Intra- and Extra-cellular Proteome Analyses of Steroid-Producer Mycobacteria.

PubMed

Barreiro, Carlos; Morales, Alejandro; Vázquez-Iglesias, Inés; Sola-Landa, Alberto

2017-01-01

The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. In contrast, those industrially relevant mycobacteria have received less attention, even though the steroids market sales in 2011, in example, were estimated in $8 billion.The extra-cellular proteome, due to its relevance in the sterols processing and uptake; as well as the intra-cellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. As a proof of concept, the obtaining methods for both sub-proteomes of Mycobacterium neoaurum NRRL B-3805, a relevant industrial strain involved in steroids production, have been developed. Thus, procedures and relevant key points of these proteomes analyses are fully described.

The International Proteomics Tutorial Programme--reaching out to the next generation proteome scientists.

PubMed

James, Peter; Marko-Varga, György A

2011-08-05

One of the most critical functions of the various Proteomics organizations is the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with the other local proteomics associations are therefore launching a joint Tutorial Program to meet these needs. The level is aimed at Masters/PhD level students with good basic training in biology, biochemistry, mathematics and statistics. The Tutorials will consist of a review/teaching article with an accompanying talk slide presentation for classroom teaching. The Tutorial Program will cover core techniques and basics as an introduction to scientists new to the field. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organizations homepages.

Proteomic Analyses of Ethanol Tolerance in Lactobacillus buchneri NRRL B-30929

USDA-ARS?s Scientific Manuscript database

The Lactobacillus buchneri NRRL B-30929 strain, isolated from a fuel ethanol production facility, exhibits high tolerance to environmental ethanol concentrations. In this study, the ethanol tolerance trait was elucidated at the molecular level by using proteomics comparison and analyses. Cellular p...

Facile preparation of salivary extracellular vesicles for cancer proteomics

NASA Astrophysics Data System (ADS)

Sun, Yan; Xia, Zhijun; Shang, Zhi; Sun, Kaibo; Niu, Xiaomin; Qian, Liqiang; Fan, Liu-Yin; Cao, Cheng-Xi; Xiao, Hua

2016-04-01

Extracellular vesicles (EVs) are membrane surrounded structures released by cells, which have been increasingly recognized as mediators of intercellular communication. Recent reports indicate that EVs participate in important biological processes and could serve as potential source for cancer biomarkers. As an attractive EVs source with merit of non-invasiveness, human saliva is a unique medium for clinical diagnostics. Thus, we proposed a facile approach to prepare salivary extracellular vesicles (SEVs). Affinity chromatography column combined with filter system (ACCF) was developed to efficiently remove the high abundant proteins and viscous interferences of saliva. Protein profiling in the SEVs obtained by this strategy was compared with conventional centrifugation method, which demonstrated that about 70% more SEVs proteins could be revealed. To explore its utility for cancer proteomics, we analyzed the proteome of SEVs in lung cancer patients and normal controls. Shotgun proteomic analysis illustrated that 113 and 95 proteins have been identified in cancer group and control group, respectively. Among those 63 proteins that have been consistently discovered only in cancer group, 12 proteins are lung cancer related. Our results demonstrated that SEVs prepared through the developed strategy are valuable samples for proteomics and could serve as a promising liquid biopsy for cancer.

The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community.

PubMed

James, Peter

2011-09-01

The most critical functions of the various proteomics organisations are the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts are therefore launching the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computer applications making rapid advances in high throughput microbial proteomics (HTMP).

PubMed

Anandkumar, Balakrishna; Haga, Steve W; Wu, Hui-Fen

2014-02-01

The last few decades have seen the rise of widely-available proteomics tools. From new data acquisition devices, such as MALDI-MS and 2DE to new database searching softwares, these new products have paved the way for high throughput microbial proteomics (HTMP). These tools are enabling researchers to gain new insights into microbial metabolism, and are opening up new areas of study, such as protein-protein interactions (interactomics) discovery. Computer software is a key part of these emerging fields. This current review considers: 1) software tools for identifying the proteome, such as MASCOT or PDQuest, 2) online databases of proteomes, such as SWISS-PROT, Proteome Web, or the Proteomics Facility of the Pathogen Functional Genomics Resource Center, and 3) software tools for applying proteomic data, such as PSI-BLAST or VESPA. These tools allow for research in network biology, protein identification, functional annotation, target identification/validation, protein expression, protein structural analysis, metabolic pathway engineering and drug discovery.

