electrokinetic enrichment in micro-nanofluidic chips are given. Various enrichment applications including protein analysis, DNA analysis, bacteria analysis, viruses analysis and cell analysis are illustrated and discussed. The advantages and difficulties of each enrichment method are expatiated. This paper will provide a particularly convenient and valuable reference to those who intend to research the electrokinetic enrichment based on micro-nanofluidic chips.

  8. Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease.

    PubMed

    Mayers, Michael D; Moon, Clara; Stupp, Gregory S; Su, Andrew I; Wolan, Dennis W

    2017-02-03

    Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across two mouse cohorts as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control, thereby limiting genetic and environmental variables that influence microbiome composition. The data generated highlight quantitative alterations in both host and microbial proteins due to intestinal inflammation and corroborates the observed phylogenetic changes in bacteria that accompany IBD in humans and mouse models. The combination of isotope labeling with shotgun proteomics resulted in the total identification of 4434 protein clusters expressed in the microbial proteomic environment, 276 of which demonstrated differential abundance between control and IBD mice. Notably, application of a novel cysteine-reactive probe uncovered several microbial proteases and hydrolases overrepresented in the IBD mice. Implementation of these methods demonstrated that substantial insights into the identity and dysregulation of host and microbial proteins altered in IBD can be accomplished and can be used in the interrogation of other microbiome-related diseases.

  9. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae1

    PubMed Central

    Mandel, Jennifer R.; Dikow, Rebecca B.; Funk, Vicki A.; Masalia, Rishi R.; Staton, S. Evan; Kozik, Alex; Michelmore, Richard W.; Rieseberg, Loren H.; Burke, John M.

    2014-01-01

    • Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. • Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. • Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families. PMID:25202605

  10. GC/MS method for determining carbon isotope enrichment and concentration of underivatized short-chain fatty acids by direct aqueous solution injection of biogas digester samples.

    PubMed

    Mulat, Daniel Girma; Feilberg, Anders

    2015-10-01

    In anaerobic digestion of organic matter, several metabolic pathways are involved during the simultaneous production and consumption of short-chain fatty acids (SCFA) in general and acetate in particular. Understanding the role of each pathway requires both the determination of the concentration and isotope enrichment of intermediates in conjunction with isotope labeled substrates. The objective of this study was to establish a rapid and simple GC/MS method for determining the isotope enrichment of acetate and concentration of underivatized short-chain fatty acids (SCFA) in biogas digester samples by direct liquid injection of acidified aqueous samples. Sample preparation involves only acidification, centrifugation and filtration of the aqueous solution followed by direct injection of the aqueous supernatant solution onto a polar column. With the sample preparation and GC/MS conditions employed, well-resolved and sharp peaks of underivatized SCFA were obtained in a reasonably short time. Good recovery (96.6-102.3%) as well as low detection (4-7 µmol/L) and quantification limits (14-22 µmol/L) were obtained for all the 6 SCFA studied. Good linearity was achieved for both concentration and isotope enrichment measurement with regression coefficients higher than 0.9978 and 0.9996, respectively. The method has a good intra- and inter-day precision with a relative standard deviation (RSD) below 6% for determining the tracer-to-tracee ratio (TTR) of both [2-(13)C]acetate and [U-(13)C]acetate. It has also a good intra- and inter-day precision with a RSD below 6% and 5% for determining the concentration of standard solution and biogas digester samples, respectively. Acidification of biogas digester samples with oxalic acid provided the low pH required for the protonation of SCFA and thus, allows the extraction of SCFA from the complex sample matrix. Moreover, oxalic acid was the source of formic acid which was produced in the injector set at high temperature. The produced

  11. Mixed housing with DBA/2 mice induces stress in C57BL/6 mice: implications for interventions based on social enrichment

    PubMed Central

    Kulesskaya, Natalia; Karpova, Nina N.; Ma, Li; Tian, Li; Voikar, Vootele

    2014-01-01

    Several behavioral interventions, based on social enrichment and observational learning are applied in treatment of neuropsychiatric disorders. However, the mechanism of such modulatory effect and the safety of applied methods on individuals involved in social support need further investigation. We took advantage of known differences between inbred mouse strains to reveal the effect of social enrichment on behavior and neurobiology of animals with different behavioral phenotypes. C57BL/6 and DBA/2 female mice displaying multiple differences in cognitive, social, and emotional behavior were group-housed either in same-strain or in mixed-strain conditions. Comprehensive behavioral phenotyping and analysis of expression of several plasticity- and stress-related genes were done to measure the reciprocal effects of social interaction between the strains. Contrary to our expectation, mixed housing did not change the behavior of DBA/2 mice. Nevertheless, the level of serum corticosterone and the expression of glucocorticoid receptor Nr3c1 in the brain were increased in mixed housed DBA/2 as compared with those of separately housed DBA/2 mice. In contrast, socially active C57BL/6 animals were more sensitive to the mixed housing, displaying several signs of stress: alterations in learning, social, and anxiety-like behavior and anhedonia. These behavioral impairments were accompanied by the elevated serum corticosterone and the reduced expression of Nr3c1, as well as the elevated Bdnf levels in the cortex and hippocampus. Our results demonstrate the importance of social factors in modulation of both behavior and the underlying neurobiological mechanisms in stress response, and draw attention to the potential negative impact of social interventions for individuals involved in social support. PMID:25147512

  12. Asset-Based Civics for, with, and by Immigrant Students: Three Sites of Enriched Teaching and Learning for Immigrant and Native-Born Students

    ERIC Educational Resources Information Center

    Hilburn, Jeremy

    2015-01-01

    In this qualitative collective case study with 6 high school civics teachers, I found that using an asset-based approach to teaching civics for, with, and by immigrant students enriched teaching and learning for immigrant and native-born students, although participants missed some opportunities for deeper exploration. I used a combined theoretical…

  13. Integrated and Contextual Basic Science Instruction in Preclinical Education: Problem-Based Learning Experience Enriched with Brain/Mind Learning Principles

    ERIC Educational Resources Information Center

    Gülpinar, Mehmet Ali; Isoglu-Alkaç, Ümmühan; Yegen, Berrak Çaglayan

    2015-01-01

    Recently, integrated and contextual learning models such as problem-based learning (PBL) and brain/mind learning (BML) have become prominent. The present study aimed to develop and evaluate a PBL program enriched with BML principles. In this study, participants were 295 first-year medical students. The study used both quantitative and qualitative…

  14. Augmenting Learning in an Out-of-School Context: The Cognitive and Affective Impact of Two Cryogenics-Based Enrichment Programmes on Upper Primary Students

    ERIC Educational Resources Information Center

    Caleon, Imelda S.; Subramaniam, R.

    2007-01-01

    Concepts learned in the classroom were reinforced and augmented by presenting them in a different context using cryogenics-based enrichment programmes (CBEPs) held in an out-of-school setting. The effectiveness of two CBEPs, which involve the use of liquid nitrogen and liquid oxygen, was explored. Using a sample of 265 upper primary students, it…

  15. High-Ability Students' Perspectives on an Affective Curriculum in a Diverse, University-Based Summer Residential Enrichment Program

    ERIC Educational Resources Information Center

    Jen, Enyi; Gentry, Marcia; Moon, Sidney M.

    2017-01-01

    The purpose of this study was to investigate how high-ability students experienced their participation in an affective curriculum through small-group discussions in a diverse, university-based, summer enrichment program for talented youth. The investigation included two closely related studies. The first study included 77 high-ability students…

  16. Augmenting Learning in an Out-of-School Context: The Cognitive and Affective Impact of Two Cryogenics-Based Enrichment Programmes on Upper Primary Students

    ERIC Educational Resources Information Center

    Caleon, Imelda S.; Subramaniam, R.

    2007-01-01

    Concepts learned in the classroom were reinforced and augmented by presenting them in a different context using cryogenics-based enrichment programmes (CBEPs) held in an out-of-school setting. The effectiveness of two CBEPs, which involve the use of liquid nitrogen and liquid oxygen, was explored. Using a sample of 265 upper primary students, it…

  17. Asset-Based Civics for, with, and by Immigrant Students: Three Sites of Enriched Teaching and Learning for Immigrant and Native-Born Students

    ERIC Educational Resources Information Center

    Hilburn, Jeremy

    2015-01-01

    In this qualitative collective case study with 6 high school civics teachers, I found that using an asset-based approach to teaching civics for, with, and by immigrant students enriched teaching and learning for immigrant and native-born students, although participants missed some opportunities for deeper exploration. I used a combined theoretical…

  18. Vitamin A Activity of Rice-based Weaning Foods Enriched with Germinated Cowpea Flour, Banana, Pumpkin and Milk Powder.

