DEFF Research Database (Denmark)
Kristensen, Dan Bach; Brønd, Jan Christian; Nielsen, Peter Aagaard
2004-01-01
LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which...... is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can...
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.
Hazarika, Rashmi R; De Coninck, Barbara; Yamamoto, Lidia R; Martin, Laura R; Cammue, Bruno P A; van Noort, Vera
2017-01-17
Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana. To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www.biw.kuleuven.be/CSB/ARA-PEPs ), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides. To our knowledge, this is the largest repository of plant peptides encoded by sORFs with transcript evidence, publicly available and this resource will help scientists to effortlessly navigate the list of experimentally studied peptides, the experimental and computational evidence supporting the activity of these peptides and gain new perspectives for peptide discovery.
Design and application of a data-independent precursor and product ion repository.
Thalassinos, Konstantinos; Vissers, Johannes P C; Tenzer, Stefan; Levin, Yishai; Thompson, J Will; Daniel, David; Mann, Darrin; DeLong, Mark R; Moseley, M Arthur; America, Antoine H; Ottens, Andrew K; Cavey, Greg S; Efstathiou, Georgios; Scrivens, James H; Langridge, James I; Geromanos, Scott J
2012-10-01
The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative space. Peptide ion map selection for identification and quantification is primarily based on replication and limited variation. The information is stored in a relational database and is used to create peptide- and protein-specific fragment ion maps that can be queried in a targeted fashion against the raw or time aligned ion detections. These queries can be conducted either individually or as groups, where the latter affords pathway and molecular machinery analysis of the protein complement. The presented results also suggest that peptide ionization and fragmentation efficiencies are highly conserved between experiments and practically independent of the analyzed biological sample when using similar instrumentation. Moreover, the data illustrate only minor variation in ionization efficiency with amino acid sequence substitutions occurring between species. Finally, the data and the presented results illustrate how LC-MS performance metrics can be extracted and utilized to ensure optimal performance of the employed analytical workflows.
Identification of candidate sites for a near surface repository for radioactive waste
International Nuclear Information System (INIS)
Motiejunas, S.
2004-01-01
This Report comprises results of the area survey stage, which involves regional screening to define the regions of interest and identification of potential sites within suitable regions. The main goal was to define a few sites potentially suitable for constructing of the near surface repository. It was concluded that a vicinity of Ignalina NPP is among the best suitable regions for the near surface repository. At the present investigation level a ridge in Galilauke village has the most favorable conditions. However, Apvardai site is potentially suitable for the repository too
PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra.
Edwards, Nathan J
2013-12-01
The PepArML meta-search peptide identification platform for tandem mass spectra provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores—reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies two to three times more spectra than individual search engines at 10% FDR.
DEFF Research Database (Denmark)
Hesselager, Marianne Overgaard; Codrea, Marius; Sun, Zhi
2016-01-01
Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data...... repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been...... underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within...
Optimizing the identification of citrullinated peptides by mass spectrometry
DEFF Research Database (Denmark)
Bennike, Tue; Lauridsen, Kasper B.; Olesen, Michael Kruse
2013-01-01
Citrullinated proteins have been associated with several diseases and citrullination can most likely function as a target for novel diagnostic agents and unravel disease etiologies. The correct identification of citrullinated proteins is therefore of most importance. Mass spectrometry (MS) driven...... of trypsin, digestion was performed on synthetic peptide sets containing either arginine or citrulline. The peptide sequences originated from disease-associated in vivo citrullinated proteins; some reported as being C-terminal tryptic citrullinated peptides. Furthermore, the proteolytic activity was verified...
Meyer, Jesse G.; A. Komives, Elizabeth
2012-08-01
We report the effects of supercharging reagents dimethyl sulphoxide (DMSO) and m-nitrobenzyl alcohol ( m-NBA) applied to untargeted peptide identification, with special emphasis on non-tryptic peptides. Peptides generated from a mixture of five standard proteins digested with trypsin, elastase, or pepsin were separated with nanoflow liquid chromatography using mobile phases modified with either 5 % DMSO or 0.1 % m-NBA. Eluting peptides were ionized by online electrospray and sequenced by both CID and ETD using data-dependent MS/MS. Statistically significant improvements in peptide identifications were observed with DMSO co-solvent. In order to understand this observation, we assessed the effects of supercharging reagents on the chromatographic separation and the electrospray quality. The increase in identifications was not due to supercharging, which was greater for the 0.1 % m-NBA co-solvent and not observed for the 5.0 % DMSO co-solvent. The improved MS/MS efficiency using the DMSO modified mobile phase appeared to result from charge state coalescence.
Thiele, H.; Glandorf, J.; Koerting, G.; Reidegeld, K.; Blüggel, M.; Meyer, H.; Stephan, C.
2007-01-01
In today’s proteomics research, various techniques and instrumentation bioinformatics tools are necessary to manage the large amount of heterogeneous data with an automatic quality control to produce reliable and comparable results. Therefore a data-processing pipeline is mandatory for data validation and comparison in a data-warehousing system. The proteome bioinformatics platform ProteinScape has been proven to cover these needs. The reprocessing of HUPO BPP participants’ MS data was done within ProteinScape. The reprocessed information was transferred into the global data repository PRIDE. ProteinScape as a data-warehousing system covers two main aspects: archiving relevant data of the proteomics workflow and information extraction functionality (protein identification, quantification and generation of biological knowledge). As a strategy for automatic data validation, different protein search engines are integrated. Result analysis is performed using a decoy database search strategy, which allows the measurement of the false-positive identification rate. Peptide identifications across different workflows, different MS techniques, and different search engines are merged to obtain a quality-controlled protein list. The proteomics identifications database (PRIDE), as a public data repository, is an archiving system where data are finally stored and no longer changed by further processing steps. Data submission to PRIDE is open to proteomics laboratories generating protein and peptide identifications. An export tool has been developed for transferring all relevant HUPO BPP data from ProteinScape into PRIDE using the PRIDE.xml format. The EU-funded ProDac project will coordinate the development of software tools covering international standards for the representation of proteomics data. The implementation of data submission pipelines and systematic data collection in public standards–compliant repositories will cover all aspects, from the generation of MS data
Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I; Marcotte, Edward M
2011-07-01
Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for every possible PSM and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for most proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses.
Identification of Cyclin A Binders with a Fluorescent Peptide Sensor.
Pazos, Elena; Mascareñas, José L; Vázquez, M Eugenio
2016-01-01
A peptide sensor that integrates the 4-dimethylaminophthalimide (4-DMAP) fluorophore in a short cyclin A binding sequence displays a large fluorescence emission increase upon interacting with the cyclin A Binding Groove (CBG). Competitive displacement assays of this probe allow the straightforward identification of peptides that interact with the CBG, which could potentially block the recognition of CDK/cyclin A kinase substrates.
Peptomics, identification of novel cationic Arabidopsis peptides with conserved sequence motifs
DEFF Research Database (Denmark)
Olsen, Addie Nina; Mundy, John; Skriver, Karen
2002-01-01
Arabidopsis family of 34 genes. The predicted peptides are characterized by a conserved C-terminal sequence motif and additional primary structure conservation in a core region. The majority of these genes had not previously been annotated. A subset of the predicted peptides show high overall sequence...... similarity to Rapid Alkalinization Factor (RALF), a peptide isolated from tobacco. We therefore refer to this peptide family as RALFL for RALF-Like. RT-PCR analysis confirmed that several of the Arabidopsis genes are expressed and that their expression patterns vary. The identification of a large gene family...
SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries*
Wu, Jemma X.; Song, Xiaomin; Pascovici, Dana; Zaw, Thiri; Care, Natasha; Krisp, Christoph; Molloy, Mark P.
2016-01-01
The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at three different ratios to simulate protein abundance change comparisons. SWATH-MS performance was assessed using local and external assay libraries of varying complexities and proteome compositions. These experiments demonstrated that local seed libraries integrated with external assay libraries achieve better performance than local assay libraries alone, in terms of the number of identified peptides and proteins and the specificity to detect differentially abundant proteins. Our findings show that the performance of extended assay libraries is influenced by the MS/MS feature similarity of the seed and external libraries, while statistical analysis using multiple testing corrections increases the statistical rigor needed when searching against large extended assay libraries. PMID:27161445
Directory of Open Access Journals (Sweden)
Madlung Johannes
2010-05-01
Full Text Available Abstract Background Often high-quality MS/MS spectra of tryptic peptides do not match to any database entry because of only partially sequenced genomes and therefore, protein identification requires de novo peptide sequencing. To achieve protein identification of the economically important but still unsequenced plant pathogenic oomycete Plasmopara halstedii, we first evaluated the performance of three different de novo peptide sequencing algorithms applied to a protein digests of standard proteins using a quadrupole TOF (QStar Pulsar i. Results The performance order of the algorithms was PEAKS online > PepNovo > CompNovo. In summary, PEAKS online correctly predicted 45% of measured peptides for a protein test data set. All three de novo peptide sequencing algorithms were used to identify MS/MS spectra of tryptic peptides of an unknown 57 kDa protein of P. halstedii. We found ten de novo sequenced peptides that showed homology to a Phytophthora infestans protein, a closely related organism of P. halstedii. Employing a second complementary approach, verification of peptide prediction and protein identification was performed by creation of degenerate primers for RACE-PCR and led to an ORF of 1,589 bp for a hypothetical phosphoenolpyruvate carboxykinase. Conclusions Our study demonstrated that identification of proteins within minute amounts of sample material improved significantly by combining sensitive LC-MS methods with different de novo peptide sequencing algorithms. In addition, this is the first study that verified protein prediction from MS data by also employing a second complementary approach, in which RACE-PCR led to identification of a novel elicitor protein in P. halstedii.
Li, Ming; Josephs, Ralf D; Daireaux, Adeline; Choteau, Tiphaine; Westwood, Steven; Wielgosz, Robert I; Li, Hongmei
2018-06-04
Peptides are an increasingly important group of biomarkers and pharmaceuticals. The accurate purity characterization of peptide calibrators is critical for the development of reference measurement systems for laboratory medicine and quality control of pharmaceuticals. The peptides used for these purposes are increasingly produced through peptide synthesis. Various approaches (for example mass balance, amino acid analysis, qNMR, and nitrogen determination) can be applied to accurately value assign the purity of peptide calibrators. However, all purity assessment approaches require a correction for structurally related peptide impurities in order to avoid biases. Liquid chromatography coupled to high resolution mass spectrometry (LC-hrMS) has become the key technique for the identification and accurate quantification of structurally related peptide impurities in intact peptide calibrator materials. In this study, LC-hrMS-based methods were developed and validated in-house for the identification and quantification of structurally related peptide impurities in a synthetic human C-peptide (hCP) material, which served as a study material for an international comparison looking at the competencies of laboratories to perform peptide purity mass fraction assignments. More than 65 impurities were identified, confirmed, and accurately quantified by using LC-hrMS. The total mass fraction of all structurally related peptide impurities in the hCP study material was estimated to be 83.3 mg/g with an associated expanded uncertainty of 3.0 mg/g (k = 2). The calibration hierarchy concept used for the quantification of individual impurities is described in detail. Graphical abstract ᅟ.
Tran, Trung T; Bollineni, Ravi C; Strozynski, Margarita; Koehler, Christian J; Thiede, Bernd
2017-07-07
Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant-specific peptide sequences that match to MS data. Furthermore, we combined this database without alternative splice variant-1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies were analyzed using these two databases. Several nonalternative splice variant-1-specific peptides were found in both cell lines, and some of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several nonalternative splice variant-1-specific peptides, and some of them showed clear quantitative differences between the two states.
In-Silico identification of peptides for the diagnostics of paratuberculosis
DEFF Research Database (Denmark)
Tang, Sheila Tuyet; Lund, Ole; Jungersen, Gregers
Identification of bovine MHC class II reactive peptides that are specific/unique to paratuberculosis and conserved across pathogenic variations of the paratuberculosis proteome will be of high value for development of new vaccines and immune based diagnostics. Here, we present an in silico screen...... by statistical significance. BMC Bioinformatics, 2003. 4: p. 21. 2. Nielsen, M., et al., Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol, 2008. 4(7): p. e1000107....
Yu, Wen; Taylor, J Alex; Davis, Michael T; Bonilla, Leo E; Lee, Kimberly A; Auger, Paul L; Farnsworth, Chris C; Welcher, Andrew A; Patterson, Scott D
2010-03-01
Despite recent advances in qualitative proteomics, the automatic identification of peptides with optimal sensitivity and accuracy remains a difficult goal. To address this deficiency, a novel algorithm, Multiple Search Engines, Normalization and Consensus is described. The method employs six search engines and a re-scoring engine to search MS/MS spectra against protein and decoy sequences. After the peptide hits from each engine are normalized to error rates estimated from the decoy hits, peptide assignments are then deduced using a minimum consensus model. These assignments are produced in a series of progressively relaxed false-discovery rates, thus enabling a comprehensive interpretation of the data set. Additionally, the estimated false-discovery rate was found to have good concordance with the observed false-positive rate calculated from known identities. Benchmarking against standard proteins data sets (ISBv1, sPRG2006) and their published analysis, demonstrated that the Multiple Search Engines, Normalization and Consensus algorithm consistently achieved significantly higher sensitivity in peptide identifications, which led to increased or more robust protein identifications in all data sets compared with prior methods. The sensitivity and the false-positive rate of peptide identification exhibit an inverse-proportional and linear relationship with the number of participating search engines.
Sahin, Deniz; Taflan, Sevket Onur; Yartas, Gizem; Ashktorab, Hassan; Smoot, Duane T
2018-04-25
Background: Gastric cancer is the second most common cancer among the malign cancer types. Inefficiency of traditional techniques both in diagnosis and therapy of the disease makes the development of alternative and novel techniques indispensable. As an alternative to traditional methods, tumor specific targeting small peptides can be used to increase the efficiency of the treatment and reduce the side effects related to traditional techniques. The aim of this study is screening and identification of individual peptides specifically targeted to human gastric cancer cells using a phage-displayed peptide library and designing specific peptide sequences by using experimentally-eluted peptide sequences. Methods: Here, MKN-45 human gastric cancer cells and HFE-145 human normal gastric epithelial cells were used as the target and control cells, respectively. 5 rounds of biopannning with a phage display 12-peptide library were applied following subtraction biopanning with HFE-145 control cells. The selected phage clones were established by enzyme-linked immunosorbent assay and immunofluorescence detection. We first obtain random phage clones after five biopanning rounds, determine the binding levels of each individual clone. Then, we analyze the frequencies of each amino acid in best binding clones to determine positively overexpressed amino acids for designing novel peptide sequences. Results: DE532 (VETSQYFRGTLS) phage clone was screened positive, showing specific binding on MKN-45 gastric cancer cells. DE-Obs (HNDLFPSWYHNY) peptide, which was designed by using amino acid frequencies of experimentally selected peptides in the 5th round of biopanning, showed specific binding in MKN-45 cells. Conclusion: Selection and characterization of individual clones may give us specifically binding peptides, but more importantly, data extracted from eluted phage clones may be used to design theoretical peptides with better binding properties than even experimentally selected ones
Proteome identification of the silkworm middle silk gland
Directory of Open Access Journals (Sweden)
Jian-ying Li
2016-03-01
Full Text Available To investigate the functional differentiation among the anterior (A, middle (M, and posterior (P regions of silkworm middle silk gland (MSG, their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014 [1] via the PRIDE partner repository (Vizcaino, 2013 [2] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015 [3]. Keywords: Bombyx mori, Middle silk gland, Silk protein synthesis, Shotgun proteomics, Label-free
Identification of characteristics which influence repository design domal salt, Task 1. Final report
International Nuclear Information System (INIS)
Rawlings, G.; Antonnen, G.; Chamness, M.
1984-04-01
The purpose of the complete project is to provide NRC with technical assistance to enable the focused, adequate review by NRC of the aspects related to design and construction of an underground test facility and final geologic repository as presented by the Department of Energy (DOE). The study presented in this report covers the identification of characteristics which influence design and construction of a geologic repository in domal salt. This report has identified five key issues, i.e., constructibility, thermal response, mechanical response, hydrologic response, and geochemical response. This report involves both short-term (up to closure) and long-term (post closure) effects. The characteristics of domal salt and its environment are described under the headings of stratigraphic/structural, tectonic, mechanical, thermal and hydrologic. Characteristics are separated into parameters (quantified and measured) and factors (qualitative). The characteristics are then subjectively ranked by their influence on the key issues. This takes into account the availability and suitability of conservative design/construction techniques, uncertainty in model and model sensitivity to the characteristic
Vizcaíno, Juan Antonio; Foster, Joseph M.; Martens, Lennart
2010-01-01
Despite the fact that data deposition is not a generalised fact yet in the field of proteomics, several mass spectrometry (MS) based proteomics repositories are publicly available for the scientific community. The main existing resources are: the Global Proteome Machine Database (GPMDB), PeptideAtlas, the PRoteomics IDEntifications database (PRIDE), Tranche, and NCBI Peptidome. In this review the capabilities of each of these will be described, paying special attention to four key properties: data types stored, applicable data submission strategies, supported formats, and available data mining and visualization tools. Additionally, the data contents from model organisms will be enumerated for each resource. There are other valuable smaller and/or more specialized repositories but they will not be covered in this review. Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced. PMID:20615486
Ivanov, Mark V.; Lobas, Anna A.; Levitsky, Lev I.; Moshkovskii, Sergei A.; Gorshkov, Mikhail V.
2018-02-01
In a proteogenomic approach based on tandem mass spectrometry analysis of proteolytic peptide mixtures, customized exome or RNA-seq databases are employed for identifying protein sequence variants. However, the problem of variant peptide identification without personalized genomic data is important for a variety of applications. Following the recent proposal by Chick et al. (Nat. Biotechnol. 33, 743-749, 2015) on the feasibility of such variant peptide search, we evaluated two available approaches based on the previously suggested "open" search and the "brute-force" strategy. To improve the efficiency of these approaches, we propose an algorithm for exclusion of false variant identifications from the search results involving analysis of modifications mimicking single amino acid substitutions. Also, we propose a de novo based scoring scheme for assessment of identified point mutations. In the scheme, the search engine analyzes y-type fragment ions in MS/MS spectra to confirm the location of the mutation in the variant peptide sequence.
Accelerator assisted repositories, technical issue identification and economic assessment
Energy Technology Data Exchange (ETDEWEB)
Myers, T.; Favale, A.; Berwald, D. [Northrop Grumman Corp., Bethpage, NY (United States)
1995-12-31
An investigation (technical and economic) is presented to quantify the impact of accelerator assisted repository (AAR) system on the US national nuclear repository strategy. An overview of US spent fuel policy is presented which provides a means to comparatively assess competing spent fuel disposition technologies under investigation. The advantages of an AAR system are highlighted and discussed. A companion economic analysis is presented. The results indicate that although a US geologic waste repository will continue to be required, waste partitioning and accelerator transmutation of selected actinides, and long-lived fission products, can result in substantial benefits. (author) 18 refs.
A novel algorithm for validating peptide identification from a shotgun proteomics search engine.
Jian, Ling; Niu, Xinnan; Xia, Zhonghang; Samir, Parimal; Sumanasekera, Chiranthani; Mu, Zheng; Jennings, Jennifer L; Hoek, Kristen L; Allos, Tara; Howard, Leigh M; Edwards, Kathryn M; Weil, P Anthony; Link, Andrew J
2013-03-01
Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has revolutionized the proteomics analysis of complexes, cells, and tissues. In a typical proteomic analysis, the tandem mass spectra from a LC-MS/MS experiment are assigned to a peptide by a search engine that compares the experimental MS/MS peptide data to theoretical peptide sequences in a protein database. The peptide spectra matches are then used to infer a list of identified proteins in the original sample. However, the search engines often fail to distinguish between correct and incorrect peptides assignments. In this study, we designed and implemented a novel algorithm called De-Noise to reduce the number of incorrect peptide matches and maximize the number of correct peptides at a fixed false discovery rate using a minimal number of scoring outputs from the SEQUEST search engine. The novel algorithm uses a three-step process: data cleaning, data refining through a SVM-based decision function, and a final data refining step based on proteolytic peptide patterns. Using proteomics data generated on different types of mass spectrometers, we optimized the De-Noise algorithm on the basis of the resolution and mass accuracy of the mass spectrometer employed in the LC-MS/MS experiment. Our results demonstrate De-Noise improves peptide identification compared to other methods used to process the peptide sequence matches assigned by SEQUEST. Because De-Noise uses a limited number of scoring attributes, it can be easily implemented with other search engines.
A peptide affinity column for the identification of integrin alpha IIb-binding proteins.
Daxecker, Heide; Raab, Markus; Bernard, Elise; Devocelle, Marc; Treumann, Achim; Moran, Niamh
2008-03-01
To understand the regulation of integrin alpha(IIb)beta(3), a critical platelet adhesion molecule, we have developed a peptide affinity chromatography method using the known integrin regulatory motif, LAMWKVGFFKR. Using standard Fmoc chemistry, this peptide was synthesized onto a Toyopearl AF-Amino-650 M resin on a 6-aminohexanoic acid (Ahx) linker. Peptide density was controlled by acetylation of 83% of the Ahx amino groups. Four recombinant human proteins (CIB1, PP1, ICln and RN181), previously identified as binding to this integrin regulatory motif, were specifically retained by the column containing the integrin peptide but not by a column presenting an irrelevant peptide. Hemoglobin, creatine kinase, bovine serum albumin, fibrinogen and alpha-tubulin failed to bind under the chosen conditions. Immunodetection methods confirmed the binding of endogenous platelet proteins, including CIB1, PP1, ICln RN181, AUP-1 and beta3-integrin, from a detergent-free platelet lysate. Thus, we describe a reproducible method that facilitates the reliable extraction of specific integrin-binding proteins from complex biological matrices. This methodology may enable the sensitive and specific identification of proteins that interact with linear, membrane-proximal peptide motifs such as the integrin regulatory motif LAMWKVGFFKR.
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
DEFF Research Database (Denmark)
Nielsen, Henrik; Engelbrecht, Jacob; Brunak, Søren
1997-01-01
We have developed a new method for the identification of signal peptides and their cleavage based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence. The method performs significantly better than previous prediction schemes and can easily be applied on genome...
Nongonierma, Alice B; FitzGerald, Richard J
2018-06-01
Milk proteins have been extensively studied for their ability to yield a range of bioactive peptides following enzymatic hydrolysis/digestion. However, many hurdles still exist regarding the widespread utilization of milk protein-derived bioactive peptides as health enhancing agents for humans. These mostly arise from the fact that most milk protein-derived bioactive peptides are not highly potent. In addition, they may be degraded during gastrointestinal digestion and/or have a low intestinal permeability. The targeted release of bioactive peptides during the enzymatic hydrolysis of milk proteins may allow the generation of particularly potent bioactive hydrolysates and peptides. Therefore, the development of milk protein hydrolysates capable of improving human health requires, in the first instance, optimized targeted release of specific bioactive peptides. The targeted hydrolysis of milk proteins has been aided by a range of in silico tools. These include peptide cutters and predictive modeling linking bioactivity to peptide structure [i.e., molecular docking, quantitative structure activity relationship (QSAR)], or hydrolysis parameters [design of experiments (DOE)]. Different targeted enzymatic release strategies employed during the generation of milk protein hydrolysates are reviewed herein and their limitations are outlined. In addition, specific examples are provided to demonstrate how in silico tools may help in the identification and discovery of potent milk protein-derived peptides. It is anticipated that the development of novel strategies employing a range of in silico tools may help in the generation of milk protein hydrolysates containing potent and bioavailable peptides, which in turn may be used to validate their health promoting effects in humans. Graphical abstract The targeted enzymatic hydrolysis of milk proteins may allow the generation of highly potent and bioavailable bioactive peptides.
Identification of ligand-selective peptidic ActRIIB-antagonists using phage display technology
Directory of Open Access Journals (Sweden)
Kotaro Sakamoto
2017-09-01
Full Text Available ActRIIB (activin receptor type-2B is an activin receptor subtype constitutively expressed in the whole body, playing a role in cellular proliferation, differentiation, and metabolism. For its various physiological activities, ActRIIB interacts with activin and multiple other ligands including myostatin (MSTN, growth differentiation factor 11 (GDF11, and bone morphogenetic protein 9 (BMP9. Notably, the protein-protein interaction (PPI between ActRIIB and MSTN negatively controls muscular development. Therefore, this PPI has been targeted for effective treatment of muscle degenerative diseases such as muscular dystrophy and sarcopenia. Here, we report the identification of ligand-selective peptidic ActRIIB-antagonists by phage display technology. Our peptides bound to the extracellular domain of ActRIIB, inhibited PPIs between ActRIIB expressed on the cell surface and its ligands, and subsequently suppressed activation of Smad that serves as the downstream signal of the ActRIIB pathway. Interestingly, these peptidic antagonists displayed different ligand selectivities; the AR2mini peptide inhibited multiple ligands (activin A, MSTN, GDF11, and BMP9, AR9 inhibited MSTN and GDF11, while AR8 selectively inhibited MSTN. This is the first report of artificial peptidic ActRIIB-antagonists possessing ligand-selectivity.
Thangakani, A Mary; Nagarajan, R; Kumar, Sandeep; Sakthivel, R; Velmurugan, D; Gromiha, M Michael
2016-01-01
Accurate distinction between peptide sequences that can form amyloid-fibrils or amorphous β-aggregates, identification of potential aggregation prone regions in proteins, and prediction of change in aggregation rate of a protein upon mutation(s) are critical to research on protein misfolding diseases, such as Alzheimer's and Parkinson's, as well as biotechnological production of protein based therapeutics. We have developed a Curated Protein Aggregation Database (CPAD), which has collected results from experimental studies performed by scientific community aimed at understanding protein/peptide aggregation. CPAD contains more than 2300 experimentally observed aggregation rates upon mutations in known amyloidogenic proteins. Each entry includes numerical values for the following parameters: change in rate of aggregation as measured by fluorescence intensity or turbidity, name and source of the protein, Uniprot and Protein Data Bank codes, single point as well as multiple mutations, and literature citation. The data in CPAD has been supplemented with five different types of additional information: (i) Amyloid fibril forming hexa-peptides, (ii) Amorphous β-aggregating hexa-peptides, (iii) Amyloid fibril forming peptides of different lengths, (iv) Amyloid fibril forming hexa-peptides whose crystal structures are available in the Protein Data Bank (PDB) and (v) Experimentally validated aggregation prone regions found in amyloidogenic proteins. Furthermore, CPAD is linked to other related databases and resources, such as Uniprot, Protein Data Bank, PUBMED, GAP, TANGO, WALTZ etc. We have set up a web interface with different search and display options so that users have the ability to get the data in multiple ways. CPAD is freely available at http://www.iitm.ac.in/bioinfo/CPAD/. The potential applications of CPAD have also been discussed.
Piehowski, Paul D; Petyuk, Vladislav A; Sandoval, John D; Burnum, Kristin E; Kiebel, Gary R; Monroe, Matthew E; Anderson, Gordon A; Camp, David G; Smith, Richard D
2013-03-01
For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Identification of small peptides arising from hydrolysis of meat proteins in dry fermented sausages.
López, Constanza M; Bru, Elena; Vignolo, Graciela M; Fadda, Silvina G
2015-06-01
In this study, proteolysis and low molecular weight (LMW) peptides (<3kDa) from commercial Argentinean fermented sausages were characterized by applying a peptidomic approach. Protein profiles and peptides obtained by Tricine-SDS-PAGE and RP-HPLC-MS, respectively, allowed distinguishing two different types of fermented sausages, although no specific biomarkers relating to commercial brands or quality were recognized. From electrophoresis, α-actin, myoglobin, creatine kinase M-type and L-lactate dehydrogenase were degraded at different intensities. In addition, a partial characterization of fermented sausage peptidome through the identification of 36 peptides, in the range of 1000-2100 Da, arising from sarcoplasmic (28) and myofibrillar (8) proteins was achieved. These peptides had been originated from α-actin, myoglobin, and creatine kinase M-type, but also from the hydrolysis of other proteins not previously reported. Although muscle enzymes exerted a major role on peptidogenesis, microbial contribution cannot be excluded as it was postulated herein. This work represents a first peptidomic approach for fermented sausages, thereby providing a baseline to define key peptides acting as potential biomarkers. Copyright © 2015 Elsevier Ltd. All rights reserved.
Identification of human embryonic progenitor cell targeting peptides using phage display.
Directory of Open Access Journals (Sweden)
Paola A Bignone
Full Text Available Human pluripotent stem (hPS cells are capable of differentiation into derivatives of all three primary embryonic germ layers and can self-renew indefinitely. They therefore offer a potentially scalable source of replacement cells to treat a variety of degenerative diseases. The ability to reprogram adult cells to induced pluripotent stem (iPS cells has now enabled the possibility of patient-specific hPS cells as a source of cells for disease modeling, drug discovery, and potentially, cell replacement therapies. While reprogramming technology has dramatically increased the availability of normal and diseased hPS cell lines for basic research, a major bottleneck is the critical unmet need for more efficient methods of deriving well-defined cell populations from hPS cells. Phage display is a powerful method for selecting affinity ligands that could be used for identifying and potentially purifying a variety of cell types derived from hPS cells. However, identification of specific progenitor cell-binding peptides using phage display may be hindered by the large cellular heterogeneity present in differentiating hPS cell populations. We therefore tested the hypothesis that peptides selected for their ability to bind a clonal cell line derived from hPS cells would bind early progenitor cell types emerging from differentiating hPS cells. The human embryonic stem (hES cell-derived embryonic progenitor cell line, W10, was used and cell-targeting peptides were identified. Competition studies demonstrated specificity of peptide binding to the target cell surface. Efficient peptide targeted cell labeling was accomplished using multivalent peptide-quantum dot complexes as detected by fluorescence microscopy and flow cytometry. The cell-binding peptides were selective for differentiated hPS cells, had little or no binding on pluripotent cells, but preferential binding to certain embryonic progenitor cell lines and early endodermal hPS cell derivatives. Taken
DEFF Research Database (Denmark)
Bundgaard, Louise; Jacobsen, Stine; Sørensen, Mette Aamand
2014-01-01
Progress in MS-based methods for veterinary research and diagnostics is lagging behind compared to the human research, and proteome data of domestic animals is still not well represented in open source data repositories. This is particularly true for the equine species. Here we present a first...... Equine PeptideAtlas encompassing high-resolution tandem MS analyses of 51 samples representing a selection of equine tissues and body fluids from healthy and diseased animals. The raw data were processed through the Trans-Proteomic Pipeline to yield high quality identification of proteins and peptides....... The current release comprises 24 131 distinct peptides representing 2636 canonical proteins observed at false discovery rates of 0.2% at the peptide level and 1.4% at the protein level. Data from the Equine PeptideAtlas are available for experimental planning, validation of new datasets, and as a proteomic...
Complex mixture analysis of peptides using LC/LC-MS/MS and data-dependent protein identification
International Nuclear Information System (INIS)
Wasinger, V.; Corthals, G.
2001-01-01
The comprehensive identification of proteins within complex solutions by mass-spectrometry largely depends on the sensitivity, resolving power and sampling efficiency of the technology. An integrated orthogonal approach using Strong Cation Exchange-Reverse Phase-MS/MS (SCX-RP-MS/MS) was used to evaluate the data-dependent Collision Induced Dissociation (CID) of yeast peptides. Reverse phase gradient times of 4, 10. 30, 90, and 180 minutes allowed the identification of hundreds of proteins in a nearly automated fashion from nuclear, membrane, and cytosolic distributions. Many proteins from typically difficult to resolve regions of two-dimensional gels, such as >100kDa, > pI 9.0 and Codon Adaptation Index < 0.2, were also identified using this multi-dimensional separation technology. Few low mass proteins (<10kDa) were identified. The impact of scan-range and duty-cycle on CID of peptides will be discussed
Directory of Open Access Journals (Sweden)
Fabrice Bertile
2007-01-01
Full Text Available Mass spectrometry-based analyses are essential tools in the field of biomarker research. However, detection and characterization of plasma low abundance and/or low molecular weight peptides is challenged by the presence of highly abundant proteins, salts and lipids. Numerous strategies have already been tested to reduce the complexity of plasma samples. The aim of this study was to enrich the low molecular weight fraction of rat plasma. To this end, we developed and compared simple protocols based on membrane filtration, solid phase extraction, and a combination of both. As assessed by UV absorbance, an albumin depletion 99% was obtained. The multistep fractionation strategy (including reverse phase HPLC allowed detection, in a reproducible manner (CV [1] 30%–35%, of more than 450 peaks below 3000 Da by MALDI-TOF/MS. A MALDI-TOF/MS-determined LOD as low as 1 fmol/μL was obtained, thus allowing nanoLC-Chip/ MS/MS identification of spiked peptides representing ∼10–6% of total proteins, by weight. Signal peptide recovery ranged between 5%–100% according to the spiked peptide considered. Tens of peptide sequence tags from endogenous plasma peptides were also obtained and high confidence identifications of low abundance fibrinopeptide A and B are reported here to show the efficiency of the protocol. It is concluded that the fractionation protocol presented would be of particular interest for future differential (high throughput analyses of the plasma low molecular weight fraction.
Smith, B Eugene; Johnston, Mark K; Lücking, Robert
2016-01-01
Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of
"Design and application of a data-independent precursor and product ion repository."
Thalassinos, K.; Vissers, J.P.; Tenzer, S.; Levin, Y.; Thompson, J.W.; Daniel, D.; Mann, D.; Delong, M.R.; Moseley, M.A.; America, A.H.P.; Ottens, A.K.; Cavey, G.S.; Efstathiou, G.; Scrivens, J.H.; Langridge, J.I.; Geromanos, S.J.
2012-01-01
The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments
Berglund, Sten; Bosson, Emma; Selroos, Jan-Olof; Sassner, Mona
2013-05-01
This paper describes solute transport modeling carried out as a part of an assessment of the long-term radiological safety of a planned deep rock repository for spent nuclear fuel in Forsmark, Sweden. Specifically, it presents transport modeling performed to locate and describe discharge areas for groundwater potentially carrying radionuclides from the repository to the surface where man and the environment could be affected by the contamination. The modeling results show that topography to large extent determines the discharge locations. Present and future lake and wetland objects are central for the radionuclide transport and dose calculations in the safety assessment. Results of detailed transport modeling focusing on the regolith and the upper part of the rock indicate that the identification of discharge areas and objects considered in the safety assessment is robust in the sense that it does not change when a more detailed model representation is used.
Directory of Open Access Journals (Sweden)
Novák Jiří
2013-12-01
Full Text Available The similarity search in theoretical mass spectra generated from protein sequence databases is a widely accepted approach for identification of peptides from query mass spectra produced by shotgun proteomics. Growing protein sequence databases and noisy query spectra demand database indexing techniques and better similarity measures for the comparison of theoretical spectra against query spectra. We employ a modification of previously proposed parameterized Hausdorff distance for comparisons of mass spectra. The new distance outperforms the original distance, the angle distance and state-of-the-art peptide identification tools OMSSA and X!Tandem in the number of identified peptides even though the q-value is only 0.001. When a precursor mass filter is used as a database indexing technique, our method outperforms OMSSA in the speed of search. When variable modifications are not searched, the search time is similar to X!Tandem. We show that the precursor mass filter is an efficient database indexing technique for high-accuracy data even though many variable modifications are being searched. We demonstrate that the number of identified peptides is bigger when variable modifications are searched separately by more search runs of a peptide identification engine. Otherwise, the false discovery rates are affected by mixing unmodified and modified spectra together resulting in a lower number of identified peptides. Our method is implemented in the freely available application SimTandem which can be used in the framework TOPP based on OpenMS.
Rojas, José Manuel; McArdle, Stephanie E B; Horton, Roger B V; Bell, Matthew; Mian, Shahid; Li, Geng; Ali, Selman A; Rees, Robert C
2005-03-01
Because of the central role of CD4(+) T cells in antitumour immunity, the identification of the MHC class II-restricted peptides to which CD4(+) T cells respond has become a priority of tumour immunologists. Here, we describe a strategy permitting us to rapidly determine the immunogenicity of candidate HLA-DR-restricted peptides using peptide immunisation of HLA-DR-transgenic mice, followed by assessment of the response in vitro. This strategy was successfully applied to the reported haemaglutinin influenza peptide HA(307-319), and then extended to three candidate HLA-DR-restricted p53 peptides predicted by the evidence-based algorithm SYFPEITHI to bind to HLA-DRbeta1*0101 (HLA-DR1) and HLA-DRbeta1*0401 (HLA-DR4) molecules. One of these peptides, p53(108-122), consistently induced responses in HLA-DR1- and in HLA-DR4-transgenic mice. Moreover, this peptide was naturally processed by dendritic cells (DCs), and induced specific proliferation in the splenocytes of mice immunised with p53 cDNA, demonstrating that immune responses could be naturally mounted to the peptide. Furthermore, p53(108-122) peptide was also immunogenic in HLA-DR1 and HLA-DR4 healthy donors. Thus, the use of this transgenic model permitted the identification of a novel HLA-DR-restricted epitope from p53 and constitutes an attractive approach for the rapid identification of novel immunogenic MHC class II-restricted peptides from tumour antigens, which can ultimately be incorporated in immunotherapeutic protocols.
Protein identification by peptide mass fingerprinting
DEFF Research Database (Denmark)
Hjernø, Karin
2007-01-01
Peptide mass fingerprinting is an effective way of identifying, e.g., gel-separated proteins, by matching experimentally obtained peptide mass data against large databases. However, several factors are known to influence the quality of the resulting matches, such as proteins contaminating the s...
Directory of Open Access Journals (Sweden)
David Lennartsson
2004-01-01
Full Text Available A novel approach to signal peptide identification is presented. We use an evolutionary algorithm for automatic evolution of classification programs, so-called programmatic motifs. The variant of evolutionary algorithm used is called genetic programming where a population of solution candidates in the form of full computer programs is evolved, based on training examples consisting of signal peptide sequences. The method is compared with a previous work using artificial neural network (ANN approaches. Some advantages compared to ANNs are noted. The programmatic motif can perform computational tasks beyond that of feed-forward neural networks and has also other advantages such as readability. The best motif evolved was analyzed and shown to detect the h-region of the signal peptide. A powerful parallel computer cluster was used for the experiment.
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Magdalena Montowska
2016-01-01
Full Text Available New approaches to rapid examination of proteins and peptides in complex food matrices are of great interest to the community of food scientists. The aim of the study is to examine the influence of microwave irradiation on the acceleration of enzymatic cleavage and enzymatic digestion of denatured proteins in cooked meat of five species (cattle, horse, pig, chicken and turkey and processed meat products (coarsely minced, smoked, cooked and semi-dried sausages. Severe protein aggregation occurred not only in heated meat under harsh treatment at 190 °C but also in processed meat products. All the protein aggregates were thoroughly hydrolyzed aft er 1 h of trypsin treatment with short exposure times of 40 and 20 s to microwave irradiation at 138 and 303 W. There were much more missed cleavage sites observed in all microwave-assisted digestions. Despite the incompleteness of microwave-assisted digestion, six unique peptide markers were detected, which allowed unambiguous identification of processed meat derived from the examined species. Although the microwave-assisted tryptic digestion can serve as a tool for rapid and high-throughput protein identification, great caution and pre-evaluation of individual samples is recommended in protein quantitation.
Peptide de novo sequencing of mixture tandem mass spectra
DEFF Research Database (Denmark)
Gorshkov, Vladimir; Hotta, Stéphanie Yuki Kolbeck; Braga, Thiago Verano
2016-01-01
they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co-isolation and thus prone to false identifications. The deconvolution approach matched...... complementary b-, y-ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co-isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced...... peptides. The improvement was in the range of 20–35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight...
Kirkpatrick, Christine L.; Parsley, Nicole C.; Bartges, Tessa E.; Cooke, Madeline E.; Evans, Wilaysha S.; Heil, Lilian R.; Smith, Thomas J.; Hicks, Leslie M.
2018-05-01
Fungal secondary metabolites represent a rich and largely untapped source for bioactive molecules, including peptides with substantial structural diversity and pharmacological potential. As methods proceed to take a deep dive into fungal genomes, complimentary methods to identify bioactive components are required to keep pace with the expanding fungal repertoire. We developed PepSAVI-MS to expedite the search for natural product bioactive peptides and herein demonstrate proof-of-principle applicability of the pipeline for the discovery of bioactive peptides from fungal secretomes via identification of the antifungal killer toxin KP4 from Ustilago maydis P4. This work opens the door to investigating microbial secretomes with a new lens, and could have broad applications across human health, agriculture, and food safety. [Figure not available: see fulltext.
500 year concrete for a radioactive waste repository
International Nuclear Information System (INIS)
Philipose, K.E.
1988-03-01
The IRUS (Intrusion resistant underground structure) repository planned at Chalk River for the belowground disposal of low level radioactive waste relies on the durability of concrete for the required 500 year service life. A research program for the IRUS repository to design a durable concrete and also to predict its longevity under the repository environment is in progress. The methodology involves the identification of major degradation agents, and the assessment of the rate of diffusion of corrosive ions and/or the rate of advancement of the reaction front into the concrete. Accelerated test methods are being used on laboratory specimens in conjunction with extrapolation procedures to predict long-term durability from short-term data. The inherent limitations are also examined
Wang, Amy Y; Lancaster, William J; Wyatt, Matthew C; Rasmussen, Luke V; Fort, Daniel G; Cimino, James J
2017-01-01
A major challenge in using electronic health record repositories for research is the difficulty matching subject eligibility criteria to query capabilities of the repositories. We propose categories for study criteria corresponding to the effort needed for querying those criteria: "easy" (supporting automated queries), mixed (initial automated querying with manual review), "hard" (fully manual record review), and "impossible" or "point of enrollment" (not typically in health repositories). We obtained a sample of 292 criteria from 20 studies from ClinicalTrials.gov. Six independent reviewers, three each from two academic research institutions, rated criteria according to our four types. We observed high interrater reliability both within and between institutions. The analysis demonstrated typical features of criteria that map with varying levels of difficulty to repositories. We propose using these features to improve enrollment workflow through more standardized study criteria, self-service repository queries, and analyst-mediated retrievals.
DEFF Research Database (Denmark)
Wang, Mingjun; Tang, Sheila Tuyet; Stryhn, Anette
2011-01-01
Major histocompatibility complex (MHC) class I restricted cytotoxic T lymphocytes (CTL) are known to play an important role in the control of Mycobacterium tuberculosis infection so identification of CTL epitopes from M. tuberculosis is of importance for the development of effective peptide...
Directory of Open Access Journals (Sweden)
Lajla Bruntse Hansen
Full Text Available We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2. Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA and from rabbit serum albumin (RSA were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.
Hansen, Lajla Bruntse; Buus, Soren; Schafer-Nielsen, Claus
2013-01-01
We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2). Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA) as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids) at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA) and from rabbit serum albumin (RSA) were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.
A feedback framework for protein inference with peptides identified from tandem mass spectra
Directory of Open Access Journals (Sweden)
Shi Jinhong
2012-11-01
Full Text Available Abstract Background Protein inference is an important computational step in proteomics. There exists a natural nest relationship between protein inference and peptide identification, but these two steps are usually performed separately in existing methods. We believe that both peptide identification and protein inference can be improved by exploring such nest relationship. Results In this study, a feedback framework is proposed to process peptide identification reports from search engines, and an iterative method is implemented to exemplify the processing of Sequest peptide identification reports according to the framework. The iterative method is verified on two datasets with known validity of proteins and peptides, and compared with ProteinProphet and PeptideProphet. The results have shown that not only can the iterative method infer more true positive and less false positive proteins than ProteinProphet, but also identify more true positive and less false positive peptides than PeptideProphet. Conclusions The proposed iterative method implemented according to the feedback framework can unify and improve the results of peptide identification and protein inference.
SwePep, a database designed for endogenous peptides and mass spectrometry.
Fälth, Maria; Sköld, Karl; Norrman, Mathias; Svensson, Marcus; Fenyö, David; Andren, Per E
2006-06-01
A new database, SwePep, specifically designed for endogenous peptides, has been constructed to significantly speed up the identification process from complex tissue samples utilizing mass spectrometry. In the identification process the experimental peptide masses are compared with the peptide masses stored in the database both with and without possible post-translational modifications. This intermediate identification step is fast and singles out peptides that are potential endogenous peptides and can later be confirmed with tandem mass spectrometry data. Successful applications of this methodology are presented. The SwePep database is a relational database developed using MySql and Java. The database contains 4180 annotated endogenous peptides from different tissues originating from 394 different species as well as 50 novel peptides from brain tissue identified in our laboratory. Information about the peptides, including mass, isoelectric point, sequence, and precursor protein, is also stored in the database. This new approach holds great potential for removing the bottleneck that occurs during the identification process in the field of peptidomics. The SwePep database is available to the public.
Data for identification of GPI-anchored peptides and ω-sites in cancer cell lines
Directory of Open Access Journals (Sweden)
Yusuke Masuishi
2016-06-01
Full Text Available We present data obtained using a focused proteomics approach to identify the glycosylphosphatidylinositol (GPI-anchored peptides in 19 human cancer cell lines. GPI-anchored proteins (GPI-APs, which localize to the outer leaflet of the membrane microdomains commonly referred to as lipid rafts play important roles in diverse biological processes. Due to the complex structure of the GPI-anchor moiety, it has been difficult to identify GPI-anchored peptide sequences on the proteomic scale by database searches using tools such as MASCOT. Here we provide data from 73 ω-sites derived from 49 GPI-APs in 19 human cancer cell lines. This article contains data related to the research article entitled “Identification of glycosylphosphatidylinositol-anchored proteins and ω-sites using TiO2-based affinity purification followed by hydrogen fluoride treatment” (Masuishi et al., 2016 [1].
Shen, Bingquan; Zhang, Wanjun; Shi, Zhaomei; Tian, Fang; Deng, Yulin; Sun, Changqing; Wang, Guangshun; Qin, Weijie; Qian, Xiaohong
2017-07-01
O-GlcNAcylation is a kind of dynamic O-linked glycosylation of nucleocytoplasmic and mitochondrial proteins. It serves as a major nutrient sensor to regulate numerous biological processes including transcriptional regulation, cell metabolism, cellular signaling, and protein degradation. Dysregulation of cellular O-GlcNAcylated levels contributes to the etiologies of many diseases such as diabetes, neurodegenerative disease and cancer. However, deeper insight into the biological mechanism of O-GlcNAcylation is hampered by its extremely low stoichiometry and the lack of efficient enrichment approaches for large-scale identification by mass spectrometry. Herein, we developed a novel strategy for the global identification of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry analysis. Standard O-GlcNAc peptides can be efficiently enriched even in the presence of 500-fold more abundant non-O-GlcNAc peptides and identified by mass spectrometry with a low nanogram detection sensitivity. This strategy successfully achieved the first large-scale enrichment and characterization of O-GlcNAc proteins and peptides in human urine. A total of 474 O-GlcNAc peptides corresponding to 457 O-GlcNAc proteins were identified by mass spectrometry analysis, which is at least three times more than that obtained by commonly used enrichment methods. A large number of unreported O-GlcNAc proteins related to cell cycle, biological regulation, metabolic and developmental process were found in our data. The above results demonstrated that this novel strategy is highly efficient in the global enrichment and identification of O-GlcNAc peptides. These data provide new insights into the biological function of O-GlcNAcylation in human urine, which is correlated with the physiological states and pathological changes of human body and therefore indicate the potential of this strategy for biomarker discovery from human urine. Copyright
Directory of Open Access Journals (Sweden)
Yun Li
2016-06-01
Full Text Available Angiotensin I-converting enzyme (ACE inhibitory activity of razor clam hydrolysates produced using five proteases, namely, pepsin, trypsin, alcalase, flavourzyme and proteases from Actinomucor elegans T3 was investigated. Flavourzyme hydrolysate showed the highest level of degree of hydrolysis (DH (45.87% followed by A. elegans T3 proteases hydrolysate (37.84% and alcalase (30.55%. The A. elegans T3 proteases was observed to be more effective in generating small peptides with ACE-inhibitory activity. The 3 kDa membrane permeate of A. elegans T3 proteases hydrolysate showed the highest ACE-inhibitory activity with an IC50 of 0.79 mg/mL. After chromatographic separation by Sephadex G-15 gel filtration and reverse phase-high performance liquid chromatography, the potent fraction was subjected to MALDI/TOF-TOF MS/MS for identification. A novel ACE-inhibitory peptide (VQY was identified exhibiting an IC50 of 9.8 μM. The inhibitory kinetics investigation by Lineweaver-Burk plots demonstrated that the peptide acts as a competitive ACE inhibitor. The razor clam hydrolysate obtained by A. elegans T3 proteases could serve as a source of functional peptides with ACE-inhibitory activity for physiological benefits.
DEFF Research Database (Denmark)
Denholt, Charlotte Lund; Hansen, Paul Robert; Pedersen, Nina
2009-01-01
We report here, the design and synthesis of a positional scanning synthetic combinatorial library for the identification of novel peptide ligands targeted against the cancer-specific epidermal growth factor tyrosine kinase receptor mutation variant III (EGFRvIII). This receptor is expressed in se...
Medicago PhosphoProtein Database: a repository for Medicago truncatula phosphoprotein data
Directory of Open Access Journals (Sweden)
Christopher M. Rose
2012-06-01
Full Text Available The ability of legume crops to fix atmospheric nitrogen via a symbiotic association with soil rhizobia makes them an essential component of many agricultural systems. Initiation of this symbiosis requires protein phosphorylation-mediated signaling in response to rhizobial signals named Nod factors. Medicago truncatula (Medicago is the model system for studying legume biology, making the study of its phosphoproteome essential. Here, we describe the Medicago Phosphoprotein Database (http://phospho.medicago.wisc.edu, a repository built to house phosphoprotein, phosphopeptide, and phosphosite data specific to Medicago. Currently, the Medicago Phosphoprotein Database holds 3,457 unique phosphopeptides that contain 3,404 non-redundant sites of phosphorylation on 829 proteins. Through the web-based interface, users are allowed to browse identified proteins or search for proteins of interest. Furthermore, we allow users to conduct BLAST searches of the database using both peptide sequences and phosphorylation motifs as queries. The data contained within the database are available for download to be investigated at the user’s discretion. The Medicago Phosphoprotein Database will be updated continually with novel phosphoprotein and phosphopeptide identifications, with the intent of constructing an unparalleled compendium of large-scale Medicago phosphorylation data.
Zhang, Zhenbin; Yan, Xiaojing; Sun, Liangliang; Zhu, Guijie; Dovichi, Norman J
2015-04-21
A detachable sulfonate-silica hybrid strong cation-exchange monolith was synthesized in a fused silica capillary, and used for solid phase extraction with online pH gradient elution during capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) proteomic analysis. Tryptic digests were prepared in 50 mM formic acid and loaded onto the strong cation-exchange monolith. Fractions were eluted using a series of buffers with lower concentration but higher pH values than the 50 mM formic acid background electrolyte. This combination of elution and background electrolytes results in both sample stacking and formation of a dynamic pH junction and allows use of relatively large elution buffer volumes while maintaining reasonable peak efficiency and resolution. A series of five pH bumps were applied to elute E. coli tryptic peptides from the monolith, followed by analysis using CZE coupled to an LTQ-Orbitrap Velos mass spectrometer; 799 protein groups and 3381 peptides were identified from 50 ng of the digest in a 2.5 h analysis, which approaches the identification rate for this organism that was obtained with an Orbitrap Fusion. We attribute the improved numbers of peptide and protein identifications to the efficient fractionation by the online pH gradient elution, which decreased the complexity of the sample in each elution step and improved the signal intensity of low abundance peptides. We also performed a comparative analysis using a nanoACQUITY UltraPerformance LCH system. Similar numbers of protein and peptide identifications were produced by the two methods. Protein identifications showed significant overlap between the two methods, whereas peptide identifications were complementary.
Spudy, Björn; Sönnichsen, Frank D; Waetzig, Georg H; Grötzinger, Joachim; Jung, Sascha
2012-10-12
Antimicrobial peptides participate in the first line of defence of many organisms against pathogens. In humans, the family of β-defensins plays a pivotal role in innate immunity. Two human β-defensins, β-defensin-2 and -3 (HBD2 and HBD3), show substantial sequence identity and structural similarity. However, HBD3 kills Staphylococcus (S.) aureus with a 4- to 8-fold higher efficiency compared to HBD2, whereas their activities against Escherichia (E.) coli are very similar. The generation of six HBD2/HBD3-chimeric molecules led to the identification of distinct molecular regions which mediate their divergent killing properties. One of the chimeras (chimera C3) killed both E. coli and S. aureus with an even higher efficacy compared to the wild-type molecules. Due to the broad spectrum of its antimicrobial activity against many human multidrug-resistant pathogens, this HBD2/HBD3-chimeric peptide represents a promising candidate for a new class of antibiotics. In order to investigate the structural basis of its exceptional antimicrobial activity, the peptide's tertiary structure was determined by NMR spectroscopy, which allowed its direct comparison to the published structures of HBD2 and HBD3 and the identification of the activity-increasing molecular features. Copyright © 2012 Elsevier Inc. All rights reserved.
Directory of Open Access Journals (Sweden)
Flanagan Keith
2014-06-01
Full Text Available The rapid and cost-effective identification of bacterial species is crucial, especially for clinical diagnosis and treatment. Peptide aptamers have been shown to be valuable for use as a component of novel, direct detection methods. These small peptides have a number of advantages over antibodies, including greater specificity and longer shelf life. These properties facilitate their use as the detector components of biosensor devices. However, the identification of suitable aptamer targets for particular groups of organisms is challenging. We present a semi-automated processing pipeline for the identification of candidate aptamer targets from whole bacterial genome sequences. The pipeline can be configured to search for protein sequence fragments that uniquely identify a set of strains of interest. The system is also capable of identifying additional organisms that may be of interest due to their possession of protein fragments in common with the initial set. Through the use of Cloud computing technology and distributed databases, our system is capable of scaling with the rapidly growing genome repositories, and consequently of keeping the resulting data sets up-to-date. The system described is also more generically applicable to the discovery of specific targets for other diagnostic approaches such as DNA probes, PCR primers and antibodies.
Flanagan, Keith; Cockell, Simon; Harwood, Colin; Hallinan, Jennifer; Nakjang, Sirintra; Lawry, Beth; Wipat, Anil
2014-06-30
The rapid and cost-effective identification of bacterial species is crucial, especially for clinical diagnosis and treatment. Peptide aptamers have been shown to be valuable for use as a component of novel, direct detection methods. These small peptides have a number of advantages over antibodies, including greater specificity and longer shelf life. These properties facilitate their use as the detector components of biosensor devices. However, the identification of suitable aptamer targets for particular groups of organisms is challenging. We present a semi-automated processing pipeline for the identification of candidate aptamer targets from whole bacterial genome sequences. The pipeline can be configured to search for protein sequence fragments that uniquely identify a set of strains of interest. The system is also capable of identifying additional organisms that may be of interest due to their possession of protein fragments in common with the initial set. Through the use of Cloud computing technology and distributed databases, our system is capable of scaling with the rapidly growing genome repositories, and consequently of keeping the resulting data sets up-to-date. The system described is also more generically applicable to the discovery of specific targets for other diagnostic approaches such as DNA probes, PCR primers and antibodies.
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.
Olexiouk, Volodimir; Van Criekinge, Wim; Menschaert, Gerben
2018-01-04
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs. Furthermore, a novel noise filtering algorithm was designed, able to distinguish sORFs with true ribosomal activity from simulated noise, consequently reducing the false positive identification rate. The inclusion of other species also led to the development of an inner BLAST pipeline, assessing sequence similarity between sORFs in the repository. Building on the proof of concept model in the initial release of sORFs.org, a full PRIDE-ReSpin pipeline was now released, reprocessing publicly available MS-based proteomics PRIDE datasets, reporting on true translation events. Next to reporting those identified peptides, sORFs.org allows visual inspection of the annotated spectra within the Lorikeet MS/MS viewer, thus enabling detailed manual inspection and interpretation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Unwin, Ian; Jansen-van der Vliet, Martine; Westenbrink, Susanne; Presser, Karl; Infanger, Esther; Porubska, Janka; Roe, Mark; Finglas, Paul
2016-02-15
The EuroFIR Document and Data Repositories are being developed as accessible collections of source documents, including grey literature, and the food composition data reported in them. These Repositories will contain source information available to food composition database compilers when selecting their nutritional data. The Document Repository was implemented as searchable bibliographic records in the Europe PubMed Central database, which links to the documents online. The Data Repository will contain original data from source documents in the Document Repository. Testing confirmed the FoodCASE food database management system as a suitable tool for the input, documentation and quality assessment of Data Repository information. Data management requirements for the input and documentation of reported analytical results were established, including record identification and method documentation specifications. Document access and data preparation using the Repositories will provide information resources for compilers, eliminating duplicated work and supporting unambiguous referencing of data contributing to their compiled data. Copyright © 2014 Elsevier Ltd. All rights reserved.
Cimino, James J; Lancaster, William J; Wyatt, Mathew C
2017-01-01
One of the challenges to using electronic health record (EHR) repositories for research is the difficulty mapping study subject eligibility criteria to the query capabilities of the repository. We sought to characterize criteria as "easy" (searchable in a typical repository), "hard" (requiring manual review of the record data), and "impossible" (not typically available in EHR repositories). We obtained 292 criteria from 20 studies available from Clinical Trials.gov and rated them according to our three types, plus a fourth "mixed" type. We had good agreement among three independent reviewers and chose 274 criteria that were characterized by single types for further analysis. The resulting analysis showed typical features of criteria that do and don't map to repositories. We propose that these features be used to guide researchers in specifying eligibility criteria to improve development of enrollment workflow, including the definition of EHR repository queries for self-service or analyst-mediated retrievals.