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

PubMed Central

Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L.

2015-01-01

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include mass spectrometry to define protein sequence, protein:protein interactions, and protein post-translational modifications. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative mass spectrometry proteomics. It supports all major operating systems and instrument vendors via open data formats. Here we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of tandem mass spectrometry datasets, as well as some major upcoming features. PMID:25631240

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

PubMed

Deutsch, Eric W; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L

2015-08-01

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include MS to define protein sequence, protein:protein interactions, and protein PTMs. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics. It supports all major operating systems and instrument vendors via open data formats. Here, we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomics for understanding miRNA biology

PubMed Central

Huang, Tai-Chung; Pinto, Sneha M.; Pandey, Akhilesh

2013-01-01

MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in posttranscriptional regulation of gene expression. Mature miRNAs associate with the RNA interference silencing complex to repress mRNA translation and/or degrade mRNA transcripts. Mass spectrometry-based proteomics has enabled identification of several core components of the canonical miRNA processing pathway and their posttranslational modifications which are pivotal in miRNA regulatory mechanisms. The use of quantitative proteomic strategies has also emerged as a key technique for experimental identification of miRNA targets by allowing direct determination of proteins whose levels are altered because of translational suppression. This review focuses on the role of proteomics and labeling strategies to understand miRNA biology. PMID:23125164

Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

PubMed Central

Kerou, Melina; Offre, Pierre; Valledor, Luis; Abby, Sophie S.; Melcher, Michael; Nagler, Matthias; Weckwerth, Wolfram; Schleper, Christa

2016-01-01

Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile “Ca. Nitrosotalea devanaterra” revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and “Ca. Nitrosopelagicus brevis” proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs. PMID:27864514

Proteome Analysis of Cytoplasmatic and Plastidic β-Carotene Lipid Droplets in Dunaliella bardawil1[OPEN

PubMed Central

Davidi, Lital; Levin, Yishai; Ben-Dor, Shifra; Pick, Uri

2015-01-01

The halotolerant green alga Dunaliella bardawil is unique in that it accumulates under stress two types of lipid droplets: cytoplasmatic lipid droplets (CLD) and β-carotene-rich (βC) plastoglobuli. Recently, we isolated and analyzed the lipid and pigment compositions of these lipid droplets. Here, we describe their proteome analysis. A contamination filter and an enrichment filter were utilized to define core proteins. A proteome database of Dunaliella salina/D. bardawil was constructed to aid the identification of lipid droplet proteins. A total of 124 and 42 core proteins were identified in βC-plastoglobuli and CLD, respectively, with only eight common proteins. Dunaliella spp. CLD resemble cytoplasmic droplets from Chlamydomonas reinhardtii and contain major lipid droplet-associated protein and enzymes involved in lipid and sterol metabolism. The βC-plastoglobuli proteome resembles the C. reinhardtii eyespot and Arabidopsis (Arabidopsis thaliana) plastoglobule proteomes and contains carotene-globule-associated protein, plastid-lipid-associated protein-fibrillins, SOUL heme-binding proteins, phytyl ester synthases, β-carotene biosynthesis enzymes, and proteins involved in membrane remodeling/lipid droplet biogenesis: VESICLE-INDUCING PLASTID PROTEIN1, synaptotagmin, and the eyespot assembly proteins EYE3 and SOUL3. Based on these and previous results, we propose models for the biogenesis of βC-plastoglobuli and the biosynthesis of β-carotene within βC-plastoglobuli and hypothesize that βC-plastoglobuli evolved from eyespot lipid droplets. PMID:25404729