    PubMed

    Hashim, N; Pongjata, J

    2000-03-01

    The objective of this study was to identify the effect of different drying methods on vitamin A activity of formulated weaning food. Weaned foods on vitamin A activity of formulated using treated cowpea flour, locally available rice flour, banana-pumpkin, skim milk powder and sugar in the ratio 35:35:15:15:5. Treated cowpea flour consisted of original cowpea flour, 24 h germinated cowpea flour. Each treated flour was mixed separately with the other ingredients and cooked into a slurry. Each mixture was either oven-dried or freeze-dried to produce a dry flaky mixture. The carotenoid composition of the product was determined by HPLC. Vitamin A activity of oven-dried weaning food was significantly reduced (p<0.05) compared to freeze-dried weaning food. The freeze-dried weaning foods showed a higher retinol equivalent than oven-dried weaning foods for all treatments. The results of the study found that an intake of 100 g of freeze-dried weaning foods enriched with banana-pumpkin and cowpea flour provided an adequate amount of the recommended daily allowance (RDA) of vitamin A for infants.

  19. On-plate glycoproteins/glycopeptides selective enrichment and purification based on surface pattern for direct MALDI MS analysis.

    PubMed

    Zeng, Zhoufang; Wang, Yandong; Guo, Xinhua; Wang, Ling; Lu, Nan

    2013-05-21

    In this paper, a novel method has been proposed to achieve selective enrichment and purification of glycoproteins/glycopeptides on a surface patterned sample support, which consists of a hydrophobic outer layer (F-SAM) and an internal boronic acid-modified gold microspot (900 μm). Upon deposition, the sample solution is firstly concentrated in a small area by repulsion of the hydrophobic outer layer, and then the glycoproteins/glycopeptides are selectively captured through boronic acid covalently binding in the inner layer. However, the non-glycosylated proteins/peptides or high concentration salts are removed after rinsing with alkaline solution. As a result, the detection sensitivity is improved by an order of magnitude greater than when using a stainless steel MALDI plate. With surface patterned sample support, the glycoproteins/glycopeptides can be detected even under interference from the excessive existing non-glycosylated proteins/peptides (10 times more than glycoproteins/glycopeptides). Simultaneously, high-quality mass spectra can be obtained even in the presence of urea (1 M), NaCl (1 M), or NH4HCO3 (200 mM). Therefore, this novel technique may be applied to high-throughput analysis of low-abundance glycoproteins/glycopeptides in complicated proteome research.

  20. A novel method for the simultaneous enrichment, identification, and quantification of phosphopeptides and sialylated glycopeptides applied to a temporal profile of mouse brain development.

    PubMed

    Palmisano, Giuseppe; Parker, Benjamin L; Engholm-Keller, Kasper; Lendal, Sara Eun; Kulej, Katarzyna; Schulz, Melanie; Schwämmle, Veit; Graham, Mark E; Saxtorph, Henrik; Cordwell, Stuart J; Larsen, Martin R

    2012-11-01

    We describe a method that combines an optimized titanium dioxide protocol and hydrophilic interaction liquid chromatography to simultaneously enrich, identify and quantify phosphopeptides and formerly N-linked sialylated glycopeptides to monitor changes associated with cell signaling during mouse brain development. We initially applied the method to enriched membrane fractions from HeLa cells, which allowed the identification of 4468 unique phosphopeptides and 1809 formerly N-linked sialylated glycopeptides. We subsequently combined the method with isobaric tagging for relative quantification to compare changes in phosphopeptide and formerly N-linked sialylated glycopeptide abundance in the developing mouse brain. A total of 7682 unique phosphopeptide sequences and 3246 unique formerly sialylated glycopeptides were identified. Moreover 669 phosphopeptides and 300 formerly N-sialylated glycopeptides differentially regulated during mouse brain development were detected. This strategy allowed us to reveal extensive changes in post-translational modifications from postnatal mice from day 0 until maturity at day 80. The results of this study confirm the role of sialylation in organ development and provide the first extensive global view of dynamic changes between N-linked sialylation and phosphorylation.

  1. Base-compositional biases and the bat problem. II. DNA-hybridization trees based on AT- and GC-enriched tracers.

    PubMed Central

    Kirsch, J A; Pettigrew, J D

    1998-01-01

    We conducted a series of parallel DNA-hybridization experiments on a small group of bats (species of Pteropus, Rhinolophus, Noctilio and Pteronotus) and outgroups (Lemur, Cynocephalus, Didelphis), using whole-genome labels and tracers made from extracts enriched with AT and two levels of GC content. FITCH (additive phylogenetic trees) topologies were constructed from the four sets of comparisons, indexed as both delta Tmode and delta NPHs (normalized percentage of hybridization). Based on our previous work showing that the shared AT bias of pteropodids and some microchiropterans may affect the rank-ordering of taxa based on either AT- or GC-rich labels, our expectation was that the resulting trees would show differing topologies when generated from tracers made with the variously enriched DNA extracts. Whereas there was some variation among the trees, most of them grouped the bats together, and almost all paired the representative megachiropteran and rhinolophoid microchiropteran as sister-taxa in contrast to the other microchiropterans. As the pteropodid-rhinolophoid relationship is an unexpected and unlikely one, we attribute this association to an AT bias that was not obviated even by our most GC-rich labels, and suggest that such a bias may compromise the truth of some molecular trees. Accordingly, we believe the broader issue of bat monophyly remains unresolved by DNA-hybridization and probably also by gene-sequencing studies. PMID:9569431

  2. Lutein-enriched emulsion-based delivery systems: Influence of pH and temperature on physical and chemical stability.

    PubMed

    Davidov-Pardo, Gabriel; Gumus, Cansu Ekin; McClements, David Julian

    2016-04-01

    Lutein may be utilized in foods as a natural pigment or nutraceutical ingredient to improve eye health. Nevertheless, its use is limited by its poor water-solubility and chemical instability. We evaluated the effect of storage temperature and pH on the physical and chemical stability of lutein-enriched emulsions prepared using caseinate. The emulsions (initial droplet diameter=232 nm) remained physically stable at all incubation temperatures (5-70 °C); however the chemical degradation of lutein increased with increasing temperature (activation energy=38 kJ/mol). Solution pH had a major impact on the physical stability of the emulsions, causing droplet aggregation at pH 4 and 5. Conversely, the chemical stability of lutein was largely independent of the pH, with only a slight decrease in degradation at pH 8. This work provides important information for the rational design of emulsion-based delivery systems for a lipophilic natural dye and nutraceutical.

  3. Screening key genes and pathways in glioma based on gene set enrichment analysis and meta-analysis.

    PubMed

    Tang, Yanyan; He, Wenwu; Wei, Yunfei; Qu, Zhanli; Zeng, Jinming; Qin, Chao

    2013-06-01

    Glioma is a highly invasive, rapidly spreading form of brain cancer, while its etiology is largely unknown. A few recently reported studies have been developed using gene expression microarrays of glioma to identify differentially expressed genes from several to hundreds. This study was designed to analyze vast amounts of glioma-related microarray data and screen the key genes and pathways related to the development and progression of glioma. We used gene set enrichment analysis (GSEA) and meta-analysis of seven included studies after standardized microarray preprocessing, which increased concordance between these gene datasets. After GSEA, there were 14 mixing pathways including 13 up- and 1 down-regulated pathways. Based on the meta-analysis, 268 significant genes were screened out (P < 0.05); there were 249 genes identified by Kyoto Encyclopedia of Genes and Genomes (KEGG), and 27 KEGG pathways closely related to the set of the imported genes were identified. At last, six consistent pathways and key genes in these pathways related to glioma were obtained with combined GSEA and meta-analysis. The gene pathways that we identified could provide insight concerning the development of glioma. Further studies are needed to determine the biological function for the positive genes.

  4. Family, Employment, and Individual Resource-Based Antecedents of Maternal Work-Family Enrichment from Infancy through Middle Childhood

    PubMed Central

    Zhou, Nan; Buehler, Cheryl

    2015-01-01

    This study used data from the NICHD Study of Early Child Care and Youth Development (N = 1,019) to examine family, employment, and individual antecedents of maternal work-family enrichment from infancy through middle childhood. Work-family conflict and important confounding factors were controlled. From the family domain, higher income-to-needs ratio and social support were associated with higher work-family enrichment. From the employment domain, greater job rewards, benefits of employment for children, and work commitment were associated with higher work-family enrichment. From the individual domain, higher maternal education and extroversion were associated with higher work-family enrichment. No family, employment, and individual characteristics were associated with work-family conflict across time except for partner intimacy. In general, the results supported antecedents of work-family enrichment that supply needed resources. The present study contributed to the literature by identifying antecedents of maternal work-family enrichment across early child developmental stages, which goes beyond examinations of particular life stages and a work-family conflict perspective. Implications for theory and practice are discussed. PMID:26641483

  5. Family, employment, and individual resource-based antecedents of maternal work-family enrichment from infancy through middle childhood.

    PubMed

    Zhou, Nan; Buehler, Cheryl

    2016-07-01

    This study used data from the National Institute of Child Health and Human Development (NICHD) Study of Early Child Care and Youth Development (N = 1,019) to examine family, employment, and individual antecedents of maternal work-family enrichment from infancy through middle childhood. Work-family conflict and important confounding factors were controlled. From the family domain, higher income-to-needs ratio and social support were associated with higher work-family enrichment. From the employment domain, greater job rewards, benefits of employment for children, and work commitment were associated with higher work-family enrichment. From the individual domain, higher maternal education and extroversion were associated with higher work-family enrichment. No family, employment, and individual characteristics were associated with work-family conflict across time except for partner intimacy. In general, the results supported antecedents of work-family enrichment that supply needed resources. The present study contributed to the literature by identifying antecedents of maternal work-family enrichment across early child developmental stages, which goes beyond examinations of particular life stages and a work-family conflict perspective. Implications for theory and practice are discussed. (PsycINFO Database Record

  6. Simultaneous and specific enrichment of several amphenicol antibiotics residues in food based on novel aptamer functionalized magnetic adsorbents using HPLC-DAD.