The preparation and identification of peptide imaging agent of lung cancer
International Nuclear Information System (INIS)
Chu Liping; Wang Yan; Wang Yueying; Liu Jinjian; Wu Hongying; Liu Jianfeng
2010-01-01
Objective: To screen in vivo lung cancer specific binding 7-peptide from T7 phage display random peptide library and prepare peptide imaging agent in early in early diagnosis of lung cancer. Methods: Used phage display in vivo technology to get the 7-peptide phage that can bind the lung cancer specifically, then sequenced and synthesized 7-peptide. After being labeled by 125 I, this 7-peptide was injected into mice via vein and the distribution in the mice tumor mold was observed. Results: One 7-peptide was obtained after four rounds of screening, and the peptide could bind lung cancer tissue specifically. Metabolism of this peptide in mice was fast and imaging of lung cancer was best two hours later after injection. The distribution in vivo decreased and almost disappeared after six hours. Conclusion: This 7-peptide could be used to image and diagnose of lung cancer effectively. (authors)
Preliminary screening and identification of the hepatocarcinoma cell-binding peptide
International Nuclear Information System (INIS)
Zhu Xiaohua; Wu Hua
2004-01-01
Objective: To explore the feasibility of screening and isolating homing peptides that bind specifically, or preferentially, to hepatocarcinoma cells using phage display random peptide library and to develop a new peptide which may be potentially used as targeting delivery carrier in the biological targeted diagnosis or therapy for liver cancer. Methods: A 12-mer peptide phage display library was used to screen and isolate peptides that bind to human hepatocarcinoma cells, and four rounds of subtractive panning were carried out with the human hepatocarcinoma cell line HepG2 as the target. The affinities of selected phage clones for human hepatocarcinoma cells were determined with enzyme-linked immunosorbent assay (ELISA) and compared with that to human liver cell and other tumor cells of different tissue origins, respectively. In addition, the binding site in the tumor cells was observed with immunofluorescence analysis under confocal light microscopy. The amino acid sequences of phages that bind HepG2 specifically were deduced through DNA sequencing. Based on the results of DNA sequence, a 16-mer peptide (WH16) was designed and synthesized. Binding ability of the new peptide, WH16, was determined with competitive inhibition test. Results: After four rounds of panning, the phages that were bound to and internalized in human hepatocarcinoma cells were isolated. ELISA and immunofluorescence analysis confirmed the affinity of these phages for hepatocarcinoma cells. 56.67%(17/30) of the isolated phages displayed repeated sequence FLLEPHLMDTSM, and FLEP was defined as conservative motif . Binding of the selected phage to HepG2 cells was inhibited by synthesized peptide WH16, that strongly support that cellular binding of the phage is mediated through its displayed peptide, and WH16 can also bind to HepG2. Conclusions: It is feasible to screen and isolate homing peptides that bind specifically, or preferentially, to hepatocarcinoma cells using phage display random peptide
Preliminary screening and identification of the hepatocarcinoma cell-binding peptide
Energy Technology Data Exchange (ETDEWEB)
Xiaohua, Zhu; Hua, Wu [Department of Nuclear Medicine, Tongji Hospital, Tongji Medical College, Huazhong Univ. of Science and Technology, Wuhan (China)
2004-12-15
Objective: To explore the feasibility of screening and isolating homing peptides that bind specifically, or preferentially, to hepatocarcinoma cells using phage display random peptide library and to develop a new peptide which may be potentially used as targeting delivery carrier in the biological targeted diagnosis or therapy for liver cancer. Methods: A 12-mer peptide phage display library was used to screen and isolate peptides that bind to human hepatocarcinoma cells, and four rounds of subtractive panning were carried out with the human hepatocarcinoma cell line HepG2 as the target. The affinities of selected phage clones for human hepatocarcinoma cells were determined with enzyme-linked immunosorbent assay (ELISA) and compared with that to human liver cell and other tumor cells of different tissue origins, respectively. In addition, the binding site in the tumor cells was observed with immunofluorescence analysis under confocal light microscopy. The amino acid sequences of phages that bind HepG2 specifically were deduced through DNA sequencing. Based on the results of DNA sequence, a 16-mer peptide (WH16) was designed and synthesized. Binding ability of the new peptide, WH16, was determined with competitive inhibition test. Results: After four rounds of panning, the phages that were bound to and internalized in human hepatocarcinoma cells were isolated. ELISA and immunofluorescence analysis confirmed the affinity of these phages for hepatocarcinoma cells. 56.67%(17/30) of the isolated phages displayed repeated sequence FLLEPHLMDTSM, and FLEP was defined as conservative motif . Binding of the selected phage to HepG2 cells was inhibited by synthesized peptide WH16, that strongly support that cellular binding of the phage is mediated through its displayed peptide, and WH16 can also bind to HepG2. Conclusions: It is feasible to screen and isolate homing peptides that bind specifically, or preferentially, to hepatocarcinoma cells using phage display random peptide
Lafarga, Tomas; O'Connor, Paula; Hayes, Maria
2014-09-01
Angiotensin-I-converting enzyme (ACE-I, EC 3.4.15.1), renin (EC 3.4.23.15), and dipeptidyl peptidase-IV (DPP-IV, EC 3.4.14.5) play key roles in the control of hypertension and the development of type-2 diabetes and other diseases associated with metabolic syndrome. The aim of this work was to utilize known in silico methodologies, peptide databases and software including ProtParam (http://web.expasy.org/protparam/), Basic Local Alignment Tool (BLAST), ExPASy PeptideCutter (http://web.expasy.org/peptide_cutter/) and BIOPEP (http://www.uwm.edu.pl/biochemia/index.php/pl/biopep) to assess the release of potentially bioactive DPP-IV, renin and ACE-I inhibitory peptides from bovine and porcine meat proteins including hemoglobin, collagen and serum albumin. These proteins were chosen as they are found commonly in meat by-products such as bone, blood and low-value meat cuts. In addition, the bioactivities of identified peptides were confirmed using chemical synthesis and in vitro bioassays. The concentration of peptide required to inhibit the activity of ACE-I and DPP-IV by 50% was determined for selected, active peptides. Novel ACE-I and DPP-IV inhibitory peptides were identified in this study using both in silico analysis and a literature search to streamline enzyme selection for peptide production. These novel peptides included the ACE-I inhibitory tri-peptide Ile-Ile-Tyr and the DPP-IV inhibitory tri-peptide Pro-Pro-Leu corresponding to sequences f (182-184) and f (326-328) of both porcine and bovine serum albumin which can be released following hydrolysis with the enzymes papain and pepsin, respectively. This work demonstrates that meat proteins are a suitable resource for the generation of bioactive peptides and further demonstrates the usefulness of in silico methodologies to streamline identification and generation of bioactive peptides. Copyright © 2014 Elsevier Inc. All rights reserved.
THPdb: Database of FDA-approved peptide and protein therapeutics.
Directory of Open Access Journals (Sweden)
Salman Sadullah Usmani
Full Text Available THPdb (http://crdd.osdd.net/raghava/thpdb/ is a manually curated repository of Food and Drug Administration (FDA approved therapeutic peptides and proteins. The information in THPdb has been compiled from 985 research publications, 70 patents and other resources like DrugBank. The current version of the database holds a total of 852 entries, providing comprehensive information on 239 US-FDA approved therapeutic peptides and proteins and their 380 drug variants. The information on each peptide and protein includes their sequences, chemical properties, composition, disease area, mode of activity, physical appearance, category or pharmacological class, pharmacodynamics, route of administration, toxicity, target of activity, etc. In addition, we have annotated the structure of most of the protein and peptides. A number of user-friendly tools have been integrated to facilitate easy browsing and data analysis. To assist scientific community, a web interface and mobile App have also been developed.
DEFF Research Database (Denmark)
Kryuchkov, Fedor; Verano-Braga, Thiago; Hansen, Thomas Aarup
2013-01-01
-resolution orbitrap mass spectrometry, an increase in the number of peptide identifications was obtained relative to the original CAD MS/MS spectra when intensified golden complementary (+18.6%) and CAD complementary pairs (+17.2%) were submitted to the Mascot search engine. This also exceeded the results obtained...
Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.
Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver
2011-08-05
Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine. This approach allows the estimation of p-values for each candidate peptide and their combination across all search engines. The consensus approach works better than any single search engine across all different instrument types considered in this study. Improvements vary strongly from platform to platform and from search engine to search engine. Compared to the industry standard MASCOT, our approach can identify up to 60% more peptides. The software for consensus predictions is implemented in C++ as part of OpenMS, a software framework for mass spectrometry. The source code is available in the current development version of OpenMS and can easily be used as a command line application or via a graphical pipeline designer TOPPAS.
Proteomics data exchange and storage: the need for common standards and public repositories.
Jiménez, Rafael C; Vizcaíno, Juan Antonio
2013-01-01
Both the existence of data standards and public databases or repositories have been key factors behind the development of the existing "omics" approaches. In this book chapter we first review the main existing mass spectrometry (MS)-based proteomics resources: PRIDE, PeptideAtlas, GPMDB, and Tranche. Second, we report on the current status of the different proteomics data standards developed by the Proteomics Standards Initiative (PSI): the formats mzML, mzIdentML, mzQuantML, TraML, and PSI-MI XML are then reviewed. Finally, we present an easy way to query and access MS proteomics data in the PRIDE database, as a representative of the existing repositories, using the workflow management system (WMS) tool Taverna. Two different publicly available workflows are explained and described.
Peptidomic Identification of Cysteine-Rich Peptides from Plants.
Hemu, Xinya; Serra, Aida; Darwis, Dina A; Cornvik, Tobias; Sze, Siu Kwan; Tam, James P
2018-01-01
Plant cysteine-rich peptides (CRPs) constitute a majority of plant-derived peptides with high molecular diversity. This protocol describes a rapid and efficient peptidomic approach to identify a whole spectrum of CRPs in a plant extract and decipher their molecular diversity and bioprocessing mechanism. Cyclotides from C. ternatea are used as the model CRPs to demonstrate our methodology. Cyclotides exist naturally in both cyclic and linear forms, although the linear forms (acyclotide) are generally present at much lower concentrations. Both cyclotides and acyclotides require linearization of their backbone prior to fragmentation and sequencing. A novel and practical three-step chemoenzymatic treatment was developed to linearize and distinguish both forms: (1) N-terminal acetylation that pre-labels the acyclotides; (2) conversion of Cys into pseudo-Lys through aziridine-mediated S-alkylation to reduce disulfide bonds and to increase the net charge of peptides; and (3) opening of cyclic backbones by the novel asparaginyl endopeptidase butelase 2 that cleaves at the native bioprocessing site. The treated peptides are subsequently analyzed by liquid chromatography coupled to mass spectrometry using electron transfer dissociation fragmentation and sequences are identified by matching the MS/MS spectra directly with the transcriptomic database.
Material control and accountability procedures for a waste isolation repository
International Nuclear Information System (INIS)
Jenkins, J.D.; Allen, E.J.; Blakeman, E.D.
1978-05-01
The material control and accountability needs of a waste isolation repository are examined. Three levels of control are discussed: (1) item identification and control, (2) tamper indication, and (3) quantitative material assay. A summary of waste characteristics is presented and, based on these, plus a consideration of the accessibility of the various types of waste, material control by item identification and accountability (where the individual waste container is the basic unit) is recommended. Tamper indicating procedures are also recommended for the intermediate and low level waste categories
International Nuclear Information System (INIS)
1977-06-01
Results of our mining, geological and geotechnical studies provided in support of the development of site suitability criteria for the high level waste repository are presented. The primary purpose of the work was the identification and development of appropriate geotechnical descriptors and coefficients required for the Site Suitability Repository Model. This model was developed by The Analytic Sciences Corporation (TASC) of Reading, Massachusetts and is not described in this report
Energy Technology Data Exchange (ETDEWEB)
1977-06-01
Results of our mining, geological and geotechnical studies provided in support of the development of site suitability criteria for the high level waste repository are presented. The primary purpose of the work was the identification and development of appropriate geotechnical descriptors and coefficients required for the Site Suitability Repository Model. This model was developed by The Analytic Sciences Corporation (TASC) of Reading, Massachusetts and is not described in this report.
Directory of Open Access Journals (Sweden)
King Nichole L
2009-02-01
Full Text Available Abstract Background Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments. Results In this manuscript, we present the Drosophila melanogaster PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal http://www.drosophila-peptideatlas.org allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s in which it was observed. Conclusion PeptideAtlas is an open access database for the Drosophila community that has several features and applications that support (1 reduction of the complexity inherently associated with performing targeted proteomic studies, (2 designing and accelerating shotgun proteomics experiments, (3 confirming or questioning gene models, and (4 adjusting gene models such that they are in line with observed Drosophila peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.
Identification of binding peptides of the ADAM15 disintegrin domain ...
Indian Academy of Sciences (India)
Madhsudhan
ADAM15 disintegrin domain (RADD) that could inhibit melanoma cell adhesion by using Escherichia coli. Second, four specific binding peptides (peptides A, B, C, and D) were selected using a phage display 12-mer peptide library. The screening protocol involved 4 rounds of positive panning on RADD and 2 rounds of ...
Bi, Jianjun; Song, Rengang; Yang, Huilan; Li, Bingling; Fan, Jianyong; Liu, Zhongrong; Long, Chaoqin
2011-01-01
Identification of immunodominant epitopes is the first step in the rational design of peptide vaccines aimed at T-cell immunity. To date, however, it is yet a great challenge for accurately predicting the potent epitope peptides from a pool of large-scale candidates with an efficient manner. In this study, a method that we named StepRank has been developed for the reliable and rapid prediction of binding capabilities/affinities between proteins and genome-wide peptides. In this procedure, instead of single strategy used in most traditional epitope identification algorithms, four steps with different purposes and thus different computational demands are employed in turn to screen the large-scale peptide candidates that are normally generated from, for example, pathogenic genome. The steps 1 and 2 aim at qualitative exclusion of typical nonbinders by using empirical rule and linear statistical approach, while the steps 3 and 4 focus on quantitative examination and prediction of the interaction energy profile and binding affinity of peptide to target protein via quantitative structure-activity relationship (QSAR) and structure-based free energy analysis. We exemplify this method through its application to binding predictions of the peptide segments derived from the 76 known open-reading frames (ORFs) of herpes simplex virus type 1 (HSV-1) genome with or without affinity to human major histocompatibility complex class I (MHC I) molecule HLA-A*0201, and find that the predictive results are well compatible with the classical anchor residue theory and perfectly match for the extended motif pattern of MHC I-binding peptides. The putative epitopes are further confirmed by comparisons with 11 experimentally measured HLA-A*0201-restrcited peptides from the HSV-1 glycoproteins D and K. We expect that this well-designed scheme can be applied in the computational screening of other viral genomes as well.
NPP Krsko: LILW Repository or Long Term Storage
International Nuclear Information System (INIS)
Lokner, V.; Subasic, D.; Levanat, I.
2008-01-01
Construction of the facilities for LILW and SF management, as planned in Decommissioning and LILW and SF management program for NPP Krsko, would be a rather expensive and challenging project for such a small nuclear program. In order to accommodate waste arising from a single nuclear power plant, one LILW repository should be constructed before the end of the NPP operation, then one SF dry storage, and finally one geological repository. This requires relatively urgent identification within Slovenian/Croatian territory of three locations that meet the criteria for establishment of such facilities and are acceptable to the local communities. There are very few such potential locations. The siting process for the first of the three facilities is well under way in Slovenia, because the country wants to have its LILW repository in operation by the year 2013. In order to facilitate public acceptance, Slovenian government has introduced financial incentives to local communities for the repository construction and operation. These 'compensations for limited land use' may significantly increase the overall costs of disposal if the repository is in operation for a long period. In the recent years, however, a possibility of long term storage (LTS) is gaining an increased attention in the waste management community, and has already been introduced e.g. in the Netherlands. It is a particularly viable option for limited waste quantities. Disposal remains the final solution, but present technologies have made possible a relatively inexpensive storage up to about hundred years, which can accommodate LILW, HLW and SF from nuclear programs as well as research reactor waste and NORM. Such storage would be a safe and simple temporary solution, encompassing all immediate and near future waste management needs. In addition, it would increase flexibility and reduce financing requirements for the final waste disposal: providing additional time for reduction of radiation emission and heat
Repository performance confirmation
International Nuclear Information System (INIS)
Hansen, Francis D.
2011-01-01
Yucca Mountain license application identified a broad suite of monitoring activities. A revision of the plan was expected to winnow the number of activities down to a manageable size. As a result, an objective process for the next stage of performance confirmation planning was developed as an integral part of an overarching long-term testing and monitoring strategy. The Waste Isolation Pilot Plant compliance monitoring program at once reflects its importance to stakeholders while demonstrating adequate understanding of relevant monitoring parameters. The compliance criteria were stated by regulation and are currently monitored as part of the regulatory rule for disposal. At the outset, the screening practice and parameter selection were not predicated on a direct or indirect correlation to system performance metrics, as was the case for Yucca Mountain. Later on, correlation to performance was established, and the Waste Isolation Pilot Plant continues to monitor ten parameters originally identified in the compliance certification documentation. The monitoring program has proven to be effective for the technical intentions and societal or public assurance. The experience with performance confirmation in the license application process for Yucca Mountain helped identify an objective, quantitative methodology for this purpose. Revision of the existing plan would be based on findings of the total system performance assessment. Identification and prioritization of confirmation activities would then derive from performance metrics associated with performance assessment. Given the understanding of repository performance confirmation, as reviewed in this paper, it is evident that the performance confirmation program for the Yucca Mountain project could be readily re-engaged if licensing activities resumed.
Geotechnical materials considerations for conceptual repository design in the Palo Duro Basin, Texas
International Nuclear Information System (INIS)
Versluis, W.S.; Balderman, M.A.
1984-01-01
The Palo Duro Basin is only one of numerous potential repository locations for placement of a nuclear waste repository. Conceptual designs in the Palo Duro Basin involve considerations of the character and properties of the geologic materials found on several sites throughout the Basin. The first consideration presented includes current basin exploration results and interpretations of engineering properties for the basin geologic sequences. The next consideration presented includes identification of the characteristics of rock taken from the geologic sequence of interest through laboratory and field testing. Values for materials properties of representative samples are obtained for input into modeling of the material response to repository placement. Conceptual designs which respond to these geotechnical considerations are discussed. 4 references, 4 figures, 4 tables
Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio
2015-03-01
Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Lehman, Rosemary
2007-01-01
This chapter looks at the development and nature of learning objects, meta-tagging standards and taxonomies, learning object repositories, learning object repository characteristics, and types of learning object repositories, with type examples. (Contains 1 table.)
Preliminary screening and identification of the peptide binding to hepatocarcinoma cell
International Nuclear Information System (INIS)
Zhu Xiaohua; Wu Ha
2004-01-01
Objective: The present study was performed to screen and isolate homing peptides that bind specifically, or preferentially, to hepatocarcinoma cells using phage display of random peptide library with the purpose of developing a new peptide which may be potentially used as target delivery carrier in the biological target diagnosis or therapy for liver cancer. Methods: A peptide 12-mer phage display library was used to screen and isolate peptide that bind to human hepatocarcinoma cell, and four rounds subtractive panning were carried out with the human hepatocarcinoma cell line HepG2 as the target. The affinities of selected phage clones to human hepatocarcinoma cell were determined with ELISA and compared with human liver cell and other tumor cells of different tissue origins respectively. In addition, the binding site in the tumor cells was observed with immunofluorescence analysis under confocal light microscopy. The amino acid sequences of phages that bind HepG2 specifically were deduced though DNA sequencing. Based on the results of DNA sequence, a 16-mer peptide (WH16) was designed and synthesized. Binding ability of the new peptide WH16 was determined with competitive inhibition test. Results: After four rounds panning, the phages that bound to and internalized in human hepatocarcinoma cell were isolated. ELISA and immunofluorescence analysis confirmed the affinity of these phages to hepatpcarcinoma cells 56.57%(17/30) of the isolated phages displayed repeated sequence FLLEPHLMDTSM, and FLEP was defined as conservative motif. Binding of the selected phage to HepG2 cells was inhibited by synthesized peptide WH16, which strongly support that cellular binding of phage is mediated though its displayed peptide and WH16 can also bind to HepG2. Conclusion: It is feasible to screen and isolate homing peptides that bind specifically, or preferentially, to hepatocarcinoma cells using phage display of random peptide libraries. The sequence of peptide that can bind to
Preliminary screening and identification of the peptide binding to hepatocarcinoma cell
Energy Technology Data Exchange (ETDEWEB)
Xiaohua, Zhu; Ha, Wu [Department of Nuclear Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan (China)
2004-07-01
Objective: The present study was performed to screen and isolate homing peptides that bind specifically, or preferentially, to hepatocarcinoma cells using phage display of random peptide library with the purpose of developing a new peptide which may be potentially used as target delivery carrier in the biological target diagnosis or therapy for liver cancer. Methods: A peptide 12-mer phage display library was used to screen and isolate peptide that bind to human hepatocarcinoma cell, and four rounds subtractive panning were carried out with the human hepatocarcinoma cell line HepG2 as the target. The affinities of selected phage clones to human hepatocarcinoma cell were determined with ELISA and compared with human liver cell and other tumor cells of different tissue origins respectively. In addition, the binding site in the tumor cells was observed with immunofluorescence analysis under confocal light microscopy. The amino acid sequences of phages that bind HepG2 specifically were deduced though DNA sequencing. Based on the results of DNA sequence, a 16-mer peptide (WH16) was designed and synthesized. Binding ability of the new peptide WH16 was determined with competitive inhibition test. Results: After four rounds panning, the phages that bound to and internalized in human hepatocarcinoma cell were isolated. ELISA and immunofluorescence analysis confirmed the affinity of these phages to hepatpcarcinoma cells 56.57%(17/30) of the isolated phages displayed repeated sequence FLLEPHLMDTSM, and FLEP was defined as conservative motif. Binding of the selected phage to HepG2 cells was inhibited by synthesized peptide WH16, which strongly support that cellular binding of phage is mediated though its displayed peptide and WH16 can also bind to HepG2. Conclusion: It is feasible to screen and isolate homing peptides that bind specifically, or preferentially, to hepatocarcinoma cells using phage display of random peptide libraries. The sequence of peptide that can bind to
Identification of key radionuclides in a nuclear waste repository in basalt
International Nuclear Information System (INIS)
Barney, G.S.; Wood, B.J.
1980-05-01
Radionuclides were identified which appear to pose the greatest potential hazard to man during long-term storage of nuclear waste in a repository mined in the Columbia Plateau basalt formation. The criteria used to select key radionuclides were as follows: quantity of radionuclide in stored waste; biological toxicity; leach rate of the wastes into groundwater; and transport rate via groundwater flow. The waste forms were assumed to be either unreprocessed spent fuel or borosilicate glass containing reprocessed high-level waste. The nuclear waste composition was assumed to be that from a light water reactor. Radionuclides were ranked according to quantity, toxicity, and release rate from the repository. These rankings were combined to obtain a single list of key radionuclides. The ten most important radionuclides in order of decreasing hazard are: 99 Tc, 129 I, 237 Np, 226 Ra, 107 Pd, 230 Th, 210 Pb, 126 Sn, 79 Se, and 242 Pu. Safety assessment studies and the design of engineered barriers should concentrate on containment of radionuclides in this list
Aquatic ecosystem characterisation strategy at a repository site
Energy Technology Data Exchange (ETDEWEB)
Kangasniemi, Ville; Ikonen, Ari T.K. [Environmental Research and Assessment EnviroCase, Ltd., Hallituskatu 1 D 4, 28100 Pori (Finland); Lahdenperae, Anne-Maj [Saanio and Riekkola Oy, Laulukuja 4, 00420 Helsinki (Finland); Kirkkala, Teija [Pyhaejaervi Institute, Sepaentie 7, 27500 Kauttua (Finland); Koivunen, Sari [Water and Environment Research of South-West Finland, Telekatu 16, 20360 Turku (Finland)
2014-07-01
Olkiluoto Island on the western coast of Finland has been selected as a repository site for spent nuclear fuel disposal. According to regulatory requirements, the safety assessment for the repository should have an assessment timeframe of several millennia. Due to the post-glacial land uplift, the relatively shallow sea areas around Olkiluoto Island will change gradually to lakes, rivers and terrestrial areas. As there are no limnic systems at present Olkiluoto site, the reference area was delineated and reference lakes and rivers were selected as an analogue. For the modelling of the transport and accumulation of possible radionuclide releases in the surface environment, aquatic ecosystems were identified and divided into biotopes. Despite the number of available templates, the division of aquatic environment for the biosphere assessment of the Olkiluoto spent fuel repository was necessary to made separately. In this contribution, the processes behind the identification of aquatic ecosystems (e.g. legislation, physical and chemical properties) together with the biotope selection methodology (e.g. light and bottom conditions) and the challenges related to the amount of variable input parameters for each biotope in the modelling are presented. (authors)
Identification and screening of potent antimicrobial peptides in arthropod genomes.
Duwadi, Deepesh; Shrestha, Anishma; Yilma, Binyam; Kozlovski, Itamar; Sa-Eed, Munaya; Dahal, Nikesh; Jukosky, James
2018-05-01
Using tBLASTn and BLASTp searches, we queried recently sequenced arthropod genomes and expressed sequence tags (ESTs) using a database of known arthropod cecropins, defensins, and attacins. We identified and synthesized 6 potential AMPs and screened them for antimicrobial activity. Using radial diffusion assays and microtiter antimicrobial assays, we assessed the in vitro antimicrobial effects of these peptides against several human pathogens including Gram-positive and Gram-negative bacteria and fungi. We also conducted hemolysis assays to examine the cytotoxicity of these peptides to mammalian cells. Four of the six peptides identified showed antimicrobial effects in these assays. We also created truncated versions of these four peptides to assay their antimicrobial activity. Two cecropins derived from the monarch butterfly genome (Danaus plexippus), DAN1 and DAN2, showed minimum inhibitory concentrations (MICs) in the range of 2-16 μg/ml when screened against Gram-negative bacteria. HOLO1 and LOUDEF1, two defensin-like peptides derived from red flour beetle (Tribolium castaneum) and human body louse (Pediculus humanus humanus), respectively, exhibited MICs in the range of 13-25 μg/ml against Gram-positive bacteria. Furthermore, HOLO1 showed an MIC less than 5 μg/ml against the fungal species Candida albicans. These peptides exhibited no hemolytic activity at concentrations up to 200 μg/ml. The truncated peptides derived from DAN2 and HOLO1 showed very little antimicrobial activity. Our experiments show that the peptides DAN1, DAN2, HOLO1, and LOUDEF1 showed potent antimicrobial activity in vitro against common human pathogens, did not lyse mammalian red blood cells, and indicates their potential as templates for novel therapeutic agents against microbial infection. Copyright © 2018 Elsevier Inc. All rights reserved.
Identification of ageing-associated naturally occurring peptides in human urine
Nkuipou-Kenfack, Esther; Bhat, Akshay; Klein, Julie; Jankowski, Vera; Mullen, William; Vlahou, Antonia; Dakna, Mohammed; Koeck, Thomas; Schanstra, Joost P.; Zürbig, Petra; Rudolph, Karl L.; Schumacher, Björn; Pich, Andreas; Mischak, Harald
2015-01-01
To assess normal and pathological peptidomic changes that may lead to an improved understanding of molecular mechanisms underlying ageing, urinary peptidomes of 1227 healthy and 10333 diseased individuals between 20 and 86 years of age were investigated. The diseases thereby comprised diabetes mellitus, renal and cardiovascular diseases. Using age as a continuous variable, 116 peptides were identified that significantly (p age in the healthy cohort. The same approach was applied to the diseased cohort. Upon comparison of the peptide patterns of the two cohorts 112 common age-correlated peptides were identified. These 112 peptides predominantly originated from collagen, uromodulin and fibrinogen. While most fibrillar and basement membrane collagen fragments showed a decreased age-related excretion, uromodulin, beta-2-microglobulin and fibrinogen fragments showed an increase. Peptide-based in silico protease analysis was performed and 32 proteases, including matrix metalloproteinases and cathepsins, were predicted to be involved in ageing. Identified peptides, predicted proteases and patient information were combined in a systems biology pathway analysis to identify molecular pathways associated with normal and/or pathological ageing. While perturbations in collagen homeostasis, trafficking of toll-like receptors and endosomal pathways were commonly identified, degradation of insulin-like growth factor-binding proteins was uniquely identified in pathological ageing. PMID:26431327
International Nuclear Information System (INIS)
Hartman, D.J.; Miller, D.D.; Klamerus, L.J.
1991-10-01
This study recommends which structures, systems, and components of the potential repository at Yucca Mountain are important to safety. The assessment was completed in April 1990 and uses the reference repository configuration in the Site Characterization Plan Conceptual Design Report and follows the methodology required at that time by DOE Procedure AP6.10-Q. Failures of repository items during the preclosure period are evaluated to determine the potential offsite radiation doses and associated probabilities. Items are important to safety if, in the event they fail to perform their intended function, an accident could result which causes a dose commitment greater than 0.5 rem to the whole body or any organ of an individual in an unrestricted area. This study recommends that these repository items include the structures that house spent fuel and high-level waste, the associated filtered ventilation exhaust systems, certain waste- handling equipment, the waste containers, the waste treatment building structure, the underground waste transporters, and other items listed in this report. This work was completed April 1990. 27 refs., 7 figs., 9 tabs
Tu, Chengjian; Sheng, Quanhu; Li, Jun; Ma, Danjun; Shen, Xiaomeng; Wang, Xue; Shyr, Yu; Yi, Zhengping; Qu, Jun
2015-11-06
The two key steps for analyzing proteomic data generated by high-resolution MS are database searching and postprocessing. While the two steps are interrelated, studies on their combinatory effects and the optimization of these procedures have not been adequately conducted. Here, we investigated the performance of three popular search engines (SEQUEST, Mascot, and MS Amanda) in conjunction with five filtering approaches, including respective score-based filtering, a group-based approach, local false discovery rate (LFDR), PeptideProphet, and Percolator. A total of eight data sets from various proteomes (e.g., E. coli, yeast, and human) produced by various instruments with high-accuracy survey scan (MS1) and high- or low-accuracy fragment ion scan (MS2) (LTQ-Orbitrap, Orbitrap-Velos, Orbitrap-Elite, Q-Exactive, Orbitrap-Fusion, and Q-TOF) were analyzed. It was found combinations involving Percolator achieved markedly more peptide and protein identifications at the same FDR level than the other 12 combinations for all data sets. Among these, combinations of SEQUEST-Percolator and MS Amanda-Percolator provided slightly better performances for data sets with low-accuracy MS2 (ion trap or IT) and high accuracy MS2 (Orbitrap or TOF), respectively, than did other methods. For approaches without Percolator, SEQUEST-group performs the best for data sets with MS2 produced by collision-induced dissociation (CID) and IT analysis; Mascot-LFDR gives more identifications for data sets generated by higher-energy collisional dissociation (HCD) and analyzed in Orbitrap (HCD-OT) and in Orbitrap Fusion (HCD-IT); MS Amanda-Group excels for the Q-TOF data set and the Orbitrap Velos HCD-OT data set. Therefore, if Percolator was not used, a specific combination should be applied for each type of data set. Moreover, a higher percentage of multiple-peptide proteins and lower variation of protein spectral counts were observed when analyzing technical replicates using Percolator
Anez, Melissa; Donohue, Tim; Fyson, Will; Simko, Tibor; Wilcox, David
2017-01-01
You’ve got more repository questions and we’ve got more answers! Last year’s Repository Rodeo panel was a huge success, so we’re taking the show on the road to Brisbane for OR2017. Join representatives from the DSpace, Eprints, Fedora, Hydra, and Islandora communities as we (briefly) explain what each of our repositories actually does. We'll also talk about the directions of our respective technical and community developments, and related to the conference theme of Open: Innovation Knowledge Repositories, offer brief observations about the latest, most promising and/or most surprising innovations in our space. This panel will be a great opportunity for newcomers to Open Repositories to get a crash course on the major repository options and meet representatives from each of their communities. After a brief presentation from each representative, we'll open the session up for questions from the audience.
IL17eScan: A Tool for the Identification of Peptides Inducing IL-17 Response
Directory of Open Access Journals (Sweden)
Sudheer Gupta
2017-10-01
Full Text Available IL-17 cytokines are pro-inflammatory cytokines and are crucial in host defense against various microbes. Induction of these cytokines by microbial antigens has been investigated in the case of ischemic brain injury, gingivitis, candidiasis, autoimmune myocarditis, etc. In this study, we have investigated the ability of amino acid sequence of antigens to induce IL-17 response using machine-learning approaches. A total of 338 IL-17-inducing and 984 IL-17 non-inducing peptides were retrieved from Immune Epitope Database. 80% of the data were randomly selected as training dataset and rest 20% as validation dataset. To predict the IL-17-inducing ability of peptides/protein antigens, different sequence-based machine-learning models were developed. The performance of support vector machine (SVM and random forest (RF was compared with different parameters to predict IL-17-inducing epitopes (IIEs. The dipeptide composition-based SVM-model displayed an accuracy of 82.4% with Matthews correlation coefficient = 0.62 at polynomial (t = 1 kernel on 10-fold cross-validation and outperformed RF. Amino acid residues Leu, Ser, Arg, Asn, and Phe and dipeptides LL, SL, LK, IL, LI, NL, LR, FK, SF, and LE are abundant in IIEs. The present tool helps in the identification of IIEs using machine-learning approaches. The induction of IL-17 plays an important role in several inflammatory diseases, and identification of such epitopes would be of great help to the immunologists. It is freely available at http://metagenomics.iiserb.ac.in/IL17eScan/ and http://metabiosys.iiserb.ac.in/IL17eScan/.
Monitoring during the stepwise implementation of the Swedish deep repository for spent fuel
Energy Technology Data Exchange (ETDEWEB)
Baeckblom, Goeran [Conrox (Sweden); Almen, Karl-Erik [KEA Geokonsult AB (Sweden)
2004-03-01
monitoring are to: obtain knowledge of undisturbed conditions in nature and their seasonal variations (baseline) in order to identify and evaluate the impact of activities related to the deep repository during different phases, obtain a better understanding of the function of the deep repository system to support the safety account and to test models and assumptions, monitor the environmental impact of the deep repository, provide evidence that the working environment is safe with regard to radiological and non-radiological effects, show that requirements on radioactive waste verification (safeguards) are fulfilled. The monitoring is concerned with bedrock conditions before and during construction and operation of the facilities, active design to engineer the underground facilities based on monitoring results during construction, the safe and environmental construction and operation of facilities. Experience exists from monitoring of the barrier function at SFR, the final repository for low - and intermediate level waste and at the Aespoe Hard Rock Laboratory and monitoring for safeguard at CLAB, the interim storage for spent nuclear fuel. The know-how on monitoring relates to all aspects from design, installation, operation and maintenance to decommissioning of systems. This report provides an overview of the features, processes and parameters that are collected during the site investigations to establish the Primary Baseline conditions for monitoring prior to the construction of the repository. It is also proposed that the monitoring programme should at least entail the following elements: objectives for the monitoring programme, scope for the monitoring (criteria for selection of issues to be monitored, identification of the properties, processes, phenomena and observable quantities to be monitored), identification on what methods to be used, operation of the monitoring system (identification of the duration and frequency of monitoring, including criteria for when
EEI/UWASTE oversight of the DOE Repository Program by the Repository Information Exchange Team
International Nuclear Information System (INIS)
Henkel, C.J.; Supko, E.M.; Schwartz, M.H.
1993-01-01
The Utility Nuclear Waste and Transportation Program of the Edison Electric Institute (EEI/UWASTE) has conducted reviews of the US DOE's repository program through its Repository Information Exchange Team (RIET or Team). Eight such reviews have been conducted since 1985 covering topics that include repository program management and control; repository schedule; repository budget; quality assurance; site characterization; repository licensing; environmental issues; and institutional and public information activities. The utility industry has used these repository program reviews as a forum for providing DOE's Office of Civilian Radioactive Waste Management (OCRWM) with comments on the direction of the repository program, advice for future actions regarding quality assurance activities and repository licensing, and suggestions for management and control of the Repository Program. The most significant recommendations made by the utility industry through the RIET are discussed along with any subsequent action by OCRWM in response to or subsequent to utility industry recommendations. The process used by the RIET to develop its recommendations to OCRWM regarding the repository program is also discussed
Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry.
Yao, Jingwen; Utsunomiya, Shin-Ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi
2014-01-01
A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/).
Energy Technology Data Exchange (ETDEWEB)
Zhang, Qibin; Monroe, Matthew E.; Schepmoes, Athena A.; Clauss, Therese RW; Gritsenko, Marina A.; Meng, Da; Petyuk, Vladislav A.; Smith, Richard D.; Metz, Thomas O.
2011-07-01
Non-enzymatic glycation of proteins is implicated in diabetes mellitus and its related complications. In this report, we extend our previous development and refinement of proteomics-based methods for the analysis of non-enzymatically glycated proteins to comprehensively identify glycated proteins in normal and diabetic human plasma and erythrocytes. Using immunodepletion, enrichment, and fractionation strategies, we identified 7749 unique glycated peptides, corresponding to 3742 unique glycated proteins. Semi-quantitative comparisons revealed a number of proteins with glycation levels significantly increased in diabetes relative to control samples and that erythrocyte proteins are more extensively glycated than plasma proteins. A glycation motif analysis revealed amino acids that are favored more than others in the protein primary structures in the vicinity of the glycation sites in both sample types. The glycated peptides and corresponding proteins reported here provide a foundation for the potential identification of novel markers for diabetes, glycemia, or diabetic complications.
Interpretation of tandem mass spectra of posttranslationally modified peptides
DEFF Research Database (Denmark)
Bunkenborg, J.; Matthiesen, R.
2013-01-01
spectra and protein database search engines have been developed to match the experimental data to peptide candidates. In most studies there is a schism between discarding perfectly valid data and including nonsensical peptide identifications-this is currently a major bottleneck in data...
Hormone action. Part I. Peptide hormones
International Nuclear Information System (INIS)
Birnbaumer, L.; O'Malley, B.W.
1985-01-01
The major sections of this book on the hormonal action of peptide hormones cover receptor assays, identification of receptor proteins, methods for identification of internalized hormones and hormone receptors, preparation of hormonally responsive cells and cell hybrids, purification of membrane receptors and related techniques, assays of hormonal effects and related functions, and antibodies in hormone action
Alkotaini, Bassam; Anuar, Nurina; Kadhum, Abdul Amir Hassan; Sani, Asmahani Azira Abdu
2014-04-01
A wild-type, Gram-positive, rod-shaped, endospore-forming and motile bacteria has been isolated from palm oil mill sludge in Malaysia. Molecular identification using 16S rRNA gene sequence analysis indicated that the bacteria belonged to genus Paenibacillus. With 97 % similarity to P. alvei (AUG6), the isolate was designated as P. alvei AN5. An antimicrobial compound was extracted from P. alvei AN5-pelleted cells using 95 % methanol and was then lyophilized. Precipitates were re-suspended in phosphate buffered saline (PBS), producing an antimicrobial crude extract (ACE). The ACE showed antimicrobial activity against Salmonella enteritidis ATCC 13076, Escherichia coli ATCC 29522, Bacillus cereus ATCC 14579 and Lactobacillus plantarum ATCC 8014. By using SP-Sepharose cation exchange chromatography, Sephadex G-25 gel filtration and Tricine SDS-PAGE, the ACE was purified, which produced a ~2-kDa active band. SDS-PAGE and infrared (IR) spectroscopy indicated the proteinaceous nature of the antimicrobial compound in the ACE, and liquid chromatography electrospray ionization mass spectroscopy and de novo sequencing using an automatic, Q-TOF premier system detected a peptide with the amino acid sequence F-C-K-S-L-P-L-P-L-S-V-K (1,330.7789 Da). This novel peptide was designated as AN5-2. The antimicrobial peptide exhibited stability from pH 3 to 12 and maintained its activity after being heated to 90 °C. It also remained active after incubation with denaturants (urea, SDS and EDTA).
An Optimal Centralized Carbon Dioxide Repository for Florida, USA
Directory of Open Access Journals (Sweden)
Brandon Poiencot
2011-03-01
Full Text Available For over a decade, the United States Department of Energy, and engineers, geologists, and scientists from all over the world have investigated the potential for reducing atmospheric carbon emissions through carbon sequestration. Numerous reports exist analyzing the potential for sequestering carbon dioxide at various sites around the globe, but none have identified the potential for a statewide system in Florida, USA. In 2005, 83% of Florida’s electrical energy was produced by natural gas, coal, or oil (e.g., fossil fuels, from power plants spread across the state. In addition, only limited research has been completed on evaluating optimal pipeline transportation networks to centralized carbon dioxide repositories. This paper describes the feasibility and preliminary locations for an optimal centralized Florida-wide carbon sequestration repository. Linear programming optimization modeling is used to plan and route an idealized pipeline network to existing Florida power plants. Further analysis of the subsurface geology in these general locations will provide insight into the suitability of the subsurface conditions and the available capacity for carbon sequestration at selected possible repository sites. The identification of the most favorable site(s is also presented.
Signal peptide discrimination and cleavage site identification using SVM and NN.
Kazemian, H B; Yusuf, S A; White, K
2014-02-01
About 15% of all proteins in a genome contain a signal peptide (SP) sequence, at the N-terminus, that targets the protein to intracellular secretory pathways. Once the protein is targeted correctly in the cell, the SP is cleaved, releasing the mature protein. Accurate prediction of the presence of these short amino-acid SP chains is crucial for modelling the topology of membrane proteins, since SP sequences can be confused with transmembrane domains due to similar composition of hydrophobic amino acids. This paper presents a cascaded Support Vector Machine (SVM)-Neural Network (NN) classification methodology for SP discrimination and cleavage site identification. The proposed method utilises a dual phase classification approach using SVM as a primary classifier to discriminate SP sequences from Non-SP. The methodology further employs NNs to predict the most suitable cleavage site candidates. In phase one, a SVM classification utilises hydrophobic propensities as a primary feature vector extraction using symmetric sliding window amino-acid sequence analysis for discrimination of SP and Non-SP. In phase two, a NN classification uses asymmetric sliding window sequence analysis for prediction of cleavage site identification. The proposed SVM-NN method was tested using Uni-Prot non-redundant datasets of eukaryotic and prokaryotic proteins with SP and Non-SP N-termini. Computer simulation results demonstrate an overall accuracy of 0.90 for SP and Non-SP discrimination based on Matthews Correlation Coefficient (MCC) tests using SVM. For SP cleavage site prediction, the overall accuracy is 91.5% based on cross-validation tests using the novel SVM-NN model. © 2013 Published by Elsevier Ltd.
Flanking signal and mature peptide residues influence signal peptide cleavage
Directory of Open Access Journals (Sweden)
Ranganathan Shoba
2008-12-01
Full Text Available Abstract Background Signal peptides (SPs mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is crucial to the medical, food and beverage and biotechnology industries yet our understanding of these peptides remains limited. This paper examines the most common type of signal peptides cleavable by the endoprotease signal peptidase I (SPase I, and the residues flanking the cleavage sites of three groups of signal peptide sequences, namely (i eukaryotes (Euk (ii Gram-positive (Gram+ bacteria, and (iii Gram-negative (Gram- bacteria. Results In this study, 2352 secretory peptide sequences from a variety of organisms with amino-terminal SPs are extracted from the manually curated SPdb database for analysis based on physicochemical properties such as pI, aliphatic index, GRAVY score, hydrophobicity, net charge and position-specific residue preferences. Our findings show that the three groups share several similarities in general, but they display distinctive features upon examination in terms of their amino acid compositions and frequencies, and various physico-chemical properties. Thus, analysis or prediction of their sequences should be separated and treated as distinct groups. Conclusion We conclude that the peptide segment recognized by SPase I extends to the start of the mature protein to a limited extent, upon our survey of the amino acid residues surrounding the cleavage processing site. These flanking residues possibly influence the cleavage processing and contribute to non-canonical cleavage sites. Our findings are applicable in defining more accurate prediction tools for recognition and identification of cleavage site of SPs.
Towards Interoperable Preservation Repositories: TIPR
Directory of Open Access Journals (Sweden)
Priscilla Caplan
2010-07-01
Full Text Available Towards Interoperable Preservation Repositories (TIPR is a project funded by the Institute of Museum and Library Services to create and test a Repository eXchange Package (RXP. The package will make it possible to transfer complex digital objects between dissimilar preservation repositories. For reasons of redundancy, succession planning and software migration, repositories must be able to exchange copies of archival information packages with each other. Every different repository application, however, describes and structures its archival packages differently. Therefore each system produces dissemination packages that are rarely understandable or usable as submission packages by other repositories. The RXP is an answer to that mismatch. Other solutions for transferring packages between repositories focus either on transfers between repositories of the same type, such as DSpace-to-DSpace transfers, or on processes that rely on central translation services. Rather than build translators between many dissimilar repository types, the TIPR project has defined a standards-based package of metadata files that can act as an intermediary information package, the RXP, a lingua franca all repositories can read and write.
Repository simulation model: Final report
International Nuclear Information System (INIS)
1988-03-01
This report documents the application of computer simulation for the design analysis of the nuclear waste repository's waste handling and packaging operations. The Salt Repository Simulation Model was used to evaluate design alternatives during the conceptual design phase of the Salt Repository Project. Code development and verification was performed by the Office of Nuclear Waste Isolation (ONWL). The focus of this report is to relate the experience gained during the development and application of the Salt Repository Simulation Model to future repository design phases. Design of the repository's waste handling and packaging systems will require sophisticated analysis tools to evaluate complex operational and logistical design alternatives. Selection of these design alternatives in the Advanced Conceptual Design (ACD) and License Application Design (LAD) phases must be supported by analysis to demonstrate that the repository design will cost effectively meet DOE's mandated emplacement schedule and that uncertainties in the performance of the repository's systems have been objectively evaluated. Computer simulation of repository operations will provide future repository designers with data and insights that no other analytical form of analysis can provide. 6 refs., 10 figs
Monitoring during the stepwise implementation of the Swedish deep repository for spent fuel
International Nuclear Information System (INIS)
Baeckblom, Goeran; Almen, Karl-Erik
2004-03-01
to: obtain knowledge of undisturbed conditions in nature and their seasonal variations (baseline) in order to identify and evaluate the impact of activities related to the deep repository during different phases, obtain a better understanding of the function of the deep repository system to support the safety account and to test models and assumptions, monitor the environmental impact of the deep repository, provide evidence that the working environment is safe with regard to radiological and non-radiological effects, show that requirements on radioactive waste verification (safeguards) are fulfilled. The monitoring is concerned with bedrock conditions before and during construction and operation of the facilities, active design to engineer the underground facilities based on monitoring results during construction, the safe and environmental construction and operation of facilities. Experience exists from monitoring of the barrier function at SFR, the final repository for low - and intermediate level waste and at the Aespoe Hard Rock Laboratory and monitoring for safeguard at CLAB, the interim storage for spent nuclear fuel. The know-how on monitoring relates to all aspects from design, installation, operation and maintenance to decommissioning of systems. This report provides an overview of the features, processes and parameters that are collected during the site investigations to establish the Primary Baseline conditions for monitoring prior to the construction of the repository. It is also proposed that the monitoring programme should at least entail the following elements: objectives for the monitoring programme, scope for the monitoring (criteria for selection of issues to be monitored, identification of the properties, processes, phenomena and observable quantities to be monitored), identification on what methods to be used, operation of the monitoring system (identification of the duration and frequency of monitoring, including criteria for when monitoring may
Directory of Open Access Journals (Sweden)
Nicolás Sarute
Full Text Available Canine distemper virus (CDV; Paramyxoviridae, Morbillivirus is the etiologic agent of a multisystemic infectious disease affecting all terrestrial carnivore families with high incidence and mortality in domestic dogs. Sequence analysis of the hemagglutinin (H gene has been widely employed to characterize field strains, permitting the identification of nine CDV lineages worldwide. Recently, it has been established that the sequences of the fusion protein signal-peptide (Fsp coding region are extremely variable, suggesting that analysis of its sequence might be useful for strain characterization studies. However, the divergence of Fsp sequences among worldwide strains and its phylogenetic resolution has not yet been evaluated. We constructed datasets containing the Fsp-coding region and H gene sequences of the same strains belonging to eight CDV lineages. Both datasets were used to evaluate their phylogenetic resolution. The phylogenetic analysis revealed that both datasets clustered the same strains into eight different branches, corresponding to CDV lineages. The inter-lineage amino acid divergence was fourfold greater for the Fsp peptide than for the H protein. The likelihood mapping revealed that both datasets display strong phylogenetic signals in the region of well-resolved topologies. These features indicate that Fsp-coding region sequence analysis is suitable for evolutionary studies as it allows for straightforward identification of CDV lineages.
Sarute, Nicolás; Calderón, Marina Gallo; Pérez, Ruben; La Torre, José; Hernández, Martín; Francia, Lourdes; Panzera, Yanina
2013-01-01
Canine distemper virus (CDV; Paramyxoviridae, Morbillivirus) is the etiologic agent of a multisystemic infectious disease affecting all terrestrial carnivore families with high incidence and mortality in domestic dogs. Sequence analysis of the hemagglutinin (H) gene has been widely employed to characterize field strains, permitting the identification of nine CDV lineages worldwide. Recently, it has been established that the sequences of the fusion protein signal-peptide (Fsp) coding region are extremely variable, suggesting that analysis of its sequence might be useful for strain characterization studies. However, the divergence of Fsp sequences among worldwide strains and its phylogenetic resolution has not yet been evaluated. We constructed datasets containing the Fsp-coding region and H gene sequences of the same strains belonging to eight CDV lineages. Both datasets were used to evaluate their phylogenetic resolution. The phylogenetic analysis revealed that both datasets clustered the same strains into eight different branches, corresponding to CDV lineages. The inter-lineage amino acid divergence was fourfold greater for the Fsp peptide than for the H protein. The likelihood mapping revealed that both datasets display strong phylogenetic signals in the region of well-resolved topologies. These features indicate that Fsp-coding region sequence analysis is suitable for evolutionary studies as it allows for straightforward identification of CDV lineages.
Use of synthetic peptide libraries for the H-2Kd binding motif identification.
Quesnel, A; Casrouge, A; Kourilsky, P; Abastado, J P; Trudelle, Y
1995-01-01
To identify Kd-binding peptides, an approach based on small peptide libraries has been developed. These peptide libraries correspond to all possible single-amino acid variants of a particular Kd-binding peptide, SYIPSAEYI, an analog of the Plasmodium berghei 252-260 antigenic peptide SYIPSAEKI. In the parent sequence, each position is replaced by all the genetically encoded amino acids (except cysteine). The multiple analog syntheses are performed either by the Divide Couple and Recombine method or by the Single Resin method and generate mixtures containing 19 peptides. The present report deals with the synthesis, the purification, the chemical characterization by amino acid analysis and electrospray mass spectrometry (ES-MS), and the application of such mixtures in binding tests with a soluble, functionally empty, single-chain H-2Kd molecule denoted SC-Kd. For each mixture, bound peptides were eluted and analyzed by sequencing. Since the binding tests were realized in noncompetitive conditions, our results show that a much broader set of peptides bind to Kd than expected from previous studies. This may be of practical importance when looking for low affinity peptides such as tumor peptides capable of eliciting protective immune response.
Lamer, S; Jungblut, P R
2001-03-10
In theory, peptide mass fingerprinting by matrix assisted laser desorption-ionization mass spectrometry (MALDI-MS) has the potential to identify all of the proteins detected by silver staining on gels. In practice, if the genome of the organism investigated is completely sequenced, using current techniques, all proteins stained by Coomassie Brilliant Blue can be identified. This loss of identification sensitivity of ten to hundred-fold is caused by loss of peptides by surface contacts. Therefore, we performed digestion and transfer of peptides in the lower microl range and reduced the number of steps. The peptide mix obtained from in-gel or on-blot digestion was analyzed directly after digestion or after concentration on POROS R2 beads. Eight protein spots of a 2-DE gel from Mycobacterium bovis BCG were identified using these four preparation procedures for MALDI-MS. Overall, on-blot digestion was as effective as in-gel digestion. Whereas higher signal intensities resulted after concentration, hydrophilic peptides are better detected by direct measurement of the peptide mix without POROS R2 concentration.
Energy Technology Data Exchange (ETDEWEB)
Freire, Carolina Braccini; Tello, Cledola Cassia Oliveira de [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)]. E-mails: cbf@cdtn.br; tellocc@cdtn.br
2007-11-15
The use of the nuclear energy is increasing in all areas. Then the radioactive waste management is in continuous development to comply the national and international established requirements. The final objective is to assure that it will not have any contamination of the public or the environmental, and that the exposition doses will be lower than the radiological protection limits. The multi barrier concept for the repository is internationally recognized. Among the repository types, the most used are: near surface, geological formations and of deposition in rock cavities. This article explains the concept and the types of repository and gives some examples of them. (author)
DEFF Research Database (Denmark)
Zhang, Guang Lan; DeLuca, David S.; Keskin, Derin B.
2011-01-01
binding peptides and immunological hotspots in an intuitive manner and also to provide a global view of results as heat maps. Another function of MULTIPRED2, which has direct relevance to vaccine design, is the calculation of population coverage. Currently it calculates population coverage in five major...... groups in North America. MULTIPRED2 is an important tool to complement wet-lab experimental methods for identification of T-cell epitopes. It is available at http://cvc.dfci.harvard.edu/multipred2/....
The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments
Directory of Open Access Journals (Sweden)
Tradigo Giuseppe
2007-07-01
Full Text Available Abstract Background Isotope-coded affinity tags (ICAT is a method for quantitative proteomics based on differential isotopic labeling, sample digestion and mass spectrometry (MS. The method allows the identification and relative quantification of proteins present in two samples and consists of the following phases. First, cysteine residues are either labeled using the ICAT Light or ICAT Heavy reagent (having identical chemical properties but different masses. Then, after whole sample digestion, the labeled peptides are captured selectively using the biotin tag contained in both ICAT reagents. Finally, the simplified peptide mixture is analyzed by nanoscale liquid chromatography-tandem mass spectrometry (LC-MS/MS. Nevertheless, the ICAT LC-MS/MS method still suffers from insufficient sample-to-sample reproducibility on peptide identification. In particular, the number and the type of peptides identified in different experiments can vary considerably and, thus, the statistical (comparative analysis of sample sets is very challenging. Low information overlap at the peptide and, consequently, at the protein level, is very detrimental in situations where the number of samples to be analyzed is high. Results We designed a method for improving the data processing and peptide identification in sample sets subjected to ICAT labeling and LC-MS/MS analysis, based on cross validating MS/MS results. Such a method has been implemented in a tool, called EIPeptiDi, which boosts the ICAT data analysis software improving peptide identification throughout the input data set. Heavy/Light (H/L pairs quantified but not identified by the MS/MS routine, are assigned to peptide sequences identified in other samples, by using similarity criteria based on chromatographic retention time and Heavy/Light mass attributes. EIPeptiDi significantly improves the number of identified peptides per sample, proving that the proposed method has a considerable impact on the protein
Mass-spectrometric identification of a novel angiotensin peptide in human plasma
DEFF Research Database (Denmark)
Jankowski, Vera; Vanholder, Raymond; van der Giet, Markus
2007-01-01
Angiotensin peptides play a central role in cardiovascular physiology and pathology. Among these peptides, angiotensin II (Ang II) has been investigated most intensively. However, further angiotensin peptides such as Ang 1-7, Ang III, and Ang IV also contribute to vascular regulation, and may eli...... elicit additional, different, or even opposite effects to Ang II. Here, we describe a novel Ang II-related, strong vasoconstrictive substance in plasma from healthy humans and end-stage renal failure patients....
Use FlowRepository to share your clinical data upon study publication.
Spidlen, Josef; Brinkman, Ryan R
2018-01-01
A fundamental tenet of scientific research is that published results including underlying data should be open to independent validation and refutation. Data sharing encourages collaboration, facilitates quality and reduces redundancy in data production. Authors submitting manuscripts to several journals have already adopted the habit of sharing their underlying flow cytometry data by deposition to FlowRepository-a data repository that is jointly supported by the International Society for Advancement of Cytometry, the International Clinical Cytometry Society and the European Society for Clinical Cell Analysis. De-identification is required for publishing data from clinical studies and we discuss ways to satisfy data sharing requirements and patient privacy requirements simultaneously. Scientific communities in the fields of microarray, proteomics, and sequencing have been benefiting from reuse and re-exploration of data in public repositories for over decade. We believe it is time that clinicians follow suit and that de-identified clinical data also become routinely available along with published cytometry-based findings. © 2016 International Clinical Cytometry Society. © 2016 International Clinical Cytometry Society.
[Tissue repositories for research at Sheba Medical Center(SMC].
Cohen, Yehudit; Barshack, Iris; Onn, Amir
2013-06-01
Cancer is the number one cause of death in both genders. Breakthroughs in the understanding of cancer biology, the identification of prognostic factors, and the development of new treatments are increasingly dependent on access to human cancer tissues with linked clinicopathological data. Access to human tumor samples and a large investment in translational research are needed to advance this research. The SMC tissue repositories provide researchers with biological materials, which are essential tools for cancer research. SMC tissue repositories for research aim to collect, document and preserve human biospecimens from patients with cancerous diseases. This is in order to provide the highest quality and well annotated biological biospecimens, used as essential tools to achieve the growing demands of scientific research needs. Such repositories are partners in acceLerating biomedical research and medical product development through clinical resources, in order to apply best options to the patients. Following Institutional Review Board approval and signing an Informed Consent Form, the tumor and tumor-free specimens are coLLected by a designated pathologist at the operating room only when there is a sufficient amount of the tumor, in excess of the routine needs. Blood samples are collected prior to the procedure. Other types of specimens collected include ascites fluid, pleural effusion, tissues for Optimal Cutting Temperature [OCT] and primary culture etc. Demographic, clinical, pathologicaL, and follow-up data are collected in a designated database. SMC has already established several organ or disease-specific tissue repositories within different departments. The foundation of tissue repositories requires the concentrated effort of a multidisciplinary team composed of paramedical, medical and scientific professionals. Research projects using these specimens facilitate the development of 'targeted therapy', accelerate basic research aimed at clarifying molecular
Cardioprotective peptides from marine sources.
Harnedy, Padraigín A; FitzGerald, Richard J
2013-05-01
Elevated blood pressure or hypertension is one of the fastest growing health problems worldwide. Although the etiology of essential hypertension has a genetic component, dietary factors play an important role. With the high costs and adverse side-effects associated with synthetic antihypertensive drugs and the awareness of the link between diet and health there has been increased focus on identification of food components that may contribute to cardiovascular health. In recent years special interest has been paid to the cardioprotective activity of peptides derived from food proteins including marine proteins. These peptides are latent within the sequence of the parent protein and only become active when released by proteolytic digestion during gastrointestinal digestion or through food processing. Current data on antihypertensive activity of marine-derived protein hydrolysates/peptides in animal and human studies is reviewed herein. Furthermore, products containing protein hydrolysates/peptides from marine origin with antihypertensive effects are discussed.
Directory of Open Access Journals (Sweden)
Paula Regina Ventura Amorim Gonçalez
2017-04-01
Full Text Available Introduction: Considering the guidelines of ISO 16363: 2012 (Space data and information transfer systems -- Audit and certification of trustworthy digital repositories and the text of CONARQ Resolution 39 for certification of Reliable Digital Archival Repository (RDC-Arq, verify the technical recommendations should be used as the basis for a digital archival repository to be considered reliable. Objective: Identify requirements for the creation of Reliable Digital Archival Repositories with emphasis on access to information from the ISO 16363: 2012 and CONARQ Resolution 39. Methodology: For the development of the study, the methodology consisted of an exploratory, descriptive and documentary theoretical investigation, since it is based on ISO 16363: 2012 and CONARQ Resolution 39. From the perspective of the problem approach, the study is qualitative and quantitative, since the data were collected, tabulated, and analyzed from the interpretation of their contents. Results: We presented a set of Checklist Recommendations for reliability measurement and/or certification for RDC-Arq with a clipping focused on the identification of requirements with emphasis on access to information is presented. Conclusions: The right to information as well as access to reliable information is a premise for Digital Archival Repositories, so the set of recommendations is directed to archivists who work in Digital Repositories and wish to verify the requirements necessary to evaluate the reliability of the Digital Repository or still guide the information professional in collecting requirements for repository reliability certification.
Managing and Evaluating Digital Repositories
Zuccala, Alesia; Oppenheim, Charles; Dhiensa, Rajveen
2008-01-01
Introduction: We examine the role of the digital repository manager, discuss the future of repository management and evaluation and suggest that library and information science schools develop new repository management curricula. Method: Face-to-face interviews were carried out with managers of five different types of repositories and a Web-based…
International Nuclear Information System (INIS)
Wicks, G.G.; Bibler, N.E.; Jantzen, C.M.; Plodinec, M.J.
1984-01-01
The repository simulation experiments described in this paper are designed to assess the performance of SRP waste glass under the most realistic repository conditions that can be obtained in the laboratory. These tests simulate the repository environment as closely as possible and introduce systematically the variability of the geology, groundwater chemistry, and waste package components during the leaching of the waste glass. The tests evaluate waste form performance under site-specific conditions, which differ for each of the geologic repositories under consideration. Data from these experiments will aid in the development of a realistic source term that can describe the release of radionuclides from SRP waste glass as a component of proposed waste packages. Hence, this information can be useful to optimize waste package design for SRP waste glass and to provide data for predicting long-term performance and subsequent conformance to regulations. The repository simulation tests also help to bridge the gap in interpreting results derived from tests performed under the control of the laboratory to the uncertainity and variability of field tests. In these experiments, site-specific repository components and conditions are emphasized and only the site specific materials contact the waste forms. An important feature of these tests is that both actual and simulated waste glasses are tested identically. 7 figures, 2 tables
International Nuclear Information System (INIS)
Cormenzana Lopez, J.L.; Cunado, M.A.; Lopez, M.T.