P2P proteomics -- data sharing for enhanced protein identification

PubMed Central

2012-01-01

Background In order to tackle the important and challenging problem in proteomics of identifying known and new protein sequences using high-throughput methods, we propose a data-sharing platform that uses fully distributed P2P technologies to share specifications of peer-interaction protocols and service components. By using such a platform, information to be searched is no longer centralised in a few repositories but gathered from experiments in peer proteomics laboratories, which can subsequently be searched by fellow researchers. Methods The system distributively runs a data-sharing protocol specified in the Lightweight Communication Calculus underlying the system through which researchers interact via message passing. For this, researchers interact with the system through particular components that link to database querying systems based on BLAST and/or OMSSA and GUI-based visualisation environments. We have tested the proposed platform with data drawn from preexisting MS/MS data reservoirs from the 2006 ABRF (Association of Biomolecular Resource Facilities) test sample, which was extensively tested during the ABRF Proteomics Standards Research Group 2006 worldwide survey. In particular we have taken the data available from a subset of proteomics laboratories of Spain's National Institute for Proteomics, ProteoRed, a network for the coordination, integration and development of the Spanish proteomics facilities. Results and Discussion We performed queries against nine databases including seven ProteoRed proteomics laboratories, the NCBI Swiss-Prot database and the local database of the CSIC/UAB Proteomics Laboratory. A detailed analysis of the results indicated the presence of a protein that was supported by other NCBI matches and highly scored matches in several proteomics labs. The analysis clearly indicated that the protein was a relatively high concentrated contaminant that could be present in the ABRF sample. This fact is evident from the information that could be derived from the proposed P2P proteomics system, however it is not straightforward to arrive to the same conclusion by conventional means as it is difficult to discard organic contamination of samples. The actual presence of this contaminant was only stated after the ABRF study of all the identifications reported by the laboratories. PMID:22293032

Proteomics/qPCR approach on estimating physical ages of wild male oriental fruit flies

USDA-ARS?s Scientific Manuscript database

Male fruit flies reared in the laboratory in DKI-PBARC rearing facility in Hilo, Hawaii, were collected and whole insects were run through standard proteomic analysis. An odorant binding protein 99b (OBP) (Bdor0907381) located at molecular weight between 9226 dalton and PI 4.56 was identified throug...

The amino acid's backup bone - storage solutions for proteomics facilities.

PubMed

Meckel, Hagen; Stephan, Christian; Bunse, Christian; Krafzik, Michael; Reher, Christopher; Kohl, Michael; Meyer, Helmut Erich; Eisenacher, Martin

2014-01-01

Proteomics methods, especially high-throughput mass spectrometry analysis have been continually developed and improved over the years. The analysis of complex biological samples produces large volumes of raw data. Data storage and recovery management pose substantial challenges to biomedical or proteomic facilities regarding backup and archiving concepts as well as hardware requirements. In this article we describe differences between the terms backup and archive with regard to manual and automatic approaches. We also introduce different storage concepts and technologies from transportable media to professional solutions such as redundant array of independent disks (RAID) systems, network attached storages (NAS) and storage area network (SAN). Moreover, we present a software solution, which we developed for the purpose of long-term preservation of large mass spectrometry raw data files on an object storage device (OSD) archiving system. Finally, advantages, disadvantages, and experiences from routine operations of the presented concepts and technologies are evaluated and discussed. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013. Published by Elsevier B.V.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics

PubMed Central

Kumar, Rajinder; Musiyenko, Alla; Oldenburg, Anja; Adams, Brian; Barik, Sailen

2004-01-01

Background Although the complete genome sequences of a large number of organisms have been determined, the exact proteomes need to be characterized. More specifically, the extent to which post-translational processes such as proteolysis affect the synthesized proteins has remained unappreciated. We examined this issue in selected protein phosphatases of the protease-rich malaria parasite, Plasmodium falciparum. Results P. falciparum encodes a number of Ser/Thr protein phosphatases (PP) whose catalytic subunits are composed of a catalytic core and accessory domains essential for regulation of the catalytic activity. Two examples of such regulatory domains are found in the Ca+2-regulated phosphatases, PP7 and PP2B (calcineurin). The EF-hand domains of PP7 and the calmodulin-binding domain of PP2B are essential for stimulation of the phosphatase activity by Ca+2. We present biochemical evidence that P. falciparum generates these full-length phosphatases as well as their catalytic cores, most likely as intermediates of a proteolytic degradation pathway. While the full-length phosphatases are activated by Ca+2, the processed cores are constitutively active and either less responsive or unresponsive to Ca+2. The processing is extremely rapid, specific, and occurs in vivo. Conclusions Post-translational cleavage efficiently degrades complex full-length phosphatases in P. falciparum. In the course of such degradation, enzymatically active catalytic cores are produced as relatively stable intermediates. The universality of such proteolysis in other phosphatases or other multi-domain proteins and its potential impact on the overall proteome of a cell merits further investigation. PMID:15230980

AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress.