    PubMed

    Huang, Shengfeng; Gan, Ning; Liu, Haibo; Zhou, You; Chen, Yinji; Cao, Yuting

    2017-08-15

    In this work, a novel aptamer functionalized magnetic adsorbent was developed and combined with magnetic dispersive solid phase extraction (MDSPE) for selective enrichment of several amphenicol antibiotics residues (chloramphenicol(CAP), thiamphenicol(TAP) and florphenicol(FF)) in foodstuff then determined by High Performance Liquid Chromatography (HPLC)-Diode array detector(DAD). Firstly, a magnetic silica-coated Fe3O4 microsphere(Fe3O4@SiO2) was synthetized by sol-gel method, then it was functionalized by amino groups through 3-Aminopropyltriethoxysilane (APTES) reagent to form Fe3O4@SiO2-NH2; Thirdly, the amino group on Fe3O4@SiO2-NH2 was transferred to carboxylic group via the succinic anhydride to form Fe3O4@SiO2-COOH. Finally a kind of DNA aptamer with amino group which can simultaneously recognize CAP, TAP, FF, was functionalized on Fe3O4@SiO2-COOH through adding the EDC/sulfo-NHS coupling reagent (Fe3O4@SiO2@Apt). Therefore, a very stable and useful adsorbent was synthesized for the detection of chloramphenicol series antibiotics. This adsorbent can specifically and simultaneously recognize and enrich CAP, TAP, and FF with high adsorption amount from some complicated food matrix, e.g. milk based on the high affinity of aptamer towards the analytes. The saturated extraction capacities for CAP, TAP and FF by the adsorbent were 2.82, 2.56, 2.72μg/g (mass of target/adsorbent)respectively and the enrichment folds were more than 100 times. Afterwards, the target analytes were washed away by pH 8.5 0.1M Tris-HCl buffer solution and detected by HPLC-DAD. The parameters including extraction temperature, extraction capacity, extraction & desorption pH, extraction & desorption time were investigated. With the optimized conditions, the limits of detection (LOD) and limits of quantitation (LOQ) were 0.12-0.17ng/ml and 0.40-0.55ng/ml for the amphenicols in milk. The adsorbent also has good reproducibility for extraction which can be reused at least for 60 cycles with

  7. Highly efficient preparation of sphingoid bases from glucosylceramides by chemoenzymatic method[S

    PubMed Central

    Gowda, Siddabasave Gowda B.; Usuki, Seigo; Hammam, Mostafa A. S.; Murai, Yuta; Igarashi, Yasuyuki; Monde, Kenji

    2016-01-01

    Sphingoid base derivatives have attracted increasing attention as promising chemotherapeutic candidates against lifestyle diseases such as diabetes and cancer. Natural sphingoid bases can be a potential resource instead of those derived by time-consuming total organic synthesis. In particular, glucosylceramides (GlcCers) in food plants are enriched sources of sphingoid bases, differing from those of animals. Several chemical methodologies to transform GlcCers to sphingoid bases have already investigated; however, these conventional methods using acid or alkaline hydrolysis are not efficient due to poor reaction yield, producing complex by-products and resulting in separation problems. In this study, an extremely efficient and practical chemoenzymatic transformation method has been developed using microwave-enhanced butanolysis of GlcCers and a large amount of readily available almond β-glucosidase for its deglycosylation reaction of lysoGlcCers. The method is superior to conventional acid/base hydrolysis methods in its rapidity and its reaction cleanness (no isomerization, no rearrangement) with excellent overall yield. PMID:26667669

  8. Three-dimensional ordered titanium dioxide-zirconium dioxide film-based microfluidic device for efficient on-chip phosphopeptide enrichment.

    PubMed

    Zhao, De; He, Zhongyuan; Wang, Gang; Wang, Hongzhi; Zhang, Qinghong; Li, Yaogang

    2016-09-15

    Microfluidic technology plays a significant role in separating biomolecules, because of its miniaturization, integration, and automation. Introducing micro/nanostructured functional materials can improve the properties of microfluidic devices, and extend their application. Inverse opal has a three-dimensional ordered net-like structure. It possesses a large surface area and exhibits good mass transport, making it a good candidate for bio-separation. This study exploits inverse opal titanium dioxide-zirconium dioxide films for on-chip phosphopeptide enrichment. Titanium dioxide-zirconium dioxide inverse opal film-based microfluidic devices were constructed from templates of 270-, 340-, and 370-nm-diameter poly(methylmethacrylate) spheres. The phosphopeptide enrichments of these devices were determined by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The device constructed from the 270-nm-diameter sphere template exhibited good comprehensive phosphopeptide enrichment, and was the best among these three devices. Because the size of opal template used in construction was the smallest, the inverse opal film therefore had the smallest pore sizes and the largest surface area. Enrichment by this device was also better than those of similar devices based on nanoparticle films and single component films. The titanium dioxide-zirconium dioxide inverse opal film-based device provides a promising approach for the efficient separation of various biomolecules. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Pressure-assisted electrokinetic injection for on-line enrichment in capillary electrophoresis-mass spectrometry: a sensitive method for measurement of ten haloacetic acids in drinking water.

    PubMed

    Zhang, Huijuan; Zhu, Jiping; Aranda-Rodriguez, Rocio; Feng, Yong-Lai

    2011-11-07

    Haloacetic acids (HAAs) are by-products of the chlorination of drinking water containing natural organic matter and bromide. A simple and sensitive method has been developed for determination of ten HAAs in drinking water. The pressure-assisted electrokinetic injection (PAEKI), an on-line enrichment technique, was employed to introduce the sample into a capillary electrophoresis (CE)-electrospray ionization-tandem mass spectrometry system (ESI-MS/MS). HAAs were monitored in selected reaction monitoring mode. With 3 min of PAEKI time, the ten major HAAs (HAA10) in drinking water were enriched up to 20,000-fold into the capillary without compromising resolution. A simple solid phase clean-up method has been developed to eliminate the influence of ionic matrices from drinking water on PAEKI. Under conditions optimized for mass spectrometry, PAEKI and capillary electrophoresis, detection limits defined as three times ratio of signal to noise have been achieved in a range of 0.013-0.12 μg L(-1) for ten HAAs in water sample. The overall recoveries for all ten HAAs in drinking water samples were between 76 and 125%. Six HAAs including monochloro- (MCAA), dichloro- (DCAA), trichloro- (TCAA), monobromo- (MBAA), bromochloro- (BCAA), and bromodichloroacetic acids (BDCAA) were found in tap water samples collected. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

  10. RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses.

    PubMed

    Shi, Mijuan; Huang, Rong; Du, Fukuan; Pei, Yongyan; Liao, Lanjie; Zhu, Zuoyan; Wang, Yaping

    2014-09-01

    Hemorrhagic disease of the grass carp, Ctenopharyngodon idella, is a fatal disease in fingerlings and yearlings caused by a reovirus, GCRV. RNA-seq data from four diseased grass carp tissues (gill, intestine, liver and spleen) were obtained at 2h before and six times after (2h, 24h, 48h, 72h, 96h and 120h) GCRV challenge. A total of 7.25±0.18 million (M) clean reads and 3.53±0.37M unique reads were obtained per RNA-seq analysis. Compared with controls, there were 9060 unique differentially expressed genes (DEGs) in the four tissues at the six time points post-GCRV challenge. Hierarchical clustering analysis of the DEGs showed that the data from the six time points fell into three branches: 2h, 24h/48h, and 72h/96h/120h. Singular (SEA) and modular enrichment analyses of DEGs per RNA-seq dataset were performed based on gene ontology. The results showed that immune responses occurred in all four tissues, indicating that GCRV probably does not target any tissue specifically. Moreover, during the course of disease, disturbances were observed in lipid and carbohydrate metabolism in each of the organs. SEA of DEGs based on the Kyoto Encyclopedia of Genes and Genomes database was also performed, and this indicated that the complement system and cellular immunity played an important role during the course of hemorrhagic disease. The qPCR of pooled samples of duplicate challenge experiment were used to confirm our RNA-seq approach. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Food Targeting: A Real-Time PCR Assay Targeting 16S rDNA for Direct Quantification of Alicyclobacillus spp. Spores after Aptamer-Based Enrichment.