1996-01-01
The methodology usually used to evaluate the behaviour of deep geological repositories for high-level radioactive wastes comprises three phases: Identification of factors (processes, characteristics and events) that can affect the repository. Generation of scenarios. In general, a normal evolution scenario (Reference Scenario) and various disruptive scenarios (earthquake, human intrusion, etc) are considered. Evaluation of the behaviour of the repository in each scenario. The normal evolution scenario taking into account all factors with a high probability of occurrence is the first to be analysed. The performance assessment of behaviour being carried out by ENRESA for the AGP Granite has led to the identification of 63 of these factors. To analyse repository behaviour in the normal evolution scenario, it is necessary to first of all create an integrated model of the global system. This is a qualitative model including the 63 factors identified. For a global view of a such a complex system, it is very useful to graphically display the relationship between factors in an Influence Diagram. This paper shows the Influence Diagram used in the analysis of the AGP Granite Reference Scenario. (Author)
The repository ecology an approach to understanding repository and service interactions
CERN. Geneva; Hagemann, Melissa
2007-01-01
An increasing number of university institutions and other organisations are deciding to deploy repositories and a growing number of formal and informal distributed services are supporting or capitalising on the information these repositories provide. Despite reasonably well understood technical architectures, early majority adopters may struggle to articulate their place within the actualities of a wider information environment. The idea of a repository ecology provides developers and administrators with a useful way of articulating and analysing their place in the information environment, and the technical and organisational interactions they have, or are developing, with other parts of such an environment. This presentation will provide an overview of the concept of a repository ecology and examine some examples from the domains of scholarly communications and elearning.
International Nuclear Information System (INIS)
Forsberg, C.; Miller, W.F.
2013-01-01
The historical repository siting strategy in the United States has been a top-down approach driven by federal government decision making but it has been a failure. This policy has led to dispatching fuel cycle facilities in different states. The U.S. government is now considering an alternative repository siting strategy based on voluntary agreements with state governments. If that occurs, state governments become key decision makers. They have different priorities. Those priorities may change the characteristics of the repository and the fuel cycle. State government priorities, when considering hosting a repository, are safety, financial incentives and jobs. It follows that states will demand that a repository be the center of the back end of the fuel cycle as a condition of hosting it. For example, states will push for collocation of transportation services, safeguards training, and navy/private SNF (Spent Nuclear Fuel) inspection at the repository site. Such activities would more than double local employment relative to what was planned for the Yucca Mountain-type repository. States may demand (1) the right to take future title of the SNF so if recycle became economic the reprocessing plant would be built at the repository site and (2) the right of a certain fraction of the repository capacity for foreign SNF. That would open the future option of leasing of fuel to foreign utilities with disposal of the SNF in the repository but with the state-government condition that the front-end fuel-cycle enrichment and fuel fabrication facilities be located in that state
Low and medium level radioactive waste repository: risk perception
International Nuclear Information System (INIS)
Aquino, Afonso Rodrigues de; Bueno, Lilian de Oliveira; Vieira, Martha Marques Ferreira; Fonseca, Edvaldo Roberto Paiva da; Bellintani, Sandra Aparecida
2009-01-01
This paper focuses on the risk perception associated to the installation of low and intermediate level radioactive waste (LLRW and ILRW) disposal facilities. The purpose is to give support for the implementation of a repository in Brazil. Public acceptance results from a long term work and trust is vital for the process as it takes long to be conquered but might be shortly lost. Therefore, it is essential to care about the way each step is conducted. The knowledge about the system and the risks, the comprehension about these risks, the commitment with safety, adequate support systems for the project (legislation, involved institutions) and the excellence as a goal to be reached are extremely important parameters. The involvement of all interested parties in the decision-making process is condition for a successful and publicly acceptable implementation of such project. The steps for public acceptance of a repository are summarized as follow: Risk perception: to verify how the local population understand and feel the installation of a repository in the region. Media observatory: to continuously follow the news reaching the region where the repository will be installed, including different media. Local population social/economical/cultural profile identification: to determine the local population social/economical/cultural profile; to conduct a survey to know their expectations, allowing the proposal of compensation and incentives to fully account for their expectations. Finally, the philosophy governing this Project is: on doubt, the public must be heard and only after this public hearing the policies concerning the project shall be formulated. (author)
Low and medium level radioactive waste repository: risk perception
Energy Technology Data Exchange (ETDEWEB)
Aquino, Afonso Rodrigues de; Bueno, Lilian de Oliveira; Vieira, Martha Marques Ferreira; Fonseca, Edvaldo Roberto Paiva da; Bellintani, Sandra Aparecida [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)], e-mail: araquino@ipen.br, e-mail: lbueno@ipen.br, e-mail: mmvieira@ipen.br, e-mail: efonseca@ipen.br, e-mail: sbellint@ipen.br
2009-07-01
This paper focuses on the risk perception associated to the installation of low and intermediate level radioactive waste (LLRW and ILRW) disposal facilities. The purpose is to give support for the implementation of a repository in Brazil. Public acceptance results from a long term work and trust is vital for the process as it takes long to be conquered but might be shortly lost. Therefore, it is essential to care about the way each step is conducted. The knowledge about the system and the risks, the comprehension about these risks, the commitment with safety, adequate support systems for the project (legislation, involved institutions) and the excellence as a goal to be reached are extremely important parameters. The involvement of all interested parties in the decision-making process is condition for a successful and publicly acceptable implementation of such project. The steps for public acceptance of a repository are summarized as follow: Risk perception: to verify how the local population understand and feel the installation of a repository in the region. Media observatory: to continuously follow the news reaching the region where the repository will be installed, including different media. Local population social/economical/cultural profile identification: to determine the local population social/economical/cultural profile; to conduct a survey to know their expectations, allowing the proposal of compensation and incentives to fully account for their expectations. Finally, the philosophy governing this Project is: on doubt, the public must be heard and only after this public hearing the policies concerning the project shall be formulated. (author)
Energy Technology Data Exchange (ETDEWEB)
Skagius, K; Wiborgh, M [Kemakta, Stockholm (Sweden); Stroem, A [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)
1995-11-01
The basic device in the Rock Engineering Systems approach, the interaction matrix, has been used to identify, structure and rank Features, Events, and Processes (FEPs) describing barrier performance and radionuclide behaviour in the far-field of a deep geologic repository for spent fuel. The result is a first version of the Process System (PS), for the far-field of a deep repository, structured in an interaction matrix with supporting documentation. The documentation is compiled in databases, one containing matrix specific information and one containing general FEP descriptions. The study has shown that an interaction matrix is feasible to use both for the structuring of the PS and for visualisation of the PS. The developed documentation system increases the transparency of the system description and makes it possible to trace back the judgements made during the construction of the matrix. This will facilitate review work and future revisions as well as consistent treatment of different issues in the system. This study is a first step in the application of a systematic method to establish a structured description of the PS for a deep repository for spent fuel. The work could be seen as a part of the preparation for the forthcoming performance and safety analysis. The next step would be to develop the PS for the remaining parts of the repository system to the same level as has been done for the far-field system. Before the PS is evaluated for different selected system premises, a scientific review of the contents of the PS for the whole repository system would be beneficial. 5 refs.
International Nuclear Information System (INIS)
Skagius, K.; Wiborgh, M.; Stroem, A.
1995-11-01
The basic device in the Rock Engineering Systems approach, the interaction matrix, has been used to identify, structure and rank Features, Events, and Processes (FEPs) describing barrier performance and radionuclide behaviour in the far-field of a deep geologic repository for spent fuel. The result is a first version of the Process System (PS), for the far-field of a deep repository, structured in an interaction matrix with supporting documentation. The documentation is compiled in databases, one containing matrix specific information and one containing general FEP descriptions. The study has shown that an interaction matrix is feasible to use both for the structuring of the PS and for visualisation of the PS. The developed documentation system increases the transparency of the system description and makes it possible to trace back the judgements made during the construction of the matrix. This will facilitate review work and future revisions as well as consistent treatment of different issues in the system. This study is a first step in the application of a systematic method to establish a structured description of the PS for a deep repository for spent fuel. The work could be seen as a part of the preparation for the forthcoming performance and safety analysis. The next step would be to develop the PS for the remaining parts of the repository system to the same level as has been done for the far-field system. Before the PS is evaluated for different selected system premises, a scientific review of the contents of the PS for the whole repository system would be beneficial. 5 refs
Cell-Penetrating Ability of Peptide Hormones: Key Role of Glycosaminoglycans Clustering
Directory of Open Access Journals (Sweden)
Armelle Tchoumi Neree
2015-11-01
Full Text Available Over the last two decades, the potential usage of cell-penetrating peptides (CPPs for the intracellular delivery of various molecules has prompted the identification of novel peptidic identities. However, cytotoxic effects and unpredicted immunological responses have often limited the use of various CPP sequences in the clinic. To overcome these issues, the usage of endogenous peptides appears as an appropriate alternative approach. The hormone pituitary adenylate-cyclase-activating polypeptide (PACAP38 has been recently identified as a novel and very efficient CPP. This 38-residue polycationic peptide is a member of the secretin/glucagon/growth hormone-releasing hormone (GHRH superfamily, with which PACAP38 shares high structural and conformational homologies. In this study, we evaluated the cell-penetrating ability of cationic peptide hormones in the context of the expression of cell surface glycosaminoglycans (GAGs. Our results indicated that among all peptides evaluated, PACAP38 was unique for its potent efficiency of cellular uptake. Interestingly, the abilities of the peptides to reach the intracellular space did not correlate with their binding affinities to sulfated GAGs, but rather to their capacity to clustered heparin in vitro. This study demonstrates that the uptake efficiency of a given cationic CPP does not necessarily correlate with its affinity to sulfated GAGs and that its ability to cluster GAGs should be considered for the identification of novel peptidic sequences with potent cellular penetrating properties.
The repository ecology: an approach to understanding repository and service interactions
CERN. Geneva
2007-01-01
An increasing number of university institutions and other organisations are deciding to deploy repositories and a growing number of formal and informal distributed services are supporting or capitalising on the information these repositories provide. Despite reasonably well understood technical architectures, early majority adopters may struggle to articulate their place within the actualities of a wider information environment. The idea of a repository ecology provides developers and administrators with a useful way of articulating and analysing their place in the information environment, and the technical and organisational interactions they have, or are developing, with other parts of such an environment. This presentation will provide an overview of the concept of a repository ecology and examine some examples from the domains of scholarly communications and elearning. View John Robertson's biography
Directory of Open Access Journals (Sweden)
Patricia Martorell
Full Text Available BACKGROUND: Cocoa and cocoa-based products contain different compounds with beneficial properties for human health. Polyphenols are the most frequently studied, and display antioxidant properties. Moreover, protein content is a very interesting source of antioxidant bioactive peptides, which can be used therapeutically for the prevention of age-related diseases. METHODOLOGY/PRINCIPAL FINDINGS: A bioactive peptide, 13L (DNYDNSAGKWWVT, was obtained from a hydrolyzed cocoa by-product by chromatography. The in vitro inhibition of prolyl endopeptidase (PEP was used as screening method to select the suitable fraction for peptide identification. Functional analysis of 13L peptide was achieved using the transgenic Caenorhabditis elegans strain CL4176 expressing the human Aβ₁₋₄₂ peptide as a pre-clinical in vivo model for Alzheimer's disease. Among the peptides isolated, peptide 13L (1 µg/mL showed the highest antioxidant activity (P≤0.001 in the wild-type strain (N2. Furthermore, 13L produced a significant delay in body paralysis in strain CL4176, especially in the 24-47 h period after Aβ₁₋₄₂ peptide induction (P≤0.0001. This observation is in accordance with the reduction of Aβ deposits in CL4176 by western blot. Finally, transcriptomic analysis in wild-type nematodes treated with 13L revealed modulation of the proteosomal and synaptic functions as the main metabolic targets of the peptide. CONCLUSIONS/SIGNIFICANCE: These findings suggest that the cocoa 13L peptide has antioxidant activity and may reduce Aβ deposition in a C. elegans model of Alzheimer's disease; and therefore has a putative therapeutic potential for prevention of age-related diseases. Further studies in murine models and humans will be essential to analyze the effectiveness of the 13L peptide in higher animals.
Hiemstra, H S; van Veelen, P A; Schloot, N C; Geluk, A; van Meijgaarden, K E; Willemen, S J; Leunissen, J A; Benckhuijsen, W E; Amons, R; de Vries, R R; Roep, B O; Ottenhoff, T H; Drijfhout, J W
1998-10-15
Progress has recently been made in the use of synthetic peptide libraries for the identification of T cell-stimulating ligands. T cell epitopes identified from synthetic libraries are mimics of natural epitopes. Here we show how the mimicry epitopes obtained from synthetic peptide libraries enable unambiguous identification of natural T cell Ags. Synthetic peptide libraries were screened with Mycobacterium tuberculosis-reactive and -autoreactive T cell clones. In two cases, database homology searches with mimicry epitopes isolated from a dedicated synthetic peptide library allowed immediate identification of the natural antigenic protein. In two other cases, an amino acid pattern that reflected the epitope requirements of the T cell was determined by substitution and omission mixture analysis. Subsequently, the natural Ag was identified from databases using this refined pattern. This approach opens new perspectives for rapid and reliable Ag definition, representing a feasible alternative to the biochemical and genetic approaches described thus far.
Delivery systems for antimicrobial peptides
DEFF Research Database (Denmark)
Nordström, Randi; Malmsten, Martin
2017-01-01
Due to rapidly increasing resistance development against conventional antibiotics, finding novel approaches for the treatment of infections has emerged as a key health issue. Antimicrobial peptides (AMPs) have attracted interest in this context, and there is by now a considerable literature...... on the identification such peptides, as well as on their optimization to reach potent antimicrobial and anti-inflammatory effects at simultaneously low toxicity against human cells. In comparison, delivery systems for antimicrobial peptides have attracted considerably less interest. However, such delivery systems...... are likely to play a key role in the development of potent and safe AMP-based therapeutics, e.g., through reducing chemical or biological degradation of AMPs either in the formulation or after administration, by reducing adverse side-effects, by controlling AMP release rate, by promoting biofilm penetration...
Identification of a peptide binding protein that plays a role in antigen presentation
International Nuclear Information System (INIS)
Lakey, E.K.; Margoliash, E.; Pierce, S.K.
1987-01-01
The helper T-cell response to globular proteins appears, in general, to require intracellular processing of the antigen, such that a peptide fragment containing the T-cell antigenic determinant is released and transported to and held on the surface of an Ia-expressing, antigen-presenting cell. However, the molecular details underlying these phenomena are largely unknown. The means by which antigenic peptides are anchored on the antigen-presenting cell surface was investigated. A cell surface protein is identified that was isolated by it ability to bind to a 24-amino acid peptide fragment of pigeon cytochrome c, residues 81-104, containing the major antigenic determinant for B10.A mouse T cells. This peptide binding protein, purified from [ 35 S]methionine-labeled cells, appears as two discrete bands of ≅72 and 74 kDa after NaDodSO 4 /PAGE. The protein can be eluted from the peptide affinity column with equivalent concentrations of either the antigenic pigeon cytochrome c peptide or the corresponding nonantigenic peptide of mouse cytochrome c. However, it does not bind to the native cytochromes c, either of pigeon or mouse, and thus the protein appears to recognize some structure available only in the free peptides. This protein plays a role in antigen presentation. Its expression is not major histocompatibility complex-restricted in that the blocking activity of the antisera can be absorbed on spleen cells from mice of different haplotypes. This peptide binding protein can be isolated from a variety of cell types, including B cells, T cells, and fibroblasts. The anchoring of processed peptides on the cell surface by such a protein may play a role in antigen presentation
SAPIERR Paves the way towards European regional repository
International Nuclear Information System (INIS)
Stefula, V.; McCombie, C.
2004-01-01
development to be carried out in future. High profile will be given to so-called co-operative scenario, which is most appropriate for the European context. The identification of the potential host country was deliberately excluded from the scope of SAPIERR project in this first phase. The working group participants will correspond throughout the two year duration of the study and will meet again towards the end of the project at an international seminar in Brussels in October 2005. The objective of the seminar will be to review and disseminate results of the project to a wide audience and to agree on subsequent steps on the way towards the European Regional Repository.(author)
Post-staining electroblotting for efficient and reliable peptide blotting.
Lee, Der-Yen; Chang, Geen-Dong
2015-01-01
Post-staining electroblotting has been previously described to transfer Coomassie blue-stained proteins from polyacrylamide gel onto polyvinylidene difluoride (PVDF) membranes. Actually, stained peptides can also be efficiently and reliably transferred. Because of selective staining procedures for peptides and increased retention of stained peptides on the membrane, even peptides with molecular masses less than 2 kDa such as bacitracin and granuliberin R are transferred with satisfactory results. For comparison, post-staining electroblotting is about 16-fold more sensitive than the conventional electroblotting for visualization of insulin on the membrane. Therefore, the peptide blots become practicable and more accessible to further applications, e.g., blot overlay detection or immunoblotting analysis. In addition, the efficiency of peptide transfer is favorable for N-terminal sequence analysis. With this method, peptide blotting can be normalized for further analysis such as blot overlay assay, immunoblotting, and N-terminal sequencing for identification of peptide in crude or partially purified samples.
Repository operational criteria analysis
International Nuclear Information System (INIS)
Hageman, J.P.; Chowdhury, A.H.
1992-08-01
The objective of the ''Repository Operational Criteria (ROC) Feasibility Studies'' (or ROC task) was to conduct comprehensive and integrated analyses of repository design, construction, and operations criteria in 10 CFR Part 60 regulations, considering the interfaces and impacts of any potential changes to those regulations. The study addresses regulatory criteria related to the preclosure aspects of the geologic repository. The study task developed regulatory concepts or potential repository operational criteria (PROC) based on analysis of a repository's safety functions and other regulations for similar facilities. These regulatory concepts or PROC were used as a basis to assess the sufficiency and adequacy of the current criteria in 10 CFR Part 60. Where the regulatory concepts were same as current operational criteria, these criteria were referenced. The operations criteria referenced or the PROC developed are given in this report. Detailed analyses used to develop the regulatory concepts and any necessary PROC for those regulations that may require a minor change are also presented. The results of the ROC task showed a need for further analysis and possible major rule change related to the design bases of a geologic repository operations area, siting, and radiological emergency planning
Consortial routes to effective repositories
Moyle, M.; Proudfoot, R.
2009-01-01
A consortial approach to the establishment of repository services can help a group of Higher Education Institutions (HEIs) to share costs, share technology and share expertise. Consortial repository work can tap into existing structures, or it can involve new groupings of institutions with a common interest in exploring repository development. This Briefing Paper outlines some of the potential benefits of collaborative repository activity, and highlights some of the technical and organisation...
Energy Technology Data Exchange (ETDEWEB)
Claiborne, H.C.; Croff, A.G.; Griess, J.C.; Smith, F.J.
1987-09-01
This document provides specifications for models/methodologies that could be employed in determining postclosure repository environmental parameters relevant to the performance of high-level waste packages for the Basalt Waste Isolation Project (BWIP) at Richland, Washington, the tuff at Yucca Mountain by the Nevada Test Site, and the bedded salt in Deaf Smith County, Texas. Guidance is provided on the identify of the relevant repository environmental parameters; the models/methodologies employed to determine the parameters, and the input data base for the models/methodologies. Supporting studies included are an analysis of potential waste package failure modes leading to identification of the relevant repository environmental parameters, an evaluation of the credible range of the repository environmental parameters, and a summary of the review of existing models/methodologies currently employed in determining repository environmental parameters relevant to waste package performance. 327 refs., 26 figs., 19 tabs.
International Nuclear Information System (INIS)
Claiborne, H.C.; Croff, A.G.; Griess, J.C.; Smith, F.J.
1987-09-01
This document provides specifications for models/methodologies that could be employed in determining postclosure repository environmental parameters relevant to the performance of high-level waste packages for the Basalt Waste Isolation Project (BWIP) at Richland, Washington, the tuff at Yucca Mountain by the Nevada Test Site, and the bedded salt in Deaf Smith County, Texas. Guidance is provided on the identify of the relevant repository environmental parameters; the models/methodologies employed to determine the parameters, and the input data base for the models/methodologies. Supporting studies included are an analysis of potential waste package failure modes leading to identification of the relevant repository environmental parameters, an evaluation of the credible range of the repository environmental parameters, and a summary of the review of existing models/methodologies currently employed in determining repository environmental parameters relevant to waste package performance. 327 refs., 26 figs., 19 tabs
RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration
Directory of Open Access Journals (Sweden)
Ogurtsov Aleksey Y
2008-10-01
Full Text Available Abstract Background Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through consideration of amino acid substitutions/modifications as well as information from disease studies. Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies. Description We have integrated from various sources annotated single amino acid polymorphisms, post-translational modifications, and their documented disease associations (if they exist into one enhanced database per organism. We have also augmented our peptide identification software RAId_DbS to take into account this information while analyzing a tandem mass spectrum. In principle, one may choose to respect or ignore the correlation of amino acid polymorphisms/modifications within each protein. The former leads to targeted searches and avoids scoring of unnecessary polymorphism/modification combinations; the latter explores possible polymorphisms in a controlled fashion. To facilitate new discoveries, RAId_DbS also allows users to conduct searches permitting novel polymorphisms as well as to search a knowledge database created by the users. Conclusion We have finished constructing enhanced databases for 17 organisms. The web link to RAId_DbS and the enhanced databases is http://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/RAId_DbS/index.html. The relevant databases and binaries of RAId_DbS for Linux, Windows, and Mac OS X are available for download from the same web page.
Energy Technology Data Exchange (ETDEWEB)
John, C M
1982-01-01
Various technical issues of radioactive waste design are addressed in this paper. Two approaches to repository design considered herein are: (1) design to minimize the disturbance of the hot rock; and (2) designs that intentionally modify the hot rock to insure better containment of the wastes. The latter designs range from construction of a highly impermeable barrier around a spherical cavern to creating a matrix of tunnels and boreholes to form a cage within which the hydraulic pressure is nearly constant. Examples of these design alternatives are described in some detail. It is concluded that proposed designs for repositories illustrate that performance criteria considered acceptable for such facilities can be met by appropriate site selection and repository engineering. With these technically feasible design concepts, it is also felt that socioeconomic and institutional issues can be better resolved. (BLM)
Furuya, K; Liao, S; Reynolds, S E; Ota, R B; Hackett, M; Schooley, D A
1993-12-01
We isolated several cardioactive peptides from extracts of whole heads of the mealworm, Tenebrio molitor, and the southern armyworm, Spodoptera eridania, using a semi-isolated heart of Manduca sexta for bioassay. We have now isolated from each species the peptide with the strongest effect on rate of contraction of the heart. The peptides were identified using micro Edman sequencing and mass spectrometric methods. This cardioactive peptide has the same primary structure from both species: Pro-Phe-Cys-Asn-Ala-Phe-Thr-Gly-Cys-NH2, a cyclic nonapeptide which is identical to crustacean cardioactive peptide (CCAP) originally isolated from the shore crab, Carcinus maenas, and subsequently isolated from Locusta migratoria and Manduca sexta. This is additional evidence that CCAP has widespread occurrence in arthropoda.
Yu, Jie; Hu, Yuanliang; Xue, Mingxiong; Dun, Yaohao; Li, Shenao; Peng, Nan; Liang, Yunxiang; Zhao, Shumao
2016-07-28
The aim of this study was to isolate antioxidant peptides from an enzymatic hydrolysate of Spirulina platensis. A novel antioxidant peptide was obtained by ultrafiltration, gel filtration chromatography, and reverse-phase high-performance liquid chromatography, with the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging assay used to measure the antioxidant activity, and the sequence was determined to be Pro-Asn-Asn (343.15 Da) by electrospray ionization tandem mass spectrometry. This peptide was synthesized to confirm its antioxidant properties, and it exhibited 81.44 ± 0.43% DPPH scavenging activity at 100 µg/ml, which was similar to that of glutathione (82.63 ± 0.56%). Furthermore, the superoxide anion and hydroxyl free-radical scavenging activities and the SOD activity of the peptide were 47.84 ± 0.49%, 54.01 ± 0.82%, and 12.55 ± 0.75%, respectively, at 10 mg/ml. These results indicate that S. platensis is a good source of antioxidant peptides, and that its hydrolysate may have important applications in the pharmaceutical and food industries.
Pathogen identification using peptide nanotube biosensors and impedance AFM
Maccuspie, Robert I.
Pathogen identification at highly sensitive levels is crucial to meet urgent needs in fighting the spread of disease or detecting bioterrorism events. Toward that end, a new method for biosensing utilizing fluorescent antibody nanotubes is proposed. Fundamental studies on the self-assembly of these peptide nanotubes are performed, as are applications of aligning these nanotubes on surfaces. As biosensors, these nanotubes incorporate recognition units with antibodies at their ends and fluorescent signaling units at their sidewalls. When viral pathogens were mixed with these antibody nanotubes in solution, the nanotubes rapidly aggregated around the viruses. The size of the aggregates increased as the concentration of viruses increased, as detected by flow cytometry on the order of attomolar concentrations by changes in fluorescence and light scattering intensities. This enabled determination of the concentrations of viruses at trace levels (102 to 106 pfu/mL) within 30 minutes from the receipt of samples to the final quantitative data analysis, as demonstrated on Adenovirus, Herpes Simplex Virus, Influenza, and Vaccinia virus. As another separate approach, impedance AFM is used to study the electrical properties of individual viruses and nanoparticles used as model systems. The design, development, and implementation of the impedance AFM for an Asylum Research platform is described, as well as its application towards studying the impedance of individual nanoparticles as a model system for understanding the fundamental science of how the life cycle of a virus affects its electrical properties. In combination, these approaches fill a pressing need to quantify viruses both rapidly and sensitively.
Scala, Maria Carmina; Sala, Marina; Pietrantoni, Agostina; Spensiero, Antonia; Di Micco, Simone; Agamennone, Mariangela; Bertamino, Alessia; Novellino, Ettore; Bifulco, Giuseppe; Gomez-Monterrey, Isabel M; Superti, Fabiana; Campiglia, Pietro
2017-09-06
Bovine lactoferrin is a biglobular multifunctional iron binding glycoprotein that plays an important role in innate immunity against infections. We have previously demonstrated that selected peptides from bovine lactoferrin C-lobe are able to prevent both Influenza virus hemagglutination and cell infection. To deeper investigate the ability of lactoferrin derived peptides to inhibit Influenza virus infection, in this study we identified new bovine lactoferrin C-lobe derived sequences and corresponding synthetic peptides were synthesized and assayed to check their ability to prevent viral hemagglutination and infection. We identified three tetrapeptides endowed with broad anti-Influenza activity and able to inhibit viral infection in a concentration range femto- to picomolar. Our data indicate that these peptides may constitute a non-toxic tool for potential applications as anti-Influenza therapeutics.
Centralized mouse repositories.
Donahue, Leah Rae; Hrabe de Angelis, Martin; Hagn, Michael; Franklin, Craig; Lloyd, K C Kent; Magnuson, Terry; McKerlie, Colin; Nakagata, Naomi; Obata, Yuichi; Read, Stuart; Wurst, Wolfgang; Hörlein, Andreas; Davisson, Muriel T
2012-10-01
Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world.
Jurtz, Vanessa; Paul, Sinu; Andreatta, Massimo; Marcatili, Paolo; Peters, Bjoern; Nielsen, Morten
2017-11-01
Cytotoxic T cells are of central importance in the immune system's response to disease. They recognize defective cells by binding to peptides presented on the cell surface by MHC class I molecules. Peptide binding to MHC molecules is the single most selective step in the Ag-presentation pathway. Therefore, in the quest for T cell epitopes, the prediction of peptide binding to MHC molecules has attracted widespread attention. In the past, predictors of peptide-MHC interactions have primarily been trained on binding affinity data. Recently, an increasing number of MHC-presented peptides identified by mass spectrometry have been reported containing information about peptide-processing steps in the presentation pathway and the length distribution of naturally presented peptides. In this article, we present NetMHCpan-4.0, a method trained on binding affinity and eluted ligand data leveraging the information from both data types. Large-scale benchmarking of the method demonstrates an increase in predictive performance compared with state-of-the-art methods when it comes to identification of naturally processed ligands, cancer neoantigens, and T cell epitopes. Copyright © 2017 by The American Association of Immunologists, Inc.
Demystifying the institutional repository for success
Buehler, Marianne
2013-01-01
Institutional repositories remain key to data storage on campus, fulfilling the academic needs of various stakeholders. Demystifying the Institutional Repository for Success is a practical guide to creating and sustaining an institutional repository through marketing, partnering, and understanding the academic needs of all stakeholders on campus. This title is divided into seven chapters, covering: traditional scholarly communication and open access publishing; the academic shift towards open access; what the successful institutional repository looks like; institutional repository collaboratio
The European Repository Landscape 2008 Inventory of Digital Repositories for Research Output
Van der Graaf, Maurits
2009-01-01
It is widely acknowledged that a common knowledge base for European research is necessary. Research repositories are an important innovation to the scientific information infrastructure. In 2006, digital repositories in the 27 countries of the European we
International Nuclear Information System (INIS)
1986-01-01
The scope and work which served as the basis for this report included the following major activities; (1) A review and summary of the screening methodologies utilized by DOE for the selection of proposed nuclear waste repository sites, including a description of the inherent weakness in those methodologies. (2) A description of the geologic and hydrologic features of the rock bodies selected by DOE and an identification of those features which could result in hazardous conditions as a result of the location of a high-level nuclear waste repository. (3) An assessment of potential environmental impacts of the repository and discussion of endanged species in the proposed repository project areas. This report is organized in three major sections in relationship to the scope of work. A list of references is also included at the end of this report. 37 refs., 2 figs
Characterization of trypsin-derived peptides acrylamide-adducted hemoglobin
International Nuclear Information System (INIS)
Springer, D.L.; Goheen, S.C.; Edmonds, C.G.; McCulloch, M.; Sylvester, D.M.; Sander, C.; Bull, R.J.
1991-01-01
Even though there are a number of sources for human exposure to acrylamide, reliable biomarkers of exposure are not available. In an effort to develop such a biomarker, the authors are characterizing peptides derived from trypsin digests of acrylamide-adducted hemoglobin. For this, radiolabeled acrylamide was incubated with this, radiolabeled acrylamide was incubated with purified human hemoglobin (Ao) and decomposition products removed by dialysis. When the adducted hemoglobin was separated by reverse-phase HPLC, radioactivity eluted with the α and β subunits, suggesting covalent binding. Digestion of individual subunits with trypsin followed by reverse phase HPLC, indicated that most of the radioactivity associated with the α subunit co-eluted with a single peptide. Similar results were observed for the β subunit except that significant amounts of radioactivity eluted with the solvent front, suggesting that radioactivity was released by trypsin digestion. Currently, these preparation are under further characterization by electrospray ionization mass spectrometry. This approach will aid in the identification of the adducted will aid in the identification of the adducted peptide and subsequent preparation of an acrylamide-specific antibody
García, M C; Puchalska, P; Esteve, C; Marina, M L
2013-03-15
Despite less explored than foods from animal origin, plant derived foods also contain biologically active proteins and peptides. Bioactive peptides can be present as an independent entity in the food or, more frequently, can be in a latent state as part of the sequence of a protein. Release from that protein requires protein hydrolysis by enzymatic digestion, fermentation or autolysis. Different methodologies have been used to test proteins and peptides bioactivities. Fractionation, separation, and identification techniques have also been employed for the isolation and identification of bioactive proteins or peptides. In this work, proteins and peptides from plant derived foods exerting antihypertensive, antioxidant, hypocholesterolemic, antithrombotic, and immunostimulating capacities or ability to reduce food intake have been reviewed. Copyright © 2013 Elsevier B.V. All rights reserved.
Office of Geologic Repositories quality assurance plan for high-level radioactive waste repositories
International Nuclear Information System (INIS)
1986-08-01
This document sets forth geologic repository program-wide quality assurance program requirements and defines management's quality assurance responsibilities for the Office of Geologic Repositories and its projects. (LM)
Virtual patient repositories--a comparative analysis.
Küfner, Julia; Kononowicz, Andrzej A; Hege, Inga
2014-01-01
Virtual Patients (VPs) are an important component of medical education. One way to reduce the costs for creating VPs is sharing through repositories. We conducted a literature review to identify existing repositories and analyzed the 17 included repositories in regards to the search functions and metadata they provide. Most repositories provided some metadata such as title or description, whereas other data, such as educational objectives, were less frequent. Future research could, in cooperation with the repository provider, investigate user expectations and usage patterns.
Technology overview of mined repositories
International Nuclear Information System (INIS)
Gimera, R.; Thirumalai, K.
1982-01-01
Mined repositories present an environmentally viable option for permanent disposal of nuclear waste. This paper reviews the state-of-the-art mining technologies and identifies technological issues and developments necessary to mine a repository in basalt. The thermal loading, isolation, and retrieval requirements of a repository present unique technological challenges unknown to conventional mining practice. The technology issues and developments required in the areas of excavation, roof and ground support, equipment development, instrumentation development, and sealing are presented. Performance assessment methods must be developed to evaluate the adequacies of technologies developed to design, construct, operate, and decommission a repository. A stepwise test-and-development approach is used in the Basalt Waste Isolation Project to develop cost-effective technologies for a repository
Breast Cancer Tissue Repository
National Research Council Canada - National Science Library
Iglehart, J
1997-01-01
The Breast Tissue Repository at Duke enters its fourth year of finding. The purpose of the Repository at Duke is to provide substantial quantities of frozen tissue for explorative molecular studies...
VerSi - A Methodology for a Comparison of Potential Repository Sites
International Nuclear Information System (INIS)
Hund, Wilhelm
2010-09-01
In the year 2000 the moratorium on the exploration of the Gorleben salt dome as a potential repository for all kinds of radioactive waste became effective as a result of the consensus agreement between the Federal Government and the utilities about phasing out nuclear energy in Germany. All exploration activities were interrupted for at maximum ten years to clarify conceptual and safety relevant questions. A new set of safety requirements for the final disposal of heat-generating radioactive waste in deep geological formations was established in July 2009 by the Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU). As the BMU intended to carry out a comparison of potential repository sites it was necessary to initiate the development of a methodology for the identification of the site with the highest level of safety. A comparison of different repository sites requires a tool ensuring most confident and objective criteria for the comparison, whereas up to present long-term safety analyses were focused on confirming the suitability of sites by meeting the protection objectives by the measures of dose and risk. Within the 2006 established project VerSi a methodology for comparing different sites in different host rocks will be developed on the basis of long-term safety analyses taking into account geoscientific databases, inventory of radioactive waste, waste containers, corresponding disposal concepts and the feasibility of appropriate backfilling and closure concepts. The development of the method is aiming at providing measures other than dose and risk for the evaluation of the level of safety. For testing the tools a HLW-repository hosted in a salt dome (Gorleben) will be compared with a generic HLW-repository in consolidated clay as a host rock. As until now in Germany no clay stone site has been investigated for hosting a HLW repository, the required data are transferred from international research projects and repository concepts
re3data.org - a global registry of research data repositories
Pampel, Heinz; Vierkant, Paul; Elger, Kirsten; Bertelmann, Roland; Witt, Michael; Schirmbacher, Peter; Rücknagel, Jessika; Kindling, Maxi; Scholze, Frank; Ulrich, Robert
2016-04-01
re3data.org - the registry of research data repositories lists over 1,400 research data repositories from all over the world making it the largest and most comprehensive online catalog of research data repositories on the web. The registry is a valuable tool for researchers, funding organizations, publishers and libraries. re3data.org provides detailed information about research data repositories, and its distinctive icons help researchers to easily identify relevant repositories for accessing and depositing data sets [1]. Funding agencies, like the European Commission [2] and research institutions like the University of Bielefeld [3] already recommend the use of re3data.org in their guidelines and policies. Several publishers and journals like Copernicus Publications, PeerJ, and Nature's Scientific Data recommend re3data.org in their editorial policies as a tool for the easy identification of appropriate data repositories to store research data. Project partners in re3data.org are the Library and Information Services department (LIS) of the GFZ German Research Centre for Geosciences, the Computer and Media Service at the Humboldt-Universität zu Berlin, the Purdue University Libraries and the KIT Library at the Karlsruhe Institute of Technology (KIT). After its fusion with the U.S. American DataBib in 2014, re3data.org continues as a service of DataCite from 2016 on. DataCite is the international organization for the registration of Digital Object Identifiers (DOI) for research data and aims to improve their citation. The poster describes the current status and the future plans of re3data.org. [1] Pampel H, et al. (2013) Making Research Data Repositories Visible: The re3data.org Registry. PLoS ONE 8(11): e78080. doi:10.1371/journal.pone.0078080. [2] European Commission (2015): Guidelines on Open Access to Scientific Publications and Research Data in Horizon 2020. Available: http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi
Tabb, David L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Variyath, Asokan Mulayath; Ham, Amy-Joan L.; Bunk, David M.; Kilpatrick, Lisa E.; Billheimer, Dean D.; Blackman, Ronald K.; Cardasis, Helene L.; Carr, Steven A.; Clauser, Karl R.; Jaffe, Jacob D.; Kowalski, Kevin A.; Neubert, Thomas A.; Regnier, Fred E.; Schilling, Birgit; Tegeler, Tony J.; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fisher, Susan J.; Gibson, Bradford W.; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Stein, Steven E.; Tempst, Paul; Paulovich, Amanda G.; Liebler, Daniel C.; Spiegelman, Cliff
2009-01-01
The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproducibility, but aberrant performance occasionally erased these gains. Even the simplest protein digestions yielded more peptide ions than LC-MS/MS could identify during a single experiment. We observed that peptide lists from pairs of technical replicates overlapped by 35–60%, giving a range for peptide-level repeatability in these experiments. Sample complexity did not appear to affect peptide identification repeatability, even as numbers of identified spectra changed by an order of magnitude. Statistical analysis of protein spectral counts revealed greater stability across technical replicates for Orbitraps, making them superior to LTQ instruments for biomarker candidate discovery. The most repeatable peptides were those corresponding to conventional tryptic cleavage sites, those that produced intense MS signals, and those that resulted from proteins generating many distinct peptides. Reproducibility among different instruments of the same type lagged behind
Shazly, Ahmed Behdal; He, Zhiyong; El-Aziz, Mahmoud Abd; Zeng, Maomao; Zhang, Shuang; Qin, Fang; Chen, Jie
2017-10-01
Buffalo and bovine caseins were hydrolysed by alcalase and trypsin to produce novel antioxidant peptides. The casein hydrolysates were purified using ultrafiltration (UF) and further characterized by RP-HPLC. The fractions produced higher antioxidant activities were identified for their peptides using LC MS/MS. All UF-VI (MWcasein (UF-VI with 54.84-fold purification) showed higher antioxidant activity than that obtained by trypsin. Trypsin hydrolysate contained high amount of hydrophobic amino acids while alcalase hydrolysate consisted mainly of Ser, Arg, Ala and Leu. The antioxidant peptides identified by LC MS/MS were RELEE, MEDNKQ and TVA, EQL in buffalo casein hydrolysates produced by trypsin and alcalase, respectively. Mechanism and reaction pathways of selected antioxidant peptides with ABTS were proposed. Conclusively, buffalo casein provided antioxidant peptides similar to bovine, suggesting that buffalo casein is a novel source of antioxidant. Copyright © 2017 Elsevier Ltd. All rights reserved.
Wang, Jiao; Song, Jingjing; Zhou, Shuimei; Fu, Yourong; Bailey, Jeffrey A; Shen, Changxin
2018-01-16
Identification of RhD antigen epitopes is a key component in understanding the pathogenesis of haemolytic disease of the foetus and newborn. Research has indicated that phage display libraries are useful tools for identifying novel mimic epitopes (mimotopes) which may help to determine antigen specificity. We selected the mimotopes of blood group RhD antigen by affinity panning a phage display library using monoclonal anti-D. After three rounds of biopanning, positive phage clones were identified by enzyme-linked immunosorbent assay (ELISA) and then sent for sequencing and peptides synthesis. Next, competitive ELISA and erythrocyte haemagglutination inhibition tests were carried out to confirm the inhibitory activity of the synthetic peptide. To evaluate the diagnostic performance of the synthetic peptide, a diagnostic ELISA was examined. Fourteen of 35 phage clones that were chosen randomly from the titering plate were considered to be positive. Following DNA sequencing and translation, 11 phage clones were found to represent the same peptide - RMKMLMMLMRRK (P4) - whereas each of the other three clones represented a unique peptide. Through the competitive ELISA and erythrocyte haemagglutination inhibition tests, the peptide (P4) was verified to have the ability to mimic the RhD antigen. The diagnostic ELISA for P4 proved to be sensitive (82.61%) and specific (88.57%). This study reveals that the P4 peptide can mimic RhD antigen and paves the way for the development of promising targeted diagnostic and therapeutic platforms for haemolytic disease of the foetus and newborn.
Al-Mahrous, Mohammed M; Jack, Ralph W; Sandiford, Stephanie K; Tagg, John R; Beatson, Scott A; Upton, Mathew
2011-08-01
Our interest in Staphylococcus epidermidis strain A487 was prompted by the unusual nature of its inhibitory activity in screening tests against methicillin-resistant Staphylococcus aureus isolates. The inhibitory activity was detected in deferred antagonism tests only if the agar plate was preheated for at least 35 min at ≥ 55 °C before inoculation of the indicator bacteria, this phenomenon indicating possible involvement of a heat-labile immunity agent or protease. The inhibitor was purified to homogeneity by ammonium sulphate precipitation, followed by cation-exchange and reversed-phase chromatography. Tandem MS revealed a novel peptide of molecular weight 2588.4 Da. The draft genome sequence of strain A487 was determined using 454 GS FLX technology, allowing the identification of the structural gene (hlp) encoding the mature peptide MQFITDLIKKAVDFFKGLFGNK. The deduced amino acid sequence of peptide 487 exhibited 70.8% similarity to that of a putative haemolysin from Staphylococcus cohnii. Analysis of the genome of strain A487 showed several additional inhibitor-encoding genes, including hld, the determinant for staphylococcal δ-lysin. This work indicates that potentially useful inhibitors could be overlooked in agar-based inhibitor screening programmes lacking a heat pretreatment step and also highlights the utility of draft genome sequence examination in antibacterial agent discovery. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
INSTITUTIONAL REPOSITORY: EMPLOYMENT IN EDUCATION
Directory of Open Access Journals (Sweden)
Vasyl P. Oleksyuk
2012-11-01
Full Text Available The article investigated the concept of «institutional repository» and determined the aspects of institutional repositories in higher education. Institutional Repositories are information systems that allow preserving, storing and disseminating scientific knowledge produced in higher education and scientific research institutions. This study presented the main aspects using institutional repositories in educational process (such as storage of scientific and educational information, means of organization activity of students, object of studying. This article produced the structure of communities and collections of the institutional. It is described the experience of implementing of DSpace in the learning process.
Directory of Open Access Journals (Sweden)
Xiaoli Guo
2017-02-01
Full Text Available Stem cell pools in the SAM (shoot apical meristem, RAM (root apical meristem and vascular procambium/cambium are regulated by CLE-receptor kinase-WOX signaling modules. Previous data showed that cyst nematode CLE-like effector proteins delivered into host cells through a stylet, act as ligand mimics of plant A-type CLE peptides and are pivotal for successful parasitism. Here we report the identification of a new class of CLE peptides from cyst nematodes with functional similarity to the B-type CLE peptide TDIF (tracheary element differentiation inhibitory factor encoded by the CLE41 and CLE44 genes in Arabidopsis. We further demonstrate that the TDIF-TDR (TDIF receptor-WOX4 pathway, which promotes procambial meristem cell proliferation, is involved in beet cyst nematode Heterodera schachtii parasitism. We observed activation of the TDIF pathway in developing feeding sites, reduced nematode infection in cle41 and tdr-1 wox4-1 mutants, and compromised syncytium size in cle41, tdr-1, wox4-1 and tdr-1 wox4-1 mutants. By qRT-PCR and promoter:GUS analyses, we showed that the expression of WOX4 is decreased in a clv1-101 clv2-101 rpk2-5 mutant, suggesting that WOX4 is a potential downstream target of nematode CLEs. Exogenous treatment with both nematode A-type and B-type CLE peptides induced massive cell proliferation in wild type roots, suggesting that the two types of CLEs may regulate cell proliferation during feeding site formation. These findings highlight an important role of the procambial cell proliferation pathway in cyst nematode feeding site formation.
Directory of Open Access Journals (Sweden)
Elizabeth Yakel
2013-06-01
Full Text Available ISO 16363:2012, Space Data and Information Transfer Systems - Audit and Certification of Trustworthy Digital Repositories (ISO TRAC, outlines actions a repository can take to be considered trustworthy, but research examining whether the repository’s designated community of users associates such actions with trustworthiness has been limited. Drawing from this ISO document and the management and information systems literatures, this paper discusses findings from interviews with 66 archaeologists and quantitative social scientists. We found similarities and differences across the disciplines and among the social scientists. Both disciplinary communities associated trust with a repository’s transparency. However, archaeologists mentioned guarantees of preservation and sustainability more frequently than the social scientists, who talked about institutional reputation. Repository processes were also linked to trust, with archaeologists more frequently citing metadata issues and social scientists discussing data selection and cleaning processes. Among the social scientists, novices mentioned the influence of colleagues on their trust in repositories almost twice as much as the experts. We discuss the implications our findings have for identifying trustworthy repositories and how they extend the models presented in the management and information systems literatures.
MALDI-based identification of stable hazelnut protein derived tryptic marker peptides.
Cucu, T; De Meulenaer, B; Devreese, B
2012-01-01
Food allergy is an important health problem especially in industrialised countries. Tree nuts, among which are hazelnuts (Corylus avellana), are typically causing serious and life-threatening symptoms in sensitive subjects. Hazelnut is used as a food ingredient in pastry, confectionary products, ice cream and meat products, therefore undeclared hazelnut can be often present as a cross-contaminant representing a threat for allergic consumers. Mass spectrometric techniques are used for the detection of food allergens in processed foods, but limited information regarding stable tryptic peptide markers for hazelnut is available. The aim of this study was to detect stable peptide markers from modified hazelnut protein through the Maillard reaction and oxidation in a buffered solution. Peptides ³⁹⁵Gly-Arg⁴⁰³ from Cor a 11 and ²⁰⁹Gln-Arg²¹⁷, ³⁵¹Ile-Arg³⁶³, ⁴⁶⁴Ala-Arg⁴⁷⁸ and ⁴⁰¹Val-Arg⁴¹⁷ from Cor a 9 hazelnut allergens proved to be the most stable and could be detected and confirmed with high scores in most of the modified samples. The identified peptides can be further used as analytical targets for the development of more robust quantitative methods for hazelnut detection in processed foods.
Huser, Vojtech; Cimino, James J
2013-01-01
Integrated data repositories (IDRs) are indispensable tools for numerous biomedical research studies. We compare three large IDRs (Informatics for Integrating Biology and the Bedside (i2b2), HMO Research Network's Virtual Data Warehouse (VDW) and Observational Medical Outcomes Partnership (OMOP) repository) in order to identify common architectural features that enable efficient storage and organization of large amounts of clinical data. We define three high-level classes of underlying data storage models and we analyze each repository using this classification. We look at how a set of sample facts is represented in each repository and conclude with a list of desiderata for IDRs that deal with the information storage model, terminology model, data integration and value-sets management.
Identification of a peptide inhibitor for the histone methyltransferase WHSC1.
Directory of Open Access Journals (Sweden)
Michael J Morrison
Full Text Available WHSC1 is a histone methyltransferase that is responsible for mono- and dimethylation of lysine 36 on histone H3 and has been implicated as a driver in a variety of hematological and solid tumors. Currently, there is a complete lack of validated chemical matter for this important drug discovery target. Herein we report on the first fully validated WHSC1 inhibitor, PTD2, a norleucine-containing peptide derived from the histone H4 sequence. This peptide exhibits micromolar affinity towards WHSC1 in biochemical and biophysical assays. Furthermore, a crystal structure was solved with the peptide in complex with SAM and the SET domain of WHSC1L1. This inhibitor is an important first step in creating potent, selective WHSC1 tool compounds for the purposes of understanding the complex biology in relation to human disease.
Process mining software repositories
Poncin, W.; Serebrenik, A.; Brand, van den M.G.J.
2011-01-01
Software developers' activities are in general recorded in software repositories such as version control systems, bug trackers and mail archives. While abundant information is usually present in such repositories, successful information extraction is often challenged by the necessity to
The Ec prototype repository project: implications of assessments for refining repository design
International Nuclear Information System (INIS)
Svemar, C.
2004-01-01
The most important issue in the evaluation of the repository performance is the long term safety of the repository. Analyses for this issue focuses on the 'steady state' conditions which start at the time when the repository has been saturated and the groundwater table returned to its normal level. The bentonite buffer around the canisters is saturated and homogeneous, and the canister is located exactly in the centre of the buffer. The backfill in the tunnel has been saturated as well and fills the earlier open spaces in the tunnel completely. The task of the activities taking places prior to the start of the 'steady state' conditions, like excavation, deposition, backfilling and sealing, with due consideration to the processes a consequences they may cause in the long run, is to provide for these 'ideal' conditions, as close as possible. While studying these activities in detail it has become obvious that development of methods and techniques needs to be carefully addressed before the decision is made on how to apply them in the repository. One general finding is that the situation in engineering of details is not that much different from the situation in geological characterisation of a site in detail; one more detail of engineering and the consequences it brings often complicates the situation rather than supports the solution prioritized so far. Many of the practical issues have been studied in the Prototype Repository project in the AEspoe Hard Rock Laboratory (Pusch et al., 2000). The Prototype Repository consists of two sections with four respectively two deposition holes with bentonite buffer and canister, the latter holding electrical heaters. The sections are separated by a concrete plug, and the whole test is to be separated from the rest of the laboratory by an outer plug. The project has two objectives: 1. To demonstrate the integrated function of tile deep repository components under realistic conditions and to compare results with models and
DEFF Research Database (Denmark)
Wang, Mingjun; Bai, Fang; Pries, Mette
2006-01-01
PURPOSE: To identify H-2 Kb/Db-binding immunogenic peptides derived from retinal proteins. METHODS: Computer-based prediction was used to identify potentially H-2 Kb/Db-binding peptides derived from the interphotoreceptor retinol-binding protein (IRBP), soluble retinal antigen (S...... on day 21 after immunization with IRBP or IRBP and the immunogenic peptides. RESULTS: All the 21 predicted peptides were found to upregulate expression of H-2 Kb/Db on RMA-S cells. Five peptides, the two IRBP-derived peptides IRBP89-96 and IRBP(101-108), and the three PEDF-derived peptides, PEDF389....... The immunogenic peptides alone did not induce inflammation in the eyes, but they could enhance severity of uveitis induced by IRBP. CONCLUSIONS: Five of 21 H-2 Kb/Db-binding retinal protein-derived peptides were found to be immunogenic, suggesting that these peptides could function as autoantigenic epitopes...
48 CFR 227.7108 - Contractor data repositories.
2010-10-01
... repositories. 227.7108 Section 227.7108 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS... Technical Data 227.7108 Contractor data repositories. (a) Contractor data repositories may be established when permitted by agency procedures. The contractual instrument establishing the data repository must...
Identification of novel peptides for horse meat speciation in highly processed foodstuffs.
Claydon, Amy J; Grundy, Helen H; Charlton, Adrian J; Romero, M Rosario
2015-01-01
There is a need for robust analytical methods to support enforcement of food labelling legislation. Proteomics is emerging as a complementary methodology to existing tools such as DNA and antibody-based techniques. Here we describe the development of a proteomics strategy for the determination of meat species in highly processed foods. A database of specific peptides for nine relevant animal species was used to enable semi-targeted species determination. This principle was tested for horse meat speciation, and a range of horse-specific peptides were identified as heat stable marker peptides for the detection of low levels of horse meat in mixtures with other species.
Urban-Kowalczyk, M; Śmigielski, J; Strzelecki, D
2017-03-01
The relationship between the olfactory system and emotional processing is an area of growing interest in schizophrenia research. Both the orbitofrontal cortex and amygdala are involved in the processing of olfactory information, and olfactory deficits may be also influenced by endogenous opioids and calcitonin gene-related peptide (CGRP), which is probably involved in dopaminergic transmission. However, the relationship between endorphins and dopaminergic transmission has not been fully explored. Odor identification performance and valence interaction was evaluated among 50 schizophrenic patients and 50 controls. Schizophrenia symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS). All study participants were subjected to the University of Pennsylvania Smell Identification Test (UPSIT), blood β-endorphin (BE) and CGRP measurement. Insignificantly higher BE concentrations were observed in the patient group, while significantly higher UPSIT scores were seen in controls (mean UPSIT 32.48 vs 26.82). The patients demonstrated significantly more identification errors for pleasant (P=0.000) and neutral (P=0.055) odors than for unpleasant odors. Patients with higher BE concentrations made more identification errors concerning pleasant (R s =-0.292; P=0.04) and neutral odors (R s =-0.331; P=0.019). Although the concentration of CGRP was significantly higher in the patient sample (Pidentification by valence for pleasant and neutral odors (UPSIT n/16: R s =-0.450, P=0.001; UPSIT n/15: R s =-0.586, P=0.000), and a weak negative correlation between PANSS N score and identification of unpleasant odors (UPSIT n/9: R s =-0.325, P=0.021). Schizophrenic patients present a unique pattern of smell identification characterized by aberrant hedonic ratings for pleasant odors but not unpleasant ones. Individuals with predominant negative symptoms and higher BE concentrations are most able to identify negative odors. Copyright © 2016 Elsevier Masson SAS. All rights
International Nuclear Information System (INIS)
Glasbergen, P.; Hamstra, J.
1981-01-01
A review is presented of the long-term scenarios used in the safety analysis which was carried out for the disposal of radioactive waste in salt domes in the Netherlands. The long-term analysis involved the following natural processes or events: climatological and sea-level changes, glacial erosion, diapirism, subsidence, faulting and dissolution. The model calculations which were carried out showed the dominant parameters: the rate of diapirism and the rate of subsurface dissolution of rock salt. During the operational period the intrusion of water in the repository was considered to be the most hazardous event. Because the layout of the disposal mine, the disposal geometry and the disposal mining procedures were still under consideration, the first approach of a release scenario was made on a generic basis. A generic scenario is presented for the events during the flooding of the repository. The transport ways of water through the repository and its surroundings are indicated. It is concluded that release scenario analysis for long-term periods and for the operational period provides essential information to optimize the overall disposal system in an iterative process
Identification of dipeptidyl peptidase-IV inhibitory peptides from mare whey protein hydrolysates.
Song, J J; Wang, Q; Du, M; Ji, X M; Mao, X Y
2017-09-01
Inhibition of dipeptidyl peptidase-IV (DPP-IV) activity is a promising strategy for treatment of type 2 diabetes. In the current study, DPP-IV inhibitory peptides were identified from mare whey protein hydrolysates obtained by papain. The results showed that all the mare whey protein hydrolysates obtained at various hydrolysis durations possessed more potent DPP-IV inhibitory activity compared with intact whey protein. The 4-h hydrolysates showed the greatest DPP-IV inhibitory activity with half-maximal inhibitory concentration of 0.18 mg/mL. The 2 novel peptides from 4-h hydrolysate fractions separated by successive chromatographic steps were characterized by liquid chromatography-electrospray ionization tandem mass spectrometry. The novel peptides Asn-Leu-Glu-Ile-Ile-Leu-Arg and Thr-Gln-Met-Val-Asp-Glu-Glu-Ile-Met-Glu-Lys-Phe-Arg, which corresponded to β-lactoglobulin 1 f(71-77) and β-lactoglobulin 1 f(143-155), demonstrated DPP-IV inhibitory activity with half-maximal inhibitory concentrations of 86.34 and 69.84 μM, respectively. The DPP-IV inhibitory activity of the 2 peptides was retained or even improved after simulated gastrointestinal digestion in vitro. Our findings indicate that mare whey protein-derived peptides may possess potential as functional food ingredients in the management of type 2 diabetes. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
Rock support for nuclear waste repositories
International Nuclear Information System (INIS)
Abramson, L.W.; Schmidt, B.
1984-01-01
The design of rock support for underground nuclear waste repositories requires consideration of special construction and operation requirements, and of the adverse environmental conditions in which some of the support is placed. While repository layouts resemble mines, design, construction and operation are subject to quality assurance and public scrutiny similar to what is experienced for nuclear power plants. Exploration, design, construction and operation go through phases of review and licensing by government agencies as repositories evolve. This paper discusses (1) the various stages of repository development; (2) the environment that supports must be designed for; (3) the environmental effects on support materials; and (4) alternative types of repository rock support
National Radwaste Repository Mochovce
International Nuclear Information System (INIS)
2000-01-01
In this leaflet the National Radioactive Waste Repository in Mochovce (Repository) is described. The Mochovce National Radioactive Waste Repository is a surface multi-barrier type storage facility for solid and treated solidified radioactive wastes generated from the Slovak Republic nuclear power plants operation and decommissioning, research institutes, laboratories and hospitals. The Repository comprises a system of single- and double-row storage boxes. The first double-row is enclosed by a steel-structure building. The 18 x 6 x 5.5 m storage boxes are made of reinforced concrete. The wall thickness is 600 mm. Two-double-rows, i.e. 80 storage boxes were built as part of Stage I (1 row = 20 storage boxes). Each storage box has a storage capacity of 90 fibre concrete containers of 3.1 m 3 volume. The total storage capacity is 7200 containers with the overall storage volume of 22320 m 3
Mudgil, Priti; Kamal, Hina; Yuen, Gan Chee; Maqsood, Sajid
2018-09-01
In-vitro inhibitory properties of peptides released from camel milk proteins against dipeptidyl peptidase-IV (DPP-IV), porcine pancreatic α-amylase (PPA), and porcine pancreatic lipase (PPL) were studied. Results revealed that upon hydrolysis by different enzymes, camel milk proteins displayed dramatic increase in inhibition of DPP-IV and PPL, but slight improvement in PPA inhibition was noticed. Peptide sequencing revealed a total of 20 and 3 peptides for A9 and B9 hydrolysates respectively, obtained the score of 0.8 or more on peptide ranker and were categorized as potential DPP-IV inhibitory peptides. KDLWDDFKGL in A9 and MPSKPPLL in B9 were identified as most potent PPA inhibitory peptide. For PPL inhibition only 7 and 2 peptides qualified as PPL inhibitory peptides from hydrolysates A9 and B9, respectively. The present study report for the first time PPA and PPL inhibitory and only second for DPP-IV inhibitory potential of protein hydrolysates from camel milk. Copyright © 2018 Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
Korhan Levent Ertürk
2012-03-01
Full Text Available After the declaration of the Budapest Open Access Initiative in 2001, institutional open repositories are known as the most important tool of the self archiving, which is also known as green road. There are 26 institutional repositories, which are all compatible to international standards. All the institutional open repositories of Turkey mentioned before are listed in international open archive directories. In this study institutional open repository of Dokuz Eylül University is examined and institutional open repositories of Turkey are discussed.
Reformulating Component Identification as Document Analysis Problem
Gross, H.G.; Lormans, M.; Zhou, J.
2007-01-01
One of the first steps of component procurement is the identification of required component features in large repositories of existing components. On the highest level of abstraction, component requirements as well as component descriptions are usually written in natural language. Therefore, we can
Radioactive waste repository of high ecological safety
International Nuclear Information System (INIS)
Sobolev, I.; Barinov, A.; Prozorov, L.