PubMed

Liu, Yu; Fares, Matthew; Dunham, Noah P; Gao, Zi; Miao, Kun; Jiang, Xueyuan; Bollinger, Samuel S; Boal, Amie K; Zhang, Xin

2017-07-17

Drug-induced proteome stress that involves protein aggregation may cause adverse effects and undermine the safety profile of a drug. Safety of drugs is regularly evaluated using cytotoxicity assays that measure cell death. However, these assays provide limited insights into the presence of proteome stress in live cells. A fluorogenic protein sensor is reported to detect drug-induced proteome stress prior to cell death. An aggregation prone Halo-tag mutant (AgHalo) was evolved to sense proteome stress through its aggregation. Detection of such conformational changes was enabled by a fluorogenic ligand that fluoresces upon AgHalo forming soluble aggregates. Using 5 common anticancer drugs, we exemplified detection of differential proteome stress before any cell death was observed. Thus, this sensor can be used to evaluate drug safety in a regime that the current cytotoxicity assays cannot cover and be generally applied to detect proteome stress induced by other toxins. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomic analysis of formalin-fixed paraffin embedded tissue by MALDI imaging mass spectrometry

PubMed Central

Casadonte, Rita; Caprioli, Richard M

2012-01-01

Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informational resource for proteomic studies. Multiple FFPE core biopsies can be assembled in a single block to form tissue microarrays (TMAs). We describe a protocol for analyzing protein in FFPE -TMAs using matrix-assisted laser desorption/ionization (MAL DI) imaging mass spectrometry (IMS). The workflow incorporates an antigen retrieval step following deparaffinization, in situ trypsin digestion, matrix application and then mass spectrometry signal acquisition. The direct analysis of FFPE -TMA tissue using IMS allows direct analysis of multiple tissue samples in a single experiment without extraction and purification of proteins. The advantages of high speed and throughput, easy sample handling and excellent reproducibility make this technology a favorable approach for the proteomic analysis of clinical research cohorts with large sample numbers. For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis. PMID:22011652

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

PubMed

Uszkoreit, Julian; Maerkens, Alexandra; Perez-Riverol, Yasset; Meyer, Helmut E; Marcus, Katrin; Stephan, Christian; Kohlbacher, Oliver; Eisenacher, Martin

2015-07-02

Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.

Metrics for Success: Strategies for Enabling Core Facility Performance and Assessing Outcomes

PubMed Central

Hockberger, Philip E.; Meyn, Susan M.; Nicklin, Connie; Tabarini, Diane; Auger, Julie A.

2016-01-01

Core Facilities are key elements in the research portfolio of academic and private research institutions. Administrators overseeing core facilities (core administrators) require assessment tools for evaluating the need and effectiveness of these facilities at their institutions. This article discusses ways to promote best practices in core facilities as well as ways to evaluate their performance across 8 of the following categories: general management, research and technical staff, financial management, customer base and satisfaction, resource management, communications, institutional impact, and strategic planning. For each category, we provide lessons learned that we believe contribute to the effective and efficient overall management of core facilities. If done well, we believe that encouraging best practices and evaluating performance in core facilities will demonstrate and reinforce the importance of core facilities in the research and educational mission of institutions. It will also increase job satisfaction of those working in core facilities and improve the likelihood of sustainability of both facilities and personnel. PMID:26848284

Metrics for Success: Strategies for Enabling Core Facility Performance and Assessing Outcomes.

PubMed

Turpen, Paula B; Hockberger, Philip E; Meyn, Susan M; Nicklin, Connie; Tabarini, Diane; Auger, Julie A

2016-04-01

Core Facilities are key elements in the research portfolio of academic and private research institutions. Administrators overseeing core facilities (core administrators) require assessment tools for evaluating the need and effectiveness of these facilities at their institutions. This article discusses ways to promote best practices in core facilities as well as ways to evaluate their performance across 8 of the following categories: general management, research and technical staff, financial management, customer base and satisfaction, resource management, communications, institutional impact, and strategic planning. For each category, we provide lessons learned that we believe contribute to the effective and efficient overall management of core facilities. If done well, we believe that encouraging best practices and evaluating performance in core facilities will demonstrate and reinforce the importance of core facilities in the research and educational mission of institutions. It will also increase job satisfaction of those working in core facilities and improve the likelihood of sustainability of both facilities and personnel.

Proteomics for understanding miRNA biology.