    PubMed

    Hünniger, Tim; Felbinger, Christine; Wessels, Hauke; Mast, Sophia; Hoffmann, Antonia; Schefer, Anna; Märtlbauer, Erwin; Paschke-Kratzin, Angelika; Fischer, Markus

    2015-05-06

    Spore-forming Alicyclobacillus spp. are able to form metabolites that induce even in small amounts an antiseptical or medicinal off-flavor in fruit juices. Microbial contaminations could occur by endospores, which overcame the pasteurization process. The current detection method for Alicyclobacillus spp. can take up to 1 week because of microbiological enrichment. In a previous study, DNA aptamers were selected and characterized for an aptamer-driven rapid enrichment of Alicyclobacillus spp. spores from orange juice by magnetic separation. In the present work, a direct quantification assay for Alicyclobacillus spp. spores was developed to complete the two-step approach of enrichment and detection. After mechanical treatment of the spores, the isolated DNA was quantified in a real-time PCR-assay targeting 16S rDNA. The assay was evaluated by the performance requirements of the European Network of Genetically Modified Organisms Laboratories (ENGL). Hence, the presented method is applicable for direct spore detection from orange juice in connection with an enrichment step.

  12. Transforming students' views of gerontological nursing: realising the potential of 'enriched' environments of learning and care: a multi-method longitudinal study.

    PubMed

    Brown, Jayne; Nolan, Mike; Davies, Sue; Nolan, Janet; Keady, John

    2008-08-01

    Gerontological nursing is often viewed as unchallenging and is rarely a positive career choice for student nurses. Issues of recruitment and retention in gerontological nursing are a global phenomenon and strategies are needed to encourage more students to opt for this area of work. To identify the role and influence of students' learning experiences on shaping their predispositions to work with older people and to identify the characteristics of a positive learning environment that might promote a more favourable view of gerontological nursing. The study was a 312-year longitudinal investigation using multiple methods of data collection and analysis, including an extensive review of the literature, large-scale postal surveys, focus groups and case studies of clinical placements. The design of the study was emergent and essentially constructivist, and participants, especially student nurses, were actively engaged in the on-going process of data analysis. The results suggest that students do not necessarily enter nurse training with negative predispositions towards work with older adults, but that such negative views develop during their training largely as a result of clinical placements and extra-curricula paid work. Student nurses are often exposed to 'impoverished' environments of care in which they witness poor standards of care and negative attitudes towards older people. However, if they experienced 'enriched' environments they are far more likely to view gerontological nursing in a favourable light. The characteristics of an enriched environment can be understood using the Senses Framework as an analytic lens to interpret students' learning experiences. The study reinforces the vital role that the placement experience plays in helping students to identify with a particular area of practice. The promotion of an 'enriched' environment of learning and care can be used to help ensure that students have a positive experience of learning to care for older people.

  13. Ru-TsDPEN with formic acid/Hunig's base for asymmetric transfer hydrogenation, a practical synthesis of optically enriched N-propyl pantolactam.

    PubMed

    Zhang, Ji; Blazecka, Peter G; Bruendl, Michelle M; Huang, Yun

    2009-02-06

    The Noyori-Ikariya catalysts, Ru-TsDPEN 1 or 2, in combination with HCOOH/Hunig's base (5:2) have been successfully utilized for catalytic asymmetric transfer hydrogenation of alpha-ketopantolactam, and optically enriched N-substituted pantolactam was prepared (S/C = 500, up to 95% ee and 99% conversion in HCOOH/Hunig's base condition). More than 2 kg of this key intermediate 9 has been synthesized efficiently with excellent chemical yield and chiral purity.

  14. Pathway Enrichment Analysis with Networks.

    PubMed

    Liu, Lu; Wei, Jinmao; Ruan, Jianhua

    2017-09-28

    Detecting associations between an input gene set and annotated gene sets (e.g., pathways) is an important problem in modern molecular biology. In this paper, we propose two algorithms, termed NetPEA and NetPEA', for conducting network-based pathway enrichment analysis. Our algorithms consider not only shared genes but also gene-gene interactions. Both algorithms utilize a protein-protein interaction network and a random walk with a restart procedure to identify hidden relationships between an input gene set and pathways, but both use different randomization strategies to evaluate statistical significance and as a result emphasize different pathway properties. Compared to an over representation-based method, our algorithms can identify more statistically significant pathways. Compared to an existing network-based algorithm, EnrichNet, our algorithms have a higher sensitivity in revealing the true causal pathways while at the same time achieving a higher specificity. A literature review of selected results indicates that some of the novel pathways reported by our algorithms are biologically relevant and important. While the evaluations are performed only with KEGG pathways, we believe the algorithms can be valuable for general functional discovery from high-throughput experiments.

  15. Enriching Careers and Lives: Introducing a Positive, Holistic, and Narrative Career Counseling Method that Bridges Theory and Practice

    ERIC Educational Resources Information Center

    Zikic, Jelena; Franklin, Mark

    2010-01-01

    CareerCycles (CC) career counseling framework and method of practice integrates and builds on aspects of positive psychology. Through its holistic and narrative approach, the CC method seeks to collaboratively identify and understand clients' career and life stories. It focuses on their strengths, desires, preferences, assets, future…

  16. Enriching Careers and Lives: Introducing a Positive, Holistic, and Narrative Career Counseling Method that Bridges Theory and Practice

    ERIC Educational Resources Information Center

    Zikic, Jelena; Franklin, Mark

    2010-01-01

    CareerCycles (CC) career counseling framework and method of practice integrates and builds on aspects of positive psychology. Through its holistic and narrative approach, the CC method seeks to collaboratively identify and understand clients' career and life stories. It focuses on their strengths, desires, preferences, assets, future…

  17. Development of a microprocessing-assisted cell-systematic evolution of ligands by exponential enrichment method for human umbilical vein endothelial cells

    NASA Astrophysics Data System (ADS)

    Terazono, Hideyuki; Kim, Hyonchol; Nomura, Fumimasa; Yasuda, Kenji

    2016-06-01

    We developed a microprocessing-assisted technique to select single-strand DNA aptamers that bind to unknown targets on the cell surface by modifying the conventional systematic evolution of ligands by exponential enrichment (cell-SELEX). Our technique involves 1) the specific selection of target-cell-surface-bound aptamers without leakage of intracellular components by trypsinization and 2) cloning of aptamers by microprocessing-assisted picking of single cells using magnetic beads. After cell-SELEX, the enriched aptamers were conjugated with magnetic beads. The aptamer-magnetic beads conjugates attached to target cells were collected individually by microassisted procedures using microneedles under a microscope. After that, the sequences of the collected magnetic-bead-bound aptamers were identified. As a result, a specific aptamer for the surface of target cells, e.g., human umbilical vein endothelial cells (HUVECs), was chosen and its specificity was examined using other cell types, e.g., HeLa cells. The results indicate that this microprocessing-assisted cell-SELEX method for identifying aptamers is applicable in biological research and clinical diagnostics.

  18. GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis.

    PubMed

    Powell, Justin Andrew Christiaan

    2014-05-17

    Despite the widespread use of high throughput expression platforms and the availability of a desktop implementation of Gene Set Enrichment Analysis (GSEA) that enables non-experts to perform gene set based analyses, the availability of the necessary precompiled gene sets is rare for species other than human. A software tool (GO2MSIG) was implemented that combines data from various publicly available sources and uses the Gene Ontology (GO) project term relationships to produce GSEA compatible hierarchical GO based gene sets for all species for which association data is available. Annotation sources include the GO association database (which contains data for over 200000 species), the Entrez gene2go table, and various manufacturers' array annotation files. This enables the creation of gene sets from the most up-to-date annotation data available. Additional features include the ability to restrict by evidence code, to remap gene descriptors, to filter by set size and to speed up repeat queries by caching the GO term hierarchy. Synonymous GO terms are remapped to the version preferred by the GO ontology supplied. The tool can be used in standalone form, or via a web interface. Prebuilt gene set collections constructed from the September 2013 GO release are also available for common species including human. In contrast human GO based sets available from the Broad Institute itself date from 2008. GO2MSIG enables the bioinformatician and non-bioinformatician alike to generate gene sets required for GSEA analysis for almost any organism for which GO term association data exists. The output gene sets may be used directly within GSEA and do not require knowledge of programming languages such as Perl, R or Python. The output sets can also be used with other analysis software such as ErmineJ that accept gene sets in the same format. Source code can be downloaded and installed locally from http://www.bioinformatics.org/go2msig/releases/ or used via the web interface at http

  19. Research on BOM based composable modeling method

    NASA Astrophysics Data System (ADS)

    Zhang, Mingxin; He, Qiang; Gong, Jianxing

    2013-03-01

    Composable modeling method has been a research hotpot in the area of Modeling and Simulation for a long time. In order to increase the reuse and interoperability of BOM based model, this paper put forward a composable modeling method based on BOM, studied on the basic theory of composable modeling method based on BOM, designed a general structure of the coupled model based on BOM, and traversed the structure of atomic and coupled model based on BOM. At last, the paper introduced the process of BOM based composable modeling and made a conclusion on composable modeling method based on BOM. From the prototype we developed and accumulative model stocks, we found this method could increase the reuse and interoperability of models.