2000-01-01
With the purpose to construct a radioactive waste repository of high ecological safety and reliable containment, MosNPO 'Radon' specialists have developed an advanced type repository - large diameter well (LBD) one. A project is started for the development of a technology for LDW repository construction and pilot operation of the new repository for 25-30 years. The 2 LDW repositories constructed at the 'Radon' site and the developed monitoring system are described
Consistency analysis of network traffic repositories
Lastdrager, Elmer; Lastdrager, E.E.H.; Pras, Aiko
Traffic repositories with TCP/IP header information are very important for network analysis. Researchers often assume that such repositories reliably represent all traffic that has been flowing over the network; little thoughts are made regarding the consistency of these repositories. Still, for
Sellafield repository design concept
International Nuclear Information System (INIS)
1998-01-01
Between 1989 and 1997, UK Nirex Ltd carried out a programme of investigations to evaluate the potential of a site adjacent to the BNFL Sellafield works to host a deep repository for the United Kingdom's intermediate-level and certain low-level radioactive waste. The programme of investigations was wound down following the decision in March 1997 to uphold the rejection of the Company's planning application for the Rock Characterisation Facility (RCF), an underground laboratory which would have allowed further investigations to confirm whether or not the site would be suitable. Since that time, the Company's efforts in relation to the Sellafield site have been directed towards documenting and publishing the work carried out. The design concept for a repository at Sellafield was developed in parallel with the site investigations through an iterative process as knowledge of the site and understanding of the repository system performance increased. This report documents the Sellafield repository design concept as it had been developed, from initial design considerations in 1991 up to the point when the RCF planning application was rejected. It shows, from the context of a project at that particular site, how much information and experience has been gained that will be applicable to the development of a deep waste repository at other potential sites
Pangestuti, Ratih; Ryu, Bomi; Himaya, Swa; Kim, Se-Kwon
2013-08-01
Hippocampus trimaculatus is one of the most heavily traded seahorse species for traditional medicine purposes in many countries. In the present study, we showed neuroprotective effects of peptide derived from H. trimaculatus against amyloid-β42 (Aβ42) toxicity which are central to the pathogenesis of Alzheimer's diseases (AD). Firstly, H. trimaculatus was separately hydrolyzed by four different enzymes and tested for their protective effect on Aβ42-induced neurotoxicity in differentiated PC12 cells. Pronase E hydrolysate exerted highest protection with cell viability value of 88.33 ± 3.33 %. Furthermore, we used response surface methodology to optimize pronase E hydrolysis conditions and found that temperature at 36.69 °C with the hydrolysis time 20.01 h, enzyme to substrate (E/S) ratio of 2.02 % and pH 7.34 were the most optimum conditions. Following several purification steps, H. trimaculatus-derived neuroprotective peptides (HTP-1) sequence was identified as Gly-Thr-Glu-Asp-Glu-Leu-Asp-Lys (906.4 Da). HTP-1 protected PC12 cells from Aβ42-induced neuronal death with the cell viability value of 85.52 ± 2.22 % and up-regulated pro-survival gene (Bcl-2) expressions. These results suggest that HTP-1 has the potential to be used in treatment of neurodegenerative diseases, particularly AD. Identification, characterization, and synthesis of bioactive components derived from H. trimaculatus have the potential to replace or at least complement the use of seahorse as traditional medicine, which further may become an approach to minimize seahorse exploitation in traditional medicine.
Marine Peptides and Their Anti-Infective Activities
Directory of Open Access Journals (Sweden)
Hee Kyoung Kang
2015-01-01
Full Text Available Marine bioresources are a valuable source of bioactive compounds with industrial and nutraceutical potential. Numerous clinical trials evaluating novel chemotherapeutic agents derived from marine sources have revealed novel mechanisms of action. Recently, marine-derived bioactive peptides have attracted attention owing to their numerous beneficial effects. Moreover, several studies have reported that marine peptides exhibit various anti-infective activities, such as antimicrobial, antifungal, antimalarial, antiprotozoal, anti-tuberculosis, and antiviral activities. In the last several decades, studies of marine plants, animals, and microbes have revealed tremendous number of structurally diverse and bioactive secondary metabolites. However, the treatments available for many infectious diseases caused by bacteria, fungi, and viruses are limited. Thus, the identification of novel antimicrobial peptides should be continued, and all possible strategies should be explored. In this review, we will present the structures and anti-infective activity of peptides isolated from marine sources (sponges, algae, bacteria, fungi and fish from 2006 to the present.
Influence analysis of Github repositories.
Hu, Yan; Zhang, Jun; Bai, Xiaomei; Yu, Shuo; Yang, Zhuo
2016-01-01
With the support of cloud computing techniques, social coding platforms have changed the style of software development. Github is now the most popular social coding platform and project hosting service. Software developers of various levels keep entering Github, and use Github to save their public and private software projects. The large amounts of software developers and software repositories on Github are posing new challenges to the world of software engineering. This paper tries to tackle one of the important problems: analyzing the importance and influence of Github repositories. We proposed a HITS based influence analysis on graphs that represent the star relationship between Github users and repositories. A weighted version of HITS is applied to the overall star graph, and generates a different set of top influential repositories other than the results from standard version of HITS algorithm. We also conduct the influential analysis on per-month star graph, and study the monthly influence ranking of top repositories.
Identification of pro-opiomelanocortin and secretion of its peptide fragments in bovine adrenals
Energy Technology Data Exchange (ETDEWEB)
Tennov, A.V.; Dmitriev, A.D.; Kizim, E.A.; Ustinova, E.E.
1986-01-01
This paper describes the results of an investigation to show that biosynthesis of POMC, its proteolytic processing, an secretion of the peptide products of that processing take place in the bovine adrenals. Rabbit antisera against endorphins were obtained and used for radioimmunoassay of peptides. I 125-labeled peptides were obtained by the chloramine method and purified from free I 125 on Sephadex G-10 (0.7 x 5 cm, centrifugation for 10 min at 1500 g). To detect secretion of peptide fragments of POMC in the adrenals experiments were undertaken to determine the beta-endorphin content in perfusates obtained during retrograde perfusion of the bovine adrenals. It was found that immunoreactive compounds, indistinguishable in their immunochemical properties from beta-endorphin, are present in the perfusates, just as in the tissue extracts.
Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features
Wang, Bing; Zhang, Jun; Chen, Peng; Ji, Zhiwei; Deng, Shuping; Li, Chi
2013-01-01
Background: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics.Results: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model.Conclusions: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques. 2013 Wang et al.; licensee BioMed Central Ltd.
Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features
Wang, Bing
2013-05-09
Background: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics.Results: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model.Conclusions: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques. 2013 Wang et al.; licensee BioMed Central Ltd.
CRIS and Institutional Repositories
Directory of Open Access Journals (Sweden)
A Asserson
2010-04-01
Full Text Available CRIS (Current Research Information Systems provide researchers, research managers, innovators, and others with a view over the research activity of a domain. IRs (institutional repositories provide a mechanism for an organisation to showcase through OA (open access its intellectual property. Increasingly, organizations are mandating that their employed researchers deposit peer-reviewed published material in the IR. Research funders are increasingly mandating that publications be deposited in an open access repository: some mandate a central (or subject-based repository, some an IR. In parallel, publishers are offering OA but replacing subscription-based access with author (or author institution payment for publishing. However, many OA repositories have metadata based on DC (Dublin Core which is inadequate; a CERIF (Common-European Research Information Format CRIS provides metadata describing publications with formal syntax and declared semantics thus facilitating interoperation or homogeneous access over heterogeneous sources. The formality is essential for research output metrics, which are increasingly being used to determine future funding for research organizations.
Directory of Open Access Journals (Sweden)
Jaana E. Laine
2015-01-01
Full Text Available Qualitative trapping profile of reactive metabolites arising from six structurally different compounds was tested with three different d-peptide isomers (Peptide 1, gly–tyr–pro–cys–pro–his-pro; Peptide 2, gly–tyr–pro–ala–pro–his–pro; Peptide 3, gly–tyr–arg–pro–cys–pro–his–lys–pro and glutathione (GSH using mouse and human liver microsomes as the biocatalyst. The test compounds were classified either as clinically “safe” (amlodipine, caffeine, ibuprofen, or clinically as “risky” (clozapine, nimesulide, ticlopidine; i.e., associated with severe clinical toxicity outcomes. Our working hypothesis was as follows: could the use of short different amino acid sequence containing d-peptides in adduct detection confer any add-on value to that obtained with GSH? All “risky” agents’ resulted in the formation of several GSH adducts in the incubation mixture and with at least one peptide adduct with both microsomal preparations. Amlodipine did not form any adducts with any of the trapping agents. No GSH and peptide 2 and 3 adducts were found with caffeine, but with peptide 1 one adduct with human liver microsomes was detected. Ibuprofen produced one Peptide 1-adduct with human and mouse liver microsomes but not with GSH. In conclusion, GSH still remains the gold trapping standard for reactive metabolites. However, targeted d-peptides could provide additional information about protein binding potential of electrophilic agents, but their clinical significance needs to be clarified using a wider spectrum of chemicals together with other safety estimates.
Bioinformatics Tools for the Discovery of New Nonribosomal Peptides
DEFF Research Database (Denmark)
Leclère, Valérie; Weber, Tilmann; Jacques, Philippe
2016-01-01
-dimensional structure of the peptides can be compared with the structural patterns of all known NRPs. The presented workflow leads to an efficient and rapid screening of genomic data generated by high throughput technologies. The exploration of such sequenced genomes may lead to the discovery of new drugs (i......This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes...... and the deciphering of the domain architecture of the nonribosomal peptide synthetases (NRPSs). In the next step, candidate peptides synthesized by these NRPSs are predicted in silico, considering the specificity of incorporated monomers together with their isomery. To assess their novelty, the two...
Identification of Cellular Binding Sites for a Novel Human Anti-Breast Cancer Peptide
National Research Council Canada - National Science Library
DeFreest, Lori
2004-01-01
... breast cancer growth. We have developed and optimized an affinity chromatography procedure to identify the receptor for AFPep by using the peptide as "bait" to isolate proteins from solublized cells which have an affinity for the peptide...
Álvarez, Claudio Andrés; Barriga, Andrés; Albericio, Fernando; Romero, María Soledad; Guzmán, Fanny
2018-04-27
The elder ( Sambucus spp.) tree has a number of uses in traditional medicine. Previous studies have demonstrated the antimicrobial properties of elderberry liquid extract against human pathogenic bacteria and also influenza viruses. These properties have been mainly attributed to phenolic compounds. However, other plant defense molecules, such as antimicrobial peptides (AMPs), may be present. Here, we studied peptide extracts from flowers of Sambucus nigra L. The mass spectrometry analyses determined peptides of 3 to 3.6 kDa, among them, cysteine-rich peptides were identified with antimicrobial activity against various Gram-negative bacteria, including recurrent pathogens of Chilean aquaculture. In addition, membrane blebbing on the bacterial surface after exposure to the cyclotide was visualized by SEM microscopy and SYTOX Green permeabilization assay showed the ability to disrupt the bacterial membrane. We postulate that these peptides exert their action by destroying the bacterial membrane.
Nuclear waste repository design and construction
International Nuclear Information System (INIS)
Bohlke, B.M.; Monsees, J.E.
1987-01-01
Extensive underground excavation will be required for construction of a mined geologic repository for nuclear waste. Hundreds of thousands of feet of drift will be required based on the conceptual layout design for each candidate nuclear waste repository. Comparison of boring and blasting excavation methods are discussed, as are special design and construction requirements (e.g., quality assurance procedures and performance assessment) for the nuclear waste repository. Comparisons are made between boring and blasting construction methods for the repository designs proposed for salt, volcanic tuff, and basalt
Oliveira, Kenneth; Procop, Gary W.; Wilson, Deborah; Coull, James; Stender, Henrik
2002-01-01
A new fluorescence in situ hybridization (FISH) method with peptide nucleic acid (PNA) probes for identification of Staphylococcus aureus directly from positive blood culture bottles that contain gram-positive cocci in clusters (GPCC) is described. The test (the S. aureus PNA FISH assay) is based on a fluorescein-labeled PNA probe that targets a species-specific sequence of the 16S rRNA of S. aureus. Evaluations with 17 reference strains and 48 clinical isolates, including methicillin-resistant and methicillin-susceptible S. aureus species, coagulase-negative Staphylococcus species, and other clinically relevant and phylogenetically related bacteria and yeast species, showed that the assay had 100% sensitivity and 96% specificity. Clinical trials with 87 blood cultures positive for GPCC correctly identified 36 of 37 (97%) of the S. aureus-positive cultures identified by standard microbiological methods. The positive and negative predictive values were 100 and 98%, respectively. It is concluded that this rapid method (2.5 h) for identification of S. aureus directly from blood culture bottles that contain GPCC offers important information for optimal antibiotic therapy. PMID:11773123
Venomics-Accelerated Cone Snail Venom Peptide Discovery
Himaya, S. W. A.
2018-01-01
Cone snail venoms are considered a treasure trove of bioactive peptides. Despite over 800 species of cone snails being known, each producing over 1000 venom peptides, only about 150 unique venom peptides are structurally and functionally characterized. To overcome the limitations of the traditional low-throughput bio-discovery approaches, multi-omics systems approaches have been introduced to accelerate venom peptide discovery and characterisation. This “venomic” approach is starting to unravel the full complexity of cone snail venoms and to provide new insights into their biology and evolution. The main challenge for venomics is the effective integration of transcriptomics, proteomics, and pharmacological data and the efficient analysis of big datasets. Novel database search tools and visualisation techniques are now being introduced that facilitate data exploration, with ongoing advances in related omics fields being expected to further enhance venomics studies. Despite these challenges and future opportunities, cone snail venomics has already exponentially expanded the number of novel venom peptide sequences identified from the species investigated, although most novel conotoxins remain to be pharmacologically characterised. Therefore, efficient high-throughput peptide production systems and/or banks of miniaturized discovery assays are required to overcome this bottleneck and thus enhance cone snail venom bioprospecting and accelerate the identification of novel drug leads. PMID:29522462
Venomics-Accelerated Cone Snail Venom Peptide Discovery
Directory of Open Access Journals (Sweden)
S. W. A. Himaya
2018-03-01
Full Text Available Cone snail venoms are considered a treasure trove of bioactive peptides. Despite over 800 species of cone snails being known, each producing over 1000 venom peptides, only about 150 unique venom peptides are structurally and functionally characterized. To overcome the limitations of the traditional low-throughput bio-discovery approaches, multi-omics systems approaches have been introduced to accelerate venom peptide discovery and characterisation. This “venomic” approach is starting to unravel the full complexity of cone snail venoms and to provide new insights into their biology and evolution. The main challenge for venomics is the effective integration of transcriptomics, proteomics, and pharmacological data and the efficient analysis of big datasets. Novel database search tools and visualisation techniques are now being introduced that facilitate data exploration, with ongoing advances in related omics fields being expected to further enhance venomics studies. Despite these challenges and future opportunities, cone snail venomics has already exponentially expanded the number of novel venom peptide sequences identified from the species investigated, although most novel conotoxins remain to be pharmacologically characterised. Therefore, efficient high-throughput peptide production systems and/or banks of miniaturized discovery assays are required to overcome this bottleneck and thus enhance cone snail venom bioprospecting and accelerate the identification of novel drug leads.
Peptide chemistry toolbox - Transforming natural peptides into peptide therapeutics.
Erak, Miloš; Bellmann-Sickert, Kathrin; Els-Heindl, Sylvia; Beck-Sickinger, Annette G
2018-06-01
The development of solid phase peptide synthesis has released tremendous opportunities for using synthetic peptides in medicinal applications. In the last decades, peptide therapeutics became an emerging market in pharmaceutical industry. The need for synthetic strategies in order to improve peptidic properties, such as longer half-life, higher bioavailability, increased potency and efficiency is accordingly rising. In this mini-review, we present a toolbox of modifications in peptide chemistry for overcoming the main drawbacks during the transition from natural peptides to peptide therapeutics. Modifications at the level of the peptide backbone, amino acid side chains and higher orders of structures are described. Furthermore, we are discussing the future of peptide therapeutics development and their impact on the pharmaceutical market. Copyright © 2018 Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
San Jiun Chai
Full Text Available Nasopharyngeal carcinoma (NPC is highly prevalent in South East Asia and China. The poor outcome is due to late presentation, recurrence, distant metastasis and limited therapeutic options. For improved treatment outcome, immunotherapeutic approaches focusing on dendritic and autologous cytotoxic T-cell based therapies have been developed, but cost and infrastructure remain barriers for implementing these in low-resource settings. As our prior observations had found that four-jointed box 1 (FJX1, a tumor antigen, is overexpressed in NPCs, we investigated if short 9-20 amino acid sequence specific peptides matching to FJX1 requiring only intramuscular immunization to train host immune systems would be a better treatment option for this disease. Thus, we designed 8 FJX1-specific peptides and implemented an assay system to first, assess the binding of these peptides to HLA-A2 molecules on T2 cells. After, ELISPOT assays were used to determine the peptides immunogenicity and ability to induce potential cytotoxicity activity towards cancer cells. Also, T-cell proliferation assay was used to evaluate the potential of MHC class II peptides to stimulate the expansion of isolated T-cells. Our results demonstrate that these peptides are immunogenic and peptide stimulated T-cells were able to induce peptide-specific cytolytic activity specifically against FJX1-expressing cancer cells. In addition, we demonstrated that the MHC class II peptides were capable of inducing T-cell proliferation. Our results suggest that these peptides are capable of inducing specific cytotoxic cytokines secretion against FJX1-expressing cancer cells and serve as a potential vaccine-based therapy for NPC patients.
Chai, San Jiun; Yap, Yoke Yeow; Foo, Yoke Ching; Yap, Lee Fah; Ponniah, Sathibalan; Teo, Soo Hwang; Cheong, Sok Ching; Patel, Vyomesh; Lim, Kue Peng
2015-01-01
Nasopharyngeal carcinoma (NPC) is highly prevalent in South East Asia and China. The poor outcome is due to late presentation, recurrence, distant metastasis and limited therapeutic options. For improved treatment outcome, immunotherapeutic approaches focusing on dendritic and autologous cytotoxic T-cell based therapies have been developed, but cost and infrastructure remain barriers for implementing these in low-resource settings. As our prior observations had found that four-jointed box 1 (FJX1), a tumor antigen, is overexpressed in NPCs, we investigated if short 9–20 amino acid sequence specific peptides matching to FJX1 requiring only intramuscular immunization to train host immune systems would be a better treatment option for this disease. Thus, we designed 8 FJX1-specific peptides and implemented an assay system to first, assess the binding of these peptides to HLA-A2 molecules on T2 cells. After, ELISPOT assays were used to determine the peptides immunogenicity and ability to induce potential cytotoxicity activity towards cancer cells. Also, T-cell proliferation assay was used to evaluate the potential of MHC class II peptides to stimulate the expansion of isolated T-cells. Our results demonstrate that these peptides are immunogenic and peptide stimulated T-cells were able to induce peptide-specific cytolytic activity specifically against FJX1-expressing cancer cells. In addition, we demonstrated that the MHC class II peptides were capable of inducing T-cell proliferation. Our results suggest that these peptides are capable of inducing specific cytotoxic cytokines secretion against FJX1-expressing cancer cells and serve as a potential vaccine-based therapy for NPC patients. PMID:26536470
National radioactive wasterRepository Mochovce
International Nuclear Information System (INIS)
2000-01-01
In this leaflet the scheme of the Mochovce National radioactive waste repository for the Slovak Republic is presented. The National radioactive waste repository in Mochovce is a surface type storage facility. It is intended for final disposal of solid and solidified low and intermediate radioactive waste produced during the operation of nuclear power plants and institutions located within the territory of the Slovak Republic. The Repository site is situated about 2 km northwest to the Mochovce NPP
Biological Web Service Repositories Review.
Urdidiales-Nieto, David; Navas-Delgado, Ismael; Aldana-Montes, José F
2017-05-01
Web services play a key role in bioinformatics enabling the integration of database access and analysis of algorithms. However, Web service repositories do not usually publish information on the changes made to their registered Web services. Dynamism is directly related to the changes in the repositories (services registered or unregistered) and at service level (annotation changes). Thus, users, software clients or workflow based approaches lack enough relevant information to decide when they should review or re-execute a Web service or workflow to get updated or improved results. The dynamism of the repository could be a measure for workflow developers to re-check service availability and annotation changes in the services of interest to them. This paper presents a review on the most well-known Web service repositories in the life sciences including an analysis of their dynamism. Freshness is introduced in this paper, and has been used as the measure for the dynamism of these repositories. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
LC-MS/MS Identification of Species-Specific Muscle Peptides in Processed Animal Proteins.
Marchis, Daniela; Altomare, Alessandra; Gili, Marilena; Ostorero, Federica; Khadjavi, Amina; Corona, Cristiano; Ru, Giuseppe; Cappelletti, Benedetta; Gianelli, Silvia; Amadeo, Francesca; Rumio, Cristiano; Carini, Marina; Aldini, Giancarlo; Casalone, Cristina
2017-12-06
An innovative analytical strategy has been applied to identify signature peptides able to distinguish among processed animal proteins (PAPs) derived from bovine, pig, fish, and milk products. Proteomics was first used to elucidate the proteome of each source. Starting from the identified proteins and using a funnel based approach, a set of abundant and well characterized peptides with suitable physical-chemical properties (signature peptides) and specific for each source was selected. An on-target LC-ESI-MS/MS method (MRM mode) was set up using standard peptides and was then applied to selectively identify the PAP source and also to distinguish proteins from bovine carcass and milk proteins. We believe that the method described meets the request of the European Commission which has developed a strategy for gradually lifting the "total ban" toward "species to species ban", therefore requiring official methods for species-specific discrimination in feed.
IAEA safeguards for geological repositories
International Nuclear Information System (INIS)
Moran, B.W.
2005-01-01
In September. 1988, the IAEA held its first formal meeting on the safeguards requirements for the final disposal of spent fuel and nuclear material-bearing waste. The consensus recommendation of the 43 participants from 18 countries at this Advisory Group Meeting was that safeguards should not terminate of spent fuel even after emplacement in, and closure of, a geologic repository.' As a result of this recommendation, the IAEA initiated a series of consultants' meetings and the SAGOR Programme (Programme for the Development of Safeguards for the Final Disposal of Spent Fuel in Geologic Repositories) to develop an approach that would permit IAEA safeguards to verify the non-diversion of spent fuel from a geologic repository. At the end of this process, in December 1997, a second Advisory Group Meeting, endorsed the generic safeguards approach developed by the SAGOR Programme. Using the SAGOR Programme results and consultants' meeting recommendations, the IAEA Department of Safeguards issued a safeguards policy paper stating the requirements for IAEA safeguards at geologic repositories. Following approval of the safeguards policy and the generic safeguards approach, the Geologic Repository Safeguards Experts Group was established to make recommendations on implementing the safeguards approach. This experts' group is currently making recommendations to the IAEA regarding the safeguards activities to be conducted with respect to Finland's repository programme. (author)
CrossWork: Software-assisted identification of cross-linked peptides
DEFF Research Database (Denmark)
Rasmussen, Morten; Refsgaard, Jan; Peng, Li
2011-01-01
Work searches batches of tandem mass-spectrometric data, and identifies cross-linked and non-cross-linked peptides using a standard PC. We tested CrossWork by searching mass-spectrometric datasets of cross-linked complement factor C3 against small (1 protein) and large (1000 proteins) search spaces, and show...
To date, some biological activities have been confirmed as different named peptides, however, most FXPRLamide peptides are still poorly understood although these peptides are found in all insects. So, the study of receptors for these peptides is particularly important. Receptors of FXPRLamide peptid...
Repository site characterization
International Nuclear Information System (INIS)
Voss, J.W.; Pentz, D.L.
1987-01-01
The characterization of candidate repository sites has a number of programmatic objectives. Principal among these is the acquisition of data: a) to determine the suitability of a site relative to the DOE repository siting guidelines, b) to support model development and calculations to determine the suitability of a site relative to the post closure criteria of the NRC and EPA, c) to support the design of a disposal system, including the waste package and the engineered barrier system, as well as the shafts and underground openings of the repository. In meeting the gaols of site characterization, the authors have an obligation to conduct their investigations within an appropriate budget and schedule. This mandates that a well-constructed and systematic plan for field investigations be developed. Such a plan must fully account for the mechanisms which will control the radiologic performance in the repository. The plan must also flexibly and dynamically respond to the results of each step of field investigation, responding to the spatial variability of earth as well as to enhanced understandings of the performance of the disposal system. Such a plan must ensure that sufficient data are available to support the necessary probabilistic calculations of performance. This paper explores the planning for field data acquisition with specific reference to requirements for demonstrations of the acceptable performance for disposal systems
Gas generation in repositories
International Nuclear Information System (INIS)
Biddle, P.; Rees, J.H.; McGahan, D.; Rushbrook, P.E.
1987-09-01
The nature and quantities of gases likely to be produced by various processes in repositories for low level and intermediate level radioactive wastes are examined in this preliminary study. Many simplifying assumptions are made where published or experimental data is unavailable. The corrosion of the canisters and metallic components in wastes is likely to be the major gas production process in both types of repository. A significant contribution from microbiological activity is expected to occur in low level repositories, predominantly where no cement grouting of the cans has been carried out. A number of areas for further research, required before a more comprehensive study could be carried out, have been identified. (author)
SUBSURFACE REPOSITORY INTEGRATED CONTROL SYSTEM DESIGN
International Nuclear Information System (INIS)
Randle, D.C.
2000-01-01
The primary purpose of this document is to develop a preliminary high-level functional and physical control system architecture for the potential repository at Yucca Mountain. This document outlines an overall control system concept that encompasses and integrates the many diverse process and communication systems being developed for the subsurface repository design. This document presents integrated design concepts for monitoring and controlling the diverse set of subsurface operations. The Subsurface Repository Integrated Control System design will be composed of a series of diverse process systems and communication networks. The subsurface repository design contains many systems related to instrumentation and control (I andC) for both repository development and waste emplacement operations. These systems include waste emplacement, waste retrieval, ventilation, radiological and air monitoring, rail transportation, construction development, utility systems (electrical, lighting, water, compressed air, etc.), fire protection, backfill emplacement, and performance confirmation. Each of these systems involves some level of I andC and will typically be integrated over a data communications network throughout the subsurface facility. The subsurface I andC systems will also interface with multiple surface-based systems such as site operations, rail transportation, security and safeguards, and electrical/piped utilities. In addition to the I andC systems, the subsurface repository design also contains systems related to voice and video communications. The components for each of these systems will be distributed and linked over voice and video communication networks throughout the subsurface facility. The scope and primary objectives of this design analysis are to: (1) Identify preliminary system-level functions and interfaces (Section 6.2). (2) Examine the overall system complexity and determine how and on what levels the engineered process systems will be monitored
International Nuclear Information System (INIS)
2014-01-01
National radioactive waste repository programmes are collecting large amounts of data to support the long-term management of their nations' radioactive wastes. The data and related records increase in number, type and quality as programmes proceed through the successive stages of repository development: pre-siting, siting, characterisation, construction, operation and finally closure. Regulatory and societal approvals are included in this sequence. Some programmes are also documenting past repository projects and facing a challenge in allowing both current and future generations to understand actions carried out in the past. Metadata allows context to be stored with data and information so that it can be located, used, updated and maintained. Metadata helps waste management organisations better utilise their data in carrying out their statutory tasks and can also help verify and demonstrate that their programmes are appropriately driven. The NEA Radioactive Waste Repository Metadata Management (RepMet) initiative aims to bring about a better understanding of the identification and administration of metadata - a key aspect of data management - to support national programmes in managing their radioactive waste repository data, information and records in a way that is both harmonised internationally and suitable for long-term management and use. This is a summary record of the 1. meeting of the RepMet initiative. The actions and decisions from this meeting were sent separately to the group after the meeting, but are also included in this document (Annex A). The list of participants is attached as well (Annex B)
Preliminary design of the repository. Stage 2
International Nuclear Information System (INIS)
Saanio, T.; Kirkkomaeki, T.; Keto, P.; Kukkola, T.; Raiko, H.
2007-04-01
Spent nuclear fuel from Finnish nuclear power plants will be disposed of in deep bedrock in Olkiluoto, Eurajoki. The repository is planned to be excavated at a depth of 400 - 500 metres. Access routes to the repository include a 1:10 inclined access tunnel, and vertical shafts. The fuel is encapsulated in the encapsulation plant above ground and transferred to the repository in the canister lift. Deposition tunnels, central tunnels and technical rooms are excavated at the disposal level. The canisters are deposited in deposition holes that are covered with bentonite blocks. The deposition holes are bored in the floors of the deposition tunnels. The central tunnel system consists of two parallel central tunnels that are inter-connected at certain distances. Two parallel central tunnels improve the fire safety of the rooms and also allow flexible backfilling and closing of the deposition tunnels in stages at the operational phase of the repository. An underground rock characterization facility, ONKALO, is excavated at the disposal level to support and confirm investigations carried out from above ground. ONKALO is designed so that it can later serve as part of the repository. ONKALO excavations were started in 2004. The repository will be excavated in the 2010s and operation will start in 2020. The fifth nuclear power unit makes the operational phase of the repository very long. Parts of the repository will be excavated and closed over the long operational period. The repository can be constructed at one or several levels. The one-storey alternative is the so-called reference alternative in this preliminary design report. The two-storey alternative is also taken into account in the ONKALO designs. The preliminary designs of the repository are presented as located in Olkiluoto. The location of the repository will be revised when more information on the bedrock has been gained. More detailed data of the circumstances will be obtained from above ground investigations
Preliminary design of the repository, stage 2
International Nuclear Information System (INIS)
Saanio, T.; Kirkkomaeki, T.; Keto, P.; Kukkola, T.; Raiko, H.
2007-01-01
Spent nuclear fuel from Finnish nuclear power plants will be disposed of in deep bedrock in Olkiluoto, Eurajoki. The repository is planned to be excavated at a depth of 400 - 500 metres. Access routes to the repository include a 1:10 inclined access tunnel, and vertical shafts. The fuel is encapsulated in the encapsulation plant above ground and transferred to the repository in the canister lift. Deposition tunnels, central tunnels and technical rooms are excavated at the disposal level. The canisters are deposited in deposition holes that are covered with bentonite blocks. The deposition holes are bored in the floors of the deposition tunnels. The central tunnel system consists of two parallel central tunnels that are inter-connected at certain distances. Two parallel central tunnels improve the fire safety of the rooms and also allow flexible backfilling and closing of the deposition tunnels in stages at the operational phase of the repository. An underground rock characterization facility, ONKALO, is excavated at the disposal level to support and confirm investigations carried out from above ground. ONKALO is designed so that it can later serve as part of the repository. ONKALO excavations were started in 2004. The repository will be excavated in the 2010s and operation will start in 2020. The fifth nuclear power unit makes the operational phase of the repository very long. Parts of the repository will be excavated and closed over the long operational period. The repository can be constructed at one or several levels. The one-storey alternative is the so-called reference alternative in this preliminary design report. The two-storey alternative is also taken into account in the ONKALO designs. The preliminary designs of the repository are presented as located in Olkiluoto. The location of the repository will be revised when more information on the bedrock has been gained. More detailed data of the circumstances will be obtained from above ground investigations
Nuclear waste repository siting
International Nuclear Information System (INIS)
Soloman, B.D.; Cameron, D.M.
1987-01-01
This paper discusses the geopolitics of nuclear waste disposal in the USA. Constitutional choice and social equity perspectives are used to argue for a more open and just repository siting program. The authors assert that every potential repository site inevitably contains geologic, environmental or other imperfections and that the political process is the correct one for determining sites selected
Granite-repository - geochemical environment
International Nuclear Information System (INIS)
1979-04-01
Some geochemical data of importance for a radioactive waste repository in hard rock are reviewed. The ground water composition at depth is assessed. The ground water chemistry in the vicinity of uranium ores is discussed. The redox system in Swedish bedrock is described. Influences of extreme climatic changes and of repository mining and construction are also evaluated
Workshop: Creating Your Institutional Research Repository
Grenz, Daryl M.
2016-11-08
In 2002, the Scholarly Publishing and Academic Resources Coalition (SPARC) proposed the concept of an institutional repository to simultaneously disrupt and enhance the state of scholarly communications in the academic world. Thirteen years later, thousands of universities and other institutions have answered this call, but many more have not due to gaps in budgets, awareness and, most of all, practical guidance on creating an institutional repository. This workshop provides you with an essential primer on what it takes to establish a fully-functioning institutional repository. Every aspect of the process will be covered, including policies, procedures, staffing guidelines, workflows and repository technologies.
Audie, J; Boyd, C
2010-01-01
The case for peptide-based drugs is compelling. Due to their chemical, physical and conformational diversity, and relatively unproblematic toxicity and immunogenicity, peptides represent excellent starting material for drug discovery. Nature has solved many physiological and pharmacological problems through the use of peptides, polypeptides and proteins. If nature could solve such a diversity of challenging biological problems through the use of peptides, it seems reasonable to infer that human ingenuity will prove even more successful. And this, indeed, appears to be the case, as a number of scientific and methodological advances are making peptides and peptide-based compounds ever more promising pharmacological agents. Chief among these advances are powerful chemical and biological screening technologies for lead identification and optimization, methods for enhancing peptide in vivo stability, bioavailability and cell-permeability, and new delivery technologies. Other advances include the development and experimental validation of robust computational methods for peptide lead identification and optimization. Finally, scientific analysis, biology and chemistry indicate the prospect of designing relatively small peptides to therapeutically modulate so-called 'undruggable' protein-protein interactions. Taken together a clear picture is emerging: through the synergistic use of the scientific imagination and the computational, chemical and biological methods that are currently available, effective peptide therapeutics for novel targets can be designed that surpass even the proven peptidic designs of nature.
Analytic framework for peptidomics applied to large-scale neuropeptide identification
DEFF Research Database (Denmark)
Secher, Anna; Kelstrup, Christian D; Conde-Frieboes, Kilian W
2016-01-01
was integrated with publically available databases. We developed and applied an algorithm that reduces the peptide complexity for identification of biologically relevant peptides. The developed pipeline was applied to rat hypothalamus and identifies thousands of neuropeptides and their post...
Safeguards for geological repositories
International Nuclear Information System (INIS)
Fattah, A.
2000-01-01
Direct disposal of spent nuclear fuel in geological repositories is a recognised option for closing nuclear fuel cycles. Geological repositories are at present in stages of development in a number of countries and are expected to be built and operated early next century. A State usually has an obligation to safely store any nuclear material, which is considered unsuitable to re-enter the nuclear fuel cycle, isolated from the biosphere. In conjunction with this, physical protection has to be accounted for to prevent inadvertent access to such material. In addition to these two criteria - which are fully under the State's jurisdiction - a third criterion reflecting international non-proliferation commitments needs to be addressed. Under comprehensive safeguards agreements a State concedes verification of nuclear material for safeguards purposes to the IAEA. The Agency can thus provide assurance to the international community that such nuclear material has been used for peaceful purposes only as declared by the State. It must be emphasised that all three criteria mentioned constitute a 'unit'. None can be sacrificed for the sake of the other, but compromises may have to be sought in order to make their combination as effective as possible. Based on comprehensive safeguards agreements signed and ratified by the State, safeguards can be terminated only when the material has been consumed or diluted in such a way that it can no longer be utilised for any nuclear activities or has become practicably irrecoverable. As such safeguards for nuclear material in geological repositories have to be continued even after the repository has been back-filled and sealed. The effective application of safeguards must assure continuity-of-knowledge that the nuclear material in the repository has not been diverted for an unknown purpose. The nuclear material disposed in a geological repository may eventually have a higher and long term proliferation risk because the inventory is
Analysis of iodinated quorum sensing peptides by LC–UV/ESI ion trap mass spectrometry
Directory of Open Access Journals (Sweden)
Yorick Janssens
2018-02-01
Full Text Available Five different quorum sensing peptides (QSP were iodinated using different iodination techniques. These iodinated peptides were analyzed using a C18 reversed phase HPLC system, applying a linear gradient of water and acetonitrile containing 0.1% (m/v formic acid as mobile phase. Electrospray ionization (ESI ion trap mass spectrometry was used for the identification of the modified peptides, while semi-quantification was performed using total ion current (TIC spectra. Non-iodinated peptides and mono- and di-iodinated peptides (NIP, MIP and DIP respectively were well separated and eluted in that order. Depending on the used iodination method, iodination yields varied from low (2% to high (57%.
Tandem MS Analysis of Selenamide-Derivatized Peptide Ions
Zhang, Yun; Zhang, Hao; Cui, Weidong; Chen, Hao
2011-09-01
Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen ( m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.
Modelling saline intrusion for repository performance assessment
International Nuclear Information System (INIS)
Jackson, C.P.
1989-04-01
UK Nirex Ltd are currently considering the possibility of disposal of radioactive waste by burial in deep underground repositories. The natural pathway for radionuclides from such a repository to return to Man's immediate environment (the biosphere) is via groundwater. Thus analyses of the groundwater flow in the neighbourhood of a possible repository, and consequent radionuclide transport form an important part of a performance assessment for a repository. Some of the areas in the UK that might be considered as possible locations for a repository are near the coast. If a repository is located in a coastal region seawater may intrude into the groundwater flow system. As seawater is denser than fresh water buoyancy forces acting on the intruding saline water may have significant effects on the groundwater flow system, and consequently on the time for radionuclides to return to the biosphere. Further, the chemistry of the repository near-field may be strongly influenced by the salinity of the groundwater. It is therefore important for Nirex to have a capability for reliably modelling saline intrusion to an appropriate degree of accuracy in order to make performance assessments for a repository in a coastal region. This report describes work undertaken in the Nirex Research programme to provide such a capability. (author)
Analisis Konten dan Kebijakan Akses Institutional Repository
Directory of Open Access Journals (Sweden)
Amirul Ulum
2016-07-01
Abstract; Institutional repository has become a major concern of higher education in Indonesia. The number of institutional respository was increased, one of the reason is the ranking web of repositories has been conducted by the Cybermetrics Lab in 2008. At that time, many institutions started to build institutional repository in order to manage the scientific work and also trying to reach the better ranks. Meanwhile, it is an achievement of institution performance which can be promote and increase visibility for the institution. University of Surabaya has also developed the institutional repository and managed by the library. The aims of this study is to analyze the content availability and access policies defined by the University of Surabaya repository providing services to the academic community and external users. The method used in this study by using observations of the institutional repository University of Surabaya with a literature review to clarify the analysis of the content and access policies. The results of this study indicate that the library's role is has the authority to manage the scientific work of academic community can be done through the institutional repository. However there is still need for library to be proactive to communicate regulations on mandatory deposit of scientific work and create intensive promotion of the institutional repository.
Process model repositories and PNML
Hee, van K.M.; Post, R.D.J.; Somers, L.J.A.M.; Werf, van der J.M.E.M.; Kindler, E.
2004-01-01
Bringing system and process models together in repositories facilitates the interchange of model information between modelling tools, and allows the combination and interlinking of complementary models. Petriweb is a web application for managing such repositories. It supports hierarchical process
Enzyme-Assisted Discovery of Antioxidant Peptides from Edible Marine Invertebrates: A Review.
Chai, Tsun-Thai; Law, Yew-Chye; Wong, Fai-Chu; Kim, Se-Kwon
2017-02-16
Marine invertebrates, such as oysters, mussels, clams, scallop, jellyfishes, squids, prawns, sea cucumbers and sea squirts, are consumed as foods. These edible marine invertebrates are sources of potent bioactive peptides. The last two decades have seen a surge of interest in the discovery of antioxidant peptides from edible marine invertebrates. Enzymatic hydrolysis is an efficient strategy commonly used for releasing antioxidant peptides from food proteins. A growing number of antioxidant peptide sequences have been identified from the enzymatic hydrolysates of edible marine invertebrates. Antioxidant peptides have potential applications in food, pharmaceuticals and cosmetics. In this review, we first give a brief overview of the current state of progress of antioxidant peptide research, with special attention to marine antioxidant peptides. We then focus on 22 investigations which identified 32 antioxidant peptides from enzymatic hydrolysates of edible marine invertebrates. Strategies adopted by various research groups in the purification and identification of the antioxidant peptides will be summarized. Structural characteristic of the peptide sequences in relation to their antioxidant activities will be reviewed. Potential applications of the peptide sequences and future research prospects will also be discussed.
Radioactive waste repository study
International Nuclear Information System (INIS)
1978-11-01
This is the second part of a report of a preliminary study for AECL. It considers the requirements for an underground waste repository for the disposal of wastes produced by the Canadian Nuclear Fuel Program. The following topics are discussed with reference to the repository: 1) geotechnical assessment, 2) hydrogeology and waste containment, 3) thermal loading and 4) rock mechanics. (author)
Open DOAR the Directory of Open Access Repositories
CERN. Geneva
2005-01-01
The last year has seen wide-spread growth in the idea of using open access repositories as a part of a research institution's accepted infrastructure. Policy development from institutions and funding bodies has also supported the growth of the repository network. The next stage of expansion will be in the provision of services and cross-repository facilities and resources. Of course, it is hoped that these will then establish a feed-back loop to encourage repository population and further repository establishment, as the potential of open access to research materials is realised. The growth of repositories has been organic, with a variety of different repositories based in departments, institutions, funding agencies or subject communities, with a range of content, both in type and subject. Existing repositories are expanding their holdings, from eprints to associated research data-sets, or with learning objects and multimedia material. This presentation will look at the development of the Directory of Open Ac...
Evaluasi Website Repositori Institusi Universitas Surabaya
Directory of Open Access Journals (Sweden)
Amirul Ulum
2015-11-01
Full Text Available The development of institutional repositories (IRs in Indonesia within the broader framework of open access has significant impact on preserving intellectual capital and scholarly communication. Institutional repositories play a fundamental role in centralizing, preserving, and making accessible institution’s intellectual capital. Evaluation of the system is to determine the functionality the system to meet the users need. Using a descriptive analysis this study wants to evaluate institutional repositories of University of Surabaya. The result is usefull for institution to develop the repository systems.
Towards a spectroscopic standard database for Pu in repository environments
International Nuclear Information System (INIS)
Amme, M.
2005-01-01
Full text of publication follows: The alteration behaviour of Pu in geological and technical environments is, although of crucial importance for example in final repository assessment procedures for high-level nuclear waste, not sufficiently investigated. Since Pu chemistry differs significantly from U behaviour (mostly due to the different stabilities of the +IV oxidation states of both elements), conclusions based on the uranium analogy cannot be extended to Pu chemistry in many cases. In order to examine precisely the alteration behaviour of Pu under repository storage conditions, customized tools for the spectroscopic identification of the element need to be developed. We are currently constructing systematically a database of Pu compounds and collect their spectra for this purpose. Pu compounds (with the element in the oxidation states +III, +IV, +V, and +VI) are synthesised, mostly by using hydrothermal synthesis techniques [1]. Compounds of high importance for repository studies are: Carbonates, (oxy)hydroxides, silicates, peroxides, and phosphates. The products are characterised by Scanning Electron Microscopy (SEM), X-Ray Photoelectron spectroscopy (XPS), and X-Ray diffraction (XRD). Furthermore, vibrational spectra (Raman and IR) of the substances will be recorded. These will allow the unambiguous identification of chemically similar compounds, once the database is compiled: Although reported for a few cases with nuclear material only, the combined investigation of solids with Raman [2,3] and SEM-EDX [3] in a combined mode, especially when spatially resolving, holds great potential An investigation with accelerator-based XAS techniques is planned within the framework of the Excellence network Actinet 6. [1] Grigorev, M., Bessonov, A., Makarenkov, V., Fedoseev, A., Model of the (PuO 2 ) 2 SiO 4 * 2H 2 O crystal structure, based on powder X-ray diffraction data, Radiochemistry, Vol. 45, No 3 (2003) 257-260. [2] M. Amme, B. Renker, B. Schmid, M. Feth, H
Consideration on safety assessment methodologies applied to the near surface repository Baita Bihor
International Nuclear Information System (INIS)
Dogaru, D.
2003-01-01
The Romanian legislation in respect of RAW management is described. The waste facilities in the country are: for low and intermediate level waste - Radioactive Waste Treatment Plant - Bucharest Magurele; Radioactive Waste Treatment Plant - Pitesti; National Repository for Radioactive Waste - Baita Bihor. for spent fuel - Intermediate dry spent fuel storage facility (DICA) - CNE Cernavoda; Intermediate wet spent fuel storage facility WWR-S - Bucharest Magurele. A detailed description of the facilities and waste characterisation are given in the report. Due o insufficient and incomplete information about site characterisation and inventory a Phare project 'Preliminary Safety Analysis for the Low-Level Radioactive Waste Repository Baita Bihor, Romania' has been approved. The project purposes are: to achieve a database with specific parameters; validation of scenarios and conceptual models for normal and altered evolution of the disposal site; validation and qualification of existing calculation methods and identification of the complementary suitable computer codes to be installed in Romania; validation and analyses of the final results expertise PSAR final results; recommendation for further completion of Integrated Performance Assessment. The results, conclusions and recommendations of the project will be included in the Preliminary Safety Analyses Report to be sent to the Romanian Authority - CNCAN for licensing of the repository operation
Preclosure Seismic Design Methodology for a Geologic Repository at Yucca Mountain
International Nuclear Information System (INIS)
K. Coppersmith
2004-01-01
This topical report describes the methodology and criteria that the U.S. Department of Energy (DOE) intends to use for preclosure seismic design of structures, systems, and components (SSCs) that are important to safety (ITS) in the geologic repository operations area. 10 Code of Federal Regulations (CFR) Part 63 [DIRS 156605], states that for a license to be issued for operation of a high-level radioactive waste repository, the U.S. Nuclear Regulatory Commission (NRC) must find that the facility will not constitute an unreasonable risk to the health and safety of the public (Section 63.41[c] [DIRS 156605]). Section 63.21(c)(5) [DIRS 156605] requires that a preclosure safety analysis (PCSA) be performed to ensure that the preclosure performance objectives (Section 63.111 [DIRS 156605]) have been met. The PCSA is a systematic examination of the site, the design, and the potential hazards (Section 63.102[f] [DIRS 156605]), including a comprehensive identification of potential event sequences. Potential naturally-occurring hazards include those event sequences that are initiated by earthquake ground motions or fault displacements due to earthquakes
Nongonierma, Alice B; Paolella, Sara; Mudgil, Priti; Maqsood, Sajid; FitzGerald, Richard J
2018-04-01
Nine novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides (FLQY, FQLGASPY, ILDKEGIDY, ILELA, LLQLEAIR, LPVP, LQALHQGQIV, MPVQA and SPVVPF) were identified in camel milk proteins hydrolysed with trypsin. This was achieved using a sequential approach combining liquid chromatography tandem mass spectrometry (LC-MS/MS), qualitative/quantitative structure activity relationship (QSAR) and confirmatory studies with synthetic peptides. The most potent camel milk protein-derived DPP-IV inhibitory peptides, LPVP and MPVQA, had DPP-IV half maximal inhibitory concentrations (IC 50 ) of 87.0 ± 3.2 and 93.3 ± 8.0 µM, respectively. DPP-IV inhibitory peptide sequences identified within camel and bovine milk protein hydrolysates generated under the same hydrolysis conditions differ. This was linked to differences in enzyme selectivity for peptide bond cleavage of camel and bovine milk proteins as well as dissimilarities in their amino acid sequences. Camel milk proteins contain novel DPP-IV inhibitory peptides which may play a role in the regulation of glycaemia in humans. Copyright © 2017 Elsevier Ltd. All rights reserved.
Zhang, Jingjing; Liang, Dong; Cheng, Qing; Cao, Li; Wu, Yun; Wang, Yan; Han, Shuping; Yu, Zhangbin; Cui, Xianwei; Xu, Tianhui; Ma, Dingyuan; Hu, Ping; Xu, Zhengfeng
2017-06-01
Tetralogy of fallot (TOF) is one of the most prevalent types of congenital heart diseases. As a category of bioactive molecules, peptides have been proved to participate in various biological processes. However, the role of endogenous peptides in the pathogenesis of TOF has not been studied. In this study, we performed a comparative peptidomic profile in the fetal heart of TOF and the control group for the first time by liquid chromatography-tandem mass spectrometry. Our data demonstrated that a total of 201 peptides derived from 176 precursor proteins were differentially expressed in the heart tissues of TOF fetuses compared with normal controls, including 41 upregulated peptides and 160 downregulated peptides. After analyzing the characteristics of these differentially expressed peptides and their precursor proteins, we found that these peptides were potentially involved in different biological processes, especially cardiogenesis and congenital anomaly of the cardiovascular system. Interestingly, we detected several extracellular matrix-derived peptides involved in our differentially expressed peptidomic profile. In summary, our study constructed a comparative peptidomic profile from the heart tissues of TOF fetuses and normal controls, and it identified a series of peptides that could potentially participate in heart development and TOF formation. The emergence of our peptidomics study indicated a new perspective to explore the pathogenesis of abnormal heart morphology, especially TOF.
Mommen, Geert P M; Frese, Christian K; Meiring, Hugo D; van Gaans-van den Brink, Jacqueline; de Jong, Ad P J M; van Els, Cécile A C M; Heck, Albert J R
2014-01-01
The identification of peptides presented by human leukocyte antigen (HLA) class I is tremendously important for the understanding of antigen presentation mechanisms under healthy or diseased conditions. Currently, mass spectrometry-based methods represent the best methodology for the identification
Alternative measure for performance of HLW geologic repository
International Nuclear Information System (INIS)
Joonhang, Ahn; Chambre, P.L.
2001-01-01
A repository performance model that can show effects of canister multiplicity and repository configuration has been developed. Masses of a radionuclide in the repository and in the far field are proposed as performance measures. Canister multiplicity has significant effects on the release of long-lived radionuclides from the repository. As more canisters are included in the same water stream, the radionuclide concentration in the stream increases, but becomes independent of the number of canisters for sufficiently many canisters. Effects of reduction of radionuclide mass in the repository on the repository performance are clearly observed if the canister multiplicity is taken into account and the mass-based measures are applied. (author)
Accelerator Physics Code Web Repository
Zimmermann, Frank; Bellodi, G; Benedetto, E; Dorda, U; Giovannozzi, Massimo; Papaphilippou, Y; Pieloni, T; Ruggiero, F; Rumolo, G; Schmidt, F; Todesco, E; Zotter, Bruno W; Payet, J; Bartolini, R; Farvacque, L; Sen, T; Chin, Y H; Ohmi, K; Oide, K; Furman, M; Qiang, J; Sabbi, G L; Seidl, P A; Vay, J L; Friedman, A; Grote, D P; Cousineau, S M; Danilov, V; Holmes, J A; Shishlo, A; Kim, E S; Cai, Y; Pivi, M; Kaltchev, D I; Abell, D T; Katsouleas, Thomas C; Boine-Frankenheim, O; Franchetti, G; Hofmann, I; Machida, S; Wei, J
2006-01-01
In the framework of the CARE HHH European Network, we have developed a web-based dynamic acceleratorphysics code repository. We describe the design, structure and contents of this repository, illustrate its usage, and discuss our future plans, with emphasis on code benchmarking.
ACCELERATION PHYSICS CODE WEB REPOSITORY.
Energy Technology Data Exchange (ETDEWEB)
WEI, J.
2006-06-26
In the framework of the CARE HHH European Network, we have developed a web-based dynamic accelerator-physics code repository. We describe the design, structure and contents of this repository, illustrate its usage, and discuss our future plans, with emphasis on code benchmarking.
Consistency of Network Traffic Repositories: An Overview
Lastdrager, E.; Lastdrager, E.E.H.; Pras, Aiko
2009-01-01
Traffc repositories with TCP/IP header information are very important for network analysis. Researchers often assume that such repositories reliably represent all traffc that has been flowing over the network; little thoughts are made regarding the consistency of these repositories. Still, for
48 CFR 227.7207 - Contractor data repositories.
2010-10-01
... repositories. 227.7207 Section 227.7207 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS... Computer Software and Computer Software Documentation 227.7207 Contractor data repositories. Follow 227.7108 when it is in the Government's interests to have a data repository include computer software or to...
Reference repository design concept for bedded salt
Energy Technology Data Exchange (ETDEWEB)
Carpenter, D.W.; Martin, R.W.
1980-10-08
A reference design concept is presented for the subsurface portions of a nuclear waste repository in bedded salt. General geologic, geotechnical, hydrologic and geochemical data as well as descriptions of the physical systems are provided for use on generic analyses of the pre- and post-sealing performance of repositories in this geologic medium. The geology of bedded salt deposits and the regional and repository horizon stratigraphy are discussed. Structural features of salt beds including discontinuities and dissolution features are presented and their effect on repository performance is discussed. Seismic hazards and the potential effects of earthquakes on underground repositories are presented. The effect on structural stability and worker safety during construction from hydrocarbon and inorganic gases is described. Geohydrologic considerations including regional hydrology, repository scale hydrology and several hydrological failure modes are presented in detail as well as the hydrological considerations that effect repository design. Operational phase performance is discussed with respect to operations, ventilation system, shaft conveyances, waste handling and retrieval systems and receival rates of nuclear waste. Performance analysis of the post sealing period of a nuclear repository is discussed, and parameters to be used in such an analysis are presented along with regulatory constraints. Some judgements are made regarding hydrologic failure scenarios. Finally, the design and licensing process, consistent with the current licensing procedure is described in a format that can be easily understood.
Reference repository design concept for bedded salt
International Nuclear Information System (INIS)
Carpenter, D.W.; Martin, R.W.
1980-01-01
A reference design concept is presented for the subsurface portions of a nuclear waste repository in bedded salt. General geologic, geotechnical, hydrologic and geochemical data as well as descriptions of the physical systems are provided for use on generic analyses of the pre- and post-sealing performance of repositories in this geologic medium. The geology of bedded salt deposits and the regional and repository horizon stratigraphy are discussed. Structural features of salt beds including discontinuities and dissolution features are presented and their effect on repository performance is discussed. Seismic hazards and the potential effects of earthquakes on underground repositories are presented. The effect on structural stability and worker safety during construction from hydrocarbon and inorganic gases is described. Geohydrologic considerations including regional hydrology, repository scale hydrology and several hydrological failure modes are presented in detail as well as the hydrological considerations that effect repository design. Operational phase performance is discussed with respect to operations, ventilation system, shaft conveyances, waste handling and retrieval systems and receival rates of nuclear waste. Performance analysis of the post sealing period of a nuclear repository is discussed, and parameters to be used in such an analysis are presented along with regulatory constraints. Some judgements are made regarding hydrologic failure scenarios. Finally, the design and licensing process, consistent with the current licensing procedure is described in a format that can be easily understood
Recent studies on the antimicrobial peptides lactoferricin and lactoferrampin.
Yin, C; Wong, J H; Ng, T B
2014-01-01
Lactoferricin and lactoferrampin, peptides derived from the whey protein lactoferrin, are antimicrobial agents with a promising prospect and are currently one of the research focuses. In this review, a basic introduction including location and solution structures of these two peptides is given. Their biological activities encompassing antiviral, antibacterial, antifungal and anti-inflammatory activities with possible mechanisms are mentioned. In terms of modification studies, research about identification of their active derivatives and crucial amino acid residues is also discussed. Various attempts at modification of lactoferricin and lactoferrampin such as introducing big hydrophobic side-chains; employing special amino acids for synthesis; N-acetylization, amidation, cyclization and peptide chimera are summarized. The studies on lactoferricin-lactoferrampin chimera are discussed in detail. Future prospects of lactoferricin and lactoferrampin are covered.
Ebner, Jennifer; Baum, Florian; Pischetsrieder, Monika
2016-09-16
Peptide profiles of different drinking milk samples were examined to study how the peptide fingerprint of milk reflects processing conditions. The combination of a simple and fast method for peptide extraction using stage tips and MALDI-TOF-MS enabled the fast and easy generation and relative quantification of peptide fingerprints for high-temperature short-time (HTST), extended shelf life (ESL) and ultra-high temperature (UHT) milk of the same dairies. The relative quantity of 16 peptides changed as a function of increasing heat load. Additional heating experiments showed that among those, the intensity of peptide β-casein 196-209 (m/z 1460.9Da) was most heavily influenced by heat treatment indicating a putative marker peptide for milk processing conditions. Storage experiments with HTST- and UHT milk revealed that the differences between different types of milk samples were not only caused by the heating process. Relevant was also the proteolytic activity of enzymes during storage, which were differently influenced by the heat treatment. These results indicate that the peptide profile may be suitable to monitor processing as well as storage conditions of milk. In the present study, peptide profiling of different types of milk was carried out by MALDI-TOF-MS after stage-tip extraction and relative quantification using an internal reference peptide. Although MALDI-TOF-MS covers only part of the peptidome, the method is easy and quick and is, therefore, suited for routine analysis to address several aspects of food authenticity. Using this method, 16 native peptides were detected in milk that could be modulated by different industrial processes. Subsequent heating and storage experiments with pasteurized and UHT milk confirmed that these peptides are indeed related to the production or storage conditions of the respective products. Furthermore, the heating experiments revealed one peptide, namely the β-casein-derived sequence β-casein 196-209, which underwent
Hydrothermal conditions around a radioactive waste repository
International Nuclear Information System (INIS)
Thunvik, R.; Braester, C.
1981-12-01
Numerical solutions for the hydrothermal conditions around a hard rock repository for nuclear fuel waste are presented. The objective of the present investigation is to illustrate in principle the effect of heat released from a hypothetical radioactive waste repository with regard to anisotropy in the rock permeability. Permeability and porosity are assumed to be constant or to decrease exponentially with depth. The hypothetical repository is situated below a horizontal ground surface or below the crest of a hill, and it is assumed that the water table follows the topography. Major interest in the analysis is directed towards the influence of anisotropy in the permeability on the flow patterns and travel times for water particles, being traced from the repository to the ground surface. The presented results show that anisotropy in the permeability may have a significant influence on the flow conditions around the repository and subsequently also on the travel times from the repository. (Authors)
Choi, Sam B.; Lombard-Banek, Camille; Muñoz-LLancao, Pablo; Manzini, M. Chiara; Nemes, Peter
2018-05-01
The ability to detect peptides and proteins in single cells is vital for understanding cell heterogeneity in the nervous system. Capillary electrophoresis (CE) nanoelectrospray ionization (nanoESI) provides high-resolution mass spectrometry (HRMS) with trace-level sensitivity, but compressed separation during CE challenges protein identification by tandem HRMS with limited MS/MS duty cycle. Here, we supplemented ultrasensitive CE-nanoESI-HRMS with reversed-phase (RP) fractionation to enhance identifications from protein digest amounts that approximate to a few mammalian neurons. An 1 to 20 μg neuronal protein digest was fractionated on a RP column (ZipTip), and 1 ng to 500 pg of peptides were analyzed by a custom-built CE-HRMS system. Compared with the control (no fractionation), RP fractionation improved CE separation (theoretical plates 274,000 versus 412,000 maximum, resp.), which enhanced detection sensitivity (2.5-fold higher signal-to-noise ratio), minimized co-isolation spectral interferences during MS/MS, and increased the temporal rate of peptide identification by up to 57%. From 1 ng of protein digest (organization. [Figure not available: see fulltext.
Liu, Yufang; Pischetsrieder, Monika
2017-03-08
Health-promoting effects of kefir may be partially caused by bioactive peptides. To evaluate their formation or degradation during gastrointestinal digestion, we monitored changes of the peptide profile in a model of (1) oral, (2) gastric, and (3) small intestinal digestion of kefir. Matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy analyses revealed clearly different profiles between digests 2/3 and kefir/digest 1. Subsequent ultraperformance liquid chromatography-electrospray ionization-tandem mass spectrometry identified 92 peptides in total (25, 25, 43, and 30, partly overlapping in kefir and digests 1, 2, and 3, respectively), including 16 peptides with ascribed bioactivity. Relative quantification in scheduled multiple reaction monitoring mode showed that many bioactive peptides were released by simulated digestion. Most prominently, the concentration of angiotensin-converting enzyme inhibitor β-casein 203-209 increased approximately 10 000-fold after combined oral, gastric, and intestinal digestion. Thus, physiological digestive processes may promote bioactive peptide formation from proteins and oligopeptides in kefir. Furthermore, bioactive peptides present in certain compartments of the gastrointestinal tract may exert local physiological effects.
Design of non-aggregating variants of Aβ peptide
Energy Technology Data Exchange (ETDEWEB)
Caine, Joanne M., E-mail: jo.caine@csiro.au [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia); Churches, Quentin; Waddington, Lynne [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Nigro, Julie; Breheney, Kerry [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia); Masters, Colin L. [CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia); Florey Institute for Neuroscience and Mental Health, 30 Royal Parade, Parkville, Victoria 3052 (Australia); Nuttall, Stewart D. [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia); Streltsov, Victor A., E-mail: victor.streltsov@csiro.au [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia)
2014-10-24
Highlights: • Non-aggregating, non-toxic variants of Aβ peptide were designed using Aβ structure. • Mutations reduce aggregation by stabilising Aβ into small non-toxic oligomers. • Identification of these residues will assist the design of future therapeutic peptides. - Abstract: Self association of the amyloid-β (Aβ{sub 42}) peptide into oligomers, high molecular weight forms, fibrils and ultimately neuritic plaques, has been correlated with progressive cognitive decline in Alzheimer’s disease. Thus, insights into the drivers of the aggregation pathway have the capacity to significantly contribute to our understanding of disease mechanism. Functional assays and a three-dimensional crystal structure of the P3 amyloidogenic region 18–41 of Aβ were used to identify residues important in self-association and to design novel non-aggregating variants of the peptide. Biophysical studies (gel filtration, SDS–PAGE, dynamic light scattering, thioflavin T assay, and electron microscopy) demonstrate that in contrast to wild type Aβ these targeted mutations lose the ability to self-associate. Loss of aggregation also correlates with reduced neuronal toxicity. Our results highlight residues and regions of the Aβ peptide important for future targeting agents aimed at the amelioration of Alzheimer’s disease.