PubMed

Huang, Tai-Chung; Pinto, Sneha M; Pandey, Akhilesh

2013-02-01

MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in posttranscriptional regulation of gene expression. Mature miRNAs associate with the RNA interference silencing complex to repress mRNA translation and/or degrade mRNA transcripts. Mass spectrometry-based proteomics has enabled identification of several core components of the canonical miRNA processing pathway and their posttranslational modifications which are pivotal in miRNA regulatory mechanisms. The use of quantitative proteomic strategies has also emerged as a key technique for experimental identification of miRNA targets by allowing direct determination of proteins whose levels are altered because of translational suppression. This review focuses on the role of proteomics and labeling strategies to understand miRNA biology. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria.

PubMed

Gray, Michael W

2015-08-18

Comparative studies of the mitochondrial proteome have identified a conserved core of proteins descended from the α-proteobacterial endosymbiont that gave rise to the mitochondrion and was the source of the mitochondrial genome in contemporary eukaryotes. A surprising result of phylogenetic analyses is the relatively small proportion (10-20%) of the mitochondrial proteome displaying a clear α-proteobacterial ancestry. A large fraction of mitochondrial proteins typically has detectable homologs only in other eukaryotes and is presumed to represent proteins that emerged specifically within eukaryotes. A further significant fraction of the mitochondrial proteome consists of proteins with homologs in prokaryotes, but without a robust phylogenetic signal affiliating them with specific prokaryotic lineages. The presumptive evolutionary source of these proteins is quite different in contending models of mitochondrial origin.

ApoptoProteomics, an integrated database for analysis of proteomics data obtained from apoptotic cells.

PubMed

Arntzen, Magnus Ø; Thiede, Bernd

2012-02-01

Apoptosis is the most commonly described form of programmed cell death, and dysfunction is implicated in a large number of human diseases. Many quantitative proteome analyses of apoptosis have been performed to gain insight in proteins involved in the process. This resulted in large and complex data sets that are difficult to evaluate. Therefore, we developed the ApoptoProteomics database for storage, browsing, and analysis of the outcome of large scale proteome analyses of apoptosis derived from human, mouse, and rat. The proteomics data of 52 publications were integrated and unified with protein annotations from UniProt-KB, the caspase substrate database homepage (CASBAH), and gene ontology. Currently, more than 2300 records of more than 1500 unique proteins were included, covering a large proportion of the core signaling pathways of apoptosis. Analysis of the data set revealed a high level of agreement between the reported changes in directionality reported in proteomics studies and expected apoptosis-related function and may disclose proteins without a current recognized involvement in apoptosis based on gene ontology. Comparison between induction of apoptosis by the intrinsic and the extrinsic apoptotic signaling pathway revealed slight differences. Furthermore, proteomics has significantly contributed to the field of apoptosis in identifying hundreds of caspase substrates. The database is available at http://apoptoproteomics.uio.no.

ApoptoProteomics, an Integrated Database for Analysis of Proteomics Data Obtained from Apoptotic Cells*

PubMed Central

Arntzen, Magnus Ø.; Thiede, Bernd

2012-01-01

Apoptosis is the most commonly described form of programmed cell death, and dysfunction is implicated in a large number of human diseases. Many quantitative proteome analyses of apoptosis have been performed to gain insight in proteins involved in the process. This resulted in large and complex data sets that are difficult to evaluate. Therefore, we developed the ApoptoProteomics database for storage, browsing, and analysis of the outcome of large scale proteome analyses of apoptosis derived from human, mouse, and rat. The proteomics data of 52 publications were integrated and unified with protein annotations from UniProt-KB, the caspase substrate database homepage (CASBAH), and gene ontology. Currently, more than 2300 records of more than 1500 unique proteins were included, covering a large proportion of the core signaling pathways of apoptosis. Analysis of the data set revealed a high level of agreement between the reported changes in directionality reported in proteomics studies and expected apoptosis-related function and may disclose proteins without a current recognized involvement in apoptosis based on gene ontology. Comparison between induction of apoptosis by the intrinsic and the extrinsic apoptotic signaling pathway revealed slight differences. Furthermore, proteomics has significantly contributed to the field of apoptosis in identifying hundreds of caspase substrates. The database is available at http://apoptoproteomics.uio.no. PMID:22067098

[Proteomics and its application to determine mechanism of action of traditional Chinese medicine].