  20. IgM-Enriched Human Intravenous Immunoglobulin-Based Treatment of Patients With Early Donor Specific Anti-HLA Antibodies After Lung Transplantation

    PubMed Central

    Ius, Fabio; Sommer, Wiebke; Kieneke, Daniela; Tudorache, Igor; Kühn, Christian; Avsar, Murat; Siemeni, Thierry; Salman, Jawad; Erdfelder, Carolin; Verboom, Murielle; Kielstein, Jan; Tecklenburg, Andreas; Greer, Mark; Hallensleben, Michael; Blasczyk, Rainer; Schwerk, Nicolaus; Gottlieb, Jens; Welte, Tobias; Haverich, Axel; Warnecke, Gregor

    2016-01-01

    Background At our institution, until April 2013, patients who showed early donor specific anti-HLA antibodies (DSA) after lung transplantation were preemptively treated with therapeutic plasma exchange (tPE) and a single dose of Rituximab. In April 2013, we moved to a therapy based on IgM-enriched human immunoglobulins (IVIG), repeated every 4 weeks, and a single dose of Rituximab. Methods This observational study was designed to evaluate the short-term patient and graft survival in patients who underwent IVIG-based DSA treatment (group A, n = 57) versus contemporary patients transplanted between April 2013 and January 2015 without DSA (group C, n = 180), as well as to evaluate DSA clearance in IVIG-treated patients versus historic patients who had undergone tPE-based treatment (group B, n = 56). Patient records were retrospectively reviewed. Follow-up ended on April 1, 2015. Results At 6 months and 1 year of follow-up, group A had a survival similar to group C (P = 0.81) but better than group B (P = 0.008). Group A showed statistically nonsignificant trends toward improved freedom from pulsed-steroid therapy and biopsy-confirmed rejection over groups B and C. The DSA clearance was better in group A than group B at treatment end (92% vs 64%; P = 0.002) and last DSA control (90% vs 75%; P = 0.04). Conclusions Patients with new early DSA but without graft dysfunction that are treated with IVIG and Rituximab have similarly good early survival as contemporary lung transplant recipients without early DSA. The IVIG yielded increased DSA clearance compared with historic tPE-based treatment, yet spontaneous clearance of new DSA also remains common. PMID:26714123

  1. EVALUATION OF CORE PHYSICS ANALYSIS METHODS FOR CONVERSION OF THE INL ADVANCED TEST REACTOR TO LOW-ENRICHMENT FUEL

    SciTech Connect

    Mark DeHart; Gray S. Chang

    2012-04-01

    Computational neutronics studies to support the possible conversion of the ATR to LEU are underway. Simultaneously, INL is engaged in a physics methods upgrade project to put into place modern computational neutronics tools for future support of ATR fuel cycle and experiment analysis. A number of experimental measurements have been performed in the ATRC in support of the methods upgrade project, and are being used to validate the new core physics methods. The current computational neutronics work is focused on performance of scoping calculations for the ATR core loaded with a candidate LEU fuel design. This will serve as independent confirmation of analyses that have been performed previously, and will evaluate some of the new computational methods for analysis of a candidate LEU fuel for ATR.

  2. Quantitative analysis of low-abundance serological proteins with peptide affinity-based enrichment and pseudo-multiple reaction monitoring by hybrid quadrupole time-of-flight mass spectrometry.

    PubMed

    Kim, Kwang Hoe; Ahn, Yeong Hee; Ji, Eun Sun; Lee, Ju Yeon; Kim, Jin Young; An, Hyun Joo; Yoo, Jong Shin

    2015-07-02

    Multiple reaction monitoring (MRM) is commonly used for the quantitative analysis of proteins during mass pectrometry (MS), and has excellent specificity and sensitivity for an analyte in a complex sample. In this study, a pseudo-MRM method for the quantitative analysis of low-abundance serological proteins was developed using hybrid quadrupole time-of-flight (hybrid Q-TOF) MS and peptide affinity-based enrichment. First, a pseudo-MRM-based analysis using hybrid Q-TOF MS was performed for synthetic peptides selected as targets and spiked into tryptic digests of human serum. By integrating multiple transition signals corresponding to fragment ions in the full scan MS/MS spectrum of a precursor ion of the target peptide, a pseudo-MRM MS analysis of the target peptide showed an increased signal-to-noise (S/N) ratio and sensitivity, as well as an improved reproducibility. The pseudo-MRM method was then used for the quantitative analysis of the tryptic peptides of two low-abundance serological proteins, tissue inhibitor of metalloproteinase 1 (TIMP1) and tissue-type protein tyrosine phosphatase kappa (PTPκ), which were prepared with peptide affinity-based enrichment from human serum. Finally, this method was used to detect femtomolar amounts of target peptides derived from TIMP1 and PTPκ, with good coefficients of variation (CV 2.7% and 9.8%, respectively), using a few microliters of human serum from colorectal cancer patients. The results suggest that pseudo-MRM using hybrid Q-TOF MS, combined with peptide affinity-based enrichment, could become a promising alternative for the quantitative analysis of low-abundance target proteins of interest in complex serum samples that avoids protein depletion.

  3. Method of recovering oil-based fluid

    SciTech Connect

    Brinkley, H.E.

    1993-07-13

    A method is described of recovering oil-based fluid, said method comprising the steps of: applying an oil-based fluid absorbent cloth of man-made fiber to an oil-based fluid, the cloth having at least a portion thereof that is napped so as to raise ends and loops of the man-made fibers and define voids; and absorbing the oil-based fluid into the napped portion of the cloth.

  4. A novel reductive graphene oxide-based magnetic molecularly imprinted poly(ethylene-co-vinyl alcohol) polymers for the enrichment and determination of polychlorinated biphenyls in fish samples.

    PubMed

    Lin, Saichai; Gan, Ning; Zhang, Jiabin; Chen, Xidong; Cao, Yuting; Li, Tianhua

    2015-06-01

    The novel reductive graphene oxide-based magnetic molecularly imprinted poly(ethylene-co-vinyl alcohol) polymers (rGO@m-MIPs) were successfully synthesized as adsorbents for six kinds of polychlorinated biphenyls (PCBs) in fish samples. rGO@m-MIPs was prepared by surface molecular imprinting technique. Besides, Fe3 O4 nanoparticles (NPs) were employed as magnetic supporters, and rGO@Fe3 O4 was in situ synthesis. Different from functional monomer and cross-linker in traditional molecularly imprinted polymer, here, 3,4-dichlorobenzidine was employed as dummy molecular and poly(ethylene-co-vinyl alcohol) was adopted as the imprinted polymers. After morphology and inner structure of the magnetic adsorbent were characterized, the adsorbent was employed for disperse solid phase extraction toward PCBs and exhibited great selectivity and high adsorption efficiency. This material was verified by determination of PCBs in fish samples combined with gas chromatography-mass spectrometry (GC-MS) method. According to the detection, the low detection limits (LODs) of PCBs were 0.0035-0.0070 µg l(-1) and spiked recoveries ranged between 79.90 and 94.23%. The prepared adsorbent can be renewable for at least 16 times and expected to be a new material for the enrichment and determination of PCBs from contaminated fish samples.

  5. The Multiple Intelligence Based Enrichment Module on the Development of Human Potential: Examining Its Impact and the Views of Teachers

    ERIC Educational Resources Information Center

    Azid, Nurulwahida Hj; Yaacob, Aizan; Shaik-Abdullah, Sarimah

    2016-01-01

    Purpose: Howard Gardners' concept of multiple intelligence (MI) offers an alternative perspective on intelligence which highlights the importance of acknowledging learner diversity, individual talents and the development of human potentials. MI has been used as a basis for the construction of modular enrichment activities to facilitate the…

  6. No Pain, No Gain? A Resource-Based Model of Work-to-Family Enrichment and Conflict

    ERIC Educational Resources Information Center

    Chen, Zheng; Powell, Gary N.

    2012-01-01

    Work-family scholars tend to work in two largely disconnected research streams, focusing on either work-family enrichment--the positive side of the work-family interface--or work-family conflict--the negative side of this interface. The purpose of this study is to suggest a reconciliation of the two research streams by proposing and testing a…

  7. Real-time pathogen monitoring during enrichment: a novel nanotechnology-based approach to food safety testing.

    PubMed

    Weidemaier, Kristin; Carruthers, Erin; Curry, Adam; Kuroda, Melody; Fallows, Eric; Thomas, Joseph; Sherman, Douglas; Muldoon, Mark

    2015-04-02

    We describe a new approach for the real-time detection and identification of pathogens in food and environmental samples undergoing culture. Surface Enhanced Raman Scattering (SERS) nanoparticles are combined with a novel homogeneous immunoassay to allow sensitive detection of pathogens in complex samples such as stomached food without the need for wash steps or extensive sample preparation. SERS-labeled immunoassay reagents are present in the cultural enrichment vessel, and the signal is monitored real-time through the wall of the vessel while culture is ongoing. This continuous monitoring of pathogen load throughout the enrichment process enables rapid, hands-free detection of food pathogens. Furthermore, the integration of the food pathogen immunoassay directly into the enrichment vessel enables fully biocontained food safety testing, thereby significantly reducing the risk of contaminating the surrounding environment with enriched pathogens. Here, we present experimental results showing the detection of E. coli, Salmonella, or Listeria in several matrices (raw ground beef, raw ground poultry, chocolate milk, tuna salad, spinach, brie cheese, hot dogs, deli turkey, orange juice, cola, and swabs and sponges used to sample a stainless steel surface) using the SERS system and demonstrate the accuracy of the approach compared to plating results.