Repository operational criteria comparative analysis
International Nuclear Information System (INIS)
Hageman, J.P.; Chowdhury, A.H.
1994-06-01
The objective of the ''Repository Operational Criteria (ROC) Feasibility Studies'' (or ROC task) was to conduct comprehensive and integrated analyses of repository design, construction, and operations criteria in 10 CFR Part 60 regulations considering the interfaces among the components of the regulations and impacts of any potential changes to those regulations. The ROC task addresses regulatory criteria and uncertainties related to the preclosure aspects of the geologic repository. Those parts of 10 CFR Part 60 that require routine guidance or minor changes to the rule were addressed in Hageman and Chowdhury, 1992. The ROC task shows a possible need for further regulatory clarity, by major changes to the rule, related to the design bases and siting of a geologic repository operations area and radiological emergency planning in order to assure defense-in-depth. The analyses, presented in this report, resulted in the development and refinement of regulatory concepts and their supporting rationale for recommendations for potential major changes to 10 CFR Pan 0 regulations
Xiao, Chuan-Le; Chen, Xiao-Zhou; Du, Yang-Li; Sun, Xuesong; Zhang, Gong; He, Qing-Yu
2013-01-04
Mass spectrometry has become one of the most important technologies in proteomic analysis. Tandem mass spectrometry (LC-MS/MS) is a major tool for the analysis of peptide mixtures from protein samples. The key step of MS data processing is the identification of peptides from experimental spectra by searching public sequence databases. Although a number of algorithms to identify peptides from MS/MS data have been already proposed, e.g. Sequest, OMSSA, X!Tandem, Mascot, etc., they are mainly based on statistical models considering only peak-matches between experimental and theoretical spectra, but not peak intensity information. Moreover, different algorithms gave different results from the same MS data, implying their probable incompleteness and questionable reproducibility. We developed a novel peptide identification algorithm, ProVerB, based on a binomial probability distribution model of protein tandem mass spectrometry combined with a new scoring function, making full use of peak intensity information and, thus, enhancing the ability of identification. Compared with Mascot, Sequest, and SQID, ProVerB identified significantly more peptides from LC-MS/MS data sets than the current algorithms at 1% False Discovery Rate (FDR) and provided more confident peptide identifications. ProVerB is also compatible with various platforms and experimental data sets, showing its robustness and versatility. The open-source program ProVerB is available at http://bioinformatics.jnu.edu.cn/software/proverb/ .
What do we mean by a cold repository?
International Nuclear Information System (INIS)
Halsey, W.G.
1994-01-01
The topic of thermal loading of a potential repository at Yucca Mountain in Nevada has been the subject of intense discussion within the project technical community. While terms such as ''Hot Repository'' and ''Cold Repository'' are frequently used, they have not been clearly defined. In particular, the definition of a cold repository has remained the opinion of each individual. This has led to confusion and misunderstanding. In this paper, a number of observed definitions for a cold repository are discussed along with the technical implications, assumptions and inconsistencies. Finally, a common language is suggested
Energy Technology Data Exchange (ETDEWEB)
MacKinnon, Robert J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-10-26
Under the auspices of the International Atomic Energy Agency (IAEA), nationally developed underground research laboratories (URLs) and associated research institutions are being offered for use by other nations. These facilities form an Underground Research Facilities (URF) Network for training in and demonstration of waste disposal technologies and the sharing of knowledge and experience related to geologic repository development, research, and engineering. In order to achieve its objectives, the URF Network regularly sponsors workshops and training events related to the knowledge base that is transferable between existing URL programs and to nations with an interest in developing a new URL. This report describes the role of URLs in the context of a general timeline for repository development. This description includes identification of key phases and activities that contribute to repository development as a repository program evolves from an early research and development phase to later phases such as construction, operations, and closure. This information is cast in the form of a matrix with the entries in this matrix forming the basis of the URF Network roadmap that will be used to identify and plan future workshops and training events.
Peptides extracted from Artemisia herba alba have antimicrobial ...
African Journals Online (AJOL)
Background: Artemisia herba alba, classified into the family of Asteraceae, is an aromatic herb that is traditionally used as a purgative and antipyretic folk medicine by rural people of south Tunisia. This study reports the first identification of antimicrobial peptides from this medicinal plant that inhibited the growth of several ...
High-Throughput Identification of Antimicrobial Peptides from Amphibious Mudskippers
Directory of Open Access Journals (Sweden)
Yunhai Yi
2017-11-01
Full Text Available Widespread existence of antimicrobial peptides (AMPs has been reported in various animals with comprehensive biological activities, which is consistent with the important roles of AMPs as the first line of host defense system. However, no big-data-based analysis on AMPs from any fish species is available. In this study, we identified 507 AMP transcripts on the basis of our previously reported genomes and transcriptomes of two representative amphibious mudskippers, Boleophthalmus pectinirostris (BP and Periophthalmus magnuspinnatus (PM. The former is predominantly aquatic with less time out of water, while the latter is primarily terrestrial with extended periods of time on land. Within these identified AMPs, 449 sequences are novel; 15 were reported in BP previously; 48 are identically overlapped between BP and PM; 94 were validated by mass spectrometry. Moreover, most AMPs presented differential tissue transcription patterns in the two mudskippers. Interestingly, we discovered two AMPs, hemoglobin β1 and amylin, with high inhibitions on Micrococcus luteus. In conclusion, our high-throughput screening strategy based on genomic and transcriptomic data opens an efficient pathway to discover new antimicrobial peptides for ongoing development of marine drugs.
High-Throughput Identification of Antimicrobial Peptides from Amphibious Mudskippers.
Yi, Yunhai; You, Xinxin; Bian, Chao; Chen, Shixi; Lv, Zhao; Qiu, Limei; Shi, Qiong
2017-11-22
Widespread existence of antimicrobial peptides (AMPs) has been reported in various animals with comprehensive biological activities, which is consistent with the important roles of AMPs as the first line of host defense system. However, no big-data-based analysis on AMPs from any fish species is available. In this study, we identified 507 AMP transcripts on the basis of our previously reported genomes and transcriptomes of two representative amphibious mudskippers, Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM). The former is predominantly aquatic with less time out of water, while the latter is primarily terrestrial with extended periods of time on land. Within these identified AMPs, 449 sequences are novel; 15 were reported in BP previously; 48 are identically overlapped between BP and PM; 94 were validated by mass spectrometry. Moreover, most AMPs presented differential tissue transcription patterns in the two mudskippers. Interestingly, we discovered two AMPs, hemoglobin β1 and amylin, with high inhibitions on Micrococcus luteus . In conclusion, our high-throughput screening strategy based on genomic and transcriptomic data opens an efficient pathway to discover new antimicrobial peptides for ongoing development of marine drugs.
International Nuclear Information System (INIS)
Farrar, Y.J.K.; Evans, R.K.; Beach, C.M.; Coleman, M.S.
1991-01-01
Terminal deoxynucleotidyl transferase (terminal transferase) was specifically modified in the DNA binding site by a photoactive DNA substrate (hetero-40-mer duplex containing eight 5-azido-dUMP residues at one 3' end). Under optimal photolabeling conditions, 27-40% of the DNA was covalently cross-linked to terminal transferase. The specificity of the DNA and protein interaction was demonstrated by protection of photolabeling at the DNA binding domain with natural DNA substrates. In order to recover high yields of modified peptides from limited amounts of starting material, protein modified with 32 P-labeled photoactive DNA and digested with trypsin was extracted 4 times with phenol followed by gel filtration chromatography. All peptides not cross-linked to DNA were extracted into the phenol phase while the photolyzed DNA and the covalently cross-linked peptides remained in the aqueous phase. The 32 P-containing peptide-DNA fraction was subjected to amino acid sequence analysis. Two sequences, Asp 221 -Lys 231 (peptide B8) and Cys 234 -Lys 249 (peptide B10), present in similar yield, were identified. Structure predictions placed the two peptides in an α-helical array of 39 angstrom which would accommodate a DNA helix span of 11 nucleotides. These peptides share sequence similarity with a region in DNA polymerase β that has been implicated in the binding of DNA template
Elucidation of Peptide-Directed Palladium Surface Structure for Biologically Tunable Nanocatalysts
Energy Technology Data Exchange (ETDEWEB)
Bedford, Nicholas M.; Ramezani-Dakhel, Hadi; Slocik, Joseph M.; Briggs, Beverly D.; Ren, Yang; Frenkel, Anatoly I.; Petkov, Valeri; Heinz, Hendrik; Naik, Rajesh R.; Knecht, Mark R.
2015-05-01
Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then eluddated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences
Radioactive waste repository study
International Nuclear Information System (INIS)
1978-11-01
This is the first part of a report of a preliminary study for Atomic Energy of Canada Limited. It considers the requirements for an underground waste repository for the disposal of wastes produced by the Canadian Nuclear Fuel Program. The following topics are discussed with reference to the repository: 1) underground layout, 2) cost estimates, 3) waste handling, 4) retrievability, decommissioning, sealing and monitoring, and 5) research and design engineering requirements. (author)
MAJOR REPOSITORY DESIGN ISSUES
International Nuclear Information System (INIS)
JACK N. BAILEY, DWAYNE CHESTNUT, JAMES COMPTON AND RICHARD D. SNELL
1997-01-01
The Yucca Mountain Project is focused on producing a four-part viability assessment in late FY98. Its four components (design, performance assessment, cost estimate, and licensing development plan) must be consistent. As a tool to compare design and performance assessment options, a series of repository pictures were developed for the sequential time phases of a repository. The boundaries of the time phases correspond to evolution in the engineered barrier system (EBS)
Identification of 11-amino acid peptides that disrupt Notch-mediated processes in Drosophila
Directory of Open Access Journals (Sweden)
Yeh Hsiao-Fong
2011-06-01
Full Text Available Abstract Background The conserved Notch signaling pathway regulates cell fate decisions and maintains stem cells in multicellular organisms. Up-regulation of Notch signaling is observed in several types of cancer and is causally involved in proliferation and survival of cancer cells. Thus, it is of great interest to look for anti-Notch reagents for therapeutic purposes. In model animal Drosophila, Notch signaling restricts selection of sensory organ precursors (SOPs during external sensory (ES organ development. To look for novel genes that can suppress Notch signaling, we performed a gain-of-function modifier screen to look for genes that enhance the phenotype of ectopic ES organs induced by overexpression of phyllopod, a gene required for SOP specification. Results From the gain-of-function screen, we discovered that overexpression of polished rice/tarsal-less (pri/tal increases the numbers of ES organs as well as SOPs. pri/tal is a polycistronic gene that contains four short open reading frames encoding three 11-amino acid and one 32-amino acid peptides. Ectopic expression of the 11 amino-acid peptides recapitulates the pri/tal misexpression phenotype in ectopic ES organ formation. In situ hybridization experiment reveals that pri/tal mRNA is expressed in the SOPs of the chemosensory organs and the stretch-sensing chordotonal organs. In Drosophila wing development, the Notch signaling pathway mediates the formation of the dorsal-ventral (DV compartmental boundary and the restriction of the vein width from the primordial veins, the proveins. We also found that pri/tal mRNA is expressed in the DV boundary and the longitudinal proveins, and overexpression of Pri/Tal peptides disrupts the DV boundary formation and helps to expand the width of the wing vein. Genetic analyses further show that a Notch loss-of-function allele strongly enhances these two phenotypes. Cut and E(splmβ are target genes of the Notch pathway in DV boundary formation and
An analysis of repository waste-handling operations
International Nuclear Information System (INIS)
Dennis, A.W.
1990-09-01
This report has been prepared to document the operational analysis of waste-handling facilities at a geologic repository for high-level nuclear waste. The site currently under investigation for the geologic repository is located at Yucca Mountain, Nye County, Nevada. The repository waste-handling operations have been identified and analyzed for the year 2011, a steady-state year during which the repository receives spent nuclear fuel containing the equivalent of 3000 metric tons of uranium (MTU) and defense high-level waste containing the equivalent of 400 MTU. As a result of this analysis, it has been determined that the waste-handling facilities are adequate to receive, prepare, store, and emplace the projected quantity of waste on an annual basis. In addition, several areas have been identified where additional work is required. The recommendations for future work have been divided into three categories: items that affect the total waste management system, operations within the repository boundary, and the methodology used to perform operational analyses for repository designs. 7 refs., 48 figs., 11 tabs
Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer.
Conlon, Kevin P; Basrur, Venkatesha; Rolland, Delphine; Wolfe, Thomas; Nesvizhskii, Alexey I; MacCoss, Michael J; Lim, Megan S; Elenitoba-Johnson, Kojo S J
2013-10-01
Chromosomal translocations encoding chimeric fusion proteins constitute one of the most common mechanisms underlying oncogenic transformation in human cancer. Fusion peptides resulting from such oncogenic chimeric fusions, though unique to specific cancer subtypes, are unexplored as cancer biomarkers. Here we show, using an approach termed fusion peptide multiple reaction monitoring mass spectrometry, the direct identification of different cancer-specific fusion peptides arising from protein chimeras that are generated from the juxtaposition of heterologous genes fused by recurrent chromosomal translocations. Using fusion peptide multiple reaction monitoring mass spectrometry in a clinically relevant scenario, we demonstrate the specific, sensitive, and unambiguous detection of a specific diagnostic fusion peptide in clinical samples of anaplastic large cell lymphoma, but not in a diverse array of benign lymph nodes or other forms of primary malignant lymphomas and cancer-derived cell lines. Our studies highlight the utility of fusion peptides as cancer biomarkers and carry broad implications for the use of protein biomarkers in cancer detection and monitoring.
Development of a dedicated peptide tandem mass spectral library for conservation science.
Fremout, Wim; Dhaenens, Maarten; Saverwyns, Steven; Sanyova, Jana; Vandenabeele, Peter; Deforce, Dieter; Moens, Luc
2012-05-30
In recent years, the use of liquid chromatography tandem mass spectrometry (LC-MS/MS) on tryptic digests of cultural heritage objects has attracted much attention. It allows for unambiguous identification of peptides and proteins, and even in complex mixtures species-specific identification becomes feasible with minimal sample consumption. Determination of the peptides is commonly based on theoretical cleavage of known protein sequences and on comparison of the expected peptide fragments with those found in the MS/MS spectra. In this approach, complex computer programs, such as Mascot, perform well identifying known proteins, but fail when protein sequences are unknown or incomplete. Often, when trying to distinguish evolutionarily well preserved collagens of different species, Mascot lacks the required specificity. Complementary and often more accurate information on the proteins can be obtained using a reference library of MS/MS spectra of species-specific peptides. Therefore, a library dedicated to various sources of proteins in works of art was set up, with an initial focus on collagen rich materials. This paper discusses the construction and the advantages of this spectral library for conservation science, and its application on a number of samples from historical works of art. Copyright © 2012 Elsevier B.V. All rights reserved.
Memory provisions for the Manche Surface Repository
International Nuclear Information System (INIS)
Dumont, Jean-Noel; Espiet-Subert, Florence
2015-01-01
The French La Manche repository site received its last radioactive waste package in 1994. In 2003, the official surveillance phase of the closed repository started under the supervision of Andra (the national industrial operator), the French Nuclear Safety Authority (ASN) and society (e.g. the local municipalities). Florence Espiet explained that information on the existence of the repository, its content, how it was operated and how it works needs to be preserved. It also is planned to review the information periodically for a minimum of 300 years. She described the creation of two documents on memory (a detailed and a summary one), both on permanent paper, and the preservation of the land registration. The latter constitutes 'passive' provisions for preserving memory. In addition, a number of 'active' provisions are and will be put in place: guided visits, exhibitions, partnerships with organisations dealing with memory preservation, and the creation of a think tank. The latter consists of local citizens and politicians, retired employees from Andra and artists that meet several times a year and reflect on memory preservation from the perspective of, for instance, local history, education, arts and rituals. Finally, two types of markers will be used to preserve the repository's memory: i) three herbaria cataloguing the plants growing on the site of the repository, including a very short description of the repository, will be stored at different sites in France; ii) a stele indicating the main characteristics of the repository, potentially linked to an art work, will be erected at the repository
Biopharmaceuticals: From peptide to drug
Hannappel, Margarete
2017-08-01
Biologics are therapeutic proteins or peptides that are produced by means of biological processes within living organisms and cells. They are highly specific molecules and play a crucial role as therapeutics for the treatment of severe and chronic diseases (e.g. cancer, rheumatoid arthritis, diabetes, autoimmune disorders). The development of new biologics and biologics-based drugs gains more and more importance in the fight against various diseases. A short overview on biotherapeutical drug development is given. Cone snails are a large group of poisonous, predatory sea snails with more than 700 species. They use a very powerful venom which rapidly inactivates and paralyzes their prey. Most bioactive venom components are small peptides (conotoxins, conopeptides) which are precisely directed towards a specific target (e.g. ion channel, receptors). Due to their small size, their precision and speed of action, naturally occurring cone snail venom peptides represent an attractive source for the identification and design of novel biological drug entities. The Jagna cone snail project is an encouraging initiative to map the ecological variety of cone snails around the island of Bohol (Philippines) and to conserve the biological information for potential future application.
Assessing high affinity binding to HLA-DQ2.5 by a novel peptide library based approach
DEFF Research Database (Denmark)
Jüse, Ulrike; Arntzen, Magnus; Højrup, Peter
2011-01-01
Here we report on a novel peptide library based method for HLA class II binding motif identification. The approach is based on water soluble HLA class II molecules and soluble dedicated peptide libraries. A high number of different synthetic peptides are competing to interact with a limited amount...... library. The eluted sequences fit very well with the previously described HLA-DQ2.5 peptide binding motif. This novel method, limited by library complexity and sensitivity of mass spectrometry, allows the analysis of several thousand synthetic sequences concomitantly in a simple water soluble format....
International Nuclear Information System (INIS)
1986-01-01
Two documents related to the Crystalline Repository Project have been reviewed. Comments and concerns related to the review of the ''Region-To-Area Screening Methodology'' and the ''Draft Area Recommendation Report'' are presented. These comments will be considered in preparation of the Final Area Recommendation Report, which will serve to formally identify potentially acceptable sites for a second repository in crystalline rock. Following a detailed review of the aforementioned documents, it is concluded that the identification of proposed potentially acceptable sites in the Draft Area Recommendation Report is based on questionable screening methodology and often incomplete data. As a result, ''favorable characteristics'' that are ascribed to each of the proposed potentially acceptable sites are, in many cases, misleading
Safety analysis in subsurface repositories
International Nuclear Information System (INIS)
1985-06-01
The development of mathematical models to represent the repository-geosphere-biosphere system, and the development of a structure for data acquisition, processing, and use to analyse the safety of subsurface repositories, are presented. To study the behavior of radionuclides in geosphere a laboratory to determine the hydrodynamic dispersion coefficient was constructed. (M.C.K.) [pt
How many geologic repositories will be needed
International Nuclear Information System (INIS)
Evans, T.J.; Halstead, R.J.
1987-01-01
DOE's postponement of site-specific work on the second repository program had rekindled debate over the number of geologic repositories needed for disposal of high level radioactive waste. The multiple repository approach grew out of the March, 1979 IRG report, which recommended co-disposal of civilian and defense HLW in a system of regional repositories. The multiple repository approach was adopted by DOE, and incorporated in the Nuclear Waste Policy Act passed by Congress in December, 1982. Since the late 1970's, the slower than anticipated growth of the nuclear power industry has substantially reduced earlier estimates of the amount of civilian spent fuel which will require geologic disposal. Reactors currently in operation (78.5 GWe) and reactors in the construction pipeline (28 GWe) are expected to discharge about 103,200 MTU of spent fuel by the year 2036, assuming no increase in fuel burnup rate. By the year 2020, defense high level radioactive wastes equivalent to as much as 27,000 MTU could require geologic disposal. Small amounts of high level waste from other sources will also require geologic disposal. Total disposal requirements appear to be less than 140,000 MTU. The five sites nominated for the first repository, as well as hypothetical sites in granite, the host rock under primary consideration for the second repository, all appear capable of accommodating up to 140,000 MTU
Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.
Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L
2017-11-13
A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.
Hagen, Reidun Anette
2009-01-01
A digital repository is a web accessible database, aimed at preserving the research material of an institution or scientific community. A digital repository serves as a tool for dissemination of research material and can increase the impact of the research by making it freely accessible. Digital repositories are often mentioned as a possible aid in relation to the Open Access debate; how research material should be freely accessible to anyone, anywhere at any time. However, for a digital repository to fully unleash its potential as a crucial component of Open Access, it is reliant on the ability to successfully collect and organize content. To a large extent this involves initiating self-archiving of research material by scientists throughout the academic world. This is not a trivial task, and many current repositories are inadequate in this respect, remaining empty, unvisited shelves. This thesis explores best practices for content recruitment to digital repositories, through the review of literature, and an...
Li, Guo-Zhong; Vissers, Johannes P C; Silva, Jeffrey C; Golick, Dan; Gorenstein, Marc V; Geromanos, Scott J
2009-03-01
A novel database search algorithm is presented for the qualitative identification of proteins over a wide dynamic range, both in simple and complex biological samples. The algorithm has been designed for the analysis of data originating from data independent acquisitions, whereby multiple precursor ions are fragmented simultaneously. Measurements used by the algorithm include retention time, ion intensities, charge state, and accurate masses on both precursor and product ions from LC-MS data. The search algorithm uses an iterative process whereby each iteration incrementally increases the selectivity, specificity, and sensitivity of the overall strategy. Increased specificity is obtained by utilizing a subset database search approach, whereby for each subsequent stage of the search, only those peptides from securely identified proteins are queried. Tentative peptide and protein identifications are ranked and scored by their relative correlation to a number of models of known and empirically derived physicochemical attributes of proteins and peptides. In addition, the algorithm utilizes decoy database techniques for automatically determining the false positive identification rates. The search algorithm has been tested by comparing the search results from a four-protein mixture, the same four-protein mixture spiked into a complex biological background, and a variety of other "system" type protein digest mixtures. The method was validated independently by data dependent methods, while concurrently relying on replication and selectivity. Comparisons were also performed with other commercially and publicly available peptide fragmentation search algorithms. The presented results demonstrate the ability to correctly identify peptides and proteins from data independent acquisition strategies with high sensitivity and specificity. They also illustrate a more comprehensive analysis of the samples studied; providing approximately 20% more protein identifications, compared to
International Nuclear Information System (INIS)
Ovsyannikova, Inna G.; Johnson, Kenneth L.; Naylor, Stephen; Muddiman, David C.; Poland, Gregory A.
2003-01-01
This is the first report of the direct identification of a HLA-DRB1*03 measles-derived peptide from measles virus infected EBV-transformed B cells. We purified HLA-DR3-peptide complexes from EBV-B cells infected with measles virus (Edmonston strain) and sequenced the HLA-DR3-peptides by mass spectrometry. A class II peptide, derived from a measles phosphoprotein, ASDVETAEGGEIHELLRLQ (P1, residues 179-197), exhibited the capacity to stimulate peripheral blood mononuclear cells to proliferate. Our data provides direct evidence that the antigenic peptide of measles virus was processed by antigen-presenting cells, presented in the context of HLA class II molecules, and was recognized by peripheral blood T cells from healthy individuals previously immunized with measles vaccine. The approach described herein provides a useful methodology for the future identification of HLA-presented pathogen-derived epitopes using mass spectrometry. The study of cell-mediated immune responses to the measles-derived peptide in immune persons should provide significant insight into the design and development of new vaccines
Building Scientific Data's list of recommended data repositories
Hufton, A. L.; Khodiyar, V.; Hrynaszkiewicz, I.
2016-12-01
When Scientific Data launched in 2014 we provided our authors with a list of recommended data repositories to help them identify data hosting options that were likely to meet the journal's requirements. This list has grown in size and scope, and is now a central resource for authors across the Nature-titled journals. It has also been used in the development of data deposition policies and recommended repository lists across Springer Nature and at other publishers. Each new addition to the list is assessed according to a series of criteria that emphasize the stability of the resource, its commitment to principles of open science and its implementation of relevant community standards and reporting guidelines. A preference is expressed for repositories that issue digital object identifiers (DOIs) through the DataCite system and that share data under the Creative Commons CC0 waiver. Scientific Data currently lists fourteen repositories that focus on specific areas within the Earth and environmental sciences, as well as the broad scope repositories, Dryad and figshare. Readers can browse and filter datasets published at the journal by the host repository using ISA-explorer, a demo tool built by the ISA-tools team at Oxford University1. We believe that well-maintained lists like this one help publishers build a network of trust with community data repositories and provide an important complement to more comprehensive data repository indices and more formal certification efforts. In parallel, Scientific Data has also improved its policies to better support submissions from authors using institutional and project-specific repositories, without requiring each to apply for listing individually. Online resources Journal homepage: http://www.nature.com/scientificdata Data repository criteria: http://www.nature.com/sdata/policies/data-policies#repo-criteria Recommended data repositories: http://www.nature.com/sdata/policies/repositories Archived copies of the list: https
Radioactive Waste Repositories and Incentives to Local Communities
International Nuclear Information System (INIS)
Knapp, A.; Medakovic, S.
2008-01-01
Public acceptance of radioactive waste (RW) repository depends on various and often community-specific factors. Although radiological risk from a properly constructed low and intermediate level waste (LILW) repository is practically negligible, routine safety considerations will favor low populated areas and therefore probably underdeveloped communities. Repository acceptance in such communities is more likely to be facilitated by prospective benefits to local economy, such as infrastructure development and increased employment, as well as by dedicated financial incentives to the community. Direct financial compensation to the local community for acceptance of the repository has been considered in some documents in countries experienced in RW management, but it has not become a widely accepted practice. In Croatia, a possibility for such compensation is mentioned in the land use plan in conjunction with the prospective RW repository site. In Slovenia, the government has already specified the annual amount of 2.33 million euro as a compensation for 'limited land use' to be shared by local communities in the vicinity of the planned LILW repository during its operation. Applicability of the Slovenian compensations to the prospective joint Slovenian-Croatian repository is not yet clear, at least in the aspect of joint funding. The joint Slovenian-Croatian Decommissioning and LILW and SF management program for NPP Krsko from 2004 did conservatively include the compensations into the repository cost estimates, but that might not be retained in subsequent revisions of the Program. According to the agreement between governments of Slovenia and Croatia on the Nuclear power plant Krsko, Croatian side has no obligations to participate in 'public expenditures' introduced after the agreement, as would be the case of community compensations for LILW repository in Slovenia. Before further decisions on joint NPP Krsko waste management are made, including the issue of LILW
A non-covalent peptide-based carrier for in vivo delivery of DNA mimics
Morris, May C.; Gros, Edwige; Aldrian-Herrada, Gudrun; Choob, Michael; Archdeacon, John; Heitz, Frederic; Divita, Gilles
2007-01-01
The dramatic acceleration in identification of new nucleic-acid-based therapeutic molecules has provided new perspectives in pharmaceutical research. However, their development is limited by their poor cellular uptake and inefficient trafficking. Here we describe a short amphipathic peptide, Pep-3, that combines a tryptophan/phenylalanine domain with a lysine/arginine-rich hydrophilic motif. Pep-3 forms stable nano-size complexes with peptide-nucleic acid analogues and promotes their efficien...
Daly, J W; Caceres, J; Moni, R W; Gusovsky, F; Moos, M; Seamon, K B; Milton, K; Myers, C W
1992-11-15
A frog used for "hunting magic" by several groups of Panoan-speaking Indians in the borderline between Brazil and Peru is identified as Phyllomedusa bicolor. This frog's skin secretion, which the Indians introduce into the body through fresh burns, is rich in peptides. These include vasoactive peptides, opioid peptides, and a peptide that we have named adenoregulin, with the sequence GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV as determined from mass spectrometry and Edman degradation. The natural peptide may contain a D amino acid residue, since it is not identical in chromatographic properties to the synthetic peptide. Adenoregulin enhances binding of agonists to A1 adenosine receptors; it is accompanied in the skin secretion by peptides that inhibit binding. The vasoactive peptide sauvagine, the opioid peptides, and adenoregulin and related peptides affect behavior in mice and presumably contribute to the behavioral sequelae observed in humans.
Henninge, John; Pepaj, Milaim; Hullstein, Ingunn; Hemmersbach, Peter
2010-01-01
Several peptide drugs are being manufactured illicitly, and in some cases they are being made available to the public before entering or completing clinical trials. At the request of Norwegian police and customs authorities, unknown pharmaceutical preparations suspected to contain peptide drugs are regularly subjected to analysis. In 2009, an unknown pharmaceutical preparation was submitted for analysis by liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS). The preparation was found to contain a 29 amino acid peptide with a C-terminal amide function. Based on the interpretation of mass spectrometric data, an amino acid sequence was proposed. The sequence is consistent with a peptide currently marketed under the name CJC-1295. CJC-1295 is a releasing factor for growth hormone and is therefore considered a Prohibited Substance under Section S2 of the WADA Prohibited List. This substance has potential performance-enhancing effects, it is readily available, and there is reason to believe that it is being used within the bodybuilding community. Copyright © 2010 John Wiley & Sons, Ltd.
Management of radioactive waste at Novi Han Repository
International Nuclear Information System (INIS)
Stefanova, I.G.; Mateeva, M.D.; Milanov, M.V.
2002-01-01
The Novi Han Repository is the only existing repository in Bulgaria for the disposal of radioactive waste from nuclear applications in industry, medicine and research. The repository was constructed in the early sixties according to the existing requirements. It was operated by the Institute for Nuclear Research and Nuclear Energy for more than thirty years without any accident or release of radioactivity to the environment, but without any investment for upgrading. As a consequence, the Bulgarian Nuclear Safety Authority temporarily stopped the operation of the repository in 1994. The measures for upgrading the Novi Han Repository, supported by the IAEA under TC Project BUL/4/005 'Increasing Safety of Novi Han Repository', are presented in this paper. They comprise: assessment of radionuclide inventory and future waste arisings, characterisation of disposal vaults, characterisation of the site, safety assessment, upgrading of the monitoring system, option study for the selection of treatment and conditioning processes and the development of a conceptual design for low and intermediate level waste processing and storage facility, immediate measures for improvement of the existing disposal vaults and infrastructure, construction of above-ground temporary storage structures, and resuming the operation of the Novi Han Repository. The necessary activities for re-licensing of the Novi Han Repository, construction of a waste processing and storage facility and a disposal facility for spent sealed sources are discussed. (author)
U.S. Environmental Protection Agency — Compliance Assurance and Enforcement Division Document Repository (CAEDDOCRESP) provides internal and external access of Inspection Records, Enforcement Actions, and...
Upgrading of radon's type near surface repository in Latvia
International Nuclear Information System (INIS)
Abramenkovs, A.
2006-01-01
In 1959, the Soviet government decided to construct the near surface radioactive wastes repository 'Radons' near the Baldone city. It was put in operation in 1962. The changes in the development of the repository were induced by the necessarily to upgrade it for disposal of radioactive wastes from the decommissioning of the Salaspils Research Reactor (SRR). The safety assessment of repository was performed during 2000-2001 under the PHARE project for necessary upgrades of repository. The outline design for new vaults and interim storage for long lived radioactive wastes was elaborated during 2003-2004 years. The Environmental Impact Assessment (EIA) for upgrade of Baldone repository was performed during 2004-2005 years. It was found, that additional efforts must be devoted for solution of social aspects o for successful operation and upgrade of repository. It was shown by EIA, that the local population has a negative opinion against the upgrade of repository in Latvia. The main recommendations for upgrades were connected with increasing the safety of repository, increasing of PR activities for education of society and developing of compensation mechanism for local municipality. (author)
Selection of Corrosion Resistant Materials for Nuclear Waste Repositories
International Nuclear Information System (INIS)
R.B. Rebak
2006-01-01
Several countries are considering geological repositories to dispose of nuclear waste. The environment of most of the currently considered repositories will be reducing in nature, except for the repository in the US, which is going to be oxidizing. For the reducing repositories, alloys such as carbon steel, stainless steels and titanium are being evaluated. For the repository in the US, some of the most corrosion resistant commercially available alloys are being investigated. This paper presents a summary of the behavior of the different materials under consideration for the repositories and the current understanding of the degradation modes of the proposed alloys in ground water environments from the point of view of general corrosion, localized corrosion and environmentally assisted cracking
Numerical modeling of magma-repository interactions
Bokhove, Onno
2001-01-01
This report explains the numerical programs behind a comprehensive modeling effort of magma-repository interactions. Magma-repository interactions occur when a magma dike with high-volatile content magma ascends through surrounding rock and encounters a tunnel or drift filled with either a magmatic
Multinational/regional repository - an illusion or solution
International Nuclear Information System (INIS)
Mele, I.
2006-01-01
The concept and current status of multinational and regional repositories are presented in the paper. Particular emphasis is given to the results and findings of the recent EU project SAPIERR, investigating the feasibility of regional repository concepts in Europe. Prospects for further development of multinational repositories are also brought forward and the impact and potential benefits of this approach to our national disposal programme are discussed as well. (author)
Stainthorp, Paul
2010-01-01
Slideshow presentation created to promote the Lincoln Repository to staff at the University of Lincoln. Consists of ten reasons why academic authors should consider depositing copies of their work in the Repository.
International perspective on repositories for low level waste
International Nuclear Information System (INIS)
Bergstroem, Ulla; Pers, Karin; Almen, Ylva
2011-12-01
Nuclear energy production gives rise to different types of radioactive waste. The use of nuclear isotopes within the research, industry and medical sectors also generates radioactive waste. To protect man and the environment from radiation the waste is isolated and contained by deposition in repositories. These repositories may have various designs regarding location, barriers etc depending on the potential danger of the waste. In Sweden, low- and intermediate level waste (LILW) is disposed of in the SFR repository in Forsmark. The repository is located 60 metres down into the bedrock under the bottom of the sea and covered by 6 metres of water. It is planned to extend SFR to accommodate decommissioning waste from the dismantling of the Swedish nuclear power facilities and also for the additional operation waste caused by the planned prolonged operation time. When planning the extension consultations will be carried out with the host municipality, authorities, organisations and general public. In planning the extension, SKB has performed a worldwide compilation of how other countries have, or plan to, handle the final disposal of similar wastes. The aim of this report is to give a brief description of LILW repositories worldwide; including general brief descriptions of many facilities, descriptions of the waste and the barriers as well as safety assessments for a few chosen repositories which represent different designs. The latter is performed, where possible, to compare certain features against the Swedish SFR. To provide a background and context to this study, international organisations and conventions are also presented along with internationally accepted principles regarding the management of radioactive waste. Similar to SFR, suitable locations for the repositories have, in many countries, been found at sites that already have, or used to have nuclear activities, such as reactor sites. Abandoned and disused mines, such as the salt mines in Germany, also
International perspective on repositories for low level waste
Energy Technology Data Exchange (ETDEWEB)
Bergstroem, Ulla; Pers, Karin; Almen, Ylva (SKB International AB (Sweden))
2011-12-15
Nuclear energy production gives rise to different types of radioactive waste. The use of nuclear isotopes within the research, industry and medical sectors also generates radioactive waste. To protect man and the environment from radiation the waste is isolated and contained by deposition in repositories. These repositories may have various designs regarding location, barriers etc depending on the potential danger of the waste. In Sweden, low- and intermediate level waste (LILW) is disposed of in the SFR repository in Forsmark. The repository is located 60 metres down into the bedrock under the bottom of the sea and covered by 6 metres of water. It is planned to extend SFR to accommodate decommissioning waste from the dismantling of the Swedish nuclear power facilities and also for the additional operation waste caused by the planned prolonged operation time. When planning the extension consultations will be carried out with the host municipality, authorities, organisations and general public. In planning the extension, SKB has performed a worldwide compilation of how other countries have, or plan to, handle the final disposal of similar wastes. The aim of this report is to give a brief description of LILW repositories worldwide; including general brief descriptions of many facilities, descriptions of the waste and the barriers as well as safety assessments for a few chosen repositories which represent different designs. The latter is performed, where possible, to compare certain features against the Swedish SFR. To provide a background and context to this study, international organisations and conventions are also presented along with internationally accepted principles regarding the management of radioactive waste. Similar to SFR, suitable locations for the repositories have, in many countries, been found at sites that already have, or used to have nuclear activities, such as reactor sites. Abandoned and disused mines, such as the salt mines in Germany, also
Data repositories for medical education research: issues and recommendations.
Schwartz, Alan; Pappas, Cleo; Sandlow, Leslie J
2010-05-01
The authors explore issues surrounding digital repositories with the twofold intention of clarifying their creation, structure, content, and use, and considering the implementation of a global digital repository for medical education research data sets-an online site where medical education researchers would be encouraged to deposit their data in order to facilitate the reuse and reanalysis of the data by other researchers. By motivating data sharing and reuse, investigators, medical schools, and other stakeholders might see substantial benefits to their own endeavors and to the progress of the field of medical education.The authors review digital repositories in medicine, social sciences, and education, describe the contents and scope of repositories, and present extant examples. The authors describe the potential benefits of a medical education data repository and report results of a survey of the Society for Directors of Research in Medicine Education, in which participants responded to questions about data sharing and a potential data repository. Respondents strongly endorsed data sharing, with the caveat that principal investigators should choose whether or not to share data they collect. A large majority believed that a repository would benefit their unit and the field of medical education. Few reported using existing repositories. Finally, the authors consider challenges to the establishment of such a repository, including taxonomic organization, intellectual property concerns, human subjects protection, technological infrastructure, and evaluation standards. The authors conclude with recommendations for how a medical education data repository could be successfully developed.
Implementation of the Brazilian national repository
International Nuclear Information System (INIS)
Tello, Cledola Cassia Oliveira de
2013-01-01
Ionizing radiation in Brazil is used in electricity generation, medicine, industry, agriculture and for research and development purposes. All these activities can generate radioactive waste. At this point, in Brazil, the use of nuclear energy and radioisotopes justifies the construction of a national repository for radioactive wastes of low and intermediate-level. According to Federal Law No. 10308, Brazilian National Commission for Nuclear Energy (CNEN) is responsible for designing and constructing the intermediate and final storages for radioactive wastes. Additionally, a restriction on the construction of Angra 3 is that the repository is under construction until its operation start, attaining some requirements of the Brazilian Environmental Regulator (IBAMA). The RBMN Project (Repository for Low and Intermediate-Level Radioactive Wastes) aims at the implantation of a National Repository for disposal of low and intermediate-level of radiation wastes. This Project has some aspects that are unique in the Brazilian context, especially referring to the time between its construction and the end of its institutional period. This time is about 360 years, when the area will be released for unrestricted uses. It means that the Repository must be safe and secure for more than three hundred years, which is longer than half of the whole of Brazilian history. This aspect is very new for the Brazilian people, bringing a new dimension to public acceptance. Another point is this will be the first repository in South America, bringing a real challenge for the continent. The current status of the Project is summarized. (author)
The development of safeguards for geological repositories
International Nuclear Information System (INIS)
Van der Meer, K.
2009-01-01
Traditionally, research and development on geological repositories for High Level Waste (HLW) focuses on the short- and long-term safety aspects of the repository. If the repository will also be used for the disposal of spent fuel, safeguards aspects have to be taken into account. Safety and safeguards requirements may be contradictory; the safety of a geological repository is based on the non-intrusion of the geological containment, while safeguards require regular inspections of position and amount of the spent fuel. Examples to reconcile these contradictory requirements are the use of information required for the safety assessment of the geological repository for safeguards purposes and the adaptation of the safeguards approach to use non-intrusive inspection techniques. The principles of an inspection approach for a geological repository are now generally accepted within the IAEA. The practical applicability of the envisaged inspection techniques is still subject to investigation. It is specifically important for the Belgian situation that an inspection technique can be used in clay, the geological medium in which Belgium intends to dispose its HLW and spent fuel. The work reported in this chapter is the result of an international cooperation in the framework of the IAEA, in which SCK-CEN participates
Creusot, N.P.; Gruppen, H.
2007-01-01
The objective of this work was to identify the dominant aggregating peptides from a whey protein hydrolysate (degree of hydrolysis of 6.8%) obtained with Bacillus licheniformis protease. The aggregating peptides were fractionated with preparative reversed-phase chromatography and identified with
Investigative study of standards for digital repositories and related services
Foulonneau, Muriel; Badolato, Anne-Marie
2008-01-01
This study is meant for institutional repository managers, service providers, repository software developers and generally, all players taking an active part in the creation of the digital repository infrastructure for e-research and e-learning. It reviews the current standards, protocols and applications in the domain of digital repositories. Special attention is being paid to the interoperability of repositories to enhance the exchange of data in repositories. It aims to stimulate discussion about these topics and supports initiatives for the integration of and, where needed, development of
International Nuclear Information System (INIS)
Moench, Christoph
2013-01-01
Part I of this article, which appeared in the preceding issue, described in general terms the background to the search for a disposal site and the result of the exploration to date of the repository, which would appear to be suitable from a mining standpoint according to the present knowledge. According to the rules in effect up to now, the exploration and construction would be financed by advance payments on the contributions of the waste producing companies, in particular the utility companies. The working draft of an 'Act on the search for and selection of a site for a repository for heat generating radioactive waste' (Gesetz zur Suche und Auswahl eines Standortes fuer ein Endlager fuer waermeentwickelnde radioaktive Abfaelle) from autumn 2012 provides for a new version of section 21b Atomic Energy Act, under which the costs for 'carrying out a repository selection procedure pursuant to the Repository Selection Act (Standort-auswahlgesetz)' would be allocated to the future users of the repository who are obliged to make contributions as a 'necessary expense'. Part II evaluates this provision of the working draft on the basis of the financial constitutional law. A comparison of sites is not a measure that could be allocated to the future users of the repository who are obliged to make contributions as a 'necessary expense'. Moreover, there is a lack of responsibility for the financing and of a legally relevant advantage that would be conferred by a cumulative alternative repository search for the later users of the repository who are obliged to provide the pre-financing. The costs can therefore not be allocated to the later users as either a contribution or a special charge, not even by way of an association with mandatory membership (Zwangsverband). They must be borne by the state. Consequently, the allocation stipulated by provision would constitute an impermissible charge under financial constitutional law. (orig.)
Institutional Repositories as Infrastructures for Long-Term Preservation
Francke, Helena; Gamalielsson, Jonas; Lundell, Björn
2017-01-01
Introduction: The study describes the conditions for long-term preservation of the content of the institutional repositories of Swedish higher education institutions based on an investigation of how deposited files are managed with regards to file format and how representatives of the repositories describe the functions of the repositories.…
Socioeconomic impacts of repositories
International Nuclear Information System (INIS)
Thomas, J.K.; Hamm, R.R.; Murdock, S.H.
1983-01-01
Federal and state decision makers, community leaders, and residents must know how communities will be changed by the impacts of a high-level nuclear waste repository. This chapter identifies the factors affecting an assessment of socioeconomic impacts and the types of impacts (economic, demographic, fiscal, community service, and social) likely to occur as a result of repository development. Each of these types can be divided into standard (those which typically results from any large-scale development) and special impact categories (those which result from the fact that radioactive materials will be handled). 3 tables
Hook, Vivian Y H
2006-01-01
The nervous system represents a key area for development of novel therapeutic agents for the treatment of neurological and neurodegenerative diseases. Recent research has demonstrated the critical importance of neuroproteases for the production of specific peptide neurotransmitters and for the production of toxic peptides in major neurodegenerative diseases that include Alzheimer, Huntington, and Parkinson diseases. This review illustrates the successful criteria that have allowed identification of proteases responsible for converting protein precursors into active peptide neurotransmitters, consisting of dual cysteine protease and subtilisin-like protease pathways in neuroendocrine cells. These peptide neurotransmitters are critical regulators of neurologic conditions, including analgesia and cognition, and numerous behaviors. Importantly, protease pathways also represent prominent mechanisms in neurodegenerative diseases, especially Alzheimer, Huntington, and Parkinson diseases. Recent studies have identified secretory vesicle cathepsin B as a novel beta-secretase for production of the neurotoxic beta-amyloid (Abeta) peptide of Alzheimer disease. Moreover, inhibition of cathepsin B reduces Abeta peptide levels in brain. These neuroproteases potentially represent new drug targets that should be explored in future pharmaceutical research endeavors for drug discovery.
Electronic Repository of Russian Historical Statistics
Tykhonov, Vyacheslav; Kessler, Gijs; Markevich, Andrei; de Vries, Jerry
2014-01-01
The Electronic Repository for Russian Historical Statistics brings together data extracted from various published and unpublished sources in one place. Its principal focus is Russian economic and social history of the last three centuries (18th-21st). The repository caters to the needs of the
Fons antic i repositoris universitaris a Espanya
Directory of Open Access Journals (Sweden)
Herrera Morillas, José Luis
2015-12-01
Full Text Available Es mostra la presència de col·leccions de fons antic en els repositoris de les biblioteques universitàries espanyoles després d'analitzar tots els repositoris. Per a aquesta anàlisi, com a part de la metodologia emprada, s'ha elaborat un model o llista que consta d'onze elements. Del conjunt de les universitats espanyoles, seixanta tenen repositoris, vint-i-vuit dels quals (16,8 % disposen de col·leccions de fons antic. Com que del concepte de repositori institucional no sembla desprendre's que tingui com a finalitat incloure aquest tipus de col·leccions, es reflexiona sobre la peculiaritat que una part dels repositoris universitaris espanyols inclogui col·leccions d'aquestes característiques.Se muestra la presencia de colecciones de fondo antiguo en los repositorios de las bibliotecas universitarias españolas después de analizar todos los repositorios. Para este análisis, como parte de la metodología empleada, se ha elaborado un modelo o lista que consta de once elementos. Del conjunto de las universidades españolas, sesenta cuentan con repositorios y, de estos, veintiocho (16,8 % disponen de colecciones de fondo antiguo. Debido a que del concepto de repositorio institucional no parece desprenderse que tenga como finalidad albergar este tipo de colecciones, se hace una reflexión sobre la peculiaridad de que parte de los repositorios universitarios españoles incluya colecciones de estas características.This paper uses an analysis of the repositories of Spanish universities to identify which institutions contain rare book and manuscript collections. The method used in this analysis involved examining each university on the basis of a list comprising eleven elements. A total of 60 universities were found to have repositories but only 28 (16.8 % of these contained rare book and manuscript collections. In the light of these figures, which suggest that Spanish university repositories do not generally consider the preservation of rare
Design approaches for access plugs in a basalt repository
International Nuclear Information System (INIS)
O'Rourke, J.; Allirot, D.; O'Connor, K.
1982-01-01
This paper describes research, laboratory testing, and analytical approaches taken toward the development of designs for sealing boreholes, shafts, and tunnels penetrating from ground surface to a deep, mined nuclear waste repository in basalt. A material selection process leading to identification of preferred sealing materials is discussed, and the laboratory testing program to define the geochemical and geotechnical performance of these materials is described. Analysis of the environmental conditions in the Columbia Plateau basalt flows leads to identification of tentative design criteria for plug systems. These design criteria include performance of the plug as a hydraulic barrier and as a radionuclide barrier. An important problem for effective performance of a plug system as a hydraulic barrier is shown to be a potentially disturbed zone surrounding the excavation in the stressed and jointed host rock. An idealized one-dimensional numerical model is described for analyzing the performance of the plug as a barrier to radionuclide transport. The preliminary analyses led to the conclusion that the composition and dimensions of practical candidate plugs can satisfy both hydraulic and radionuclide barrier criteria. Examples of candidate designs are shown for boreholes, shafts, and tunnels. 9 references, 6 figures, 6 tables
Decompression of magma into repository tunnels
Bokhove, Onno; Woods, A.W.
2002-01-01
It is nontrivial to find and design safe repository sites for nuclear waste. It appears common sense to drill tunnels as repository sites in a mountain in remote and relatively dry regions. However, erosion of the waste canisters by naturally abundant chemicals in the mountains water cycle remains a
High-resolution mass spectrometry driven discovery of peptidic danger signals in insect immunity.
Directory of Open Access Journals (Sweden)
Arton Berisha
Full Text Available The 'danger model' is an alternative concept for immune response postulating that the immune system reacts to entities that do damage (danger associated molecular patterns, DAMP and not only to entities that are foreign (pathogen-associated molecular patterns, PAMP as proposed by classical immunology concepts. In this study we used Galleria mellonella to validate the danger model in insects. Hemolymph of G. mellonella was digested with thermolysin (as a representative for virulence-associated metalloproteinases produced by humanpathogens followed by chromatographic fractionation. Immune-stimulatory activity was tested by measuring lysozyme activity with the lytic zone assays against Micrococcus luteus cell wall components. Peptides were analyzed by nano-scale liquid chromatography coupled to high-resolution Fourier transform mass spectrometers. Addressing the lack of a genome sequence we complemented the rudimentary NCBI protein database with a recently established transcriptome and de novo sequencing methods for peptide identification. This approach led to identification of 127 peptides, 9 of which were identified in bioactive fractions. Detailed MS/MS experiments in comparison with synthetic analogues confirmed the amino acid sequence of all 9 peptides. To test the potential of these putative danger signals to induce immune responses we injected the synthetic analogues into G. mellonella and monitored the anti-bacterial activity against living Micrococcus luteus. Six out of 9 peptides identified in the bioactive fractions exhibited immune-stimulatory activity when injected. Hence, we provide evidence that small peptides resulting from thermolysin-mediated digestion of hemolymph proteins function as endogenous danger signals which can set the immune system into alarm. Consequently, our study indicates that the danger model also plays a role in insect immunity.
Paper and digital repositories in the United States
Directory of Open Access Journals (Sweden)
David F. Kohl
2003-09-01
Full Text Available What you've asked me to talk about today is basically what can libraries do with all the stuff they have and continue to get. Where do we put it all; what do we do with it? As we know, libraries have three core functions: collecting, organizing and preserving the key documents of the human enterprise. And, with apologies to Saint Paul, the greatest of these is preservation. For without preservation neither of the first two ultimately matter. My assignment this morning is to bring you up to date on one specific aspect of the preservation function, library repositories, and indeed, library repository developments in the US. The plan for this morning's presentation is the following: after a brief background review to give us a context for American developments we will examine first the various kinds of print repositories and then the various initiatives for electronic repositories. Because other presentations at this conference deal with electronic repositories, the main focus today will be on U.S. print repositories.
Institutional Repository Sebagai Sarana Komunikasi Ilmiah Yang Sustainable Dan Reliable
Directory of Open Access Journals (Sweden)
Faizuddin Harliansyah
2016-07-01
Full Text Available Abstract; Institutional repositories development has drawn the attention of many scholars throughout the world. Using the keywords ‘institutional repositories’, there are over 300 peer-reviewed articles related on the topic has been indexed in Library, Information Science, & Technology Abstracts (LISTA and SCOPUS. There are also hundreds of theses, dissertations, and websites dedicated on this blooming trends. These are proofs that the importance of IR in higher education has been acknowledged by many professionals in the field. This paper aims at clarifying the role of repositories in strengthening scholarly communication in higher education and research institution and explaining some basic repositories concepts (types of repositories and their characteristics, as well as exploring its relations with open access movement, the development ideas, and resources that could be kept in repositories and deposit policies. Abstrak; Pengembangan institutional repositories telah banyak menyita perhatian dari kalangan ilmiah di seluruh dunia. Melalui kata kunci ‘institutional repositories’, ada lebih dari 300 artikel terulas mitra bestari yang berhubungan dengan topik ini, yang telah terindeks di Library, Information Science, & Technology Abstracts (LISTA, dan SCOPUS. Terdapat juga ratusan tesis, disertasi, dan website yang mengulas trend ini. Inilah bukti bahwa pentingnya institutional repositories (IR telah dipahami oleh para profesional di bidangnya. Tulisan ini akan menjelaskan aturan-aturan repository dalam memperkuat komunikasi ilmiah di perguruan tinggi dan lembaga riset, menjelaskan konsep-konsep dasar repositories, termasuk tipe-tipe repository dan karakteristiknya. Tulisan ini juga akan memperdalam konsep repositories dalam hubungannya dengan gerakan open access, pengembangan ide-ide, sumber-sumber ilmiah yang dapat disimpan di repositories, serta kebijakan penyimpanan di dalamnya.
International Nuclear Information System (INIS)
Owen, J.L.; McGinnis, J.T.; Harper, C.M.; Battelle Columbus Labs., OH)
1982-01-01
This paper presents results of an environmental assessment conducted under the direction of the Office of Nuclear Waste Isolation as part of the National Waste Terminal Storage program. The study defined a range of potential environmental effects of constructing, operating, decommissioning, and long-term isolation of a nuclear waste repository. The analytical methodology used to determine potential environmental effects required definition of a hypothetical environmental setting and repository. Potentially applicable regulatory requirements were identified and were used as guidelines to evaluate permitting feasibility. The environmental effects of repository development were analyzed for the two major time periods of concern: short term (the period of construction, operation, and decommissioning) and long term (the isolation period after decommissioning). As a result of this analysis, major environmental uncertainties and issues were identified. 11 references, 5 figures
Analysis of computational vulnerabilities in digital repositories
Directory of Open Access Journals (Sweden)
Valdete Fernandes Belarmino
2015-04-01
Full Text Available Objective. Demonstrates the results of research that aimed to analyze the computational vulnerabilities of digital directories in public Universities. Argues the relevance of information in contemporary societies like an invaluable resource, emphasizing scientific information as an essential element to constitute scientific progress. Characterizes the emergence of Digital Repositories and highlights its use in academic environment to preserve, promote, disseminate and encourage the scientific production. Describes the main software for the construction of digital repositories. Method. The investigation identified and analyzed the vulnerabilities that are exposed the digital repositories using Penetration Testing running. Discriminating the levels of risk and the types of vulnerabilities. Results. From a sample of 30 repositories, we could examine 20, identified that: 5% of the repositories have critical vulnerabilities, 85% high, 25% medium and 100% lowers. Conclusions. Which demonstrates the necessity to adapt actions for these environments that promote informational security to minimizing the incidence of external and / or internal systems attacks.Abstract Grey Text – use bold for subheadings when needed.
A Review of Antioxidant Peptides Derived from Meat Muscle and By-Products
Directory of Open Access Journals (Sweden)
Rui Liu
2016-09-01
Full Text Available Antioxidant peptides are gradually being accepted as food ingredients, supplemented in functional food and nutraceuticals, to positively regulate oxidative stress in the human body against lipid and protein oxidation. Meat muscle and meat by-products are rich sources of proteins and can be regarded as good materials for the production of bioactive peptides by use of enzymatic hydrolysis or direct solvent extraction. In recent years, there has been a growing number of studies conducted to characterize antioxidant peptides or hydrolysates derived from meat muscle and by-products as well as processed meat products, including dry-cured hams. Antioxidant peptides obtained from animal sources could exert not only nutritional value but also bioavailability to benefit human health. This paper reviews the antioxidant peptides or protein hydrolysates identified in muscle protein and by-products. We focus on the procedure for the generation of peptides with antioxidant capacity including the acquisition of crude peptides, the assessment of antioxidant activity, and the purification and identification of the active fraction. It remains critical to perform validation experiments with a cell model, animal model or clinical trial to eliminate safety concerns before final application in the food system. In addition, some of the common characteristics on structure-activity relationship are also reviewed based on the identified antioxidant peptides.
A Review of Antioxidant Peptides Derived from Meat Muscle and By-Products.
Liu, Rui; Xing, Lujuan; Fu, Qingquan; Zhou, Guang-Hong; Zhang, Wan-Gang
2016-09-20
Antioxidant peptides are gradually being accepted as food ingredients, supplemented in functional food and nutraceuticals, to positively regulate oxidative stress in the human body against lipid and protein oxidation. Meat muscle and meat by-products are rich sources of proteins and can be regarded as good materials for the production of bioactive peptides by use of enzymatic hydrolysis or direct solvent extraction. In recent years, there has been a growing number of studies conducted to characterize antioxidant peptides or hydrolysates derived from meat muscle and by-products as well as processed meat products, including dry-cured hams. Antioxidant peptides obtained from animal sources could exert not only nutritional value but also bioavailability to benefit human health. This paper reviews the antioxidant peptides or protein hydrolysates identified in muscle protein and by-products. We focus on the procedure for the generation of peptides with antioxidant capacity including the acquisition of crude peptides, the assessment of antioxidant activity, and the purification and identification of the active fraction. It remains critical to perform validation experiments with a cell model, animal model or clinical trial to eliminate safety concerns before final application in the food system. In addition, some of the common characteristics on structure-activity relationship are also reviewed based on the identified antioxidant peptides.
Machtejevas, Egidijus; John, Harald; Wagner, Knut; Standker, Ludger; Marko-Varga, Gyorgy; Georg Forssmann, Wolf; Bischoff, Rainer; K. Unger, Klaus
2004-01-01
A comprehensive on-line sample clean-up with an integrated two-dimensional HPLC system was developed for the analysis of natural peptides. Samples comprised of endogenous peptides with molecular weights up to 20 kDa were generated from human hemofiltrate (HF) obtained from patients with chronic
New Roles, New Responsibilities: Examining Training Needs of Repository Staff
Directory of Open Access Journals (Sweden)
Natasha Simons
2012-05-01
Full Text Available INTRODUCTION Institutional repositories play a critical role in the research lifecycle. Funding agencies are increasingly seeking an improved return on their investment in research. Repositories facilitate this process by providing storage of, and access to, institutional research outputs and, more recently, research data. While repositories are generally managed within the academic library, repository staff require different skills and knowledge compared with traditional library roles. This study reports on a survey of Australasian institutional repository staff to identify skills and knowledge sets. METHODS Institutional repository staff working at universities in Australia and New Zealand were invited to participate in an online survey which incorporated both open and closed-ended question types. RESULTS The survey found significant gaps in the current provision of formal training and coursework related to institutional repositories, which echoed findings in the United Kingdom, Italy, and the United States. DISCUSSION There is clearly a need for more and varied training opportunities for repository professionals. Repository work requires a specific set of skills that can be difficult to find and institutions will benefit from investing in training and ongoing development opportunities for repository staff. CONCLUSION The data from this study could be used to facilitate staff recruitment, development, training, and retention strategies.
Andromeda: a peptide search engine integrated into the MaxQuant environment.
Cox, Jürgen; Neuhauser, Nadin; Michalski, Annette; Scheltema, Richard A; Olsen, Jesper V; Mann, Matthias
2011-04-01
A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides.
International Nuclear Information System (INIS)
Glass, R.S.
1981-12-01
This report explores the interaction of ionizing radiation with various environments. In particular, worst case (aqueous) environments for the proposed nuclear waste repository sites are considered. Emphasis is on the fundamental chemical and physical processes involved. The identities of possible radiolysis products (both transient and stable) have been sought through a literature search. The effect of radiation on corrosion processes is discussed. The radiation-induced chemical environment in the worst case repository sites is not well defined. Attention should therefore be given to fundamental studies exploring the interaction of such environments with components of the nuclear waste package, including the canister materials and backfills. Identification and quantification of radiolysis products would be helpful in this regard
Evaluation of repository safety
Energy Technology Data Exchange (ETDEWEB)
Sagar, B.; Patrick, W.; Dasgupta, B.; Mohanty, S. [Center for Nuclear Waste Regulatory Analyses, San Antonio (United States)
2002-07-01
The United States high-level waste program requires evaluation of radiological safety during two distinct time intervals. The first interval, commonly referred to as the preclosure period, deals with receipt of waste at the site, transfer into disposal containers, if needed, emplacement in the underground openings, monitoring and maintenance activities, backfill and closure of the underground openings, and decontamination and decommissioning of the surface facilities of the geologic repository. The preclosure period may extend from a few tens of years to as long as a few hundred of years, depending on repository design and societal norms regarding a final decision to permanently seal the repository. During the preclosure or operational period, performance confirmation studies are conducted to provide a basis for updating and reevaluating estimates of postclosure performance and, finally, to provide a basis for a closure decision. The postclosure period during which expected repository performance must meet certain standards may range from ten thousands years, as it does in the United States, to millions of years, as it does in some European nations. Waste handling operations in the preclosure period are to be evaluated in relation to their potential effect on workers, members of general public, and the general environment. During this period, releases of radioactivity are to be monitored and appropriate actions taken whenever established limits are approached or exceeded. Preclosure safety is highly dependent on facility design, operational hardware and automated systems, operational sequences, and reliability of humans involved in operations. Preclosure safety analyses conducted before operations begin play a major role in the design process, selection of equipment, and development of operational procedures. Because of the complexity, duration, and spatial scales of the operations, analyses are conducted using mathematical models implemented in computer codes
Evaluation of repository safety
International Nuclear Information System (INIS)
Sagar, B.; Patrick, W.; Dasgupta, B.; Mohanty, S.