PubMed

Xin, Ping; Kuang, Hai-Xue; Li, Xiao-Liang; Wang, Yu; Zhang, Ben-Mei; Bu, He; Wang, Zhi-Bin; Meng, Yong-Hai; Wang, Yan-Hong; Wang, Qiu-Hong

2018-03-01

There is no doubt that the traditional Chinese medicine(TCM) is effective, practical and scientific after it was used for thousands of years. However, the mechanisms of action of many TCM are still unclear because of their multi-component, multi-target and multi-level features, which hinder the modernization and internationalization of the TCM. Proteomics is to analyze the composition and activity of intracellular proteins which are changing dynamically from a holistic perspective. It is consistent with the holistic and dynamic views of the TCM and brings about the hope of clarifying the mechanism of action of the TCM. In recent years, great progress has been made in the application of proteomics to determine the mechanism of the TCM. This article introduced the core technologies of proteomics and systematically summarized the applications of proteomics in the study of the mechanism of the Chinese medicinal formulae, single Chinese medicine and monomeric compounds from the TCM to provide innovative ideas and methods for reference. Copyright© by the Chinese Pharmaceutical Association.

Hair-bundle proteomes of avian and mammalian inner-ear utricles

PubMed Central

Wilmarth, Phillip A.; Krey, Jocelyn F.; Shin, Jung-Bum; Choi, Dongseok; David, Larry L.; Barr-Gillespie, Peter G.

2015-01-01

Examination of multiple proteomics datasets within or between species increases the reliability of protein identification. We report here proteomes of inner-ear hair bundles from three species (chick, mouse, and rat), which were collected on LTQ or LTQ Velos ion-trap mass spectrometers; the constituent proteins were quantified using MS2 intensities, which are the summed intensities of all peptide fragmentation spectra matched to a protein. The data are available via ProteomeXchange with identifiers PXD002410 (chick LTQ), PXD002414 (chick Velos), PXD002415 (mouse Velos), and PXD002416 (rat LTQ). The two chick bundle datasets compared favourably to a third, already-described chick bundle dataset, which was quantified using MS1 peak intensities, the summed intensities of peptides identified by high-resolution mass spectrometry (PXD000104; updated analysis in PXD002445). The mouse bundle dataset described here was comparable to a different mouse bundle dataset quantified using MS1 intensities (PXD002167). These six datasets will be useful for identifying the core proteome of vestibular hair bundles. PMID:26645194

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

A postdoctoral position is available in Dr. Efsun Arda’s Developmental Genomics Group within the Laboratory of Receptor Biology and Gene Expression Branch at the National Cancer Institute (NCI), National Institutes of Health (NIH). Our research is focused on understanding the regulatory networks that govern pancreas cell identity and function in the context of diabetes and cancer. The lab is highly interdisciplinary and uses state-of-the-art technologies to address outstanding questions in human pancreas biology. The appointment is renewed annually upon performance evaluation for a maximum of five years. The candidate will be fully funded by a competitive intramural Center for Cancer Research (CCR) fellowship. Other fellowship opportunities outside NIH are also available and applications will be supported. CCR provides a highly collaborative, enabling environment for research fellows with more than 40 core facilities ranging from bioinformatics and computing, chemistry and structural biology, flow cytometry, genomics, imaging and microscopy, pharmacology, proteomics and single cell analysis.

Core Proteomic Analysis of Unique Metabolic Pathways of Salmonella enterica for the Identification of Potential Drug Targets.

PubMed

Uddin, Reaz; Sufian, Muhammad

2016-01-01

Infections caused by Salmonella enterica, a Gram-negative facultative anaerobic bacteria belonging to the family of Enterobacteriaceae, are major threats to the health of humans and animals. The recent availability of complete genome data of pathogenic strains of the S. enterica gives new avenues for the identification of drug targets and drug candidates. We have used the genomic and metabolic pathway data to identify pathways and proteins essential to the pathogen and absent from the host. We took the whole proteome sequence data of 42 strains of S. enterica and Homo sapiens along with KEGG-annotated metabolic pathway data, clustered proteins sequences using CD-HIT, identified essential genes using DEG database and discarded S. enterica homologs of human proteins in unique metabolic pathways (UMPs) and characterized hypothetical proteins with SVM-prot and InterProScan. Through this core proteomic analysis we have identified enzymes essential to the pathogen. The identification of 73 enzymes common in 42 strains of S. enterica is the real strength of the current study. We proposed all 73 unexplored enzymes as potential drug targets against the infections caused by the S. enterica. The study is comprehensive around S. enterica and simultaneously considered every possible pathogenic strain of S. enterica. This comprehensiveness turned the current study significant since, to the best of our knowledge it is the first subtractive core proteomic analysis of the unique metabolic pathways applied to any pathogen for the identification of drug targets. We applied extensive computational methods to shortlist few potential drug targets considering the druggability criteria e.g. Non-homologous to the human host, essential to the pathogen and playing significant role in essential metabolic pathways of the pathogen (i.e. S. enterica). In the current study, the subtractive proteomics through a novel approach was applied i.e. by considering only proteins of the unique metabolic pathways of the pathogens and mining the proteomic data of all completely sequenced strains of the pathogen, thus improving the quality and application of the results. We believe that the sharing of the knowledge from this study would eventually lead to bring about novel and unique therapeutic regimens against the infections caused by the S. enterica.