  8. An alum-based water treatment residual can reduce extractable phosphorus concentrations in three phosphorus-enriched coastal plain soils.

    PubMed

    Novak, J M; Watts, D W

    2005-01-01

    The accumulation of excess soil phosphorus (P) in watersheds under intensive animal production has been linked to increases in dissolved P concentrations in rivers and streams draining these watersheds. Reductions in water dissolved P concentrations through very strong P sorption reactions may be obtainable after land application of alum-based drinking water treatment residuals (WTRs). Our objectives were to (i) evaluate the ability of an alum-based WTR to reduce Mehlich-3 phosphorus (M3P) and water-soluble phosphorus (WSP) concentrations in three P-enriched Coastal Plain soils, (ii) estimate WTR application rates necessary to lower soil M3P levels to a target 150 mg kg(-1) soil M3P concentration threshold level, and (iii) determine the effects on soil pH and electrical conductivity (EC). Three soils containing elevated M3P (145-371 mg kg(-1)) and WSP (12.3-23.5 mg kg(-1)) concentrations were laboratory incubated with between 0 and 6% WTR (w w(-1)) for 84 d. Incorporation of WTR into the three soils caused a near linear and significant reduction in soil M3P and WSP concentrations. In two soils, 6% WTR application caused a soil M3P concentration decrease to below the soil P threshold level. An additional incubation on the third soil using higher WTR to soil treatments (10-15%) was required to reduce the mean soil M3P concentration to 178 mg kg(-1). After incubation, most treatments had less than a half pH unit decline and a slight increase in soil EC values suggesting a minimal impact on soil quality properties. The results showed that WTR incorporation into soils with high P concentrations caused larger relative reductions in extractable WSP than M3P concentrations. The larger relative reductions in the extractable WSP fraction suggest that WTR can be more effective at reducing potential runoff P losses than usage as an amendment to lower M3P concentrations.

  9. A new test method for the assessment of the arc tracking properties of wire insulation in air, oxygen enriched atmospheres and vacuum

    NASA Technical Reports Server (NTRS)

    Koenig, Dieter

    1994-01-01

    Development of a new test method suitable for the assessment of the resistance of aerospace cables to arc tracking for different specific environmental and network conditions of spacecraft is given in view-graph format. The equipment can be easily adapted for tests at different realistic electrical network conditions incorporating circuit protection and the test system works equally well whatever the test atmosphere. Test results confirm that pure Kapton insulated wire has bad arcing characteristics and ETFE insulated wire is considerably better in air. For certain wires, arc tracking effects are increased at higher oxygen concentrations and significantly increased under vacuum. All tests on different cable insulation materials and in different environments, including enriched oxygen atmospheres, resulted in a more or less rapid extinguishing of all high temperature effects at the beginning of the post-test phase. In no case was a self-maintained fire initiated by the arc.

  10. Environmental enrichment for aquatic animals.

    PubMed

    Corcoran, Mike

    2015-05-01

    Aquatic animals are the most popular pets in the United States based on the number of owned pets. They are popular display animals and are increasingly used in research settings. Enrichment of captive animals is an important element of zoo and laboratory medicine. The importance of enrichment for aquatic animals has been slower in implementation. For a long time, there was debate over whether or not fish were able to experience pain or form long-term memories. As that debate has reduced and the consciousness of more aquatic animals is accepted, the need to discuss enrichment for these animals has increased.

  11. Localization of Sphingolipid Enriched Plasma Membrane Regions and Long-Chain Base Composition during Mature-Fruit Abscission in Olive

    PubMed Central

    Parra-Lobato, Maria C.; Paredes, Miguel A.; Labrador, Juana; Saucedo-García, Mariana; Gavilanes-Ruiz, Marina; Gomez-Jimenez, Maria C.

    2017-01-01

    Sphingolipids, found in membranes of eukaryotic cells, have been demonstrated to carry out functions in various processes in plant cells. However, the roles of these lipids in fruit abscission remain to be determined in plants. Biochemical and fluorescence microscopy imaging approach has been adopted to investigate the accumulation and distribution of sphingolipids during mature-fruit abscission in olive (Olea europaea L. cv. Picual). Here, a lipid-content analysis in live protoplasts of the olive abscission zone (AZ) was made with fluorescent dyes and lipid analogs, particularly plasma membrane sphingolipid-enriched domains, and their dynamics were investigated in relation to the timing of mature-fruit abscission. In olive AZ cells, the measured proportion of both polar lipids and sphingolipids increased as well as endocytosis was stimulated during mature-fruit abscission. Likewise, mature-fruit abscission resulted in quantitative and qualitative changes in sphingolipid long-chain bases (LCBs) in the olive AZ. The total LCB increase was due essentially to the increase of t18:1(8E) LCBs, suggesting that C-4 hydroxylation and Δ8 desaturation with a preference for (E)-isomer formation were quantitatively the most important sphingolipids in olive AZ during abscission. However, our results also showed a specific association between the dihydroxylated LCB sphinganine (d18:0) and the mature-fruit abscission. These results indicate a clear correlation between the sphingolipid composition and mature-fruit abscission. Moreover, measurements of endogenous sterol levels in the olive AZ revealed that it accumulated sitosterol and campesterol with a concomitant decrease in cycloartenol during abscission. In addition, underlying the distinct sterol composition of AZ during abscission, genes for key biosynthetic enzymes for sterol synthesis, for obtusifoliol 14α-demethylase (CYP51) and C-24 sterol methyltransferase2 (SMT2), were up-regulated during mature-fruit abscission, in

  12. Localization of Sphingolipid Enriched Plasma Membrane Regions and Long-Chain Base Composition during Mature-Fruit Abscission in Olive.

    PubMed

    Parra-Lobato, Maria C; Paredes, Miguel A; Labrador, Juana; Saucedo-García, Mariana; Gavilanes-Ruiz, Marina; Gomez-Jimenez, Maria C

    2017-01-01

    Sphingolipids, found in membranes of eukaryotic cells, have been demonstrated to carry out functions in various processes in plant cells. However, the roles of these lipids in fruit abscission remain to be determined in plants. Biochemical and fluorescence microscopy imaging approach has been adopted to investigate the accumulation and distribution of sphingolipids during mature-fruit abscission in olive (Olea europaea L. cv. Picual). Here, a lipid-content analysis in live protoplasts of the olive abscission zone (AZ) was made with fluorescent dyes and lipid analogs, particularly plasma membrane sphingolipid-enriched domains, and their dynamics were investigated in relation to the timing of mature-fruit abscission. In olive AZ cells, the measured proportion of both polar lipids and sphingolipids increased as well as endocytosis was stimulated during mature-fruit abscission. Likewise, mature-fruit abscission resulted in quantitative and qualitative changes in sphingolipid long-chain bases (LCBs) in the olive AZ. The total LCB increase was due essentially to the increase of t18:1(8E) LCBs, suggesting that C-4 hydroxylation and Δ8 desaturation with a preference for (E)-isomer formation were quantitatively the most important sphingolipids in olive AZ during abscission. However, our results also showed a specific association between the dihydroxylated LCB sphinganine (d18:0) and the mature-fruit abscission. These results indicate a clear correlation between the sphingolipid composition and mature-fruit abscission. Moreover, measurements of endogenous sterol levels in the olive AZ revealed that it accumulated sitosterol and campesterol with a concomitant decrease in cycloartenol during abscission. In addition, underlying the distinct sterol composition of AZ during abscission, genes for key biosynthetic enzymes for sterol synthesis, for obtusifoliol 14α-demethylase (CYP51) and C-24 sterol methyltransferase2 (SMT2), were up-regulated during mature-fruit abscission, in

  13. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

    PubMed Central

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-01-01

    Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed). PMID:22638583

  14. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.

    PubMed

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-07-01

    Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed).

  15. Impact of McKenzie Method Therapy Enriched by Muscular Energy Techniques on Subjective and Objective Parameters Related to Spine Function in Patients with Chronic Low Back Pain

    PubMed Central

    Szulc, Paweł; Wendt, Michał; Waszak, Małgorzata; Tomczak, Maciej; Cieślik, Krystyna; Trzaska, Tadeusz

    2015-01-01

    Background The high incidence and inconsistencies in diagnostic and therapeutic process of low back pain (LBP) stimulate the continuing search for more efficient treatment modalities. Integration of the information obtained with various therapeutic methods and a holistic approach to the patient seem to be associated with positive outcomes. The aim of this study was to analyze the efficacy of combined treatment with McKenzie method and Muscle Energy Technique (MET), and to compare it with the outcomes of treatment with McKenzie method or standard physiotherapy in specific chronic lumbar pain. Material/Methods The study included 60 men and women with LBP (mean age 44 years). The patients were randomly assigned to 1 of 3 therapeutic groups, which were further treated with: 1) McKenzie method and MET, 2) McKenzie method alone, or 3) standard physiotherapy for 10 days. The extent of spinal movements (electrogoniometry), level of experienced pain (Visual Analogue Scale and Revised Oswestry Pain Questionnaire), and structure of the spinal discs (MRI) were examined prior to the intervention, immediately thereafter, and 3 months after the intervention. Results McKenzie method enriched with MET had the best therapeutic outcomes. The mobility of cervical, thoracic, and lumbar spine normalized at levels corresponding to 87.1%, 66.7%, and 95% of respective average normative values. Implementation of McKenzie method, both alone and combined with MET, was associated with a significant decrease in Oswestry Disability Index, significant alleviation of pain (VAS), and significantly reduced size of spinal disc herniation. Conclusions The combined method can be effectively used in the treatment of chronic LBP. PMID:26418868

  16. A novel tantalum-based sol-gel packed microextraction syringe for highly specific enrichment of phosphopeptides in MALDI-MS applications.