2002-01-01
The United States high-level waste program requires evaluation of radiological safety during two distinct time intervals. The first interval, commonly referred to as the preclosure period, deals with receipt of waste at the site, transfer into disposal containers, if needed, emplacement in the underground openings, monitoring and maintenance activities, backfill and closure of the underground openings, and decontamination and decommissioning of the surface facilities of the geologic repository. The preclosure period may extend from a few tens of years to as long as a few hundred of years, depending on repository design and societal norms regarding a final decision to permanently seal the repository. During the preclosure or operational period, performance confirmation studies are conducted to provide a basis for updating and reevaluating estimates of postclosure performance and, finally, to provide a basis for a closure decision. The postclosure period during which expected repository performance must meet certain standards may range from ten thousands years, as it does in the United States, to millions of years, as it does in some European nations. Waste handling operations in the preclosure period are to be evaluated in relation to their potential effect on workers, members of general public, and the general environment. During this period, releases of radioactivity are to be monitored and appropriate actions taken whenever established limits are approached or exceeded. Preclosure safety is highly dependent on facility design, operational hardware and automated systems, operational sequences, and reliability of humans involved in operations. Preclosure safety analyses conducted before operations begin play a major role in the design process, selection of equipment, and development of operational procedures. Because of the complexity, duration, and spatial scales of the operations, analyses are conducted using mathematical models implemented in computer codes
Semantic Linking of Learning Object Repositories to DBpedia
Lama, Manuel; Vidal, Juan C.; Otero-Garcia, Estefania; Bugarin, Alberto; Barro, Senen
2012-01-01
Large-sized repositories of learning objects (LOs) are difficult to create and also to maintain. In this paper we propose a way to reduce this drawback by improving the classification mechanisms of the LO repositories. Specifically, we present a solution to automate the LO classification of the Universia repository, a collection of more than 15…
Conlon, J Michael; Mechkarska, Milena; Kolodziejek, Jolanta; Leprince, Jérôme; Coquet, Laurent; Jouenne, Thierry; Vaudry, Hubert; Nowotny, Norbert; King, Jay D
2015-10-01
Peptidomic analysis of norepinephrine-stimulated skin secretions from the octoploid Mawa clawed frog Xenopus boumbaensis Loumont, 1983 led to the identification and characterization of 15 host-defense peptides belonging to the magainin (two peptides), peptide glycine-leucine-amide (PGLa; three peptides), xenopsin precursor fragment (XPF; three peptides), caerulein precursor fragment (CPF; two peptides), and caerulein precursor fragment-related peptide (CPF-RP; five peptides) families. In addition, caerulein and three peptides with structural similarity to the trefoil factor family (TFF) peptides, xP2 and xP4 from Xenopus laevis were also present in the secretions. Consistent with data from comparisons of the nucleotides sequence of mitochondrial and nuclear genes, the primary structures of the peptides suggest a close phylogenetic relationship between X. boumbaensis and the octoploid frogs Xenopus amieti and Xenopus andrei. As the three species occupy disjunct ranges within Cameroon, it is suggested that they diverged from a common ancestor by allopatric speciation. Copyright © 2015 Elsevier Inc. All rights reserved.
Directory of Open Access Journals (Sweden)
Heng-Li Chen
Full Text Available The rise of multidrug-resistant (MDR pathogens causes an increasing challenge to public health. Antimicrobial peptides are considered a possible solution to this problem. HBV core protein (HBc contains an arginine-rich domain (ARD at its C-terminus, which consists of 16 arginine residues separated into four clusters (ARD I to IV. In this study, we demonstrated that the peptide containing the full-length ARD I-IV (HBc147-183 has a broad-spectrum antimicrobial activity at micro-molar concentrations, including some MDR and colistin (polymyxin E-resistant Acinetobacter baumannii. Furthermore, confocal fluorescence microscopy and SYTOX Green uptake assay indicated that this peptide killed Gram-negative and Gram-positive bacteria by membrane permeabilization or DNA binding. In addition, peptide ARD II-IV (HBc153-176 and ARD I-III (HBc147-167 were found to be necessary and sufficient for the activity against P. aeruginosa and K. peumoniae. The antimicrobial activity of HBc ARD peptides can be attenuated by the addition of LPS. HBc ARD peptide was shown to be capable of direct binding to the Lipid A of lipopolysaccharide (LPS in several in vitro binding assays. Peptide ARD I-IV (HBc147-183 had no detectable cytotoxicity in various tissue culture systems and a mouse animal model. In the mouse model by intraperitoneal (i.p. inoculation with Staphylococcus aureus, timely treatment by i.p. injection with ARD peptide resulted in 100-fold reduction of bacteria load in blood, liver and spleen, as well as 100% protection of inoculated animals from death. If peptide was injected when bacterial load in the blood reached its peak, the protection rate dropped to 40%. Similar results were observed in K. peumoniae using an IVIS imaging system. The finding of anti-microbial HBc ARD is discussed in the context of commensal gut microbiota, development of intrahepatic anti-viral immunity and establishment of chronic infection with HBV. Our current results suggested that
U.S. Department of Health & Human Services — The NIDDK Central Repository stores biosamples, genetic and other data collected in designated NIDDK-funded clinical studies. The purpose of the NIDDK Central...
International Nuclear Information System (INIS)
1983-06-01
The interim performance specifications and data requirements presented apply to conceptual waste package designs for all waste forms which will be isolated in salt geologic repositories. The waste package performance specifications and data requirements respond to the waste package performance criteria. Subject areas treated include: containment and controlled release, operational period safety, criticality control, identification, and waste package performance testing requirements. This document was generated for use in the development of conceptual waste package designs in salt. It will be revised as additional data, analyses, and regulatory requirements become available
Researching radioactive waste disposal. [Underground repository
Energy Technology Data Exchange (ETDEWEB)
Feates, F; Keen, N [UKAEA Research Group, Harwell. Atomic Energy Research Establishment
1976-02-16
At present it is planned to use the vitrification process to convert highly radioactive liquid wastes, arising from nuclear power programme, into glass which will be contained in steel cylinders for storage. The UKAEA in collaboration with other European countries is currently assessing the relative suitability of various natural geological structures as final repositories for the vitrified material. The Institute of Geological Sciences has been commissioned to specify the geological criteria that should be met by a rock structure if it is to be used for the construction of a repository though at this stage disposal sites are not being sought. The current research programme aims to obtain basic geological data about the structure of the rocks well below the surface and is expected to continue for at least three years. The results in all the European countries will then be considered so that the United Kingdom can choose a preferred method for isolating their wastes. It is only at that stage that a firm commitment may be made to select a site for a potential repository, when a far more detailed scientific research study will be instituted. Heat transfer problems and chemical effects which may occur within and around repositories are being investigated and a conceptual design study for an underground repository is being prepared.
Cross Institutional Cooperation on a Shared Bit Repository
DEFF Research Database (Denmark)
Zierau, Eld; Kejser, Ulla Bøgvad
2013-01-01
This paper explores how independent institutions, such as archives and libraries, can cooperate on managing a shared bit repository with bit preservation, in order to use their resources for preservation in a more cost-effective way. It uses the OAIS Reference Model to provide a framework...... for systematically analysing institutions technical and organisational requirements for a remote bit repository. Instead of viewing a bit repository simply as Archival Storage for the institutions repositories, we argue for viewing it as consisting of a subset of functions from all entities defined by the OAIS...... Reference Model. The work is motivated by and used in a current Danish feasibility study for establishing a national bit repository. The study revealed that depending on their missions and the collections they hold, the institutions have varying requirements e.g. for bit safety, accessibility...
Cross Institutional Cooperation on a Shared Bit Repository
DEFF Research Database (Denmark)
Zierau, Eld; Kejser, Ulla Bøgvad
2010-01-01
This paper explores how independent institutions, such as archives and libraries, can cooperate on managing a shared bit repository with bit preservation in order to use their resources for preservation n in a more cost-effective way. It uses the OAIS Reference Model to provide a framework...... for systematically analysing the technical and organizational requirements of institutions for a remote bit repository. Instead of viewing a bit repository simply as Archival Storage for the institutions’ repositories, we argue for viewing it as consisting of a subset of functions from all entities defined...... by the OAIS Reference Model. The work is motivated by and used in a current Danish feasibility study for establishing a national bit repository. The study revealed that depending on their missions and the collections they hold, the institutions have varying requirements, such as for bit safety, accessibility...
Tools for Managing Repository Objects
Banker, Rajiv D.; Isakowitz, Tomas; Kauffman, Robert J.; Kumar, Rachna; Zweig, Dani
1993-01-01
working Paper Series: STERN IS-93-46 The past few years have seen the introduction of repository-based computer aided software engineering (CASE) tools which may finally enable us to develop software which is reliable and affordable. With the new tools come new challenges for management: Repository-based CASE changes software development to such an extent that traditional approaches to estimation, performance, and productivity assessment may no longer suffice - if they ever...
Screening and identification of novel B cell epitopes of Toxoplasma gondii SAG1
Wang, Yanhua; Wang, Guangxiang; Zhang, Delin; Yin, Hong; Wang, Meng
2013-01-01
Background The identification of protein epitopes is useful for diagnostic purposes and for the development of peptide vaccines. In this study, the epitopes of Toxoplasma gondii SAG1 were identified using synthetic peptide techniques with the aid of bioinformatics. Findings Eleven peptides derived from T. gondii SAG1 were assessed by ELISA using pig sera from different time points after infection. Four (PS4, PS6, PS10 and PS11), out of the eleven peptides tested were recognized by all sera. T...
DEFF Research Database (Denmark)
Bunkenborg, J.; Falkenby, L. G.; Harder, L. M.
2016-01-01
. Chemical modification of all peptides in a sample leads to shifts in masses depending on the chemical properties of each peptide. The identification of a native peptide sequence and its perturbed version with a different parent mass and fragment ion masses provides valuable information. Labeling all...
Di peptides of the Zeyhera digitalis roots; Dipeptideo das raizes de Zeyhera digitalis
Energy Technology Data Exchange (ETDEWEB)
Ferreira, Dalva Trevisan; Silva, Rosely Barbosa da [Universidade Estadual de Londrina, PR (Brazil). Dept. de Quimica; Oliveira, Alaide Braga de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Quimica; Isobe, Minoru [Nagoya Univ. (Japan)
1991-12-31
Systematic investigation using {sup 1} H NMR have been done on the Zeyhera digitalis roots for isolation, purification, and identification of substances with biological or medical potential activities , such as di peptides compounds 5 figs.
Di peptides of the Zeyhera digitalis roots; Dipeptideo das raizes de Zeyhera digitalis
Energy Technology Data Exchange (ETDEWEB)
Ferreira, Dalva Trevisan; Silva, Rosely Barbosa da [Universidade Estadual de Londrina, PR (Brazil). Dept. de Quimica; Oliveira, Alaide Braga de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Quimica; Isobe, Minoru [Nagoya Univ. (Japan)
1992-12-31
Systematic investigation using {sup 1} H NMR have been done on the Zeyhera digitalis roots for isolation, purification, and identification of substances with biological or medical potential activities , such as di peptides compounds 5 figs.
El Zoeiby, Ahmed; Sanschagrin, François; Darveau, André; Brisson, Jean-Robert; Levesque, Roger C
2003-03-01
The machinery of peptidoglycan biosynthesis is an ideal site at which to look for novel antimicrobial targets. Phage display was used to develop novel peptide inhibitors for MurC, an essential enzyme involved in the early steps of biosynthesis of peptidoglycan monomer. We cloned and overexpressed the murA, -B and -C genes from Pseudomonas aeruginosa in the pET expression vector, adding a His-tag to their C termini. The three proteins were overproduced in Escherichia coli and purified to homogeneity in milligram quantities. MurA and -B were combinatorially used to synthesize the MurC substrate UDP-N-acetylmuramate, the identity of which was confirmed by mass spectrometry and nuclear magnetic resonance analysis. Two phage-display libraries were screened against MurC in order to identify peptide ligands to the enzyme. Three rounds of biopanning were carried out, successively increasing elution specificity from round 1 to 3. The third round was accomplished with both non-specific elution and competitive elution with each of the three MurC substrates, UDP-N-acetylmuramic acid (UNAM), ATP and L-alanine. The DNA of 10 phage, selected randomly from each group, was extracted and sequenced, and consensus peptide sequences were elucidated. Peptides were synthesized and tested for inhibition of the MurC-catalysed reaction, and two peptides were shown to be inhibitors of MurC activity with IC(50)s of 1.5 and 0.9 mM, respectively. The powerful selection technique of phage display allowed us to identify two peptide inhibitors of the essential bacterial enzyme MurC. The peptide sequences represent the basis for the synthesis of inhibitory peptidomimetic molecules.
International Nuclear Information System (INIS)
1987-06-01
This document describes an integrated laboratory testing and model development effort for the seal system for a high-level nuclear waste repository in salt. The testing and modeling efforts are designed to determine seal material response in the repository environment, to provide models of seal system components for performance assessment, and to assist in the development of seal system designs. A code/model development and performance analysis program will be performed to predict the short- and long-term response of seal materials and seal components. The results from these analyses will be used to support the material testing activities on this contract and to support performance assessment activities that are conducted in other parts of the Salt Repository Project (SRP). 48 refs., 15 figs., 4 tabs
Gas generation and release from the VLJ repository
International Nuclear Information System (INIS)
Vieno, T.; Valkiainen, M.
1992-01-01
The VLJ repository is an underground disposal facility located at the Olkiluoto nuclear power plant site on the west coast of Finland. The repository will house low (LLW) and intermediate level radioactive wastes (MLW) from the TVO I and TVO II BWR's and the spent fuel interim store at Olkiluoto. The disposal rooms have been excavated at a depth of 60... 100 meters in the crystalline bedrock. They consist of two rock silos - one for the LLW and the other for MLW. Low level waste is usually packed in steel drums and steel boxes. Medium level wastes consists of bituminized resins in steel drums. Wastes packages are emplaced in concrete boxes before transportation into the repository. Low level wastes are emplaced in the shotcreted rock silo where no backfilling will used. For medium level wastes, a separate silo of reinforced concrete has been constructed inside the rock silo. No backfilling will be used inside the concrete silo and an opening will be made in the lid of the concrete silo for gas release. The microbial degradation of low level wastes is the principle gas generation process in the repository. The gas transport though the bedrock covering the repository is evaluated with the help of ground water flow study. It is recommended that the shotcrete lining on the ceiling of the repository cavern is partly removed before the final sealing of the repository. Provided that dissipation of gases from the disposal cavern into the rock can been assured, the overall effects of gas generation on the long-term safety of the repository are insignificant. 10 refs., 6 figs
Wu, Wenfei; Li, Bafang; Hou, Hu; Zhang, Hongwei; Zhao, Xue
2017-12-13
A calcium-chelating peptide is considered to have the ability to improve calcium absorption. In this study, Pacific cod skin gelatin hydrolysates treated with trypsin for 120 min exhibited higher calcium-chelating activity. Sequential chromatography, involving hydroxyapatite affinity chromatography and reversed phase high performance liquid chromatography, was used for the purification of calcium-chelating peptides. Two novel peptides with the typical characteristics of collagen were sequenced as GDKGESGEAGER and GEKGEGGHR based on LC-HRMS/MS, which showed a high affinity to calcium. Calcium-peptide complexation was further characterized by ESI-MS (MS and MS/MS) and FTIR spectroscopy. The results showed that the complexation of the two peptides with calcium was conducted mainly at the ratio of 1 : 1. The amino terminal group and the peptide bond of the peptide backbone as well as the amino group of the lysine side chain and the carboxylate of the glutamate side chain were the possible calcium binding sites for the two peptides. Meanwhile, several amino acid side chain groups, including the hydroxyl (Ser) and carboxylate (Asp) of GDKGESGEAGER and the imine (His) of GEKGEGGHR, were crucial in the complexation. The arginine residue in GEKGEGGHR also participated in the calcium coordination. Additionally, several active fragments with calcium-chelating activity were obtained using MS/MS spectra, including GDKGESGEAGE, GEAGER, GEK, EKG and KGE. This study suggests that gelatin-derived peptides have the potential to be used as a calcium-chelating ingredient to combat calcium deficiency.
Post-closure radiation dose assessment for Yucca Mountain repository
International Nuclear Information System (INIS)
Jia Mingyan; Zhang Xiabin; Yang Chuncai
2006-01-01
A brief introduction of post-closure long-term radiation safety assessment results was represented for the yucca mountain high-level waste geographic disposal repository. In 1 million years after repository closure, for the higher temperature repository operating mode, the peak annual dose would be 150 millirem (120 millirem under the lower-temperature operating mode) to a reasonably maximally exposed individual approximately 18 kilometers (11 miles) from the repository. The analysis of a drilling intrusion event occurring at 30,000 years indicated a peak of the mean annual dose to the reasonably maximally exposed individual approximately 18 kilometers (11 miles) downstream of the repository would be 0.002 millirem. The analysis of an igneous activity scenario, including a volcanic eruption event and igneous intrusion event indicated a peak of the mean annual dose to the reasonably maximally exposed individual approximately 18 kilometers downstream of the repository would be 0.1 millirem. (authors)
Design of repository sealing systems - 1981
International Nuclear Information System (INIS)
Ellison, R.D.; Shukla, D.K.; Kelsall, P.C.; D'Appolonia Consulting Engineers, Albuquerque, NM)
1982-01-01
Isolating nuclear waste in geologic repositories will require the sealing of penetrations such as access shafts and tunnels, disposal rooms, and exploration boreholes. This paper discusses seal designs developed for a repository in bedded salt referenced to the stratigraphy of southeastern New Mexico. Designs are based on a multiple component concept whereby individual components are designed for a specific function and location. For a repository in salt the major function of the seals is to exclude groundwater inflow. Two main types of component are included for this purpose: (1) bulk-heads are dense concrete structures keyed into the walls of the penetration and are intended to reduce flow at the interface between the seal and the salt; (2) backfills are granular materials compacted in place in the penetration. In the repository the major backfill material is crushed salt, which is expected to consolidate and recrystallize as the rooms close in response to salt creep. Densely compacted clays will be used as backfill in the shafts closer to potential sources of water inflow. 22 references, 10 figures, 1 table
Creation of Data Repositories to Advance Nursing Science.
Perazzo, Joseph; Rodriguez, Margaret; Currie, Jackson; Salata, Robert; Webel, Allison R
2017-12-01
Data repositories are a strategy in line with precision medicine and big data initiatives, and are an efficient way to maximize data utility and form collaborative research relationships. Nurse researchers are uniquely positioned to make a valuable contribution using this strategy. The purpose of this article is to present a review of the benefits and challenges associated with developing data repositories, and to describe the process we used to develop and maintain a data repository in HIV research. Systematic planning, data collection, synthesis, and data sharing have enabled us to conduct robust cross-sectional and longitudinal analyses with more than 200 people living with HIV. Our repository building has also led to collaboration and training, both in and out of our organization. We present a pragmatic and affordable way that nurse scientists can build and maintain a data repository, helping us continue to make to our understanding of health phenomena.
Pfammatter, Sibylle; Bonneil, Eric; McManus, Francis P.; Thibault, Pierre
2018-04-01
The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines. Here, we exploited the unusual structure of SUMO peptides to facilitate their separation by high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the coverage of SUMO proteome analysis. Upon trypsin digestion, branched peptides contain a SUMO remnant side chain and predominantly form triply protonated ions that facilitate their gas-phase separation using FAIMS. We evaluated the mobility characteristics of synthetic SUMO peptides and further demonstrated the application of FAIMS to profile the changes in protein SUMOylation of HEK293 cells following heat shock, a condition known to affect this modification. FAIMS typically provided a 10-fold improvement of detection limit of SUMO peptides, and enabled a 36% increase in SUMO proteome coverage compared to the same LC-MS/MS analyses performed without FAIMS. [Figure not available: see fulltext.
Reducing Psychological Resistance to Digital Repositories
Directory of Open Access Journals (Sweden)
Brian Quinn
2010-06-01
Full Text Available The potential value of digital repositories is dependent on the cooperation of scholars to deposit their work. Although many researchers have been resistant to submitting their work, the literature on digital repositories contains very little research on the psychology of resistance. This article looks at the psychological literature on resistance and explores what its implications might be for reducing the resistance of scholars to submitting their work to digital repositories. Psychologists have devised many potentially useful strategies for reducing resistance that might be used to address the problem; this article examines these strategies and how they might be applied.
Augmenting interoperability across repositories architectural ideas
CERN. Geneva
2005-01-01
The aDORe digital repository architecture designed and implemented by the Los Alamos Research Library is fully standards-based and highly modular, with the various components of the architecture interacting in a protocol-driven manner. Although aDORe was designed for use in the context of the Los Alamos Library, its modular and standards-based design has led to interesting insights regarding possible new levels of interoperability in a federation of heterogeneous repositories. The presentation will discuss these insights, and will illustrate that attractive federations of repositories can be built by introducing rather basic interoperability requirements. The presentation will also show that, once these requirements are met, a powerful service framework that overlays the federation can emerge.
Executive-style briefings on selected repository design issues
International Nuclear Information System (INIS)
1978-01-01
This document is a collection of executive-style briefings on selected repository design issues. Most of the briefings discuss differences between the US repository design bases presented in US Working Draft on Repository Physical Descriptions in a Salt Formation, prepared in support of INFCE discussions of May 1978 and the FRG-Netherlands design bases, presented in Design Study of a Radioactive Waste Repository to be Mined in a Medium-Size Salt Dome by Hamstra and Velzeboer, Netherlands Energy Research Foundation, January 1978. Advantages and disadvantages of the two sets of design bases are discussed, and the impacts of adopting either of these bases on the other's programs and positions are identified
Anti-dengue virus serotype 2 activity and mode of action of a novel peptide.
Chew, M-F; Tham, H-W; Rajik, M; Sharifah, S H
2015-10-01
To identify a novel antiviral peptide against dengue virus serotype 2 (DENV-2) by screening a phage display peptide library and to evaluate its in vitro antiviral activity and mode of action. A phage display peptide library was biopanned against purified DENV-2 and resulted in the identification and selection of a peptide (peptide gg-ww) for further investigation. ELISA was performed, and peptide gg-ww was shown to possess the highest binding affinity against DENV-2. Thus, peptide gg-ww was synthesized for cytotoxicity and antiviral assays. Virus plaque reduction assay, real-time PCR and immunofluorescence assay were used to investigate the inhibitory effect of peptide gg-ww on DENV-2 infection in Vero cells. Three different assays (pre-, simultaneous and post-treatments assays) were performed to investigate the peptide's mode of action. Results indicated that peptide gg-ww possessed strong antiviral activity with a ~96% inhibition rate, which was achieved at 250 μmol l(-1) . Viral replication was inhibited during a simultaneous treatment assay, indicating that the entry of the virus was impeded by this peptide. Peptide gg-ww displayed antiviral action against DENV-2 by targeting an early stage of viral replication (i.e. during viral entry). Peptide gg-ww may represent a new therapeutic candidate for the treatment of DENV infections and is a potential candidate to be developed as a peptide drug. © 2015 The Society for Applied Microbiology.
Repository-analog experiments of nuclear waste leaching and migration
International Nuclear Information System (INIS)
Seitz, M.G.
1982-01-01
The potential for radionuclide migration from a breached nuclear-waste repository depends on the leaching and subsequent interaction of the leached radionuclides with materials in the groundwater flow path. An attempt is made to consider all interactions using experiments that integrate repository materials. Results of a repository-analog experiment using borosilicate glass, fissured granite, and flowing water suggest: (1) plutonium was immobile possibly because of its low solubility; (2) caesium migrated down slowly because of sorption; and (3) neptunium remained oxidized even in water of low oxidation potential. By summing the effects of all interactions, not just sorption, the repository-analog experiment produced radionuclide migration that could be expected from a breached repository. (author)
Novel T-cell epitopes of ovalbumin in BALB/c mouse: Potential for peptide-immunotherapy
International Nuclear Information System (INIS)
Yang, Marie; Mine, Yoshinori
2009-01-01
The identification of food allergen T-cell epitopes provides a platform for the development of novel immunotherapies. Despite extensive knowledge of the physicochemical properties of hen ovalbumin (OVA), a major egg allergen, the complete T-cell epitope map of OVA has surprisingly not been defined in the commonly used BALB/c mouse model. In this study, spleen cells obtained from OVA-sensitized mice were incubated in the presence of 12-mer overlapping synthetic peptides, constructed using the SPOTS synthesis method. Proliferative activity was assessed by 72-h in vitro assays with use of the tetrazolium salt WST-1 and led to identification of four mitogenic sequences, i.e., A39R50, S147R158, K263E274, and A329E340. ELISA analyses of interferon (IFN)-γ and interleukin (IL)-4 productions in cell culture supernatants upon stimulation with increasing concentrations of peptides confirmed their immunogenicity. Knowledge of the complete T-cell epitope map of OVA opens the way to a number of experimental investigations, including the exploration of peptide-based immunotherapy.
Prediction of monomer isomery in Florine: a workflow dedicated to nonribosomal peptide discovery.
Directory of Open Access Journals (Sweden)
Thibault Caradec
Full Text Available Nonribosomal peptides represent a large variety of natural active compounds produced by microorganisms. Due to their specific biosynthesis pathway through large assembly lines called NonRibosomal Peptide Synthetases (NRPSs, they often display complex structures with cycles and branches. Moreover they often contain non proteogenic or modified monomers, such as the D-monomers produced by epimerization. We investigate here some sequence specificities of the condensation (C and epimerization (E domains of NRPS that can be used to predict the possible isomeric state (D or L of each monomer in a putative peptide. We show that C- and E- domains can be divided into 2 sub-regions called Up-Seq and Down-Seq. The Up-Seq region corresponds to an InterPro domain (IPR001242 and is shared by C- and E-domains. The Down-Seq region is specific to the enzymatic activity of the domain. Amino-acid signatures (represented as sequence logos previously described for complete C-and E-domains have been restricted to the Down-Seq region and amplified thanks to additional sequences. Moreover a new Down-Seq signature has been found for Ct-domains found in fungi and responsible for terminal cyclization of the peptides. The identification of these signatures has been included in a workflow named Florine, aimed to predict nonribosomal peptides from NRPS sequence analyses. In some cases, the prediction of isomery is guided by genus-specific rules. Florine was used on a Pseudomonas genome to allow the determination of the type of pyoverdin produced, the update of syringafactin structure and the identification of novel putative products.
CERN. Geneva
2007-01-01
The impact of self-archiving on journals and publishers is an important topic for all those involved in scholarly communication. There is some evidence that the physics arXiv has had no impact on physics journals, while 'economic common sense' suggests that some impact is inevitable. I shall review recent studies of librarian attitudes towards repositories and journals, and place this in the context of IOP Publishing's experiences with arXiv. I shall offer some possible reasons for the mis-match between these perspectives and then discuss how IOP has linked with arXiv and experimented with OA publishing. As well as launching OA journals we have co-operated with Cornell and the arXiv on Eprintweb.org, a platform that offers new features to repository users. View Andrew Wray's biography
Milk derived bioactive peptides and their impact on human health – A review
Directory of Open Access Journals (Sweden)
D.P. Mohanty
2016-09-01
Full Text Available Milk-derived bioactive peptides have been identified as potential ingredients of health-promoting functional foods. These bioactive peptides are targeted at diet-related chronic diseases especially the non-communicable diseases viz., obesity, cardiovascular diseases and diabetes. Peptides derived from the milk of cow, goat, sheep, buffalo and camel exert multifunctional properties, including anti-microbial, immune modulatory, anti-oxidant, inhibitory effect on enzymes, anti-thrombotic, and antagonistic activities against various toxic agents. Majority of those regulate immunological, gastrointestinal, hormonal and neurological responses, thereby playing a vital role in the prevention of cancer, osteoporosis, hypertension and other disorders as discussed in this review. For the commercial production of such novel bioactive peptides large scale technologies based on membrane separation and ion exchange chromatography methods have been developed. Separation and identification of those peptides and their pharmacodynamic parameters are necessary to transfer their potent functional properties into food applications. The present review summarizes the preliminary classes of bioactive milk-derived peptides along with their physiological functions, general characteristics and potential applications in health-care.
Business models for digital repositories
CERN. Geneva; Bjørnshauge, Lars
2007-01-01
Those setting up, or planning to set up, a digital repository may be interested to know more about what has gone before them. What is involved, what is the cost, how many people are needed, how have others made the case to their institution, and how do you get anything into it once it is built? I have recently undertaken a study of European repository business models for the DRIVER project and will present an overview of the findings.
Waste package/repository impact study: Final report
Energy Technology Data Exchange (ETDEWEB)
1985-09-01
The Waste Package/Repository Impact Study was conducted to evaluate the feasibility of using the current reference salt waste package in the salt repository conceptual design. All elements of the repository that may impact waste package parameters, i.e., (size, weight, heat load) were evaluated. The repository elements considered included waste hoist feasibility, transporter and emplacement machine feasibility, subsurface entry dimensions, feasibility of emplacement configuration, and temperature limits. The evaluations are discussed in detail with supplemental technical data included in Appendices to this report, as appropriate. Results and conclusions of the evaluations are discussed in light of the acceptability of the current reference waste package as the basis for salt conceptual design. Finally, recommendations are made relative to the salt project position on the application of the reference waste package as a basis for future design activities. 31 refs., 11 figs., 11 tabs.
Waste package/repository impact study: Final report
International Nuclear Information System (INIS)
1985-09-01
The Waste Package/Repository Impact Study was conducted to evaluate the feasibility of using the current reference salt waste package in the salt repository conceptual design. All elements of the repository that may impact waste package parameters, i.e., (size, weight, heat load) were evaluated. The repository elements considered included waste hoist feasibility, transporter and emplacement machine feasibility, subsurface entry dimensions, feasibility of emplacement configuration, and temperature limits. The evaluations are discussed in detail with supplemental technical data included in Appendices to this report, as appropriate. Results and conclusions of the evaluations are discussed in light of the acceptability of the current reference waste package as the basis for salt conceptual design. Finally, recommendations are made relative to the salt project position on the application of the reference waste package as a basis for future design activities. 31 refs., 11 figs., 11 tabs
International Nuclear Information System (INIS)
Pentz, D.L.
1984-01-01
This paper discusses exploration objectives and requirements for a nuclear repository in the U.S.A. The importance of designing the exploration program to meet the system performance objectives is emphasized and some examples of the extent of exploration required before the License Application for Construction Authorization is granted are also discussed
The use of chimeric vimentin citrullinated peptides for the diagnosis of rheumatoid arthritis.
Malakoutikhah, Morteza; Gómara, María J; Gómez-Puerta, José A; Sanmartí, Raimon; Haro, Isabel
2011-11-10
Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes inflammation and, in many cases, destruction of the joints. To prevent progressive and irreversible structural damage, early diagnosis of RA is of paramount importance. The present study addresses the search of new RA citrullinated antigens that could supplement or complement diagnostic/prognostic existing tests. With this aim, the epitope anticitrullinated vimentin antibody response was mapped using synthetic peptides. To improve the sensitivity/specificity balance, a vimentin peptide that was selected, and its cyclic analogue, were combined with fibrin- and filaggrin-related peptides to render chimeric peptides. Our findings highlight the putative application of these chimeric peptides for the design of RA diagnosis systems and imply that more than one serological test is required to classify RA patients based on the presence or absence of ACPAs. Each of the target molecules reported here (fibrin, vimentin, filaggrin) has a specific utility in the identification of a particular subset of RA patients.
Learning frameworks as an alternative to repositories
DEFF Research Database (Denmark)
Dalsgaard, Christian
2005-01-01
This paper presents the concept of ‘learning frameworks’. The purpose of the paper is to discuss and question collections of digital learning objects in large repositories and to argue for large learning frameworks which organise a number of thematically related digital learning materials. Whereas...... a learning object repository contains all kinds of materials, a learning framework consists of an organisation of materials related to a common theme. Further, a repository consists of single, self-contained objects, whereas a learning framework is an open-ended environment which presents a number...
Findeisen, Peter; Thumfart, Jörg Oliver; Costina, Victor; Hofheinz, Ralf; Neumaier, Michael
2013-09-01
To determine the preanalytical quality of serum and plasma by monitoring the time-dependent ex vivo decay of a synthetic reporter peptide (RP) with liquid chromatography/mass spectrometry (LC/MS). Serum and plasma specimens were spiked with the RP and proteolytic fragments were monitored with LC/MS at different preanalytical time points ranging from 2 to 24 hours after blood withdrawal. The concentration of fragments changed in a time-dependent manner, and respective peptide profiles were used to classify specimens according to their preanalytical time span. Classification accuracy was high, with values always above 0.89 for areas under receiver operating characteristic curves. This "proteomics degradation clock" can be used to estimate the preanalytical quality of serum and plasma and might have impact on quality control procedures of biobanking repositories.
Status of Proposed Repository for Latin-American Spent Fuel
Energy Technology Data Exchange (ETDEWEB)
Ferrada, J.J.
2004-10-04
This report compiles preliminary information that supports the premise that a repository is needed in Latin America and analyzes the nuclear situation (mainly in Argentina and Brazil) in terms of nuclear capabilities, inventories, and regional spent-fuel repositories. The report is based on several sources and summarizes (1) the nuclear capabilities in Latin America and establishes the framework for the need of a permanent repository, (2) the International Atomic Energy Agency (IAEA) approach for a regional spent-fuel repository and describes the support that international institutions are lending to this issue, (3) the current situation in Argentina in order to analyze the Argentinean willingness to find a location for a deep geological repository, and (4) the issues involved in selecting a location for the repository and identifies a potential location. This report then draws conclusions based on an analysis of this information. The focus of this report is mainly on spent fuel and does not elaborate on other radiological waste sources.
Andromeda - a peptide search engine integrated into the MaxQuant environment
DEFF Research Database (Denmark)
Cox, Jurgen; Neuhauser, Nadin; Michalski, Annette
2011-01-01
A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data Andromeda performs as well as Mascot......, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly...... phosphorylated peptides and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination...
Gabbro as a host rock for a nuclear waste repository
International Nuclear Information System (INIS)
Ahlbom, K.; Leijon, B.; Smellie, J.; Liedholm, M.
1992-09-01
As an alternative to granitic rocks, gabbro and other basic rock types have been investigated with respect to their suitability to host a nuclear waste repository. The present report summarizes and examines existing geoscientific knowledge of relevance in assessing the potential merits of gabbro as a repository host rock. Implications in terms of site selection, repository construction and post-closure repository performance are also discussed. The objective of the study is to provide a basis for decisions as regards future consideration of the gabbro alternative. It is found that there are rather few gabbro bodies in Sweden, that are potentially of sufficient size to host a repository. Thus, gabbro offers little latitude as regards site selection. In comparison to siting a repository in granitic rocks, this is a major disadvantage, and it may in fact remove gabbro from further consideration. The potential advantages of gabbro refer to repository performance, and include low hydraulic conductivity and a chemical environment promoting efficient radionuclide retardation. However, results from field investigations show that groundwater flow in gabbro bodies is largely controlled by intersecting heterogeneities, in particular granitic dykes, that are significantly more conductive to water than the gabbro. In the far-field scale significant to repository performance, this may reduce or eliminate the potential effects of favourable hydraulic and chemical characteristics of the gabbro itself. In conclusion, there are apparent difficulties associated with siting a repository in gabbro, due to lack of sufficiently large gabbro bodies. On the basis of the present state of knowledge, no decisive differences can be demonstrated when comparing gabbro with granitic rocks, neither with respects to repository construction, nor as regards repository performance. (au)
Safety assessment methodology for waste repositories in deep geological formations
International Nuclear Information System (INIS)
Chapuis, A.M.; Lewi, J.; Pradel, J.; Queniart, D.; Raimbault, P.; Assouline, M.
1986-06-01
The long term safety of a nuclear waste repository relies on the evaluation of the doses which could be transferred to man in the future. This implies a detailed knowledge of the medium where the waste will be confined, the identification of the basic phenomena which govern the migration of the radionuclides and the investigation of all possible scenarios that may affect the integrity of the barriers between the waste and the biosphere. Inside the Institute of protection and nuclear safety of the French Atomic Energy Commission (CEA/IPSN), the Department of the Safety Analysis (DAS) is currently developing a methodology for assessing the safety of future geological waste repositories, and is in charge of the modelling development, while the Department of Technical Protection (DPT) is in charge of the geological experimental studies. Both aspects of this program are presented. The methodology for risk assessment stresses the needs for coordination between data acquisition and model development which should result in the obtention of an efficient tool for safety evaluation. Progress needs to be made in source and geosphere modelling. Much more sophisticated models could be used than the ones which is described; however sensitivity analysis will determine the level of sophistication which is necessary to implement. Participation to international validation programs are also very important for gaining confidence in the approaches which have been chosen
Design and production of the KBS-3 repository
International Nuclear Information System (INIS)
Moren, Lena
2010-12-01
The report contains the common basis for a set of Production reports, presenting how the KBS-3 repository is designed, produced and inspected. The set of reports is included in the safety report for the KBS-3 repository and repository facility. The report presents the role of the Production reports within the safety report and their common purposes and objectives. An important part of the report is to present the background and sources to the principles to be applied in the design, the functions of the KBS-3 repository and the barrier functions the engineered barriers and rock. Further, the methodology to substantiate detailed design premises for the engineered barriers, underground openings and other parts of the KBS-3 repository is presented. The report also gives an overview of the KBS-3 system and its facilities and the production lines for the spent fuel, the engineered barriers and underground openings. Finally, an introduction to quality management, safety classification and their application is given
Design and production of the KBS-3 repository
Energy Technology Data Exchange (ETDEWEB)
Moren, Lena
2010-12-15
The report contains the common basis for a set of Production reports, presenting how the KBS-3 repository is designed, produced and inspected. The set of reports is included in the safety report for the KBS-3 repository and repository facility. The report presents the role of the Production reports within the safety report and their common purposes and objectives. An important part of the report is to present the background and sources to the principles to be applied in the design, the functions of the KBS-3 repository and the barrier functions the engineered barriers and rock. Further, the methodology to substantiate detailed design premises for the engineered barriers, underground openings and other parts of the KBS-3 repository is presented. The report also gives an overview of the KBS-3 system and its facilities and the production lines for the spent fuel, the engineered barriers and underground openings. Finally, an introduction to quality management, safety classification and their application is given
Energy Technology Data Exchange (ETDEWEB)
Sun Xiaonan [Department of Radiation Oncology, Sir Run Run Shaw Hospital, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou (China); Yang Chunying [Department of Radiation Oncology, Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX (United States); Liu Hai; Wang Qi [Department of Radiation Oncology, Sir Run Run Shaw Hospital, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou (China); Wu Shixiu [Department of Radiation Oncology, The First Affiliated Hospital of Wenzhou Medical College, Wenzhou (China); Li Xia; Xie Tian [Research Center of Biomedicine and Health, Hangzhou Normal University, Hangzhou (China); Brinkman, Kathryn L.; Teh, Bin S.; Butler, E. Brian [Department of Radiation Oncology, Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX (United States); Xu Bo, E-mail: bxu@tmhs.org [Department of Radiation Oncology, Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX (United States); Zheng, Shu, E-mail: zhengshu@zju.edu.cn [Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou (China)
2012-12-01
Purpose: The DNA protein kinase catalytic subunit (DNA-PKcs) is one of the critical elements involved in the DNA damage repair process. Inhibition of DNA-PKcs results in hypersensitivity to ionizing radiation (IR); therefore, this approach has been explored to develop molecular targeted radiosensitizers. Here, we aimed to develop small inhibitory peptides that could specifically target DNA-PKcs autophosphorylation, a critical step for the enzymatic activation of the kinase in response to IR. Methods and Materials: We generated several small fusion peptides consisting of 2 functional domains, 1 an internalization domain and the other a DNA-PKcs autophosphorylation inhibitory domain. We characterized the internalization, toxicity, and radiosensitization activities of the fusion peptides. Furthermore, we studied the mechanisms of the inhibitory peptides on DNA-PKcs autophosphorylation and DNA repair. Results: We found that among several peptides, the biotin-labeled peptide 3 (BTW3) peptide, which targets DNA-PKcs threonine 2647 autophosphorylation, can abrogate IR-induced DNA-PKcs activation and cause prolonged {gamma}-H2AX focus formation. We demonstrated that BTW3 exposure led to hypersensitivity to IR in DNA-PKcs-proficient cells but not in DNA-PKcs-deficient cells. Conclusions: The small inhibitory peptide BTW3 can specifically target DNA-PKcs autophosphorylation and enhance radiosensitivity; therefore, it can be further developed as a novel class of radiosensitizer.
International Nuclear Information System (INIS)
Sun Xiaonan; Yang Chunying; Liu Hai; Wang Qi; Wu Shixiu; Li Xia; Xie Tian; Brinkman, Kathryn L.; Teh, Bin S.; Butler, E. Brian; Xu Bo; Zheng, Shu
2012-01-01
Purpose: The DNA protein kinase catalytic subunit (DNA-PKcs) is one of the critical elements involved in the DNA damage repair process. Inhibition of DNA-PKcs results in hypersensitivity to ionizing radiation (IR); therefore, this approach has been explored to develop molecular targeted radiosensitizers. Here, we aimed to develop small inhibitory peptides that could specifically target DNA-PKcs autophosphorylation, a critical step for the enzymatic activation of the kinase in response to IR. Methods and Materials: We generated several small fusion peptides consisting of 2 functional domains, 1 an internalization domain and the other a DNA-PKcs autophosphorylation inhibitory domain. We characterized the internalization, toxicity, and radiosensitization activities of the fusion peptides. Furthermore, we studied the mechanisms of the inhibitory peptides on DNA-PKcs autophosphorylation and DNA repair. Results: We found that among several peptides, the biotin-labeled peptide 3 (BTW3) peptide, which targets DNA-PKcs threonine 2647 autophosphorylation, can abrogate IR-induced DNA-PKcs activation and cause prolonged γ-H2AX focus formation. We demonstrated that BTW3 exposure led to hypersensitivity to IR in DNA-PKcs-proficient cells but not in DNA-PKcs-deficient cells. Conclusions: The small inhibitory peptide BTW3 can specifically target DNA-PKcs autophosphorylation and enhance radiosensitivity; therefore, it can be further developed as a novel class of radiosensitizer.
Wilson, Karl A.; Tan-Wilson, Anna
2013-01-01
Mass spectrometry (MS) has become an important tool in studying biological systems. One application is the identification of proteins and peptides by the matching of peptide and peptide fragment masses to the sequences of proteins in protein sequence databases. Often prior protein separation of complex protein mixtures by 2D-PAGE is needed,…
10 CFR 51.67 - Environmental information concerning geologic repositories.
2010-01-01
... 10 Energy 2 2010-01-01 2010-01-01 false Environmental information concerning geologic repositories... information concerning geologic repositories. (a) In lieu of an environmental report, the Department of Energy... connection with any geologic repository developed under Subtitle A of Title I, or under Title IV, of the...
Rudashevskaya, Elena L; Breitwieser, Florian P; Huber, Marie L; Colinge, Jacques; Müller, André C; Bennett, Keiryn L
2013-02-05
The identification and validation of cross-linked peptides by mass spectrometry remains a daunting challenge for protein-protein cross-linking approaches when investigating protein interactions. This includes the fragmentation of cross-linked peptides in the mass spectrometer per se and following database searching, the matching of the molecular masses of the fragment ions to the correct cross-linked peptides. The hybrid linear trap quadrupole (LTQ) Orbitrap Velos combines the speed of the tandem mass spectrometry (MS/MS) duty circle with high mass accuracy, and these features were utilized in the current study to substantially improve the confidence in the identification of cross-linked peptides. An MS/MS method termed multiple and sequential data acquisition method (MSDAM) was developed. Preliminary optimization of the MS/MS settings was performed with a synthetic peptide (TP1) cross-linked with bis[sulfosuccinimidyl] suberate (BS(3)). On the basis of these results, MSDAM was created and assessed on the BS(3)-cross-linked bovine serum albumin (BSA) homodimer. MSDAM applies a series of multiple sequential fragmentation events with a range of different normalized collision energies (NCE) to the same precursor ion. The combination of a series of NCE enabled a considerable improvement in the quality of the fragmentation spectra for cross-linked peptides, and ultimately aided in the identification of the sequences of the cross-linked peptides. Concurrently, MSDAM provides confirmatory evidence from the formation of reporter ions fragments, which reduces the false positive rate of incorrectly assigned cross-linked peptides.
Conceptual design of repository facilities
International Nuclear Information System (INIS)
Beale, H.; Engelmann, H.J.; Souquet, G.; Mayence, M.; Hamstra, J.
1980-01-01
As part of the European Economic Communities programme of research into underground disposal of radioactive wastes repository design studies have been carried out for application in salt deposits, argillaceous formations and crystalline rocks. In this paper the design aspects of repositories are reviewed and conceptual designs are presented in relation to the geological formations under consideration. Emphasis has been placed on the disposal of vitrified high level radioactive wastes although consideration has been given to other categories of radioactive waste
GreyGuide Forum and Repository
Biagioni, Stefania; Farace, Dominic
2014-01-01
We present the GreyGuide: an online forum and repository of good practice in the field of grey literature. The launch of the GreyGuide Repository took place in December 2013 at the Fifteenth International Conference on Grey Literature. Since then, the acquisition of both proposed and published good practices are underway. The GreyGuide as an online forum is currently in a developmental stage and is influenced by the changes that have taken place in GreyNet's new infrastructure commencing in J...
Characterizing Peptide Neutral Losses Induced by Negative Electron-Transfer Dissociation (NETD)
Rumachik, Neil G.; McAlister, Graeme C.; Russell, Jason D.; Bailey, Derek J.; Wenger, Craig D.; Coon, Joshua J.
2012-01-01
We implemented negative electron-transfer dissociation (NETD) on a hybrid ion trap/Orbitrap mass spectrometer to conduct ion/ion reactions using peptide anions and radical reagent cations. In addition to sequence-informative ladders of a•- and x-type fragment ions, NETD generated intense neutral loss peaks corresponding to the entire or partial side-chain cleavage from amino acids constituting a given peptide. Thus, a critical step towards the characterization of this recently introduced fragmentation technique is a systematic study of synthetic peptides to identify common neutral losses and preferential fragmentation pathways. Examining 46 synthetic peptides with high mass accuracy and high resolution analysis permitted facile determination of the chemical composition of each neutral loss. We identified 19 unique neutral losses from 14 amino acids and three modified amino acids, and assessed the specificity and sensitivity of each neutral loss using a database of 1542 confidently identified peptides generated from NETD shotgun experiments employing high-pH separations and negative electrospray ionization. As residue-specific neutral losses indicate the presence of certain amino acids, we determined that many neutral losses have potential diagnostic utility. We envision this catalogue of neutral losses being incorporated into database search algorithms to improve peptide identification specificity and to further advance characterization of the acidic proteome. PMID:22290482
LESSONS IN DE NOVO PEPTIDE SEQUENCING BY TANDEM MASS SPECTROMETRY
Medzihradszky, Katalin F.; Chalkley, Robert J.
2015-01-01
Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are “translated” into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general. PMID:25667941
Ventilation System Strategy for a Prospective Korean Radioactive Waste Repository
International Nuclear Information System (INIS)
Kim, Jin; Kwon, Sang Ki
2005-01-01
In the stage of conceptual design for the construction and operation of the geologic repository for radioactive wastes, it is important to consider a repository ventilation system which serves the repository working environment, hygiene and safety of the public at large, and will allow safe maintenance like moisture content elimination in repository for the duration of the repositories life, construction/operation/closure, also allowing safe waste transportation and emplacement. This paper describes the possible ventilation system design criteria and requirements for the prospective Korean radioactive waste repositories with emphasis on the underground rock cavity disposal method in the both cases of low and medium-level and high-level wastes. It was found that the most important concept is separate ventilation systems for the construction (development) and waste emplacement (storage) activities. In addition, ventilation network system modeling, natural ventilation, ventilation monitoring systems and real time ventilation simulation, and fire simulation and emergency system in the repository are briefly discussed.
Identification of novel selective V2 receptor non-peptide agonists.
Del Tredici, Andria L; Vanover, Kim E; Knapp, Anne E; Bertozzi, Sine M; Nash, Norman R; Burstein, Ethan S; Lameh, Jelveh; Currier, Erika A; Davis, Robert E; Brann, Mark R; Mohell, Nina; Olsson, Roger; Piu, Fabrice
2008-10-30
Peptides with agonist activity at the vasopressin V(2) receptor are used clinically to treat fluid homeostasis disorders such as polyuria and central diabetes insipidus. Of these peptides, the most commonly used is desmopressin, which displays poor bioavailability as well as potent activity at the V(1b) receptor, with possible stress-related adverse effects. Thus, there is a strong need for the development of small molecule chemistries with selective V(2) receptor agonist activity. Using the functional cell-based assay Receptor Selection and Amplification Technology (R-SAT((R))), a screening effort identified three small molecule chemotypes (AC-94544, AC-88324, and AC-110484) with selective agonist activity at the V(2) receptor. One of these compounds, AC-94544, displayed over 180-fold selectivity at the V(2) receptor compared to related vasopressin and oxytocin receptors and no activity at 28 other G protein-coupled receptors (GPCRs). All three compounds also showed partial agonist activity at the V(2) receptor in a cAMP accumulation assay. In addition, in a rat model of central diabetes insipidus, AC-94544 was able to significantly reduce urine output in a dose-dependent manner. Thus, AC-94544, AC-88324, and AC-110484 represent novel opportunities for the treatment of disorders associated with V(2) receptor agonist deficiency.
Types of safety assessments of near surface repository for radioactive waste
International Nuclear Information System (INIS)
Mateeva, M.
2004-01-01
The purpose of this article is to presents the classification of different types safety assessments of near surface repository for low and intermediate level radioactive waste substantiated with results of safety assessments generated in Bulgaria. The different approach of safety assessments applied for old existing repository as well as for site selection for construction new repository is outlined. The regulatory requirements in Bulgaria define three main types of assessments: Safety assessment; Technical substation of repository safety; Assessment of repository influence on environment that is in form of report prepared from the Ministry of environment and waters on the base of results obtained in two first types of assessments. Additionally first type is subdivided in three categories - preliminary safety assessment, safety assessment and post closure safety assessment, which are generated using deterministic approach. The technical substation of repository safety is generated using probabilistic approach. Safety assessment results that are presented here are based on evaluation of existing old repository type 'Radon' in Novi Han and real site selection procedure for new near surface repository for low and intermediate level radioactive waste from nuclear power station in Kozloduy. The important role of safety assessment for improvement the repository safety as well as for repository licensing, correct site selection and right choice of engineer barriers and repository design is discussed using generated results. (author)
Data Stewardship: Environmental Data Curation and a Web-of-Repositories
Directory of Open Access Journals (Sweden)
Karen S. Baker
2009-10-01
Full Text Available Scientific researchers today frequently package measurements and associated metadata as digital datasets in anticipation of storage in data repositories. Through the lens of environmental data stewardship, we consider the data repository as an organizational element central to data curation. One aspect of non-commercial repositories, their distance-from-origin of the data, is explored in terms of near and remote categories. Three idealized repository types are distinguished – local, center, and archive - paralleling research, resource, and reference collection categories respectively. Repository type characteristics such as scope, structure, and goals are discussed. Repository similarities in terms of roles, activities and responsibilities are also examined. Data stewardship is related to care of research data and responsible scientific communication supported by an infrastructure that coordinates curation activities; data curation is defined as a set of repeated and repeatable activities focusing on tending data and creating data products within a particular arena. The concept of “sphere-of-context” is introduced as an aid to distinguishing repository types. Conceptualizing a “web-of-repositories” accommodates a variety of repository types and represents an ecologically inclusive approach to data curation.
A theoretical justification for single molecule peptide sequencing.
Directory of Open Access Journals (Sweden)
Jagannath Swaminathan
2015-02-01
Full Text Available The proteomes of cells, tissues, and organisms reflect active cellular processes and change continuously in response to intracellular and extracellular cues. Deep, quantitative profiling of the proteome, especially if combined with mRNA and metabolite measurements, should provide an unprecedented view of cell state, better revealing functions and interactions of cell components. Molecular diagnostics and biomarker discovery should benefit particularly from the accurate quantification of proteomes, since complex diseases like cancer change protein abundances and modifications. Currently, shotgun mass spectrometry is the primary technology for high-throughput protein identification and quantification; while powerful, it lacks high sensitivity and coverage. We draw parallels with next-generation DNA sequencing and propose a strategy, termed fluorosequencing, for sequencing peptides in a complex protein sample at the level of single molecules. In the proposed approach, millions of individual fluorescently labeled peptides are visualized in parallel, monitoring changing patterns of fluorescence intensity as N-terminal amino acids are sequentially removed, and using the resulting fluorescence signatures (fluorosequences to uniquely identify individual peptides. We introduce a theoretical foundation for fluorosequencing and, by using Monte Carlo computer simulations, we explore its feasibility, anticipate the most likely experimental errors, quantify their potential impact, and discuss the broad potential utility offered by a high-throughput peptide sequencing technology.
Harvesting NASA's Common Metadata Repository
Shum, D.; Mitchell, A. E.; Durbin, C.; Norton, J.
2017-12-01
As part of NASA's Earth Observing System Data and Information System (EOSDIS), the Common Metadata Repository (CMR) stores metadata for over 30,000 datasets from both NASA and international providers along with over 300M granules. This metadata enables sub-second discovery and facilitates data access. While the CMR offers a robust temporal, spatial and keyword search functionality to the general public and international community, it is sometimes more desirable for international partners to harvest the CMR metadata and merge the CMR metadata into a partner's existing metadata repository. This poster will focus on best practices to follow when harvesting CMR metadata to ensure that any changes made to the CMR can also be updated in a partner's own repository. Additionally, since each partner has distinct metadata formats they are able to consume, the best practices will also include guidance on retrieving the metadata in the desired metadata format using CMR's Unified Metadata Model translation software.
Bottino, Carolina G; Gomes, Luciano P; Pereira, José B; Coura, José R; Provance, David William; De-Simone, Salvatore G
2013-12-03
The identification of epitopes in proteins recognized by medically relevant antibodies is useful for the development of peptide-based diagnostics and vaccines. In this study, epitopes in the cytoplasmic repetitive antigen (CRA) and flagellar repetitive antigen (FRA) proteins from Trypanosoma cruzi were identified using synthetic peptide techniques and pooled sera from Chagasic patients. The epitopes were further assayed with an ELISA assay based on synthetic peptides. Twenty-two overlapping synthetic peptides representing the coding sequence of the T. cruzi CRA and FRA proteins were assessed by a Spot-synthesis array analysis using sera donated by patients with Chagas disease. Shorter peptides were selected that represented the determined epitopes and synthesized by solid phase synthesis to evaluate the patterns of cross-reactivities and discrimination through an ELISA-diagnostic assay. The peptide Spot-synthesis array successfully identified two IgG antigenic determinants in the CRA protein and four in FRA. Bioinformatics suggested that the CRA antigens were unique to T. cruzi while the FRA antigen showed similarity with sequences present within various proteins from Leishmania sp. Subsequently, shorter peptides representing the CRA-1, CRA-2 and FRA-1 epitopes were synthesized by solid phase synthesis and assayed by an ELISA-diagnostic assay. The CRA antigens gave a high discrimination between Chagasic, Leishmaniasis and T. cruzi-uninfected serum. A sensitivity and specificity of 100% was calculated for CRA. While the FRA antigen showed a slightly lower sensitivity (91.6%), its specificity was only 60%. The epitopes recognized by human anti-T. cruzi antibodies have been precisely located in two biomarkers of T. cruzi, CRA and FRA. The results from screening a panel of patient sera through an ELISA assay based on peptides representing these epitopes strongly suggest that the sequences from CRA would be useful for the development of diagnostic reagents that could
Core Certification of Data Repositories: Trustworthiness and Long-Term Stewardship
de Sherbinin, A. M.; Mokrane, M.; Hugo, W.; Sorvari, S.; Harrison, S.
2017-12-01
Scientific integrity and norms dictate that data created and used by scientists should be managed, curated, and archived in trustworthy data repositories thus ensuring that science is verifiable and reproducible while preserving the initial investment in collecting data. Research stakeholders including researchers, science funders, librarians, and publishers must also be able to establish the trustworthiness of data repositories they use to confirm that the data they submit and use remain useful and meaningful in the long term. Data repositories are increasingly recognized as a key element of the global research infrastructure and the importance of establishing their trustworthiness is recognised as a prerequisite for efficient scientific research and data sharing. The Core Trustworthy Data Repository Requirements are a set of universal requirements for certification of data repositories at the core level (see: https://goo.gl/PYsygW). They were developed by the ICSU World Data System (WDS: www.icsu-wds.org) and the Data Seal of Approval (DSA: www.datasealofapproval.org)—the two authoritative organizations responsible for the development and implementation of this standard to be further developed under the CoreTrustSeal branding . CoreTrustSeal certification of data repositories involves a minimally intensive process whereby repositories supply evidence that they are sustainable and trustworthy. Repositories conduct a self-assessment which is then reviewed by community peers. Based on this review CoreTrustSeal certification is granted by the CoreTrustSeal Standards and Certification Board. Certification helps data communities—producers, repositories, and consumers—to improve the quality and transparency of their processes, and to increase awareness of and compliance with established standards. This presentation will introduce the CoreTrustSeal certification requirements for repositories and offer an opportunity to discuss ways to improve the contribution of
United States Crystalline Repository Project - key research areas
International Nuclear Information System (INIS)
Patera, E.S.
1986-01-01
The Crystalline Repository Project is responsible for siting the second high-level nuclear waste repository in crystalline rock for the US Department of Energy. A methodology is being developed to define data and information needs and a way to evaluate that information. The areas of research the Crystalline Repository Project is involved in include fluid flow in a fractured network, coupled thermal, chemical and flow processes and cooperation in other nations and OECD research programs
Towards Content Development For Institutional Digital Repository ...
African Journals Online (AJOL)
The growth in Information and Communication Technology has lead to the emergence of Institutional Digital Repository, a digital archive for the preservation and dissemination of institutional research outputs. Institutional Digital Repositories make possible global dissemination of research outputs through the use of the ...