    PubMed

    Çelikbıçak, Ömür; Atakay, Mehmet; Güler, Ülkü; Salih, Bekir

    2013-08-07

    A new tantalum-based sol-gel material was synthesized using a unique sol-gel synthesis pathway by PEG incorporation into the sol-gel structure without performing a calcination step. This improved its chemical and physical properties for the high capacity and selective enrichment of phosphopeptides from protein digests in complex biological media. The specificity of the tantalum-based sol-gel material for phosphopeptides was evaluated and compared with tantalum(V) oxide (Ta2O5) in different phosphopeptide enrichment applications. The tantalum-based sol-gel and tantalum(V) oxide were characterized in detail using FT-IR spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM), and also using a surface area and pore size analyzer. In the characterization studies, the surface morphology, pore volume, crystallinity of the materials and PEG incorporation into the sol-gel structure to produce a more hydrophilic material were successfully demonstrated. The X-ray diffractograms of the two different materials were compared and it was noted that the broad signals of the tantalum-based sol-gel clearly represented the amorphous structure of the sol-gel material, which was more likely to create enough surface area and to provide more accessible tantalum atoms for phosphopeptides to be easily adsorbed when compared with the neat and more crystalline structure of Ta2O5. Therefore, the phosphopeptide enrichment performance of the tantalum-based sol-gels was found to be remarkably higher than the more crystalline Ta2O5 in our studies. Phosphopeptides at femtomole levels could be selectively enriched using the tantalum-based sol-gel and detected with a higher signal-to-noise ratio by matrix-assisted laser desorption/ionization-mass spectrometer (MALDI-MS). Moreover, phosphopeptides in a tryptic digest of non-fat bovine milk as a complex real-world biological sample were retained with higher yield using a tantalum-based sol-gel. Additionally, the sol-gel material

  17. High-Affinity DNA Aptamer Generation Targeting von Willebrand Factor A1-Domain by Genetic Alphabet Expansion for Systematic Evolution of Ligands by Exponential Enrichment Using Two Types of Libraries Composed of Five Different Bases.

    PubMed

    Matsunaga, Ken-Ichiro; Kimoto, Michiko; Hirao, Ichiro

    2017-01-11

    The novel evolutionary engineering method ExSELEX (genetic alphabet expansion for systematic evolution of ligands by exponential enrichment) provides high-affinity DNA aptamers that specifically bind to target molecules, by introducing an artificial hydrophobic base analogue as a fifth component into DNA aptamers. Here, we present a newer version of ExSELEX, using a library with completely randomized sequences consisting of five components: four natural bases and one unnatural hydrophobic base, 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds). In contrast to the limited number of Ds-containing sequence combinations in our previous library, the increased complexity of the new randomized library could improve the success rates of high-affinity aptamer generation. To this end, we developed a sequencing method for each clone in the enriched library after several rounds of selection. Using the improved library, we generated a Ds-containing DNA aptamer targeting von Willebrand factor A1-domain (vWF) with significantly higher affinity (KD = 75 pM), relative to those generated by the initial version of ExSELEX, as well as that of the known DNA aptamer consisting of only the natural bases. In addition, the Ds-containing DNA aptamer was stabilized by introducing a mini-hairpin DNA resistant to nucleases, without any loss of affinity (KD = 61 pM). This new version is expected to consistently produce high-affinity DNA aptamers.

  18. MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency

    PubMed Central

    Klonowska, Katarzyna; Handschuh, Luiza; Swiercz, Aleksandra; Figlerowicz, Marek; Kozlowski, Piotr

    2016-01-01

    Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation of the libraries in terms of exome enrichment efficiency prior to the sequencing step is of considerable importance. Here, we present a strategy for the evaluation of exome enrichment, i.e., the Multipoint Test for Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE for the analysis of subsequent steps of the Illumina TruSeq Exome Enrichment procedure. The calculated values of enrichment-associated parameters (i.e., relative enrichment, relative clearance, overall clearance, and fold enrichment) and the comparison of MTTE results with the actual enrichment revealed the high reliability of our assay. Additionally, the MTTE assay enabled the determination of the sequence-associated features that may confer bias in the enrichment of different targets. Importantly, the MTTE is low cost method that can be easily adapted to the region of interest important for a particular project. Thus, the MTTE strategy is attractive for post-capture validation in a variety of targeted/exome enrichment NGS projects. PMID:27572310

  19. Impulse-based methods for fluid flow

    SciTech Connect

    Cortez, Ricardo

    1995-05-01

    A Lagrangian numerical method based on impulse variables is analyzed. A relation between impulse vectors and vortex dipoles with a prescribed dipole moment is presented. This relation is used to adapt the high-accuracy cutoff functions of vortex methods for use in impulse-based methods. A source of error in the long-time implementation of the impulse method is explained and two techniques for avoiding this error are presented. An application of impulse methods to the motion of a fluid surrounded by an elastic membrane is presented.

  20. An enrichment technique for auxotrophs of Agrobacterium tumefaciens using a combination of carbenicillin and lysozyme.

    PubMed

    Klapwijk, P M; de Jonge, A J; Schilperoort, R A; Rörsch, A

    1975-11-01

    A procedure to enrich for auxotrophic and fermentation mutants of Agrobacterium tumefaciens is described. The method is based on the amplification of the killing power of carbenicillin by the addition of lysozyme. Isolation frequencies of some types of mutants are presented, with and without the application of the proposed procedure. The yield of mutants is usually enhanced a hundredfold per enrichment treatment.

  1. A new method for geochemical anomaly separation based on the distribution patterns of singularity indices

    NASA Astrophysics Data System (ADS)

    Liu, Yue; Zhou, Kefa; Cheng, Qiuming

    2017-08-01

    Singularity analysis is one of the most important models in the fractal/multifractal family that has been demonstrated as an efficient tool for identifying hybrid distribution patterns of geochemical data, such as normal and multifractal distributions. However, the question of how to appropriately separate these patterns using reasonable thresholds has not been well answered. In the present study, a new method termed singularity-quantile (S-Q) analysis was proposed to separate multiple geochemical anomaly populations based on integrating singularity analysis and quantile-quantile plot (QQ-plot) analysis. The new method provides excellent abilities for characterizing frequency distribution patterns of singularity indices by plotting singularity index quantiles vs. standard normal quantiles. From a perspective of geochemical element enrichment processes, distribution patterns of singularity indices can be evidently separated into three groups by means of the new method, corresponding to element enrichment, element generality and element depletion, respectively. A case study for chromitite exploration based on geochemical data in the western Junggar region (China), was employed to examine the potential application of the new method. The results revealed that the proposed method was very sensitive to the changes of singularity indices with three segments when it was applied to characterize geochemical element enrichment processes. And hence, the S-Q method can be considered as an efficient and powerful tool for separating hybrid geochemical anomalies on the basis of statistical and inherent fractal/multifractal properties.

  2. The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus

    PubMed Central

    Shafagati, Nazly; Narayanan, Aarthi; Baer, Alan; Fite, Katherine; Pinkham, Chelsea; Bailey, Charles; Kashanchi, Fatah; Lepene, Benjamin; Kehn-Hall, Kylene

    2013-01-01

    Background Rift Valley Fever Virus (RVFV) is a zoonotic virus that is not only an emerging pathogen but is also considered a biodefense pathogen due to the threat it may cause to public health and national security. The current state of diagnosis has led to misdiagnosis early on in infection. Here we describe the use of a novel sample preparation technology, NanoTrap particles, to enhance the detection of RVFV. Previous studies demonstrated that NanoTrap particles lead to both 100 percent capture of protein analytes as well as an improvement of more than 100-fold in sensitivity compared to existing methods. Here we extend these findings by demonstrating the capture and enrichment of viruses. Results Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. Importantly, NT53 capture of RVFV resulted in greater than 100-fold enrichment from low viral titers when other diagnostics assays may produce false negatives. NT53 was also capable of capturing and enhancing RVFV detection from serum samples. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Furthermore, both NP-40-lysed virus and purified RVFV RNA were bound by NT53. Importantly, NT53 protected viral RNA from RNase A degradation, which was not observed with other commercially available beads. Incubation of RVFV samples with NT53 also resulted in increased viral stability as demonstrated through preservation of infectivity at elevated temperatures. Finally, NanoTrap particles were capable of capturing VEEV and HIV, demonstrating the broad applicability of NanoTrap particles for viral diagnostics. Conclusion This study demonstrates NanoTrap particles are capable of capturing, enriching, and protecting RVFV virions. Furthermore, the use of NanoTrap particles

  3. Heart cells with regenerative potential from pediatric patients with end stage heart failure: a translatable method to enrich and propagate.