Groundwater flow modelling of an abandoned partially open repository
Energy Technology Data Exchange (ETDEWEB)
Bockgaard, Niclas (Golder Associates AB (Sweden))
2010-12-15
As a part of the license application, according to the nuclear activities act, for a final repository for spent nuclear fuel at Forsmark, the Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken a series of groundwater flow modelling studies. These represent time periods with different hydraulic conditions and the simulations carried out contribute to the overall evaluation of the repository design and long-term radiological safety. The modelling study presented here serves as an input for analyses of so-called future human actions that may affect the repository. The objective of the work was to investigate the hydraulic influence of an abandoned partially open repository. The intention was to illustrate a pessimistic scenario of the effect of open tunnels in comparison to the reference closure of the repository. The effects of open tunnels were studied for two situations with different boundary conditions: A 'temperate' case with present-day boundary conditions and a generic future 'glacial' case with an ice sheet covering the repository. The results were summarized in the form of analyses of flow in and out from open tunnels, the effect on hydraulic head and flow in the surrounding rock volume, and transport performance measures of flow paths from the repository to surface
Groundwater flow modelling of an abandoned partially open repository
International Nuclear Information System (INIS)
Bockgaard, Niclas
2010-12-01
As a part of the license application, according to the nuclear activities act, for a final repository for spent nuclear fuel at Forsmark, the Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken a series of groundwater flow modelling studies. These represent time periods with different hydraulic conditions and the simulations carried out contribute to the overall evaluation of the repository design and long-term radiological safety. The modelling study presented here serves as an input for analyses of so-called future human actions that may affect the repository. The objective of the work was to investigate the hydraulic influence of an abandoned partially open repository. The intention was to illustrate a pessimistic scenario of the effect of open tunnels in comparison to the reference closure of the repository. The effects of open tunnels were studied for two situations with different boundary conditions: A 'temperate' case with present-day boundary conditions and a generic future 'glacial' case with an ice sheet covering the repository. The results were summarized in the form of analyses of flow in and out from open tunnels, the effect on hydraulic head and flow in the surrounding rock volume, and transport performance measures of flow paths from the repository to surface
Current Status of Deep Geological Repository Development
International Nuclear Information System (INIS)
Budnitz, R J
2005-01-01
This talk provided an overview of the current status of deep-geological-repository development worldwide. Its principal observation is that a broad consensus exists internationally that deep-geological disposal is the only long-term solution for disposition of highly radioactive nuclear waste. Also, it is now clear that the institutional and political aspects are as important as the technical aspects in achieving overall progress. Different nations have taken different approaches to overall management of their highly radioactive wastes. Some have begun active programs to develop a deep repository for permanent disposal: the most active such programs are in the United States, Sweden, and Finland. Other countries (including France and Russia) are still deciding on whether to proceed quickly to develop such a repository, while still others (including the UK, China, Japan) have affirmatively decided to delay repository development for a long time, typically for a generation of two. In recent years, a major conclusion has been reached around the world that there is very high confidence that deep repositories can be built, operated, and closed safely and can meet whatever safety requirements are imposed by the regulatory agencies. This confidence, which has emerged in the last few years, is based on extensive work around the world in understanding how repositories behave, including both the engineering aspects and the natural-setting aspects, and how they interact together. The construction of repositories is now understood to be technically feasible, and no major barriers have been identified that would stand in the way of a successful project. Another major conclusion around the world is that the overall cost of a deep repository is not as high as some had predicted or feared. While the actual cost will not be known in detail until the costs are incurred, the general consensus is that the total life-cycle cost will not exceed a few percent of the value of the
Earthquakes - a danger to deep-lying repositories?
International Nuclear Information System (INIS)
2012-03-01
This booklet issued by the Swiss National Cooperative for the Disposal of Radioactive Waste NAGRA takes a look at geological factors concerning earthquakes and the safety of deep-lying repositories for nuclear waste. The geological processes involved in the occurrence of earthquakes are briefly looked at and the definitions for magnitude and intensity of earthquakes are discussed. Examples of damage caused by earthquakes are given. The earthquake situation in Switzerland is looked at and the effects of earthquakes on sub-surface structures and deep-lying repositories are discussed. Finally, the ideas proposed for deep-lying geological repositories for nuclear wastes are discussed
Stream-simulation experiments for waste-repository investigations
International Nuclear Information System (INIS)
Seitz, M.G.
1980-01-01
The potential for radionuclide migration by groundwater flow from a breached-water repository depends on the leaching process and on chemical changes that might occur as the radionuclide moves away from the repository. Therefore, migration involves the interactions of leached species with (1) the waste and canister, (2) the engineered barrier, and (3) the geologic materials surrounding the repository. Rather than attempt to synthesize each species and study it individually, another approach is to integrate all species and interactions using stream-simulation experiments. Interactions identified in these studies can then be investigated in detail in simpler experiments
Protein interaction networks by proteome peptide scanning.
Directory of Open Access Journals (Sweden)
Christiane Landgraf
2004-01-01
Full Text Available A substantial proportion of protein interactions relies on small domains binding to short peptides in the partner proteins. Many of these interactions are relatively low affinity and transient, and they impact on signal transduction. However, neither the number of potential interactions mediated by each domain nor the degree of promiscuity at a whole proteome level has been investigated. We have used a combination of phage display and SPOT synthesis to discover all the peptides in the yeast proteome that have the potential to bind to eight SH3 domains. We first identified the peptides that match a relaxed consensus, as deduced from peptides selected by phage display experiments. Next, we synthesized all the matching peptides at high density on a cellulose membrane, and we probed them directly with the SH3 domains. The domains that we have studied were grouped by this approach into five classes with partially overlapping specificity. Within the classes, however, the domains display a high promiscuity and bind to a large number of common targets with comparable affinity. We estimate that the yeast proteome contains as few as six peptides that bind to the Abp1 SH3 domain with a dissociation constant lower than 100 microM, while it contains as many as 50-80 peptides with corresponding affinity for the SH3 domain of Yfr024c. All the targets of the Abp1 SH3 domain, identified by this approach, bind to the native protein in vivo, as shown by coimmunoprecipitation experiments. Finally, we demonstrate that this strategy can be extended to the analysis of the entire human proteome. We have developed an approach, named WISE (whole interactome scanning experiment, that permits rapid and reliable identification of the partners of any peptide recognition module by peptide scanning of a proteome. Since the SPOT synthesis approach is semiquantitative and provides an approximation of the dissociation constants of the several thousands of interactions that are
Federated repositories of X-ray diffraction images.
Androulakis, Steve; Schmidberger, Jason; Bate, Mark A; DeGori, Ross; Beitz, Anthony; Keong, Cyrus; Cameron, Bob; McGowan, Sheena; Porter, Corrine J; Harrison, Andrew; Hunter, Jane; Martin, Jennifer L; Kobe, Bostjan; Dobson, Renwick C J; Parker, Michael W; Whisstock, James C; Gray, Joan; Treloar, Andrew; Groenewegen, David; Dickson, Neil; Buckle, Ashley M
2008-07-01
There is a pressing need for the archiving and curation of raw X-ray diffraction data. This information is critical for validation, methods development and improvement of archived structures. However, the relatively large size of these data sets has presented challenges for storage in a single worldwide repository such as the Protein Data Bank archive. This problem can be avoided by using a federated approach, where each institution utilizes its institutional repository for storage, with a discovery service overlaid. Institutional repositories are relatively stable and adequately funded, ensuring persistence. Here, a simple repository solution is described, utilizing Fedora open-source database software and data-annotation and deposition tools that can be deployed at any site cheaply and easily. Data sets and associated metadata from federated repositories are given a unique and persistent handle, providing a simple mechanism for search and retrieval via web interfaces. In addition to ensuring that valuable data is not lost, the provision of raw data has several uses for the crystallographic community. Most importantly, structure determination can only be truly repeated or verified when the raw data are available. Moreover, the availability of raw data is extremely useful for the development of improved methods of image analysis and data processing.
International Nuclear Information System (INIS)
Bunnell, L.R.; Shade, J.W.
1987-03-01
Packing materials should be included in waste package design for a high-level nuclear waste repository in salt. A packing material barrier would increase confidence in the waste package by alleviating possible shortcomings in the present design and prolonging confinement capabilities. Packing materials have been studied for uses in other geologic repositories; appropriately chosen, they would enhance the confinement capabilities of salt repository waste packages in several ways. Benefits of packing materials include retarding or chemically modifying brines to reduce corrosion of the waste package, providing good thermal conductivity between the waste package and host rock, retarding or absorbing radionuclides, and reducing the massiveness of the waste package. These benefits are available at low percentage of total repository cost, if the packing material is properly chosen and used. Several candidate materials are being considered, including oxides, hydroxides, silicates, cement-based mixtures, and clay mixtures. 18 refs
Representation of an open repository in groundwater flow models
International Nuclear Information System (INIS)
Painter, Scott; Sun, Alexander
2005-08-01
The effect of repository tunnels on groundwater flow has been identified as a potential issue for the nuclear waste repository being considered by SKB for a fractured granite formation in Sweden. In particular, the following pre-closure and post-closure processes have been identified as being important: inflows into open tunnels as functions of estimated grouting efficiencies, drawdown of the water table in the vicinity of the repository, upcoming of saline water, 'turnover' of surface water in the upper bedrock, and resaturation of backfilled tunnels following repository closure. The representation of repository tunnels within groundwater models is addressed in this report. The primary focus is on far-field flow that is modeled with a continuum porous medium approximation. Of particular interest are the consequences of the tunnel representation on the transient response of the groundwater system to repository operations and repository closure, as well as modeling issues such as how the water-table free surface and the coupling to near-surface hydrogeology should be handled. The overall objectives are to understand the consequences of current representations and to identify appropriate approximations for representing open tunnels in future groundwater modeling studies. The following conclusions can be drawn from the results of the simulations: 1. Two-phase flow may be induced in the vicinity of repository tunnels during repository pre-closure operations, but the formation of a two-phase flow region will not significantly affect far-field flow or inflows into tunnels. 2. The water table will be drawn down to the repository horizon and tunnel inflows will reach a steady-state value within about 5 years. 3. Steady-state inflows at the repository edge are estimated to be about 250 m 3 /year per meter of tunnel. Inflows will be greater during the transient de-watering period and less for tunnel locations closer to the repository center. 4. Significant amounts of water
Representation of an open repository in groundwater flow models
Energy Technology Data Exchange (ETDEWEB)
Painter, Scott; Sun, Alexander [Southwest Research Inst., San Antonio, TX (United States). Center for Nuclear Waste Regulatory Analyses
2005-08-01
The effect of repository tunnels on groundwater flow has been identified as a potential issue for the nuclear waste repository being considered by SKB for a fractured granite formation in Sweden. In particular, the following pre-closure and post-closure processes have been identified as being important: inflows into open tunnels as functions of estimated grouting efficiencies, drawdown of the water table in the vicinity of the repository, upcoming of saline water, 'turnover' of surface water in the upper bedrock, and resaturation of backfilled tunnels following repository closure. The representation of repository tunnels within groundwater models is addressed in this report. The primary focus is on far-field flow that is modeled with a continuum porous medium approximation. Of particular interest are the consequences of the tunnel representation on the transient response of the groundwater system to repository operations and repository closure, as well as modeling issues such as how the water-table free surface and the coupling to near-surface hydrogeology should be handled. The overall objectives are to understand the consequences of current representations and to identify appropriate approximations for representing open tunnels in future groundwater modeling studies. The following conclusions can be drawn from the results of the simulations: 1. Two-phase flow may be induced in the vicinity of repository tunnels during repository pre-closure operations, but the formation of a two-phase flow region will not significantly affect far-field flow or inflows into tunnels. 2. The water table will be drawn down to the repository horizon and tunnel inflows will reach a steady-state value within about 5 years. 3. Steady-state inflows at the repository edge are estimated to be about 250 m{sup 3}/year per meter of tunnel. Inflows will be greater during the transient de-watering period and less for tunnel locations closer to the repository center. 4. Significant
The industrial organization of the repository. Pitfall or logical?
International Nuclear Information System (INIS)
Frostenson, Magnus
2010-11-01
From a systems perspective the organization of the Swedish final repository project for nuclear waste is studied. Different aspects of organization are identified in the report, covering dimensions of geographical, operative, structural, responsibility and contextual organization. Following SKB's site selection for the applications for the final repository for spent nuclear system and the closing of the surplus value agreement, issues concerning operative, structural and contextual organization tend to become particularly pressing, which is reflected in three research questions: - How will the final repository project be organized operatively and structurally over time? - Why is the final repository project organized in this way by SKB? - What kind of contextual organization takes place in the final repository project and what are the consequences of these activities? How the different industrial units of the final repository project should be run and within which structure, for example concerning ownership and integration of units, is established in the report. SKB's reasons for choosing this kind of organization are also highlighted. Apart from legal and safety-related demands that must be met together with the demands of the owners, SKB's strategic preference for insourcing conditions organizational choices. The traditional task centred operative and structural organization of SKB is also reflected in the organizational choices for the present and future units of the final depository system. Contextual organization implies deepened actor relationships between SKB's owners and SKB on the one side and the municipalities Oesthammar and Oskarshamn on the other. Through active organizing, the final repository arena 'narrows down' and the final repository issue turns into an in many respects local issue. There is a clear tendency that the roles of SKB are multiplied in order to handle the demands that central stakeholders - in particular the municipalities - place on
Transfer systems in an underground repository
International Nuclear Information System (INIS)
Berg, H.P.; Ehrlich, D.
1991-01-01
In addition to logistic problem definitions taking into account the waste types of the wastes to be disposed of and the mining conditions, transport and handling of radioactive wastes in a repository, particularly require the keeping of safety technological marginal conditions mainly resulting from the accident analyses carried out. The realization of these safety technological aspects is described taking the planned Konrad repository as an example. (author)
Asset Reuse of Images from a Repository
Herman, Deirdre
2014-01-01
According to Markus's theory of reuse, when digital repositories are deployed to collect and distribute organizational assets, they supposedly help ensure accountability, extend information exchange, and improve productivity. Such repositories require a large investment due to the continuing costs of hardware, software, user licenses, training,…
Classifying decommissioning wastes for allocation to appropriate final repositories
International Nuclear Information System (INIS)
Alder, J.C.; Tunaboylu, K.
1982-01-01
For the safe disposal of radioactive wastes in different repositories, it is of advantage to classify them in well-defined conditioned categories, appropriate for final disposal. These categories, the so-called waste sorts are characterized by similar radionuclide distribution, similar nuclide-specific activity concentrations and similar waste matrix. A methodology is presented for classifying decommissioning wastes and is applied to the decommissioning wastes arising from a Swiss program of 6 GWe. The amounts and nuclide-specific activity inventories of the decommissioning waste sorts have been estimated. A first allocation into two different repository types has been performed. Such a classification enables one to define the source parameters for repository safety analysis and allows one to allocate the different waste categories into appropriate final repositories. This work presents a first iteration to determine which waste sorts belong to which repository type. The characteristics of waste sorts have to be better defined and the protective strength of the repository barriers has to be optimized. 7 references, 2 figures, 4 tables
Shaft placement in a bedded salt repository
International Nuclear Information System (INIS)
Klasi, M.L.
1982-10-01
Preferred shaft pillar sizes and shaft locations were determined with respect to the induced thermal stresses in a generic bedded salt repository at a depth of 610 m with a gross thermal loading of 14.8 W/m 2 . The model assumes isotropic material properties, plane strain and linear elastic behavior. Various shaft locations were analyzed over a 25 year period. The thermal results show that for this time span, the stratigraphy is unimportant except for the region immediately adjacent to the repository. The thermomechanical results show that for the given repository depth of 610 m, a minimum central shaft pillar radius of 244 m is required to equal the material strength in the barrier pillar. An assumed constant stress and constant temperature distribution creep model of the central shaft region adjacent to the repository conservatively overestimates a creep closure of 310 mm in a 6.1 m diameter centrally-located shaft
Safety analysis of the VLJ repository
International Nuclear Information System (INIS)
Vieno, T.; Nordman, H.
1991-05-01
The VLJ repository is an underground disposal facility for the low and medium level waste generated at the Olkiluoto nuclear power plant. The repository is located within 1 km from TVO I and TVO II (2 x 710 MWe) BWR's on the Olkiluoto island at the west coast of Finland. It contains two rock silos excavated at the depth of 60...100 meters in the bedrock. Low level waste will be disposed of in a shotcreted rock silo. For bituminized medium level waste, a separate silo of reinforced concrete has been built inside the shotcreted rock silo. The post-closure safety analysis has been done for the Final Safety Analysis Report (FSAR) of the VLJ repository. In addition to the normal evolution scenario, several disturbed evolution and accident scenarios have been analysed. In the reference scenario, radio-nuclides are assumed to be released from the bituminized waste within 500 years, the concrete silo is assumed to gradually disintegrate and finally to collapse at 5 000 years, all concrete in the silo is assumed to be also chemically depleted within 6 000 years, and all the seals of the repository are assumed to deteriorate within 12 000 years. The ability of alone natural barriers to restrict the release of radionuclides into the biosphere has been evaluated by means of scenarios where the degradation of engineered barriers has been assumed to take place at a still faster rate. In one of the disturbed evolution scenarios it has been assumed that the concrete silo for medium level waste is severely impaired immediately after sealing of the repository. Effects of gas generation and consequences of human intrusion have been evaluated, too. The results of the safety analysis show that radiation doses of any significance are caused only if a well is bored in the vicinity of the repository or if the groundwater discharge spot is inhabited and used for cultivation. In the reference scenario the maximum expectation value of the individual dose rate is 0.3 mSv/a
Szabó, Zalán; Oliveira Stahl, Adriana; Albers, Sonja-V.; Kissinger, Jessica C.; Driessen, Arnold J.M.; Pohlschröder, Mechthild; Pohlschroder, M.
2007-01-01
Most secreted archaeal proteins are targeted to the membrane via a tripartite signal composed of a charged N terminus and a hydrophobic domain, followed by a signal peptidase-processing site. Signal peptides of archaeal flagellins, similar to class III signal peptides of bacterial type IV pilins,
Diversion path analysis for the Swedish geological repository
International Nuclear Information System (INIS)
Fritzell, Anni; Meer, Klaas Van Der
2008-02-01
The Swedish strategy to handle the spent fuel from the nuclear power plants is direct disposal in a geological repository. The safeguards regime covering all nuclear material in the state will be expanded to cover the new repository, which will require a novel safeguards approach due mainly to the inaccessibility of the fuel after disposal. The safeguards approach must be able to provide a high level of assurance that the fuel in the repository not diverted, but must also be resource efficient. An attractive approach with regards to use of resources is to monitor only the access points to the repository, i.e. the openings. The implementation of such an approach can only be allowed if it is shown to be sufficiently secure. With the purpose of determining the applicability of this 'black box' approach, a diversion path analysis for the Swedish geological repository has been carried out. The result from the analysis shows that all credible diversion paths could be covered by the black-box safeguards approach provided that the identified boundary conditions can be met
Diversion path analysis for the Swedish geological repository
Energy Technology Data Exchange (ETDEWEB)
Fritzell, Anni (Dept. of Physics and Astronomy, Uppsala Univ., Uppsala (Sweden)); Meer, Klaas Van Der (Belgian Nuclear Research Center SCK.CEN (BG))
2008-02-15
The Swedish strategy to handle the spent fuel from the nuclear power plants is direct disposal in a geological repository. The safeguards regime covering all nuclear material in the state will be expanded to cover the new repository, which will require a novel safeguards approach due mainly to the inaccessibility of the fuel after disposal. The safeguards approach must be able to provide a high level of assurance that the fuel in the repository not diverted, but must also be resource efficient. An attractive approach with regards to use of resources is to monitor only the access points to the repository, i.e. the openings. The implementation of such an approach can only be allowed if it is shown to be sufficiently secure. With the purpose of determining the applicability of this 'black box' approach, a diversion path analysis for the Swedish geological repository has been carried out. The result from the analysis shows that all credible diversion paths could be covered by the black-box safeguards approach provided that the identified boundary conditions can be met
Salt Repository Project shaft design guide: Revision 0
International Nuclear Information System (INIS)
1987-12-01
The Salt Repository Project (SRP) Shaft Design Guide (SDG) and the accompanying SRP Input to Seismic Design define the basic approach for developing appropriate shaft designs for a high-level nuclear waste repository in salt at a proposed site in Deaf Smith County, Texas. The SDG is based on current mining industry standards and practices enhanced to meet the special needs of an underground nuclear waste repository. It provides a common approach for design of both the exploratory and repository shafts. The SDG defines shaft lining and material concepts and presents methods for calculating the loads and displacements that will be imposed on lining structures. It also presents the methodology and formulae for sizing lining components. The SDG directs the shaft designer to sources of geoscience and seismic design data for the Deaf Smith County, Texas repository site. In addition, the SDG describes methods for confirming shaft lining design by means of computer analysis, and it discusses performance monitoring needs that must be considered in the design. 113 refs., 18 figs., 14 tabs
Shared Medical Imaging Repositories.
Lebre, Rui; Bastião, Luís; Costa, Carlos
2018-01-01
This article describes the implementation of a solution for the integration of ownership concept and access control over medical imaging resources, making possible the centralization of multiple instances of repositories. The proposed architecture allows the association of permissions to repository resources and delegation of rights to third entities. It includes a programmatic interface for management of proposed services, made available through web services, with the ability to create, read, update and remove all components resulting from the architecture. The resulting work is a role-based access control mechanism that was integrated with Dicoogle Open-Source Project. The solution has several application scenarios like, for instance, collaborative platforms for research and tele-radiology services deployed at Cloud.
Design aspects of the alpha repository. II. Conceptual layouts of underground storage facilities
International Nuclear Information System (INIS)
Grams, W.H.
1975-01-01
Five conceptual repository layouts are presented: linear repository, 1 panel; bow tie repository, 2 panels; maltese cross repository, 4 panels; snowflake repository; 5 panels, and sash window repository, 8 panels. The layouts are compared with respect to excavation requirements, haulage distances, ventilation flow path designs, and safety features
Bowden, Peter; Beavis, Ron; Marshall, John
2009-11-02
A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis-identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. The many files of the Hupo blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 distinct proteins. About 6875 distinct proteins were only represented by a single distinct peptide, 2866 proteins showed 2 distinct peptides, and 3454 proteins showed at least three distinct peptides by X!TANDEM. More than 99% of the peptides were associated with proteins that had cumulative expectation values, i.e. probability of false positive identification, of one in one hundred or less. The distribution of peptides per protein from X!TANDEM was significantly different than those expected from random assignment of peptides.
Directory of Open Access Journals (Sweden)
Sahar Ahmed
2017-05-01
Full Text Available An in vitro platform to perform peptide screening against different cancer cell lines was designed. The strategy for this screening relied on the design and detection of high-affinity cancer-targeting peptides based on the sequences of NGR and P160. Evaluation of the best binding peptides was performed via incubation of the peptide array-bounded cells with MTT reagent, which is reduced to purple formazan in living cells and further quantified using an Elispot and Kodak imager. For proof of concept, a peptide library (132 spots, and 66 different peptides was designed, synthesized, and screened against different cancer cell lines. The current strategy assists in the identification of positive and negative peptides as well as the relative binding between positive ones. Better binding peptide sequences of the NGR motif were demonstrated to show up to a 2.6-fold increase in CD13+ cell lines with insignificant binding to CD13− ones. Comparable results were observed for P160 peptide sequences, to which different peptides had increased binding, with an up to 3-fold increase relative to the native P160 peptide. Based on our results, new peptide sequences for cancer targeting were identified, and the developed strategy was applied to two different peptide libraries.
Digital Repositories and the Question of Data Usefulness
Hughes, J. S.; Downs, R. R.
2017-12-01
The advent of ISO standards for trustworthy long-term digital repositories provides both a set of principles to develop long-term data repositories and the instruments to assess them for trustworthiness. Such mandatory high-level requirements are broad enough to be achievable, to some extent, by many scientific data centers, archives, and other repositories. But the requirement that the data be useful in the future, the requirement that is usually considered to be most relevant to the value of the repository for its user communities, largely remains subject to various interpretations and misunderstanding. However, current and future users will be relying on repositories to preserve and disseminate the data and information needed to discover, understand, and utilize these resources to support their research, learning, and decision-making objectives. Therefore, further study is needed to determine the approaches that can be adopted by repositories to make data useful to future communities of users. This presentation will describe approaches for enabling scientific data and related information, such as software, to be useful for current and potential future user communities and will present the methodology chosen to make one science discipline's data useful for both current and future users. The method uses an ontology-based information model to define and capture the information necessary to make the data useful for contemporary and future users.
Zhang, Fan; Briones, Andrea; Soloviev, Mikhail
2016-01-01
This chapter describes the principles of selection of antigenic peptides for the development of anti-peptide antibodies for use in microarray-based multiplex affinity assays and also with mass-spectrometry detection. The methods described here are mostly applicable to small to medium scale arrays. Although the same principles of peptide selection would be suitable for larger scale arrays (with 100+ features) the actual informatics software and printing methods may well be different. Because of the sheer number of proteins/peptides to be processed and analyzed dedicated software capable of processing all the proteins and an enterprise level array robotics may be necessary for larger scale efforts. This report aims to provide practical advice to those who develop or use arrays with up to ~100 different peptide or protein features.
Nuclear waste in a repository: amount as a factor in risk duration
International Nuclear Information System (INIS)
Zen, E.
1980-01-01
The relationship between the amount of nuclear waste in a nuclear repository and the safety of the repository is examined. It is shown that the amount of a given hazardous nuclide that is potentially leachable depends on the initial amount of waste in the repository and the time that has elapsed since the repository was put into operation. Nuclear repository safety can be enhanced if repositories are designed as modular units with leach-resistant watertight compartments
DEFF Research Database (Denmark)
Larsen, Malene Erup; Kloverpris, H.; Stryhn, A.
2011-01-01
://www.cbs.dtu.dk/services/HLArestrictor ), which is based on the highly versatile and accurate NetMHCpan predictor, which here has been optimized for the identification of both the MHC restriction element and the corresponding minimal epitope of a T cell response in a given individual. As input, it requires high-resolution (i.e., 4-digit) HLA...... HLA restrictions and minimal epitopes for about 90% of the positive peptide/patient pairs while rejecting more than 95% of the negative peptide-HLA pairs. Furthermore, for 18 peptide/HLA tetramer validated responses, HLArestrictor in all cases predicted both the HLA restriction element and minimal...
Retrievability as proposed in the US repository concept
International Nuclear Information System (INIS)
Harrington, P.G.
2000-01-01
The Nuclear Waste Policy Act states that any repository shall be designed and constructed to permit retrieval. Reasons for retrieval include public health and safety, environmental concerns, and recovery of economically valuable contents of spent nuclear fuel. The Nuclear Regulatory Commission requires that waste must be retrievable at any time up to 50 years after start of emplacement. The US Department of Energy intends to maintain a retrieval capability throughout the preclosure period. Possible preclosure periods range from a minimum of 50 years to as much as 300 years. Repository closure includes sealing all accessible portions of the repository, including ventilation shafts, access ramps and boreholes. Drip shields will be installed over the waste packages. Access to the repository after closure is not intended. The proposed repository includes horizontal emplacement drifts located in the unsaturated zone. The emplacement drift centerline spacing is 81 meters to provide a subboiling region between drifts for water drainage. A drip shield covers the waste packages. All emplacement drifts remain open until closure of the repository, providing performance benefits such as removing heat and moisture during the preclosure period and lowering postclosure temperatures. This does not impede retrieval, permitting a reversal of the emplacement process to accomplish retrieval under normal conditions. The preclosure period is therefore not to enhance retrievability, but does improve performance, and the resultant extension of the retrievability capability is a secondary effect. Information must be provided from the performance confirmation program to support a regulatory decision to close. Closure would isolate the repository from the accessible environment, preclude preferential flowpaths for water into the mountain, and minimize the possibility of inadvertent intrusion. (author)
Raucher, Drazen; Moktan, Shama; Massodi, Iqbal; Bidwell, Gene L
2009-10-01
Therapeutic peptides have great potential as anticancer agents owing to their ease of rational design and target specificity. However, their utility in vivo is limited by low stability and poor tumor penetration. The authors review the development of peptide inhibitors with potential for cancer therapy. Peptides that arrest the cell cycle by mimicking CDK inhibitors or induce apoptosis directly are discussed. The authors searched Medline for articles concerning the development of therapeutic peptides and their delivery. Inhibition of cancer cell proliferation directly using peptides that arrest the cell cycle or induce apoptosis is a promising strategy. Peptides can be designed that interact very specifically with cyclins and/or cyclin-dependent kinases and with members of apoptotic cascades. Use of these peptides is not limited by their design, as a rational approach to peptide design is much less challenging than the design of small molecule inhibitors of specific protein-protein interactions. However, the limitations of peptide therapy lie in the poor pharmacokinetic properties of these large, often charged molecules. Therefore, overcoming the drug delivery hurdles could open the door for effective peptide therapy, thus making an entirely new class of molecules useful as anticancer drugs.
Identification of coeliac disease triggering glutenin peptides in adults.
Donnelly, Suzanne C; Šuligoj, Tanja; Ellis, H Julia; Ciclitira, Paul J
2016-07-01
Coeliac disease affects approximately 1% of Northern American and European populations. It is caused by an inappropriate immune response to dietary gluten. Gluten comprises of two major protein fractions: gliadins and glutenins. Glutenins have recently been found to be toxic to coeliac individuals. Proliferation assays suggest in some but not all paediatric coeliac individuals there may be immunological stimulation with high molecular weight (HMW) glutenins. Less evidence pertains to low molecular weight (LMW) glutenins. The aim is to assess adaptive, T-cell driven, and innate immune response in adult coeliac individuals towards HMW glutenin peptide, glut04, and LMW glutenin peptide, glt156. Coeliac patients were recruited attending endoscopy for routine monitoring. Adaptive immune response towards glut04 and glt156 was measured by proliferation assays and measurement of interferon-γ secretion in 28 T-cell lines. The innate immune response was assessed by measurement of enterocyte cell height (ECH) in coeliac small intestinal biopsies following overnight incubation in organ culture chambers in a further nine individuals. There were 3/28 and 2/28 positive proliferation results using gluten-sensitive T-cells with glut04 and glt156, respectively. All coeliac biopsies tested in organ culture chambers demonstrated clear reduction in ECH with peptic-tryptic digest of whole industrial gluten, glut04 and glt156 when compared to negative control ovalbumin (p < 0.005). Three individuals had both T-cell and organ culture study data. Their proliferation assays showed no stimulation of the T-cells. This study demonstrates glutenin epitopes glut04 and glt156, while minor T-cell epitopes, are important in their ability to trigger the innate immune response.
Staged Repository Development Programmes
International Nuclear Information System (INIS)
Isaacs, T
2003-01-01
Programs to manage and ultimately dispose of high-level radioactive wastes are unique from scientific and technological as well as socio-political aspects. From a scientific and technological perspective, high-level radioactive wastes remain potentially hazardous for geological time periods-many millennia-and scientific and technological programs must be put in place that result in a system that provides high confidence that the wastes will be isolated from the accessible environment for these many thousands of years. Of course, ''proof'' in the classical sense is not possible at the outset, since the performance of the system can only be known with assurance, if ever, after the waste has been emplaced for those geological time periods. Adding to this challenge, many uncertainties exist in both the natural and engineered systems that are intended to isolate the wastes, and some of the uncertainties will remain regardless of the time and expense in attempting to characterize the system and assess its performance. What was perhaps underappreciated in the early days of waste management and repository program development were the unique and intense reactions that the institutional, political, and public bodies would have to repository program development, particularly in programs attempting to identify and then select sites for characterization, design, licensing, and ultimate development. Reactions in most nations were strong, focused, unrelenting, and often successful in hindering, derailing, and even stopping national repository programs. The reasons for such reactions and the measures to successfully respond to them are still evolving and continue to be the focus of many national program and political leaders. Adaptive Staging suggests an approach to repository program development that reflects the unique challenges associated with the disposal of high-level radioactive waste. The step-wise, incremental, learn-as-you-go approach is intended to maximize the
Industrial complementarities between interim storage and reversible geological repository - 59237
International Nuclear Information System (INIS)
Hoorelbeke, Jean-Michel
2012-01-01
The French Act voted in 2006 made the choice of deep geological disposal as the reference option for the long term management of high level (HLW) and intermediate level long-lived waste. The CIGEO repository project aims at avoiding or limiting burden to future generations, which could not be achieved by the extension in time of interim storage. The reversibility as provided by the Act will maintain a liberty of choice for waste management on a duration which is comparable to new storage facility. Interim storage is required to accommodate waste as long as the repository is not available. The commissioning of the repository in 2025 will not suppress needs for interim storage. The paper describes the complementarities between existing and future interim storage facilities and the repository project: repository operational issues and planning, HLW thermal decay, support for the reversibility, etc. It shows opportunities to prepare a global optimization of waste management including the utilization at best of storage capacities and the planning of waste emplacement in the repository in such a way to facilitate operational conditions and to limit cost. Preliminary simulations of storage-disposal scenarios are presented. Thanks to an optimal use of the waste management system, provision can be made for a progressive increase of waste emplacement flow during the first operation phase of the repository. It is then possible to stabilize the industrial activity level of the repository site. An optimal utilization of interim storage can also limit the diversity of waste packages emplaced simultaneously, which facilitates the operation of the repository. 60 years minimum interim storage duration is generally required with respect to HLW thermal output. Extending this interim storage period may reduce the underground footprint of the repository. Regarding reversibility, the capability to manage waste packages potentially retrieved from the repository should be analyzed. The
Identification and characterization of peptide: N- glycanase from Dictyostelium discoideum
Directory of Open Access Journals (Sweden)
Gosain Anuradha
2012-06-01
Full Text Available Abstract Background Peptide: N- glycanase (PNGase enzyme cleaves oligosaccharides from the misfolded glycoproteins and prepares them for degradation. This enzyme plays a role in the endoplasmic reticulum associated degradation (ERAD pathway in yeast and mice but its biological importance and role in multicellular development remain largely unknown. Results In this study, the PNGase from the cellular slime mold, Dictyostelium discoideum (DdPNGase was identified based on the presence of a common TG (transglutaminase core domain and its sequence homology with the known PNGases. The domain architecture and the sequence comparison validated the presence of probable functional domains in DdPNGase. The tertiary structure matched with the mouse PNGase. Here we show that DdPNGase is an essential protein, required for aggregation during multicellular development and a knockout strain of it results in small sized aggregates, all of which did not form fruiting bodies. The in situ hybridization and RT-PCR results show higher level of expression during the aggregate stage. The expression gets restricted to the prestalk region during later developmental stages. DdPNGase is a functional peptide:N-glycanase enzyme possessing deglycosylation activity, but does not possess any significant transamidation activity. Conclusions We have identified and characterized a novel PNGase from D. discoideum and confirmed its deglycosylation activity. The results emphasize the importance of PNGase in aggregation during multicellular development of this organism.
LIFE Materials: Fuel Cycle and Repository Volume 11
Energy Technology Data Exchange (ETDEWEB)
Shaw, H; Blink, J A
2008-12-12
The fusion-fission LIFE engine concept provides a path to a sustainable energy future based on safe, carbon-free nuclear power with minimal nuclear waste. The LIFE design ultimately offers many advantages over current and proposed nuclear energy technologies, and could well lead to a true worldwide nuclear energy renaissance. When compared with existing and other proposed future nuclear reactor designs, the LIFE engine exceeds alternatives in the most important measures of proliferation resistance and waste minimization. The engine needs no refueling during its lifetime. It requires no removal of fuel or fissile material generated in the LIFE engine. It leaves no weapons-attractive material at the end of life. Although there is certainly a need for additional work, all indications are that the 'back end' of the fuel cycle does not to raise any 'showstopper' issues for LIFE. Indeed, the LIFE concept has numerous benefits: (1) Per unit of electricity generated, LIFE engines would generate 20-30 times less waste (in terms of mass of heavy metal) requiring disposal in a HLW repository than does the current once-through fuel cycle. (2) Although there may be advanced fuel cycles that can compete with LIFE's low mass flow of heavy metal, all such systems require reprocessing, with attendant proliferation concerns; LIFE engines can do this without enrichment or reprocessing. Moreover, none of the advanced fuel cycles can match the low transuranic content of LIFE waste. (3) The specific thermal power of LIFE waste is initially higher than that of spent LWR fuel. Nevertheless, this higher thermal load can be managed using appropriate engineering features during an interim storage period, and could be accommodated in a Yucca-Mountain-like repository by appropriate 'staging' of the emplacement of waste packages during the operational period of the repository. The planned ventilation rates for Yucca Mountain would be sufficient for LIFE waste
LIFE Materials: Fuel Cycle and Repository Volume 11
International Nuclear Information System (INIS)
Shaw, H.; Blink, J.A.
2008-01-01
The fusion-fission LIFE engine concept provides a path to a sustainable energy future based on safe, carbon-free nuclear power with minimal nuclear waste. The LIFE design ultimately offers many advantages over current and proposed nuclear energy technologies, and could well lead to a true worldwide nuclear energy renaissance. When compared with existing and other proposed future nuclear reactor designs, the LIFE engine exceeds alternatives in the most important measures of proliferation resistance and waste minimization. The engine needs no refueling during its lifetime. It requires no removal of fuel or fissile material generated in the LIFE engine. It leaves no weapons-attractive material at the end of life. Although there is certainly a need for additional work, all indications are that the 'back end' of the fuel cycle does not to raise any 'showstopper' issues for LIFE. Indeed, the LIFE concept has numerous benefits: (1) Per unit of electricity generated, LIFE engines would generate 20-30 times less waste (in terms of mass of heavy metal) requiring disposal in a HLW repository than does the current once-through fuel cycle. (2) Although there may be advanced fuel cycles that can compete with LIFE's low mass flow of heavy metal, all such systems require reprocessing, with attendant proliferation concerns; LIFE engines can do this without enrichment or reprocessing. Moreover, none of the advanced fuel cycles can match the low transuranic content of LIFE waste. (3) The specific thermal power of LIFE waste is initially higher than that of spent LWR fuel. Nevertheless, this higher thermal load can be managed using appropriate engineering features during an interim storage period, and could be accommodated in a Yucca-Mountain-like repository by appropriate 'staging' of the emplacement of waste packages during the operational period of the repository. The planned ventilation rates for Yucca Mountain would be sufficient for LIFE waste to meet the thermal constraints of
Administrative Data Repository (ADR)
Department of Veterans Affairs — The Administrative Data Repository (ADR) was established to provide support for the administrative data elements relative to multiple categories of a person entity...
Investigative study of standards for Digital Repositories and related services
Foulonneau, Muriel; André, Francis
2007-01-01
This study is meant for institutional repository managers, service providers, repository software developers and generally, all players taking an active part in the creation of the digital repository infrastructure for e-research and e-learning. It reviews the current standards, protocols and
Reference Design Description for a Geologic Repository
International Nuclear Information System (INIS)
2000-01-01
One of the current major national environmental problems is the safe disposal of large quantities of spent nuclear fuel and high-level radioactive waste materials, which are rapidly accumulating throughout the country. These radioactive byproducts are generated as the result of national defense activities and from the generation of electricity by commercial nuclear power plants. At present, spent nuclear fuel is accumulating at over 70 power plant sites distributed throughout 33 states. The safe disposal of these high-level radioactive materials at a central disposal facility is a high national priority. This Reference Design Description explains the current design for a potential geologic repository that may be located at Yucca Mountain in Nevada for the disposal of spent nuclear fuel and high-level radioactive waste materials. This document describes a possible design for the three fundamental parts of a repository: a surface facility, subsurface repository, and waste packaging. It also presents the current conceptual design of the key engineering systems for the final four phases of repository processes: operations, monitoring, closure, and postclosure. In accordance with current law, this design does not include an interim storage option. In addition, this Reference Design Description reviews the expected long-term performance of the potential repository. It describes the natural barrier system which, together with the engineered systems, achieves the repository objectives. This design will protect the public and the environment by allowing the safe disposal of radioactive waste received from government-owned custodial spent fuel sites, high-level radioactive waste sites, and commercial power reactor sites. All design elements meet or exceed applicable regulations governing the disposal of high-level radioactive waste. The design will provide safe disposal of waste materials for at least a 10,000 year period. During this time interval, natural radioactive decay
Optimizing Resources for Trustworthiness and Scientific Impact of Domain Repositories
Lehnert, K.
2017-12-01
Domain repositories, i.e. data archives tied to specific scientific communities, are widely recognized and trusted by their user communities for ensuring a high level of data quality, enhancing data value, access, and reuse through a unique combination of disciplinary and digital curation expertise. Their data services are guided by the practices and values of the specific community they serve and designed to support the advancement of their science. Domain repositories need to meet user expectations for scientific utility in order to be successful, but they also need to fulfill the requirements for trustworthy repository services to be acknowledged by scientists, funders, and publishers as a reliable facility that curates and preserves data following international standards. Domain repositories therefore need to carefully plan and balance investments to optimize the scientific impact of their data services and user satisfaction on the one hand, while maintaining a reliable and robust operation of the repository infrastructure on the other hand. Staying abreast of evolving repository standards to certify as a trustworthy repository and conducting a regular self-assessment and certification alone requires resources that compete with the demands for improving data holdings or usability of systems. The Interdisciplinary Earth Data Alliance (IEDA), a data facility funded by the US National Science Foundation, operates repositories for geochemical, marine Geoscience, and Antarctic research data, while also maintaining data products (global syntheses) and data visualization and analysis tools that are of high value for the science community and have demonstrated considerable scientific impact. Balancing the investments in the growth and utility of the syntheses with resources required for certifcation of IEDA's repository services has been challenging, and a major self-assessment effort has been difficult to accommodate. IEDA is exploring a partnership model to share
Automated 2D peptide separation on a 1D nano-LC-MS system
DEFF Research Database (Denmark)
Taylor, Paul; Nielsen, Peter A; Trelle, Morten Beck
2009-01-01
the on-line separation of highly complex peptide mixtures directly coupled with mass spectrometry-based identification. Here, we present a variation of the traditional MudPIT protocol, combining highly sensitive chromatography using a nanoflow liquid chromatography system (nano-LC) with a two...
Long-term environmental impacts of geologic repositories
International Nuclear Information System (INIS)
Pigford, T.H.
1983-05-01
This paper summarizes a study of the long-term environmental impacts of geologic repositories for radioactive wastes. Conceptual repositories in basalt, granite, salt, and tuff were considered. Site-specific hydrological and geochemical parameters were used wherever possible, supplemented with generic parameters when necessary. Radiation doses to future maximally exposed individuals who use the contaminated groundwater and surface water were calculated and compared with a performance criterion of 10 -4 Sv/yr for radiation exposures from probable events. The major contributors to geologic isolation are the absence of groundwater if the repository is in natural salt, the slow dissolution of key radioelements as limited by solubility and by diffusion and convection in groundwater, long water travel times from the waste to the environment, and sorption retardation in the media surrounding the repository. In addition, dilution by surface water can considerably reduce the radiation exposures that result from the small fraction of the waste radioactivity that may ultimately reach the environment. Estimates of environmental impacts are made both for unreprocessed spent fuel and for reprocessing wastes. Accelerated dissolution of waste exposed to groundwater during the period of repository heating is also considered. This study of environmental impacts is a portion of a more comprehensive study of geologic waste disposal carried out by the Waste Isolation System Panel of the US National Research Council
Directory of Open Access Journals (Sweden)
S. Mirdamadi
2017-05-01
Full Text Available Bioactive peptides, are inactive components within the structure of the protein and when they are released by enzymatic hydrolysis, show different physiological functions. Recently, the identification and characterization of bioactive peptides derived from plant and animal sources and different microorganisms is highly regarded. They are produced during enzymatic hydrolysis by gastrointestinal enzymes or enzymes extracted from microorganisms and plants or by proteolytic starter cultures during fermentation process and exhibit different activities including: opioid, mineral binding, immunomodulatory, antioxidant, antimicrobial, anti-inflammatory, chlosterol lowering and so on. Take advantage of bioactive peptides as components of health is related to bio stability assurance, bioavailability and safety of them. The use of computer-based techniques and the use of various databases completed in laboratory studies, have provided the possibility of studying the mechanisms of action of different peptides.
De Lisa, Emilia; Salzano, Anna Maria; Moccia, Francesco; Scaloni, Andrea; Di Cosmo, Anna
2013-06-15
Marine invertebrates exhibit both chemokinesis and chemotaxis phenomena, induced in most cases by the release of water-borne peptides or pheromones. In mollusks, several peptides released during egg-laying improve both male attraction and mating. Unlike other cephalopods, Octopus vulgaris adopts an indirect internal fertilization strategy. We here report on the identification and characterization of a chemoattractant peptide isolated from mature eggs of octopus females. Using two-chamber and time-lapse microscopy assays, we demonstrate that this bioactive peptide is able to increase sperm motility and induce chemotaxis by changing the octopus spermatozoa swimming behavior in a dose-dependent manner. We also provide evidence that chemotaxis in the octopus requires the presence of extracellular calcium and membrane protein phophorylation at tyrosine. This study is the first report on a sperm-activating factor in a non-free-spawning marine animal.
International Nuclear Information System (INIS)
Mueller, Monika C.M.
2013-01-01
The documentation on the Loccum meeting 2013 includes contributions on the following topics: Public participation for the final repository search; Lessons learned from the past; Public participation: what is expected? Experiences of repository operators on public participation; The TRIPLEX concept; From Gorleben to the law on final repository search: a long and a short story; Public participation concerning radioactive waste storage; The public has to be informed on the radioactive waste problem and the possible solutions; After consensus is before consensus - German final repository conflict between legislation and simulated public participation; Political concept of public participation; A fast final repository law will not bring about social peace; Good public participation on final repository search - requirements, challenges, questions and approaches.
Computational Materials Repository
DEFF Research Database (Denmark)
Landis, David
, different abstraction levels and enables users to analyze their own results, and allows to share data with collaborators. The approach of the Computational Materials Repository (CMR) is to convert data to an internal format that maintains the original variable names without insisting on any semantics...
Wang, Huixin; Wang, Bing; Wei, Zhonglin; Zhang, Hao; Guo, Xinhua
2015-01-01
A good understanding of gas-phase fragmentation chemistry of peptides is important for accurate protein identification. Additional product ions obtained by sodiated peptides can provide useful sequence information supplementary to protonated peptides and improve protein identification. In this work, we first demonstrate that the sodiated a3 ions are abundant in the tandem mass spectra of sodium-cationized peptides although observations of a3 ions have rarely been reported in protonated peptides. Quantum chemical calculations combined with tandem mass spectrometry are used to investigate this phenomenon by using a model tetrapeptide GGAG. Our results reveal that the most stable [a3 + Na - H](+) ion is present as a bidentate linear structure in which the sodium cation coordinates to the two backbone carbonyl oxygen atoms. Due to structural inflexibility, further fragmentation of the [a3 + Na - H](+) ion needs to overcome several relatively high energetic barriers to form [b2 + Na - H](+) ion with a diketopiperazine structure. As a result, low abundance of [b2 + Na - H](+) ion is detected at relatively high collision energy. In addition, our computational data also indicate that the common oxazolone pathway to generate [b2 + Na - H](+) from the [a3 + Na - H](+) ion is unlikely. The present work provides a mechanistic insight into how a sodium ion affects the fragmentation behaviors of peptides. Copyright © 2015 John Wiley & Sons, Ltd.
Geotechnical instrumentation for repository shafts
International Nuclear Information System (INIS)
Lentell, R.L.; Byrne, J.
1993-01-01
The US Congress passed the Nuclear Waste Policy Act in 1980, which required that three distinctly different geologic media be investigated as potential candidate sites for the permanent disposal of high-level nuclear waste. The three media that were selected for study were basalt (WA), salt (TX, LA, MS, UT), and tuff (NV). Preliminary Exploratory Shaft Facilities (ESF) designs were prepared for seven candidate salt sites, including bedded and domal salt environments. A bedded-salt site was selected in Deaf Smith County, TX for detailed site characterization studies and ESF Final Design. Although Congress terminated the Salt Repository Program in 1988, Final Design for the Deaf Smith ESF was completed, and much of the design rationale can be applied to subsequent deep repository shafts. This paper presents the rationale for the geotechnical instrumentation that was designed for construction and operational performance monitoring of the deep shafts of the in-situ test facility. The instrumentation design described herein can be used as a general framework in designing subsequent instrumentation programs for future high-level nuclear waste repository shafts
Peptides, polypeptides and peptide-polymer hybrids as nucleic acid carriers.
Ahmed, Marya
2017-10-24
Cell penetrating peptides (CPPs), and protein transduction domains (PTDs) of viruses and other natural proteins serve as a template for the development of efficient peptide based gene delivery vectors. PTDs are sequences of acidic or basic amphipathic amino acids, with superior membrane trespassing efficacies. Gene delivery vectors derived from these natural, cationic and cationic amphipathic peptides, however, offer little flexibility in tailoring the physicochemical properties of single chain peptide based systems. Owing to significant advances in the field of peptide chemistry, synthetic mimics of natural peptides are often prepared and have been evaluated for their gene expression, as a function of amino acid functionalities, architecture and net cationic content of peptide chains. Moreover, chimeric single polypeptide chains are prepared by a combination of multiple small natural or synthetic peptides, which imparts distinct physiological properties to peptide based gene delivery therapeutics. In order to obtain multivalency and improve the gene delivery efficacies of low molecular weight cationic peptides, bioactive peptides are often incorporated into a polymeric architecture to obtain novel 'polymer-peptide hybrids' with improved gene delivery efficacies. Peptide modified polymers prepared by physical or chemical modifications exhibit enhanced endosomal escape, stimuli responsive degradation and targeting efficacies, as a function of physicochemical and biological activities of peptides attached onto a polymeric scaffold. The focus of this review is to provide comprehensive and step-wise progress in major natural and synthetic peptides, chimeric polypeptides, and peptide-polymer hybrids for nucleic acid delivery applications.
Safety case for Slovenian LILW near-surface repository
International Nuclear Information System (INIS)
Viršek, Sandi; Špiler, Janja; Žagar, Tomaž
2016-01-01
Conclusions: • Repository provides the fulfillment of international and national legal requirements regarding treatment and disposal of LILW; • Repository improves the conditions for life extension for NPP Krško and offers synergetic effects for the second unit of NPP Krško; • Repository provides a basis for safe, economic and reliable use of radioactive sources in science, medicine and industry in Slovenia; • All economic calculations and comparisons show a clear advantage in case of a joint Slovenian and Croatian solution
New content in digital repositories the changing research landscape
Simons, Natasha
2013-01-01
Research institutions are under pressure to make their outputs more accessible in order to meet funding requirements and policy guidelines. Libraries have traditionally played an important role by exposing research output through a predominantly institution-based digital repository, with an emphasis on storing published works. New publishing paradigms are emerging that include research data, huge volumes of which are being generated globally. Repositories are the natural home for managing, storing and describing institutional research content. New Content in Digital Repositories explores the diversity of content types being stored in digital repositories with a focus on research data, creative works, and the interesting challenges they pose.
Directory of Open Access Journals (Sweden)
Lund Ole
2009-09-01
Full Text Available Abstract Background The major histocompatibility complex (MHC molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to cytotoxic T cells, whereas MHC class II molecules stimulate cellular and humoral immunity through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting this binding event. Results Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data due to redundant binding core representation. Incorporation of information about the residues flanking the peptide-binding core is shown to significantly improve the prediction accuracy. The method is evaluated on a large-scale benchmark consisting of six independent data sets covering 14 human MHC class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods. Conclusion The NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http://www.cbs.dtu.dk/services/NetMHCII-2.0.
Impact of retrievability of repository design
International Nuclear Information System (INIS)
Heijdra, J.J.; Gaag, J. v.d.; Prij, J.
1995-01-01
In this paper the impact of the retrievability on the design of the repository will be handled. Retrievability of radioactive waste from a repository in geological formations has received increasing attention during recent years. It is obvious that this retrievability will have consequences in terms of mining engineering, safety and cost. The purpose of the present study is to evaluate cost consequences by comparing two extreme options for retrievable storage. (author). 6 refs., 3 figs
Chemical risks from nuclear waste repositories
International Nuclear Information System (INIS)
Persson, L.
1988-01-01
Studies concerning the chemical risks of nuclear waste are reviewed. The radiological toxicity of the material is of primary concern but the potential nonradiological toxicity should not be overlooked as the chemotoxic substances may reach the biosphere from a nuclear waste repository. In the report is concluded that the possible chemotoxic effects of a repository for nuclear waste should be studied as a part of the formal risk assessment of the disposal concept. (author)
Federal Laboratory Consortium — To facilitate aging research on cells in culture, the NIA provides support for the NIA Aging Cell Repository, located at the Coriell Institute for Medical Research...
Repository waste-handling operations, 1998
International Nuclear Information System (INIS)
Cottam, A.E.; Connell, L.
1986-04-01
The Civilian Radioactive Waste Management Program Mission Plan and the Generic Requirements for a Mined Geologic Disposal System state that beginning in 1998, commercial spent fuel not exceeding 70,000 metric tons of heavy metal, or a quantity of solidified high-level radioactive waste resulting from the reprocessing of such a quantity of spent fuel, will be shipped to a deep geologic repository for permanent storage. The development of a waste-handling system that can process 3000 metric tons of heavy metal annually will require the adoption of a fully automated approach. The safety and minimum exposure of personnel will be the prime goals of the repository waste handling system. A man-out-of-the-loop approach will be used in all operations including the receipt of spent fuel in shipping casks, the inspection and unloading of the spent fuel into automated hot-cell facilities, the disassembly of spent fuel assemblies, the consolidation of fuel rods, and the packaging of fuel rods into heavy-walled site-specific containers. These containers are designed to contain the radionuclides for up to 1000 years. The ability of a repository to handle more than 6000 pressurized water reactor spent-fuel rods per day on a production basis for approximately a 23-year period will require that a systems approach be adopted that combines space-age technology, robotics, and sophisticated automated computerized equipment. New advanced inspection techniques, maintenance by robots, and safety will be key factors in the design, construction, and licensing of a repository waste-handling facility for 1998
Distributed Web Service Repository
Directory of Open Access Journals (Sweden)
Piotr Nawrocki
2015-01-01
Full Text Available The increasing availability and popularity of computer systems has resulted in a demand for new, language- and platform-independent ways of data exchange. That demand has in turn led to a significant growth in the importance of systems based on Web services. Alongside the growing number of systems accessible via Web services came the need for specialized data repositories that could offer effective means of searching of available services. The development of mobile systems and wireless data transmission technologies has allowed the use of distributed devices and computer systems on a greater scale. The accelerating growth of distributed systems might be a good reason to consider the development of distributed Web service repositories with built-in mechanisms for data migration and synchronization.
FAMILY OF FLP PEPTIDES IN CAENORHABDITIS ELEGANS AND RELATED NEMATODES
Directory of Open Access Journals (Sweden)
Chris eLi
2014-10-01
Full Text Available Neuropeptides regulate all aspects of behavior in multicellular organisms. Because of their ability to act at long distances, neuropeptides can exert their effects beyond the conventional synaptic connections, thereby adding an intricate layer of complexity to the activity of neural networks. In the nematode Caenorhabditis elegans, a large number of neuropeptide genes that are expressed throughout the nervous system has been identified. The actions of these peptides supplement the synaptic connections of the 302 neurons, allowing for fine tuning of neural networks and increasing the ways in which behaviors can be regulated. In this review, we focus on a large family of genes encoding FMRFamide-related peptides. These genes, the flp genes, have been used as a starting point to identifying flp genes throughout Nematoda. Nematodes have the largest family of FMRFamide-related peptides described thus far. The challenges in the future are the elucidation of their functions and the identification of the receptors and signaling pathways through which they function.
Ventilation planning for a prospective nuclear waste repository
International Nuclear Information System (INIS)
Wallace, K.G. Jr.
1987-01-01
In 1982, the US Congress passed the Nuclear Waste Policy Act to provide for the development of underground repositories for spent nuclear fuel. This development will be managed by the United States Department of Energy. In 1986, the President selected three areas for site characterization to determine their suitability for the development of an underground repository; those sites were: (1) A site in volcanic tuff located at Yucca Mountain in Nevada, (2) a site in bedded salt located in Deaf Smith County in Texas, and (3) a site in basalt located in Hanford, Washington. At present conceptual repository designs are being developed for each site. A key element of a repository design is the underground ventilation system required to support construction, nuclear waste emplacement, and potential waste retrieval. This paper describes the preliminary ventilation systems designed for the repository in tuff. The concept provides separate ventilation systems for the construction and waste emplacement activities. The paper further describes the means by which acceptable environmental conditions will be re-established to allow re-entry into previously closed rooms for the purpose of inspection, maintenance or retrieval
Status of the implementation of Brazilian National Repository
International Nuclear Information System (INIS)
Tello, Cledola Cassia Oliveira de
2015-01-01
In Brazil, the use of nuclear energy and radioisotopes is increasing and it already justifies the construction of a national repository for radioactive wastes of low and intermediate-level. The Brazilian National Commission for Nuclear Energy (CNEN) is legally responsible for designing and constructing intermediate and final storages for radioactive wastes generated in all Country, in accordance to Federal Law No. 10308. Additionally, the Brazilian Environmental Regulator (IBAMA) lately is imposing to the implementation of new nuclear installations (e.g. Angra 3 NPP and Brazilian Multipurpose Reactor) that the National Repository should be in construction, before the start-up of those ones. In November 2009, the RBMN Project Charter was signed. The RBMN Project aims at the implantation of a National Repository to dispose the radioactive wastes of low- and intermediate-level. Some aspects about the Repository construction are very challenging, mainly due to the licensing process, which will be made for two different regulatory bodies, nuclear and environmental. The main achievements obtained till now are the establishment of the current Brazilian radioactive waste inventory, the conceptual design and the selection of candidate sites for the repository. The current status of the Project is summarized. (author)
Yu, Zhipeng; Chen, Yang; Zhao, Wenzhu; Li, Jianrong; Liu, Jingbo; Chen, Feng
2018-01-25
In order to circumvent some challenges of the classical approach, the in silico method has been applied to the discovery of angiotensin-converting enzyme (ACE) inhibitory peptides from food proteins. In this study, some convenient and efficient in silico tools were utilized to identify novel ACE inhibitory peptides from Salmo salar. Collagen from Salmo salar was digested in silico into hundreds of peptides. Results revealed that tetrapeptides PGAR and IGPR showed potent ACE inhibitory activity, with IC 50 values of 0.598 ± 0.12 and 0.43 ± 0.09 mmol L -1 , respectively. The molecular docking result showed that PGAR and IGPR interact with ACE mostly via hydrogen bonds and attractive charge. Peptide IGPR interacts with Zn + at the ACE active site, showing high inhibitory activity. Interaction with Zn + in ACE may lead to higher inhibitory activity of peptides, and Pi interactions may promote the effect of peptides on ACE. The in silico method can be an effective method to predict potent ACE inhibitory peptides from food proteins. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.
International Nuclear Information System (INIS)
James Graham, Robert Leslie; Graham, Ciaren; McClean, Stephen; Chen, Tianbao; O'Rourke, Martin; Hirst, David; Theakston, David; Shaw, Chris
2005-01-01
A novel undecapeptide has been isolated and structurally characterized from the venoms of three species of New World pit vipers from the subfamily, Crotalinae. These include the Mexican moccasin (Agkistrodon bilineatus), the prairie rattlesnake (Crotalus viridis viridis), and the South American bushmaster (Lachesis muta). The peptide was purified from all three venoms using a combination of gel permeation chromatography and reverse-phase HPLC. Automated Edman degradation sequencing and MALDI-TOF mass spectrometry established its peptide primary structure as: Thr-Pro-Pro-Ala-Gly-Pro-Asp-Val-Gly-Pro-Arg-OH, with a non-protonated molecular mass of 1063.18 Da. A synthetic replicate of the peptide was found to be an antagonist of bradykinin action at the rat vascular B2 receptor. This is the first bradykinin inhibitory peptide isolated from snake venom. Database searching revealed the peptide to be highly structurally related (10/11 residues) with a domain residing between the bradykinin-potentiating peptide and C-type natriuretic peptide domains of a recently cloned precursor from tropical rattlesnake (Crotalus durissus terrificus) venom gland. BIP thus represents a novel biological entity from snake venom
Yang, Huiping; Cuevas-Uribe, Rafael; Savage, Markita G; Walter, Ronald B; Tiersch, Terrence R
2012-09-01
Cryopreservation of sperm from Xiphophorus fishes has produced live young in three species: X. hellerii, X. couchianus, and X. maculatus. In this study, the goal was to establish protocols for sperm cryopreservation and artificial insemination to produce live young in X. variatus, and to identify needs for repository development. The objectives were to: 1) collect basic biological characteristics of males; 2) cryopreserve sperm from X. variatus, 3) harvest live young from cryopreserved sperm, and 4) discuss the requirements for establishment of sperm repositories. The 35 males used in this study had a body weight of 0.298±0.096 g (mean±SD), body length of 2.5±0.2 cm, and testis weight of 6.4±3.4 mg. The sperm production per gram of testis was 2.33±1.32×10(9) cells. After freezing, the post-thaw motility decreased significantly to 37%±17% (ranging from 5% to 70%) (p=0.000) from 57%±14% (40%-80%) of fresh sperm (N=20). Artificial insemination of post-thaw sperm produced confirmed offspring from females of X. hellerii and X. variatus. This research, taken together with previous studies, provides a foundation for development of strategies for sperm repositories of Xiphophorus fishes. This includes: 1) the need for breeding strategies for regeneration of target populations, 2) identification of minimum fertilization capacity of frozen samples, 3) identification of fish numbers necessary for sampling and their genetic relationships, 4) selection of packaging containers for labeling and biosecurity, 5) assurance of quality control and standardization of procedures, 6) information systems that can manage the data associated with cryopreserved samples, including the genetic data, 7) biological data of sampled fish, 8) inventory data associated with frozen samples, and 9) data linking germplasm samples with other related materials such as body tissues or cells saved for DNA and RNA analyses.
A Repository of Semantic Open EHR Archetypes
Directory of Open Access Journals (Sweden)
Fernando Sánchez
2015-03-01
Full Text Available This paper describes a repository of openEHR archetypes that have been translated to OWL. In the work presented here, five different CKMs (Clinical Knowledge Managers have been downloaded and the archetypes have been translated to OWL. This translation is based on an existing translator that has been improved to solve programming problems with certain structures. As part of the repository a tool has been developed to keep it always up-to-date. So, any change in one of the CKMs (addition, elimination or even change of an archetype will involve translating the changed archetypes once more. The repository is accessible through a Web interface (http://www.openehr.es/.
DEFF Research Database (Denmark)
Li, Shizhong; Bock, Elisabeth Marianne; Berezin, Vladimir
2010-01-01
of protein structure, in silico modeling and biological studies have recently resulted in the identification of FGFR binding peptides derived from various FGFs and NCAM mimicking the effects of these molecules with regard to their neuritogenic and neuroprotective properties. This review focuses on recently...
Peptide-based proteasome inhibitors in anticancer drug design.
Micale, Nicola; Scarbaci, Kety; Troiano, Valeria; Ettari, Roberta; Grasso, Silvana; Zappalà, Maria
2014-09-01
The identification of the key role of the eukaryotic 26S proteasome in regulated intracellular proteolysis and its importance as a target in many pathological conditions wherein the proteasomal activity is defective (e.g., malignancies, autoimmune diseases, neurodegenerative diseases, etc.) prompted several research groups to the development of specific inhibitors of this multicatalytic complex with the aim of obtaining valid drug candidates. In regard to the anticancer therapy, the peptide boronate bortezomib (Velcade®) represents the first molecule approved by FDA for the treatment of multiple myeloma in 2003 and mantle cell lymphoma in 2006. Since then, a plethora of molecules targeting the proteasome have been identified as potential anticancer agents and a few of them reached clinical trials or are already in the market (i.e., carfilzomib; Kyprolis®). In most cases, the design of new proteasome inhibitors (PIs) takes into account a proven peptide or pseudopeptide motif as a base structure and places other chemical entities throughout the peptide skeleton in such a way to create an efficacious network of interactions within the catalytic sites. The purpose of this review is to provide an in-depth look at the current state of the research in the field of peptide-based PIs, specifically those ones that might find an application as anticancer agents. © 2014 Wiley Periodicals, Inc.
Low- and intermediate-level waste repository-induced effects
Energy Technology Data Exchange (ETDEWEB)
Leupin, O.X.; Marschall, P.; Johnson, L.; Cloet, V.; Schneider, J. [National Cooperative for the Disposal of Radioactive Waste (NAGRA), Wettingen (Switzerland); Smith, P. [Safety Assessment Management Ltd, Henley-On-Thames, Oxfordshire (United Kingdom); Savage, D. [Savage Earth Associates Ltd, Bournemouth, Dorset (United Kingdom); Senger, R. [Intera Inc., Ennetbaden (Switzerland)
2016-10-15
This status report aims at describing and assessing the interactions of the radioactive waste emplaced in a low- and intermediate level waste (L/ILW) repository with the engineered materials and the Opalinus Clay host rock. The Opalinus Clay has a thickness of about 100 m in the proposed siting regions. Among other things the results are used to steer the RD and D programme of NAGRA. The repository-induced effects considered in this report are of the following broad types: - Thermal effects: i.e. effects arising principally from the heat generated by the waste and the setting of cement. - Rock-mechanical effects: i.e. effects arising from the mechanical disturbance to the rock caused by the excavation of the emplacement caverns and other underground structures. - Hydraulic and gas-related effects: i.e. the effects of repository resaturation and of gas generation, e.g. due to the corrosion of metals within the repository, on the host rock and engineered barriers. - Chemical effects: i.e. chemical interactions between the waste, the engineered materials and the host rock. Deep geological repositories are designed to avoid or mitigate the impact of potentially detrimental repository-induced effects on long-term safety. For the repository under consideration in the present report, an assessment of those repository-induced effects that remain shows that detrimental chemical and mechanical impacts are largely confined to the rock adjacent to the excavations, thermal impacts are minimal and gas effects can be mitigated by appropriate design measures to reduce gas production and provide pathways for gas transport that limit gas pressure build-up (engineered gas transport system, or EGTS). Specific measures that are part of the current reference design are discussed in relation to their significance with respect to repository-induced effects. The disposal system described in this report provides a system of passive barriers with multiple safety functions. The disposal
Low- and intermediate-level waste repository-induced effects
International Nuclear Information System (INIS)
Leupin, O.X.; Marschall, P.; Johnson, L.; Cloet, V.; Schneider, J.; Smith, P.; Savage, D.; Senger, R.
2016-10-01
This status report aims at describing and assessing the interactions of the radioactive waste emplaced in a low- and intermediate level waste (L/ILW) repository with the engineered materials and the Opalinus Clay host rock. The Opalinus Clay has a thickness of about 100 m in the proposed siting regions. Among other things the results are used to steer the RD and D programme of NAGRA. The repository-induced effects considered in this report are of the following broad types: - Thermal effects: i.e. effects arising principally from the heat generated by the waste and the setting of cement. - Rock-mechanical effects: i.e. effects arising from the mechanical disturbance to the rock caused by the excavation of the emplacement caverns and other underground structures. - Hydraulic and gas-related effects: i.e. the effects of repository resaturation and of gas generation, e.g. due to the corrosion of metals within the repository, on the host rock and engineered barriers. - Chemical effects: i.e. chemical interactions between the waste, the engineered materials and the host rock. Deep geological repositories are designed to avoid or mitigate the impact of potentially detrimental repository-induced effects on long-term safety. For the repository under consideration in the present report, an assessment of those repository-induced effects that remain shows that detrimental chemical and mechanical impacts are largely confined to the rock adjacent to the excavations, thermal impacts are minimal and gas effects can be mitigated by appropriate design measures to reduce gas production and provide pathways for gas transport that limit gas pressure build-up (engineered gas transport system, or EGTS). Specific measures that are part of the current reference design are discussed in relation to their significance with respect to repository-induced effects. The disposal system described in this report provides a system of passive barriers with multiple safety functions. The disposal
Making research data repositories visible: the re3data.org Registry.
Directory of Open Access Journals (Sweden)
Heinz Pampel
Full Text Available Researchers require infrastructures that ensure a maximum of accessibility, stability and reliability to facilitate working with and sharing of research data. Such infrastructures are being increasingly summarized under the term Research Data Repositories (RDR. The project re3data.org-Registry of Research Data Repositories-has begun to index research data repositories in 2012 and offers researchers, funding organizations, libraries and publishers an overview of the heterogeneous research data repository landscape. In July 2013 re3data.org lists 400 research data repositories and counting. 288 of these are described in detail using the re3data.org vocabulary. Information icons help researchers to easily identify an adequate repository for the storage and reuse of their data. This article describes the heterogeneous RDR landscape and presents a typology of institutional, disciplinary, multidisciplinary and project-specific RDR. Further the article outlines the features of re3data.org, and shows how this registry helps to identify appropriate repositories for storage and search of research data.
Making research data repositories visible: the re3data.org Registry.
Pampel, Heinz; Vierkant, Paul; Scholze, Frank; Bertelmann, Roland; Kindling, Maxi; Klump, Jens; Goebelbecker, Hans-Jürgen; Gundlach, Jens; Schirmbacher, Peter; Dierolf, Uwe
2013-01-01
Researchers require infrastructures that ensure a maximum of accessibility, stability and reliability to facilitate working with and sharing of research data. Such infrastructures are being increasingly summarized under the term Research Data Repositories (RDR). The project re3data.org-Registry of Research Data Repositories-has begun to index research data repositories in 2012 and offers researchers, funding organizations, libraries and publishers an overview of the heterogeneous research data repository landscape. In July 2013 re3data.org lists 400 research data repositories and counting. 288 of these are described in detail using the re3data.org vocabulary. Information icons help researchers to easily identify an adequate repository for the storage and reuse of their data. This article describes the heterogeneous RDR landscape and presents a typology of institutional, disciplinary, multidisciplinary and project-specific RDR. Further the article outlines the features of re3data.org, and shows how this registry helps to identify appropriate repositories for storage and search of research data.
Exploring Characterizations of Learning Object Repositories Using Data Mining Techniques
Segura, Alejandra; Vidal, Christian; Menendez, Victor; Zapata, Alfredo; Prieto, Manuel
Learning object repositories provide a platform for the sharing of Web-based educational resources. As these repositories evolve independently, it is difficult for users to have a clear picture of the kind of contents they give access to. Metadata can be used to automatically extract a characterization of these resources by using machine learning techniques. This paper presents an exploratory study carried out in the contents of four public repositories that uses clustering and association rule mining algorithms to extract characterizations of repository contents. The results of the analysis include potential relationships between different attributes of learning objects that may be useful to gain an understanding of the kind of resources available and eventually develop search mechanisms that consider repository descriptions as a criteria in federated search.
Fingerprinting Desmosine-Containing Elastin Peptides
Schräder, Christoph U.; Heinz, Andrea; Majovsky, Petra; Schmelzer, Christian E. H.
2015-05-01
Elastin is a vital protein of the extracellular matrix of jawed vertebrates and provides elasticity to numerous tissues. It is secreted in the form of its soluble precursor tropoelastin, which is subsequently cross-linked in the course of the elastic fiber assembly. The process involves the formation of the two tetrafunctional amino acids desmosine (DES) and isodesmosine (IDES), which are unique to elastin. The resulting high degree of cross-linking confers remarkable properties, including mechanical integrity, insolubility, and long-term stability to the protein. These characteristics hinder the structural elucidation of mature elastin. However, MS2 data of linear and cross-linked peptides released by proteolysis can provide indirect insights into the structure of elastin. In this study, we performed energy-resolved collision-induced dissociation experiments of DES, IDES, their derivatives, and DES-/IDES-containing peptides to determine characteristic product ions. It was found that all investigated compounds yielded the same product ion clusters at elevated collision energies. Elemental composition determination using the exact masses of these ions revealed molecular formulas of the type CxHyN, suggesting that the pyridinium core of DES/IDES remains intact even at relatively high collision energies. The finding of these specific product ions enabled the development of a similarity-based scoring algorithm that was successfully applied on LC-MS/MS data of bovine elastin digests for the identification of DES-/IDES-cross-linked peptides. This approach facilitates the straightforward investigation of native cross-links in elastin.
Studies on an advanced repository system with enhanced engineered barriers (a framework)
International Nuclear Information System (INIS)
Fujiwara, A.; Tashiro, S.; Ikari, S.; Suzuki, A.
1993-01-01
In order to propose advanced designs of repositories with enhanced engineered barriers of relatively high radioactive wastes such as burnable poisons, channel boxes, control rods and highly irradiated metals, studies started in 1987 and completed the first phase in 1992. This paper presents the framework and brief results of the first phase. The studies set preliminary design concepts of the repositories with various combinations with engineered barriers and natural barriers for different models and locations such as a silo type in shallow land or a tunnel type in intermediate depth. Through the designs, four component technics were picked up and studied for (1) construction of the components in repository; (2) performance evaluation to realize repository design; (3) improvement of circumstances inside or around repository; and (4) surveillance of repository performance to realize the repository designs. Finally, some repository systems were provided using obtained results, and then the applicability and the economy were evaluated. The studies will continue to the second phase focusing on the long-term performance of the repositories
Visual querying and analysis of large software repositories
Voinea, Lucian; Telea, Alexandru
We present a software framework for mining software repositories. Our extensible framework enables the integration of data extraction from repositories with data analysis and interactive visualization. We demonstrate the applicability of the framework by presenting several case studies performed on
Institutional Repositories in Indian Universities and Research Institutes: A Study
Krishnamurthy, M.; Kemparaju, T. D.
2011-01-01
Purpose: The purpose of this paper is to report on a study of the institutional repositories (IRs) in use in Indian universities and research institutes. Design/methodology/approach: Repositories in various institutions in India were accessed and described in a standardised way. Findings: The 20 repositories studied covered collections of diverse…
The Use of Digital Repositories for Enhancing Teacher Pedagogical Performance
Cohen, Anat; Kalimi, Sharon; Nachmias, Rafi
2013-01-01
This research examines the usage of local learning material repositories at school, as well as related teachers' attitudes and training. The study investigates the use of these repositories for enhancing teacher performance and assesses whether the assimilation of the local repositories increases their usage of and contribution to by teachers. One…
Oceanographic Data Repositories: An Analysis of the International Situation
Directory of Open Access Journals (Sweden)
Fabiano Couto Corrêa da Silva
2017-04-01
Full Text Available The preservation and organization of oceanographic research data enables the scientific community to consult and reuse information of different kinds, and this is made possible by the repositories, meaning the services that facilitate data storage and dissemination. This paper reviews the current situation of oceanographic data repositories across different countries and evaluates them according to a series of indicators. The writers propose that although interest in storing and reusing oceanographic data has increased in recent years, the repositories are still in the process of developing their systems for processing, disseminating and reusing data. The repositories also differ in terms of architecture and the organizational level of the content they offer.
Park, Gun Wook; Hwang, Heeyoun; Kim, Kwang Hoe; Lee, Ju Yeon; Lee, Hyun Kyoung; Park, Ji Yeong; Ji, Eun Sun; Park, Sung-Kyu Robin; Yates, John R; Kwon, Kyung-Hoon; Park, Young Mok; Lee, Hyoung-Joo; Paik, Young-Ki; Kim, Jin Young; Yoo, Jong Shin
2016-11-04
In the Chromosome-Centric Human Proteome Project (C-HPP), false-positive identification by peptide spectrum matches (PSMs) after database searches is a major issue for proteogenomic studies using liquid-chromatography and mass-spectrometry-based large proteomic profiling. Here we developed a simple strategy for protein identification, with a controlled false discovery rate (FDR) at the protein level, using an integrated proteomic pipeline (IPP) that consists of four engrailed steps as follows. First, using three different search engines, SEQUEST, MASCOT, and MS-GF+, individual proteomic searches were performed against the neXtProt database. Second, the search results from the PSMs were combined using statistical evaluation tools including DTASelect and Percolator. Third, the peptide search scores were converted into E-scores normalized using an in-house program. Last, ProteinInferencer was used to filter the proteins containing two or more peptides with a controlled FDR of 1.0% at the protein level. Finally, we compared the performance of the IPP to a conventional proteomic pipeline (CPP) for protein identification using a controlled FDR of <1% at the protein level. Using the IPP, a total of 5756 proteins (vs 4453 using the CPP) including 477 alternative splicing variants (vs 182 using the CPP) were identified from human hippocampal tissue. In addition, a total of 10 missing proteins (vs 7 using the CPP) were identified with two or more unique peptides, and their tryptic peptides were validated using MS/MS spectral pattern from a repository database or their corresponding synthetic peptides. This study shows that the IPP effectively improved the identification of proteins, including alternative splicing variants and missing proteins, in human hippocampal tissues for the C-HPP. All RAW files used in this study were deposited in ProteomeXchange (PXD000395).
Energy Technology Data Exchange (ETDEWEB)
Artmann, Andreas; Larue, Juergen; Seher, Holger; Weiss, Dietmar
2014-08-15
The project of application and further development of models for the final repository safety analyses on the clearance of radioactive materials for disposal is aimed to study the long-term safety using repository-specific simulation programs with respect to radiation exposure for different scenarios. It was supposed to investigate whether the 10 micro Sv criterion can be guaranteed under consideration of human intrusion scenarios. The report covers the following issues: selection and identification of models and codes and the definition of boundary conditions; applicability of conventional repository models for long-term safety analyses; modeling results for the pollutant release and transport and calculation of radiation exposure; determination of the radiation exposure.
International Nuclear Information System (INIS)
Swanson, J.S.; Reed, D.T.; Cherkouk, A.; Arnold, T.; Meleshyn, A.; Patterson, Russ
2018-01-01
For the past several decades, the Nuclear Energy Agency Salt Club has been supporting and overseeing the characterisation of rock salt as a potential host rock for deep geological repositories. This extensive evaluation of deep geological settings is aimed at determining - through a multidisciplinary approach - whether specific sites are suitable for radioactive waste disposal. Studying the microbiology of granite, basalt, tuff, and clay formations in both Europe and the United States has been an important part of this investigation, and much has been learnt about the potential influence of microorganisms on repository performance, as well as about deep subsurface microbiology in general. Some uncertainty remains, however, around the effects of microorganisms on salt-based repository performance. Using available information on the microbial ecology of hyper-saline environments, the bioenergetics of survival under high ionic strength conditions and studies related to repository microbiology, this report summarises the potential role of microorganisms in salt-based radioactive waste repositories
Effects of repository conditions on environmental impact reduction by recycling
International Nuclear Information System (INIS)
Ahn, Joonhong
2010-01-01
The environmental impacts (EI) of high-level wastes (HLW) disposed of in a water-saturated repository (WSR) and in the Yucca Mountain Repository (YMR) for various fuel cycle cases have been evaluated and compared to observe the difference in the recycling effects for differing repository conditions. With the impacts of direct spent fuel disposal in each repository as the reference level, separation of actinides by Urex+ and borosilicate vitrification clearly reduces the environmental impacts of YMR, while separation by Purex and borosilicate vitrification would not necessarily reduce the environmental impact of WSR. (authors)
International Nuclear Information System (INIS)
Stenhouse, M.J.; Miller, W.M.; Chapman, N.A.
2001-05-01
Scenario development is a key component of the performance assessment (PA) process for radioactive waste disposal, the primary objective being to ensure that all relevant factors associated with the future evolution of the repository system are properly considered in PA. As part of scenario development, a list of features, events and processes (FEPs) are identified and assembled, representing the Process System, with interactions/influences between FEPs incorporated in a Process Influence Diagram (PID). This report documents the technical work conducted between 1997 and the end of 1999 under the Systems Studies Project. The overall objective of this project has been the construction of a PID for the SFR-1 repository (final repository for reactor waste), this PID being the first stage in the identification of scenarios to describe future evolution of this repository. The PIDs discussed in this report have been created using two software applications: existing commercial software (Business Modeller, Infotool AB. Stockholm, Sweden) and, more recently, a newly developed software tool SPARTA (Enviros QuantiSci, Henley, U.K.). Although the focus of this report is on the application of SPARTA to PID development, it is important to document the work carried out prior to SPARTA being available, in order to provide a complete record of the entire SFR-1 PID development effort as well as preserving the context of the multi-year project. Following a description of the different disposal sections of the SFR-1 and the various near-field barriers, the sequential development (i.e. near-field of Silo, BMA, BLA, BTF sections; far-field; integrated near-field + far-field) of the PID for SFR-1 repository system using Business Modeller is described. Owing to the complexity of the repository, in terms of number of both different disposal sections (Silo, BLA, BMA, BTF) and barriers associated with each section, the two-dimensional (2D) PID created for SFR-1 using Business Modeller is
Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.
2015-11-01
Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.
Czech Republic. Dukovany repository
International Nuclear Information System (INIS)
2001-01-01
Full text: The repository at the Dukovany site is a structure located above the land surface. It consists of two double-rows of reinforced concrete vaults. Each double-row has dimensions 38x160x6 meters and contains 2x28 vaults. The internal dimensions of each vault are 18x6x5.4 meters. The repository serves for reactor wastes from the Dukovany and Temelin nuclear power plants (NPPs). Its capacity is 55,000 m 3 or 130,000 drums. The repository is a fully engineered facility with multiple barriers. The first engineered barrier is the waste form (in the case of waste from the Dukovany NPP, the waste form is mainly bitumen, but concrete and glass are also considered as suitable solidification products). The second barrier is the container (a 200 litre steel drum or a HIC container), whereas the third consists of cut-off reinforced concrete walls with asphalt-based hydro-insulation. The fourth barrier is a cap which should protect the vaults against infiltration of rainwater and should serve also as an intrusion and erosion barrier. The fifth barrier is a drainage system around the repository which is composed of layers of gravel and sand. The void space in drums around the waste is filled with specially composed grout. Such waste packages are emplaced into the disposal vault, which is covered by pre-fabricated panels. Thereafter, joints between the panels are sealed and a provisional coverage added; the final cover, however, will be constructed only over the whole row of 28 vaults, until all vaults are filled with waste. The final cover will encompass the following components: reinforced concrete pre-fabricated panels (500 mm); cement overcoat (30 mm); insulation foil; concrete layer for cap levelling (5-150 mm); layer of asphalto-propylene concrete (150 mm); soil (450 mm); geotextile foil with topsoil (top surface vegetation). (author)
Species identification of archaeological skin objects from Danish bogs
DEFF Research Database (Denmark)
Brandt, Luise Ørsted; Schmidt, Anne Lisbeth; Mannering, Ulla
2014-01-01
environment of peat bogs leading to morphological and molecular degradation within the samples. We compared species assignment results of twelve archaeological skin samples from Danish bogs using Mass Spectrometry (MS)-based peptide sequencing, against results obtained using light and scanning electron...... microscopy. While it was difficult to obtain reliable results using microscopy, MS enabled the identification of several species-diagnostic peptides, mostly from collagen and keratins, allowing confident species discrimination even among taxonomically close organisms, such as sheep and goat. Unlike previous...
Ashok, N R; Aparna, H S
2017-08-01
Whey based peptides are well known for their nutritional and multifunctional properties. In this context, whey proteins from buffalo colostrum & milk were digested by in vitro simulation digestion and analyzed by nano-LC-MS/MS. Functional protein association networks, gene annotations and localization of identified proteins were carried out. An ACE inhibitory peptide sorted from the library was custom synthesized and an in vitro ACE assay was performed. The study led to the identification of 74 small peptides which were clustered into 5 gene functional groups and majority of them were secretory proteins. Among the identified peptides, majority of them were found identical to angiotensin I-converting enzyme (ACE) inhibitors, antioxidant, antimicrobial, immunomodulatory and opioidal peptides. An octapeptide (m/z - 902.51, IQKVAGTW) synthesized was found to inhibit ACE with an IC 50 of 300±2µM. The present investigation thus establishes newer vista for food derived peptides having ACE inhibitory potential for nutraceutical or therapeutic applications. Copyright © 2017 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Acar, Handan [Institute; Department; Samaeekia, Ravand [Institute; Department; Schnorenberg, Mathew R. [Institute; Department; Medical; Sasmal, Dibyendu K. [Institute; Huang, Jun [Institute; Tirrell, Matthew V. [Institute; Institute; LaBelle, James L. [Department
2017-08-24
Peptides synthesized in the likeness of their native interaction domain(s) are natural choices to target protein protein interactions (PPIs) due to their fidelity of orthostatic contact points between binding partners. Despite therapeutic promise, intracellular delivery of biofunctional peptides at concentrations necessary for efficacy remains a formidable challenge. Peptide amphiphiles (PAs) provide a facile method of intracellular delivery and stabilization of bioactive peptides. PAs consisting of biofunctional peptide headgroups linked to hydrophobic alkyl lipid-like tails prevent peptide hydrolysis and proteolysis in circulation, and PA monomers are internalized via endocytosis. However, endocytotic sequestration and steric hindrance from the lipid tail are two major mechanisms that limit PA efficacy to target intracellular PPIs. To address these problems, we have constructed a PA platform consisting of cathepsin-B cleavable PAs in which a selective p53-based inhibitory peptide is cleaved from its lipid tail within endosomes, allowing for intracellular peptide accumulation and extracellular recycling of the lipid moiety. We monitor for cleavage and follow individual PA components in real time using a resonance energy transfer (FRET)-based tracking system. Using this platform, components in real time using a Forster we provide a better understanding and quantification of cellular internalization, trafficking, and endosomal cleavage of PAs and of the ultimate fates of each component.
International Nuclear Information System (INIS)
1987-07-01
This MRS Facility and Salt Repository Integration Study evaluates the impacts of an integrated MRS/Salt Repository Waste Management System on the Salt Repository Surface facilities' design, operations, cost, and schedule. Eight separate cases were studied ranging from a two phase repository design with no MRS facility to a design in which the repository only received package waste from the MRS facility for emplacement. The addition of the MRS facility to the Waste Management System significantly reduced the capital cost of the salt repository. All but one of the cases studied were capable of meeting the waste acceptance data. The reduction in the size and complexity of the Salt Repository waste handling building with the integration of the MRS facility reduces the design and operating staff requirements. 7 refs., 35 figs., 43 tabs
Automated genome mining of ribosomal peptide natural products
Energy Technology Data Exchange (ETDEWEB)
Mohimani, Hosein; Kersten, Roland; Liu, Wei; Wang, Mingxun; Purvine, Samuel O.; Wu, Si; Brewer, Heather M.; Pasa-Tolic, Ljiljana; Bandeira, Nuno; Moore, Bradley S.; Pevzner, Pavel A.; Dorrestein, Pieter C.
2014-07-31
Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity (1). In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic datasets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs and apply it for lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connection of multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 as the first natural product to be identified in an automated fashion by genome mining. The presented tool is available at cy-clo.ucsd.edu.
DEFF Research Database (Denmark)
Mucci, Juan; Carmona, Santiago J.; Volcovich, Romina
2017-01-01
Chagas Disease, caused by the protozoan Trypanosoma cruzi, is a major health and economic problem in Latin America for which no vaccine or appropriate drugs for large-scale public health interventions are yet available. Accurate diagnosis is essential for the early identification and follow up....... cruzi linear B-cell epitopes using high-density peptide chips, leading to the identification of several hundred novel sequence signatures associated to chronic Chagas Disease. Here, we performed a serological assessment of 27 selected epitopes and of their use in a novel multipeptide-based diagnostic...... method. A combination of 7 of these peptides were finally evaluated in ELISA format against a panel of 199 sera samples (Chagas-positive and negative, including sera from Leishmaniasis-positive subjects). The multipeptide formulation displayed a high diagnostic performance, with a sensitivity of 96...
Monte Carlo simulations for generic granite repository studies
Energy Technology Data Exchange (ETDEWEB)
Chu, Shaoping [Los Alamos National Laboratory; Lee, Joon H [SNL; Wang, Yifeng [SNL
2010-12-08
In a collaborative study between Los Alamos National Laboratory (LANL) and Sandia National Laboratories (SNL) for the DOE-NE Office of Fuel Cycle Technologies Used Fuel Disposition (UFD) Campaign project, we have conducted preliminary system-level analyses to support the development of a long-term strategy for geologic disposal of high-level radioactive waste. A general modeling framework consisting of a near- and a far-field submodel for a granite GDSE was developed. A representative far-field transport model for a generic granite repository was merged with an integrated systems (GoldSim) near-field model. Integrated Monte Carlo model runs with the combined near- and farfield transport models were performed, and the parameter sensitivities were evaluated for the combined system. In addition, a sub-set of radionuclides that are potentially important to repository performance were identified and evaluated for a series of model runs. The analyses were conducted with different waste inventory scenarios. Analyses were also conducted for different repository radionuelide release scenarios. While the results to date are for a generic granite repository, the work establishes the method to be used in the future to provide guidance on the development of strategy for long-term disposal of high-level radioactive waste in a granite repository.
Implementing digital preservation in repositories: Knowledge and practices
Directory of Open Access Journals (Sweden)
Caterina Groposo Pavão
2016-09-01
Full Text Available Digital preservation has to be undertaken by institutional repositories, which are responsible for the preservation of the scientific output from academic institutions. However, due to the constant evolution of the field, to gain domain knowledge and recognise best practices is a complex task for people responsible for digital preservation in those institutions. Digital preservation research, practices and solutions address specific problems, such as formats, curation, reference models, authenticity, policies and preservation plans, tools, etc., while stakeholders need an integrated, contextualized and applicable overview. This paper focuses on the implementation of digital preservation in repositories, from the perspective of the team responsible for the project, regarding the necessary knowledge and best practices. Initially, it defines and contextualizes digital preservation repositories. The following section presents a conceptual model of digital preservation, synthesized from conceptual models developed in influential projects in the field, which allows us to identify the domain knowledge in digital preservation. Finally, aspects represented in the model are discussed in the light of the performance of teams implementing digital preservation repositories. It provides recommendations, guides and examples that may be useful for the implementation of digital preservation. It points to the need to strengthen the relationship between domain knowledge in digital preservation repositories with practices developed in numerous projects developed worldwide.
Mapping of Epitopes Occurring in Bovine α(s1)-Casein Variants by Peptide Microarray Immunoassay.
Lisson, Maria; Erhardt, Georg
2016-01-01
Immunoglobulin E epitope mapping of milk proteins reveals important information about their immunologic properties. Genetic variants of αS1-casein, one of the major allergens in bovine milk, are until now not considered when discussing the allergenic potential. Here we describe the complete procedure to assess the allergenicity of αS1-casein variants B and C, which are frequent in most breeds, starting from milk with identification and purification of casein variants by isoelectric focusing (IEF) and anion-exchange chromatography, followed by in vitro gastrointestinal digestion of the casein variants, identification of the resulting peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), in silico analysis of the variant-specific peptides as allergenic epitopes, and determination of their IgE-binding properties by microarray immunoassay with cow's milk allergic human sera.
Monitoring of geological repositories for high level radioactive waste
International Nuclear Information System (INIS)
2001-04-01
Geological repositories for disposal of high level radioactive waste are designed to provide isolation of the waste from human environment for many thousands of years. This report discusses the possible purposes for monitoring geological repositories at the different stages of a repository programme, the use that may be made of the information obtained and the techniques that might be applied. This report focuses on the different objectives that monitoring might have at various stages of a programme, from the initiation of work on a candidate site, to the period after repository closure. Each objective may require somewhat different types of information, or may use the same information in different ways. Having evaluated monitoring requirements, the report concludes with a brief evaluation of available monitoring techniques
Integrating repositories with fuel cycles: The airport authority model
Energy Technology Data Exchange (ETDEWEB)
Forsberg, C. [Massachusetts Inst. of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307 (United States)
2012-07-01
The organization of the fuel cycle is a legacy of World War II and the cold war. Fuel cycle facilities were developed and deployed without consideration of the waste management implications. This led to the fuel cycle model of a geological repository site with a single owner, a single function (disposal), and no other facilities on site. Recent studies indicate large economic, safety, repository performance, nonproliferation, and institutional incentives to collocate and integrate all back-end facilities. Site functions could include geological disposal of spent nuclear fuel (SNF) with the option for future retrievability, disposal of other wastes, reprocessing with fuel fabrication, radioisotope production, other facilities that generate significant radioactive wastes, SNF inspection (navy and commercial), and related services such as SNF safeguards equipment testing and training. This implies a site with multiple facilities with different owners sharing some facilities and using common facilities - the repository and SNF receiving. This requires a different repository site institutional structure. We propose development of repository site authorities modeled after airport authorities. Airport authorities manage airports with government-owned runways, collocated or shared public and private airline terminals, commercial and federal military facilities, aircraft maintenance bases, and related operations - all enabled and benefiting the high-value runway asset and access to it via taxi ways. With a repository site authority the high value asset is the repository. The SNF and HLW receiving and storage facilities (equivalent to the airport terminal) serve the repository, any future reprocessing plants, and others with needs for access to SNF and other wastes. Non-public special-built roadways and on-site rail lines (equivalent to taxi ways) connect facilities. Airport authorities are typically chartered by state governments and managed by commissions with members
Integrating repositories with fuel cycles: The airport authority model
International Nuclear Information System (INIS)
Forsberg, C.
2012-01-01
The organization of the fuel cycle is a legacy of World War II and the cold war. Fuel cycle facilities were developed and deployed without consideration of the waste management implications. This led to the fuel cycle model of a geological repository site with a single owner, a single function (disposal), and no other facilities on site. Recent studies indicate large economic, safety, repository performance, nonproliferation, and institutional incentives to collocate and integrate all back-end facilities. Site functions could include geological disposal of spent nuclear fuel (SNF) with the option for future retrievability, disposal of other wastes, reprocessing with fuel fabrication, radioisotope production, other facilities that generate significant radioactive wastes, SNF inspection (navy and commercial), and related services such as SNF safeguards equipment testing and training. This implies a site with multiple facilities with different owners sharing some facilities and using common facilities - the repository and SNF receiving. This requires a different repository site institutional structure. We propose development of repository site authorities modeled after airport authorities. Airport authorities manage airports with government-owned runways, collocated or shared public and private airline terminals, commercial and federal military facilities, aircraft maintenance bases, and related operations - all enabled and benefiting the high-value runway asset and access to it via taxi ways. With a repository site authority the high value asset is the repository. The SNF and HLW receiving and storage facilities (equivalent to the airport terminal) serve the repository, any future reprocessing plants, and others with needs for access to SNF and other wastes. Non-public special-built roadways and on-site rail lines (equivalent to taxi ways) connect facilities. Airport authorities are typically chartered by state governments and managed by commissions with members
Peptides reproducibly released by in vivo digestion of beef meat and trout flesh in pigs.
Bauchart, Caroline; Morzel, Martine; Chambon, Christophe; Mirand, Philippe Patureau; Reynès, Christelle; Buffière, Caroline; Rémond, Didier
2007-12-01
Characterisation and identification of peptides (800 to 5000 Da) generated by intestinal digestion of fish or meat were performed using MS analyses (matrix-assisted laser desorption ionisation time of flight and nano-liquid chromatography electrospray-ionisation ion trap MS/MS). Four pigs fitted with cannulas at the duodenum and jejunum received a meal exclusively made of cooked Pectoralis profundus beef meat or cooked trout fillets. A protein-free meal, made of free amino acids, starch and fat, was used to identify peptides of endogenous origin. Peptides reproducibly detected in digesta (i.e. from at least three pigs) were evidenced predominantly in the first 3 h after the meal. In the duodenum, most of the fish- and meat-derived peptides were characteristic of a peptic digestion. In the jejunum, the majority of peptides appeared to result from digestion by chymotrypsin and trypsin. Despite slight differences in gastric emptying kinetics and overall peptide production, possibly in relation to food structure and texture, six and four similar peptides were released after ingestion of fish or meat in the duodenum and jejunum. A total of twenty-six different peptides were identified in digesta. All were fragments of major structural (actin, myosin) or sarcoplasmic (creatine kinase, glyceraldehyde-3-phosphate dehydrogenase and myoglobin) muscle proteins. Peptides were short ( digestion, some of them can be reproducibly observed in intestinal digesta.
Overly Honest Data Repository Development
Directory of Open Access Journals (Sweden)
Colleen Fallaw
2016-10-01
Full Text Available After a year of development, the library at the University of Illinois at Urbana-Champaign has launched a repository, called the Illinois Data Bank (https://databank.illinois.edu/, to provide Illinois researchers with a free, self-serve publishing platform that centralizes, preserves, and provides persistent and reliable access to Illinois research data. This article presents a holistic view of development by discussing our overarching technical, policy, and interface strategies. By openly presenting our design decisions, the rationales behind those decisions, and associated challenges this paper aims to contribute to the library community's work to develop repository services that meet growing data preservation and sharing needs.
Initial design process of the repository
International Nuclear Information System (INIS)
Osmanlioglu, A.E.
2001-01-01
The concept of the final disposal of high level wastes is to isolate the waste from the biosphere for extremely long periods of time by emplacement of wastes into deep stable geological formations. Several geological formations have been considered as candidate host environments for high level waste disposal and several techniques have been developed for repository design. In this study, interrelationships of main parameters of a general repository design have been defined and effective parameters are shown at each step. Initial design process is based on the long term stability of underground openings as disposal galleries. For this reason, this design process includes two main analyses: mechanical analysis and thermal analysis. Each of the analysis systems is directly related to each other by technical precautions. As a result of this design process, general information about the acceptable depth of the repository, layout and emplacement pattern can be taken. Final design study can be established on the result of initial design process. (author)
Geologic nuclear waste repository site selection studies in the Paradox Basin, Utah
International Nuclear Information System (INIS)
Rogers, T.H.; Conwell, F.R.
1981-01-01
During Phase I regional-level studies, a literature review was conducted to ascertain geologic characteristics pertinent to repository siting factors. On the basis of the regional screening results, four areas in southeastern Utah were selected as being suitable for more detailed study in Phase II: Elk Ridge and Gibson Dome, containing nearly horizontal bedded salt deposits; Salt Valley, containing a diapiric salt anticline; and Lisbon Valley, containing a non-diapiric salt anticline. During current Phase II area studies, the four study areas are being characterized in greater detail than in Phase I. Phase II will culminate in the identification of a potentially suitable location(s), if any, that will be recommended for study in still greater detail in a subsequent phase of work. 5 refs
International Nuclear Information System (INIS)
Jensen, M.R.
2007-01-01
Within the Deep Geologic Repository Technology Programme (DGRTP) several Geoscience activities are focused on advancing the understanding of groundwater flow system evolution and geochemical stability in a Canadian Shield setting as affected by long-term climate change. A key aspect is developing confidence in predictions of groundwater flow patterns and residence times as they relate to the safety of a deep geologic repository for used nuclear fuel waste. This is being achieved through a coordinated multi-disciplinary approach intent on: i) demonstrating coincidence between independent geo-scientific data; ii) improving the traceability of geo-scientific data and its interpretation within a conceptual descriptive model(s); iii) improving upon methods to assess and demonstrate robustness in flow domain prediction(s) given inherent flow domain uncertainties (i.e. spatial chemical/physical property distributions, boundary conditions) in time and space; and iv) improving awareness amongst geo-scientists as to the utility of various geo-scientific data in supporting a safety case for a deep geologic repository. This multi-disciplinary DGRTP approach is yielding an improved understanding of groundwater flow system evolution and stability in Canadian Shield settings that is further contributing to the geo-scientific basis for understanding and communicating aspects of DGR safety. (author)
Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping.
Mukherjee, Sumanta; Warwicker, Jim; Chandra, Nagasuma
2015-07-01
T-cell responses in humans are initiated by the binding of a peptide antigen to a human leukocyte antigen (HLA) molecule. The peptide-HLA complex then recruits an appropriate T cell, leading to cell-mediated immunity. More than 2000 HLA class-I alleles are known in humans, and they vary only in their peptide-binding grooves. The polymorphism they exhibit enables them to bind a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern, as many peptides bind to a given allele and a given peptide can be recognized by many alleles. A powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. We present a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification was obtained, with 7 supergroups, each further subclassifying to yield 72 groups. An independent clustering performed based only on similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explain the basis of clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues contributing to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants.
International Nuclear Information System (INIS)
Rojanasakul, Y.
1989-01-01
Two major aspects of corneal peptide absorption, namely the transport mechanisms and the promoting effect of some penetration enhancers, were investigated. Studies on transport mechanisms involve (a) identification of transport pathways of peptides across the cornea, (b) determination of rate-limiting barrier(s) for peptide absorption, and (c) permselective properties of the cornea. To study the transport pathways of peptides, four model peptides differing in molecular size and charge were either fluorescently or radioactively labeled and their movement across the cornea was detected by laser scanning confocal microscopy and autoradiography. Results from these studies indicate that peptides can penetrate the cornea via different pathways, depending on the physicochemical properties and membrane specificity of the peptides. In all cases, the outermost layer of the corneal epithelium presents the rate-limiting barrier for peptide absorption. The results also indicate a charge discrimination effect to transport of negatively charged peptides. In permselectivity studies, it has been shown that the cornea, due to the presence of ionizable charged groups, is amphoteric and exhibits dual selective characteristics to transport of charged molecules. At pH's above the isoelectric point, 3.2, the cornea carries a net negative charge and is selective to positively-charged molecules. Below the isoelectric pH, the reverse is valid. The promoting mechanisms of penetration enhancers were studied microscopically using confocal fluorescence microscopy with the aid of a specific fluorescent membrane probe (3,3'-dioctadecyloxacarbocyanine) and a non-permeating polar tracer. All enhancers, including chelators, non-ionic surfactants, bile salts, and cytoskeleton-active agents, significantly increase membrane permeability depending on concentration and exposure time
Qiao, Xiaoqiang; Zhou, Yuan; Hou, Chunyan; Zhang, Xiaodan; Yang, Kaiguang; Zhang, Lihua; Zhang, Yukui
2013-03-01
The cationic reagent 1-(3-aminopropyl)-3-butylimidazolium bromide (BAPI) was exploited for the derivatization of carboxyl groups on peptides. Nearly 100% derivatization efficiency was achieved with the synthetic peptide RVYVHPI (RI-7). Furthermore, the peptide derivative was stable in a 0.1% TFA/water solution or a 0.1% (v/v) TFA/acetonitrile/water solution for at least one week. The effect of BAPI derivatization on the ionization of the peptide RI-7 was further investigated, and the detection sensitivity was improved >42-fold via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), thus outperforming the commercial piperazine derivatization approach. Moreover, the charge states of the peptide were largely increased via BAPI derivatization by electrospray ionization (ESI) MS. The results indicate the potential merits of BAPI derivatization for high sensitivity peptide analysis by MS.
Digital Preservation in the Context of Institutional Repositories
Hockx-Yu, Helen
2006-01-01
Purpose: To discuss the issues and challenges of digital preservation facing institutional repositories and to illustrate the Joint Information Systems Committee's (JISC) view on institutional repositories and its key initiatives in helping UK institutions address these issues. Design/methodology/approach: A combination of published work and JISC…
General construction requirements for the deep repository in the KBS-3 system
International Nuclear Information System (INIS)
2002-10-01
The KBS-3 systems includes equipment and plants for transport of spent nuclear fuels and encapsulated spent fuels, central intermediate storage, encapsulation and deep geologic disposal. The requirements in this document concern the repository and have been put together in view of the tasks of designing, constructing and building the repository. The report presents: A general review of existing design plans; Laws and regulations relevant for the design of the repository; How the regulations have been broken down to functional demands and dimensioning requirements for the repository; How the site conditions influence the design, and how the layout of the different parts of the repository interact; Relations between the functions of the repository, the safety and the design; A foundation for developing construction plans for the repository. The requirements will be collected in a database that will develop as new knowledge is collected
Global thermo-mechanical effects from a KBS-3 type repository
International Nuclear Information System (INIS)
Hakami, E.; Olofsson, Stig-Olof
1998-01-01
The objective of this study has been to identify the global thermo-mechanical effects in the bedrock hosting a nuclear waste repository. Numerical thermo-mechanical modeling using distinct element models was performed. The number of fracture zones, the heat intensity of the waste, the material properties of the rock mass and the boundary conditions of the models were varied. Different models for multi-level repositories were also analyzed and compared to the main single-level case. Further, the global influence from the excavation of repository tunnels and deposition holes was examined by introducing weaker rock mass material properties in the repository region of one model. The maximum compression stress obtained for the main model is 44 MPa and occurs at the repository level after about 100 years of deposition. Due to thermal expansion, the rock mass displaces upward, and the maximum heave at the ground surface after 1000 years is calculated to be 16 cm. In the area close to the ground surface the horizontal stresses reduce, causing the rock to yield in tension down to a depth of about 80 meters. The fracture zones show opening displacements at shallow depths and closing and shearing at the repository level. The maximum displacements are 0.3-2.5 cm for closing, 0.0-0.8 cm for opening and 0.2-2.2 cm for shearing. The resultant stresses and displacements depend in large part on the assumptions made concerning the heat intensity of the waste. In the main model, an initial heat intensity of 10 W/m 2 is assumed, which gives larger effects than the case with 6 W/m 2 . Another important input parameter for the analysis is the Young's modulus of the rock mass. In the main model, a value of 30 GPa is assumed. Higher values of Young's modulus give larger thermo-mechanical effects. All multi-level repository layouts give rise to higher temperatures than the single-level layout, causing the compressive stresses to increase more at the repository level. The multi
Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags
DEFF Research Database (Denmark)
Hägglund, Per; Bunkenborg, Jakob; Maeda, Kenji
2014-01-01
Thioredoxins (Trx) are small redox proteins that reduce disulfide bonds in various target proteins and maintain cellular thiol redox control. Here, a thiol-specific labeling and affinity enrichment approach for identification and relative quantification of Trx target disulfides in complex protein...... reduction is determined by LC-MS/MS-based quantification of tryptic peptides labeled with "light" (12C) and "heavy" (13C) ICAT reagents. The methodology can be adapted to monitor the effect of different reductants or oxidants on the redox status of thiol/disulfide proteomes in biological systems....... extracts is described. The procedure utilizes the isotope-coded affinity tag (ICAT) reagents containing a thiol reactive iodoacetamide group and a biotin affinity tag to target peptides containing reduced cysteine residues. The identification of substrates for Trx and the extent of target disulfide...
Underground excavation methods for a high-level waste repository
International Nuclear Information System (INIS)
Peshel, J.; Gupta, D.; Nataraja, M.
1990-01-01
This paper reports on rock excavation methods for a High-Level Waste repository that should be selected to limit the potential for creating preferential pathways for groundwater to travel to the waste packages or for radionuclides to migrate to the accessible environment. The use of water and other foreign substances should be controlled so that the repository performance is not compromised. The excavated openings should remain stable so that operations can be carried out safely and the retrievability option maintained. As per the current conceptual designs presented by the Department of Energy, the exploratory shaft facility becomes a part of the repository if the Yucca Mountain site is found suitable for repository development. Therefore, the methods of constructing the underground openings should be compatible with the performance requirements for the repository. Also, the degree of damage to the rock surrounding the openings and the extent of the damage zone should not preclude adequate site characterization. The ESf construction and operation should be compatible with the site data gathering activities, such as geological, thermomechanical, hydrological and geochemical testing
Reference design description for a geologic repository. Revision 02
International Nuclear Information System (INIS)
1999-01-01
This Reference Design Description explains the current design for a potential geologic repository that may be located at Yucca Mountain in Nevada. It describes the proposed design for a surface facility, subsurface repository, and waste packaging; it also presents the current design of the key engineering systems for the final four phases: operations, monitoring, closure, and postclosure. In addition, this Reference Design Description reviews the expected long-term performance of the potential repository. In accordance with current law, this design does not include an interim storage option. This document has six major sections. Section 1 describes the physical layout of the proposed repository. The second section describes the 4-phase evolution of the development of the proposed repository. Section 3 describes the reception of waste from offsite locations. The fourth section details the various systems that will package the waste and move it below ground as well as safety monitoring and closure. Section 5 describes the systems (both physical and analytical) that ensure continued safety after closure. The final section offers design options that may be adopted to increase the margin of safety
Environmental effects on corrosion in the Tuff repository
International Nuclear Information System (INIS)
Beavers, J.A.; Thompson, N.G.
1990-02-01
Cortest Columbus is investigating the long-term performance of container materials used for high-level waste packages as part of the information needed by the Nuclear Regulatory Commission to assess the Department of Energy's application to construct a geologic repository for high-level radioactive waste. The scope of work consists of employing short-term techniques, to examine a wide range of possible failure modes. Long-term tests are being used to verify and further examine specific failure modes identified as important by the short-term studies. The original focus of the program was on the salt repository but the emphasis was shifted to the Tuff repository. This report summarizes the results of a literature survey performed under Task 1 of the program. The survey focuses on the influence of environmental variables on the corrosion behavior of candidate container materials for the Tuff repository. Environmental variables considered include: radiation, thermal and microbial effects. 80 refs., 44 figs., 44 tabs
Future extension of the Swedish repository for low and intermediate level waste (SFR)
International Nuclear Information System (INIS)
Carlsson, Jan
2006-01-01
The existing Swedish repository for low and intermediate level waste (SFR) is licensed for disposal of short-lived waste originated from operation and maintenance of Swedish nuclear power plants. The repository is foreseen to be extended to accommodate short-lived waste from the future decommissioning of the Nuclear Power Plants. Long-lived waste from operation, maintenance and eventually decommissioning will be stored some years before disposal in a geological repository. This repository can be build either as a further extension of the SFR facility or as a separate repository. This paper discusses the strategy of a step-wise extended repository where the extensions are performed during operation of the existing parts of the repository. It describes the process for licensing new parts of the repository (and re-license of the existing parts). (author)
Jappe, Emma Christine; Kringelum, Jens; Trolle, Thomas; Nielsen, Morten
2018-02-15
Peptides that bind to and are presented by MHC class I and class II molecules collectively make up the immunopeptidome. In the context of vaccine development, an understanding of the immunopeptidome is essential, and much effort has been dedicated to its accurate and cost-effective identification. Current state-of-the-art methods mainly comprise in silico tools for predicting MHC binding, which is strongly correlated with peptide immunogenicity. However, only a small proportion of the peptides that bind to MHC molecules are, in fact, immunogenic, and substantial work has been dedicated to uncovering additional determinants of peptide immunogenicity. In this context, and in light of recent advancements in mass spectrometry (MS), the existence of immunological hotspots has been given new life, inciting the hypothesis that hotspots are associated with MHC class I peptide immunogenicity. We here introduce a precise terminology for defining these hotspots and carry out a systematic analysis of MS and in silico predicted hotspots. We find that hotspots defined from MS data are largely captured by peptide binding predictions, enabling their replication in silico. This leads us to conclude that hotspots, to a great degree, are simply a result of promiscuous HLA binding, which disproves the hypothesis that the identification of hotspots provides novel information in the context of immunogenic peptide prediction. Furthermore, our analyses demonstrate that the signal of ligand processing, although present in the MS data, has very low predictive power to discriminate between MS and in silico defined hotspots. © 2018 John Wiley & Sons Ltd.
Rigby, Susan; Procop, Gary W.; Haase, Gerhard; Wilson, Deborah; Hall, Geraldine; Kurtzman, Cletus; Oliveira, Kenneth; Von Oy, Sabina; Hyldig-Nielsen, Jens J.; Coull, James; Stender, Henrik
2002-01-01
A new fluorescence in situ hybridization (FISH) method that uses peptide nucleic acid (PNA) probes for identification of Candida albicans directly from positive-blood-culture bottles in which yeast was observed by Gram staining (herein referred to as yeast-positive blood culture bottles) is described. The test (the C. albicans PNA FISH method) is based on a fluorescein-labeled PNA probe that targets C. albicans 26S rRNA. The PNA probe is added to smears made directly from the contents of the blood culture bottle and hybridized for 90 min at 55°C. Unhybridized PNA probe is removed by washing of the mixture (30 min), and the smears are examined by fluorescence microscopy. The specificity of the method was confirmed with 23 reference strains representing phylogenetically related yeast species and 148 clinical isolates covering the clinically most significant yeast species, including C. albicans (n = 72), C. dubliniensis (n = 58), C. glabrata (n = 5), C. krusei (n = 2), C. parapsilosis (n = 4), and C. tropicalis (n = 3). The performance of the C. albicans PNA FISH method as a diagnostic test was evaluated with 33 routine and 25 simulated yeast-positive blood culture bottles and showed 100% sensitivity and 100% specificity. It is concluded that this 2.5-h method for the definitive identification of C. albicans directly from yeast-positive blood culture bottles provides important information for optimal antifungal therapy and patient management. PMID:12037084
Campeiro, Joana D'Arc; Neshich, Izabella P; Sant'Anna, Osvaldo A; Lopes, Robson; Ianzer, Danielle; Assakura, Marina T; Neshich, Goran; Hayashi, Mirian A F
2015-08-01
Bradykinin-potentiating peptides (BPPs) from the South American pit viper snake venom were the first natural inhibitors of the human angiotensin I-converting enzyme (ACE) described. The pioneer characterization of the BPPs precursor from the snake venom glands by our group showed for the first time the presence of the C-type natriuretic peptide (CNP) in this same viper precursor protein. The confirmation of the BPP/CNP expression in snake brain regions correlated with neuroendocrine functions stimulated us to pursue the physiological correlates of these vasoactive peptides in mammals. Notably, several snake toxins were shown to have endogenous physiological correlates in mammals. In the present work, we expressed in bacteria the BPPs domain of the snake venom gland precursor protein, and this purified recombinant protein was used to raise specific polyclonal anti-BPPs antibodies. The correspondent single protein band immune-recognized in adult rat brain cytosol was isolated by 2D-SDS/PAGE and/or HPLC, before characterization by MS fingerprint analysis, which identified this protein as superoxide dismutase (SOD, EC 1.15.1.1), a classically known enzyme with antioxidant activity and important roles in the blood pressure modulation. In silico analysis showed the exposition of the BPP-like peptide sequences on the surface of the 3D structure of rat SOD. These peptides were chemically synthesized to show the BPP-like biological activities in ex vivo and in vivo pharmacological bioassays. Taken together, our data suggest that SOD protein have the potential to be a source for putative BPP-like bioactive peptides, which once released may contribute to the blood pressure control in mammals. Copyright © 2015 Elsevier Inc. All rights reserved.
Study of nuclear waste storage capacity at Yucca mountain repository
International Nuclear Information System (INIS)
Zhou Wei; Apted, M.; Kessler, J.H.
2008-01-01
The Yucca Mountain repository is applying license for storing 70000 MTHM nuclear waste including commercial spent nuclear fuel (CSNF) and defense high-level radioactive waste (HLW). The 70000 MTHM is a legal not the technical limit. To study the technical limit, the Electric Power Research Institute (EPRI) carried out a systematic study to explore the potential impact if the repository will accept more waste. This paper describes the model and results for evaluating the spent-fuel disposal capacity for a repository at Yucca Mountain from the thermal and hydrological point of view. Two proposed alternative repository designs are analyzed, both of which would fit into the currently well-characterized site and, therefore, not necessitating any additional site characterization at Yucca Mountain. The two- and three-dimensional models for coupled thermo-hydrological analysis extends from the surface to the water table, covering all the major and subgroup rock layers of the planned repository, as well as formations above and below the repository horizon. A dual-porosity and dual-permeability approach is used to model coupled heat and mass transfer through fracture formations. The waste package heating and ventilation are all assumed to follow those of the current design. The results show that the repository is able to accommodate three times the amount of spent fuel compared to the current design, without extra spatial expansion or exceeding current thermal and hydrological constraints. (authors)
Interoperability Across the Stewardship Spectrum in the DataONE Repository Federation
Jones, M. B.; Vieglais, D.; Wilson, B. E.
2016-12-01
Thousands of earth and environmental science repositories serve many researchers and communities, each with their own community and legal mandates, sustainability models, and historical infrastructure. These repositories span the stewardship spectrum from highly curated collections that employ large numbers of staff members to review and improve data, to small, minimal budget repositories that accept data caveat emptor and where all responsibility for quality lies with the submitter. Each repository fills a niche, providing services that meet the stewardship tradeoffs of one or more communities. We have reviewed these stewardship tradeoffs for several DataONE member repositories ranging from minimally (KNB) to highly curated (Arctic Data Center), as well as general purpose (Dryad) to highly discipline or project specific (NEON). The rationale behind different levels of stewardship reflect resolution of these tradeoffs. Some repositories aim to encourage extensive uptake by keeping processes simple and minimizing the amount of information collected, but this limits the long-term utility of the data and the search, discovery, and integration systems that are possible. Other repositories require extensive metadata input, review, and assessment, allowing for excellent preservation, discovery, and integration but at the cost of significant time for submitters and expense for curatorial staff. DataONE recognizes these different levels of curation, and attempts to embrace them to create a federation that is useful across the stewardship spectrum. DataONE provides a tiered model for repositories with growing utility of DataONE services at higher tiers of curation. The lowest tier supports read-only access to data and requires little more than title and contact metadata. Repositories can gradually phase in support for higher levels of metadata and services as needed. These tiered capabilities are possible through flexible support for multiple metadata standards and services
International Nuclear Information System (INIS)
2004-07-01
The objective of this publication is to highlight the importance of the early establishment of a comprehensive records system to manage primary level information (PLI) as an integrated set of information, not merely as a collection of information, throughout all the phases of radioactive waste management. Early establishment of a comprehensive records system to manage Primary Level Information as an integrated set of information throughout all phases of radioactive waste management is important. In addition to the information described in the waste inventory record keeping system (WIRKS), the PLI of a radioactive waste repository consists of the entire universe of information, data and records related to any aspect of the repository's life cycle. It is essential to establish PLI requirements based on integrated set of needs from Regulators and Waste Managers involved in the waste management chain and to update these requirements as needs change over time. Information flow for radioactive waste management should be back-end driven. Identification of an Authority that will oversee the management of PLI throughout all phases of the radioactive waste management life cycle would guarantee the information flow to future generations. The long term protection of information essential to future generations can only be assured by the timely establishment of a comprehensive and effective RMS capable of capturing, indexing and evaluating all PLI. The loss of intellectual control over the PLI will make it very difficult to subsequently identify the ILI and HLI information sets. At all times prior to the closure of a radioactive waste repository, there should be an identifiable entity with a legally enforceable financial and management responsibility for the continued operation of a PLI Records Management System. The information presented in this publication will assist Member States in ensuring that waste and repository records, relevant for retention after repository closure
Repository emplacement costs for Al-clad high enriched uranium spent fuel
International Nuclear Information System (INIS)
McDonell, W.R.; Parks, P.B.
1994-01-01
A range of strategies for treatment and packaging of Al-clad high-enriched uranium (HEU) spent fuels to prevent or delay the onset of criticality in a geologic repository was evaluated in terms of the number of canisters produced and associated repository costs incurred. The results indicated that strategies in which neutron poisons were added to consolidated forms of the U-Al alloy fuel generally produced the lowest number of canisters and associated repository costs. Chemical processing whereby the HEU was removed from the waste form was also a low cost option. The repository costs generally increased for isotopic dilution strategies, because of the substantial depleted uranium added. Chemical dissolution strategies without HEU removal were also penalized because of the inert constituents in the final waste glass form. Avoiding repository criticality by limiting the fissile mass content of each canister incurred the highest repository costs
Prestudy Oskarshamn. Tourism in Oskarshamn with or without a repository
International Nuclear Information System (INIS)
Nordblom, C.J.; Foghagen, C.
1998-11-01
Consequences for the tourism at Oskarshamn from siting a spent fuel repository in the community are studied. Four questionnaire/interview enquires were performed, and the analysis of the results show that no noticeable effects are expected. Still, an uncertainty about the impact of a repository is felt by the public, and more thorough information about the repository and its components is needed
Establishing managerial requirements for low-and intermediate-level waste repository
International Nuclear Information System (INIS)
Chung, C. W.; Lee, Y. K.; Kim, H. T.; Park, W. J.; Suk, T. W.; Park, S. H.
2004-01-01
This paper reviews basic considerations for establishing managerial requirements on the domestic low-and intermediate-level radioactive waste repository and presents the corresponding draft requirements. The draft emphasizes their close linking with the related regulations, standards and safety assessment for the repository. It also proposes a desirable direction towards harmonizing together with the existing waste acceptance requirements for the repository
DEFF Research Database (Denmark)
Hansen, Christian Skjødt; Østerbye, Thomas; Marcatili, Paolo
2017-01-01
-reactivity. B cell epitopes are typically classified as either linear epitopes, i.e. short consecutive segments from the protein sequence or conformational epitopes adapted through native protein folding. Recent advances in high-density peptide microarrays enable high-throughput, high-resolution identification...
Radionuclide getters in the near-field chemistry of repositories
International Nuclear Information System (INIS)
Holland, T.R.; Lee, D.J.
1993-01-01
The ultimate release of radionuclides from a radioactive waste repository will depend upon the natural and man-made barriers surrounding the site. An opportunity exists to enhance natural radionuclide retention through improved sorption, by the use of suitable additives applied to the repository backfill material. This programme of work was designed to identify problem isotopes, to search for suitable materials to enhance their retention and ultimately to provide, through experimental studies, an understanding of their effectiveness under repository conditions. (Author)