    PubMed

    Steele, Ann; Boucek, Robert J; Jacobs, Jeffrey Phillip; Steele, Peter; Asante-Korang, Alfred; Chamizo, Wilfredo; Steele, Jasmine; Chai, Paul J; Quintessenza, James A

    2012-01-01

    Background. Human cardiac-derived progenitor cells (hCPCs) have shown promise in treating heart failure (HF) in adults. The purpose of this study was to describe derivation of hCPCs from pediatric patients with end-stage HF. Methods. At surgery, discarded right atrial tissues (hAA) were obtained from HF patients (n = 25; hAA-CHF). Minced tissues were suspended in complete (serum-containing) DMEM. Cells were selected for their tissue migration and expression of stem cell factor receptor (hc-kit). Characterization of hc-kit(positive) cells included immunohistochemical screening with a panel of monoclonal antibodies. Results. Cells, including phase-bright cells identified as hc-kit(positive), spontaneously emigrated from hAA-CHF in suspended explant cultures (SEC) after Day 7. When cocultured with tissue, emigrated hc-kit(positive) cells proliferated, first as loosely attached clones and later as multicellular clusters. At Day 21~5% of cells were hc-kit(positive). Between Days 14 and 28 hc-kit(positive) cells exhibited mesodermal commitment (GATA-4(positive) and NKX2.5(positive)); then after Day 28 cardiac lineages (flk-1(positive), smooth muscle actin(positive), troponin-I(positive), and myosin light chain(positive)). Conclusions. C-kit(positive) hCPCs can be derived from atrial tissue of pediatric patients with end-stage HF. SEC is a novel culture method for derivation of migratory hc-kit(positive) cells that favors clinical translation by reducing the need for exogenously added factors to expand hCPCs in vitro.

  4. Heart Cells with Regenerative Potential from Pediatric Patients with End Stage Heart Failure: A Translatable Method to Enrich and Propagate

    PubMed Central

    Steele, Ann; Boucek, Robert J.; Jacobs, Jeffrey Phillip; Steele, Peter; Asante-Korang, Alfred; Chamizo, Wilfredo; Steele, Jasmine; Chai, Paul J.; Quintessenza, James A.

    2012-01-01

    Background. Human cardiac-derived progenitor cells (hCPCs) have shown promise in treating heart failure (HF) in adults. The purpose of this study was to describe derivation of hCPCs from pediatric patients with end-stage HF. Methods. At surgery, discarded right atrial tissues (hAA) were obtained from HF patients (n = 25; hAA-CHF). Minced tissues were suspended in complete (serum-containing) DMEM. Cells were selected for their tissue migration and expression of stem cell factor receptor (hc-kit). Characterization of hc-kitpositive cells included immunohistochemical screening with a panel of monoclonal antibodies. Results. Cells, including phase-bright cells identified as hc-kitpositive, spontaneously emigrated from hAA-CHF in suspended explant cultures (SEC) after Day 7. When cocultured with tissue, emigrated hc-kitpositive cells proliferated, first as loosely attached clones and later as multicellular clusters. At Day 21~5% of cells were hc-kitpositive. Between Days 14 and 28 hc-kitpositive cells exhibited mesodermal commitment (GATA-4positive and NKX2.5positive); then after Day 28 cardiac lineages (flk-1positive, smooth muscle actinpositive, troponin-Ipositive, and myosin light chainpositive). Conclusions. C-kitpositive hCPCs can be derived from atrial tissue of pediatric patients with end-stage HF. SEC is a novel culture method for derivation of migratory hc-kitpositive cells that favors clinical translation by reducing the need for exogenously added factors to expand hCPCs in vitro. PMID:22936950

  5. The Melt-Dilute Treatment of Al-Base Highly Enriched DOE Spent Nuclear Fuels: Principles and Practices

    SciTech Connect

    Adams, T.M.

    1998-11-25

    The melt-dilute treatment technology program is focused on the development and implementation of a treatment technology for diluting highly enriched (>20 percent 235U) aluminum spent nuclear fuel to low enriched levels (<20 percent 235U) and qualifying the LEU Al-SNF form for geologic repository storage. In order to reduce the enrichment of these assemblies prior to ultimate geologic repository disposal, the melt-dilute technology proposes to melt these SNF assemblies and then dilute with additions of depleted uranium. The benefits accrued from this treatment process include the potential for significant volume reduction, reduced criticality potential, and the potential for enhanced SNF form characteristics. The emphasis within the development program to date has been on determining the process metallurgy and off-gas system design for the treatment of all types of Al SNF (UAlx, Al-U3O8, and Al-U3Si2). In determining the process metallurgy a wide range of alloys, representative of those expected in the Al-SNF form, have been fabricated and their product characteristics, namely microstructure, homogeneity, phase composition, and "ternary" constituent effects have been analyzed. As a result of the presence of species within the melt which will possess significant vapor pressures in the desired operating temperature range an off-gas system is necessary. Of the volitile species the one of greatest concern is 137Cs.

  6. Identification of Crosslinked Peptides after Click-based Enrichment Using Sequential CID and ETD Tandem Mass Spectrometry

    PubMed Central

    Chowdhury, Saiful M.; Du, Xiuxia; Tolić, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

    2010-01-01

    Chemical crosslinking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of crosslinked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact crosslinkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under condition where the native complex structure is stable. In this study, we present a novel compact crosslinker that contains two distinct features: 1) an alkyne tag and 2) a small molecule detection tag (NO2-) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the crosslinked peptide after proteolytic cleavage after coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO2- moiety provides a secondary means of detecting crosslinked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this crosslinker, which we termed CLIP (Click-enabled Linker for Interacting Proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for crosslinked ubiquitin in highly complex E. coli cell lysates. Sequential CID-MS/MS and ETD-MS/MS of inter-crosslinked peptides (two peptides connected with a crosslinker) are also demonstrated for improved automated identification of crosslinked peptides. PMID:19496583

  7. Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry

    SciTech Connect

    Chowdhury, Saiful M.; Du, Xiuxia; Tolic, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

    2009-07-01

    Chemical cross-linking combined with mass spectrometric analysis is emerging as a powerful technique for protein-protein interaction and protein structure elucidation studies.1 Cross-linkers covalently link two interacting proteins, often with chemistries specific to certain amino acid side chains. After enzymatic digestion of the proteins, the resulting cross-linked peptides can be subjected to analysis by LC-MS(/MS) to identify cross-linked species.2,3 For studying protein interactions using chemical cross-linking towards global discovery-based applications, the critical needs are the development of cross-linkers that are highly specific, amenable to LC-MS/MS, and resulting spectra are interpretable by bioinformatics tools to automatically assign cross-linked peptides with high confidence.4-10 As recently mentioned by Aebersold and co-workers, due to the low relative abundances of cross-linking products compared to their unmodified counterparts, enrichment of cross-linked species is also highly desirable to improve the likelihood of unambiguous identification of cross-linked peptides.6 Most of the currently available enrichable cross-linkers are bulky and are not amenable to studying protein-protein interactions in vivo. To discover protein-protein interactions with high confidence, there is a need for chemical cross-linkers that can effectively label protein complexes, utilize mass spectrometry based bottom-up proteomics analysis pipelines and also contains enrichment functionality.

  8. Augmenting Learning in an Out-of-school Context: The Cognitive and Affective Impact of Two Cryogenics-based Enrichment Programmes on Upper Primary Students

    NASA Astrophysics Data System (ADS)

    Caleon, Imelda S.; Subramaniam, R.

    2007-07-01

    Concepts learned in the classroom were reinforced and augmented by presenting them in a different context using cryogenics-based enrichment programmes (CBEPs) held in an out-of-school setting. The effectiveness of two CBEPs, which involve the use of liquid nitrogen and liquid oxygen, was explored. Using a sample of 265 upper primary students, it was found that both enrichment programmes were effective in promoting the learning of science concepts. Fair improvements, albeit only transient, in two attitude constructs, enjoyment of science and career preference, due to either CBEPs were detected. The CBEPs did not have any significant impact on the attitude construct relating to students’ views on the social implications of science. The impact of CBEPs showed signs of retention, specifically in the cognitive realm, and reasonable indications of influencing subsequent learning and activities of students.

  9. Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications.

    PubMed

    Hoang, Stephen A; Xu, Xiaojiang; Bekiranov, Stefan

    2011-08-11

    The advent of ChIP-seq technology has made the investigation of epigenetic regulatory networks a computationally tractable problem. Several groups have applied statistical computing methods to ChIP-seq datasets to gain insight into the epigenetic regulation of transcription. However, methods for estimating enrichment levels in ChIP-seq data for these computational studies are understudied and variable. Since the conclusions drawn from these data mining and machine learning applications strongly depend on the enrichment level inputs, a comparison of estimation methods with respect to the performance of statistical models should be made. Various methods were used to estimate the gene-wise ChIP-seq enrichment levels for 20 histone methylations and the histone variant H2A.Z. The Multivariate Adaptive Regression Splines (MARS) algorithm was applied for each estimation method using the estimation of enrichment levels as predictors and gene expression levels as responses. The methods used to estimate enrichment levels included tag counting and model-based methods that were applied to whole genes and specific gene