A framework for managing core facilities within the research enterprise.

PubMed

Haley, Rand

2009-09-01

Core facilities represent increasingly important operational and strategic components of institutions' research enterprises, especially in biomolecular science and engineering disciplines. With this realization, many research institutions are placing more attention on effectively managing core facilities within the research enterprise. A framework is presented for organizing the questions, challenges, and opportunities facing core facilities and the academic units and institutions in which they operate. This framework is intended to assist in guiding core facility management discussions in the context of a portfolio of facilities and within the overall institutional research enterprise.

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

PubMed Central

Manolakos, Elias S.

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub. PMID:26605332

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures.

PubMed

Sharma, Anuj; Manolakos, Elias S

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub.

Human borna disease virus infection impacts host proteome and histone lysine acetylation in human oligodendroglia cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xia; Department of Neurology, The Fifth People's Hospital of Shanghai, School of Medicine, Fudan University, Shanghai, 200240; Zhao, Libo

2014-09-15

Background: Borna disease virus (BDV) replicates in the nucleus and establishes persistent infections in mammalian hosts. A human BDV strain was used to address the first time, how BDV infection impacts the proteome and histone lysine acetylation (Kac) of human oligodendroglial (OL) cells, thus allowing a better understanding of infection-driven pathophysiology in vitro. Methods: Proteome and histone lysine acetylation were profiled through stable isotope labeling for cell culture (SILAC)-based quantitative proteomics. The quantifiable proteome was annotated using bioinformatics. Histone acetylation changes were validated by biochemistry assays. Results: Post BDV infection, 4383 quantifiable differential proteins were identified and functionally annotated tomore » metabolism pathways, immune response, DNA replication, DNA repair, and transcriptional regulation. Sixteen of the thirty identified Kac sites in core histones presented altered acetylation levels post infection. Conclusions: BDV infection using a human strain impacted the whole proteome and histone lysine acetylation in OL cells. - Highlights: • A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells). • This study is the first to reveal the host proteomic and histone Kac profiles in BDV-infected OL cells. • BDV infection affected the expression of many transcription factors and several HATs and HDACs.« less

Elucidation of salt stress defense and tolerance mechanisms of crop plants using proteomics--current achievements and perspectives.

PubMed

Barkla, Bronwyn J; Castellanos-Cervantes, Thelma; de León, José L Diaz; Matros, Andrea; Mock, Hans-Peter; Perez-Alfocea, Francisco; Salekdeh, Ghasem H; Witzel, Katja; Zörb, Christian

2013-06-01

Salinity is a major threat limiting the productivity of crop plants. A clear demand for improving the salinity tolerance of the major crop plants is imposed by the rapidly growing world population. This review summarizes the achievements of proteomic studies to elucidate the response mechanisms of selected model and crop plants to cope with salinity stress. We also aim at identifying research areas, which deserve increased attention in future proteome studies, as a prerequisite to identify novel targets for breeding strategies. Such areas include the impact of plant-microbial communities on the salinity tolerance of crops under field conditions, the importance of hormone signaling in abiotic stress tolerance, and the significance of control mechanisms underlying the observed changes in the proteome patterns. We briefly highlight the impact of novel tools for future proteome studies and argue for the use of integrated approaches. The evaluation of genetic resources by means of novel automated phenotyping facilities will have a large impact on the application of proteomics especially in combination with metabolomics or transcriptomics. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Global analysis of the rat and human platelet proteome – the molecular blueprint for illustrating multi-functional platelets and cross-species function evolution

PubMed Central

Yu, Yanbao; Leng, Taohua; Yun, Dong; Liu, Na; Yao, Jun; Dai, Ying; Yang, Pengyuan; Chen, Xian

2013-01-01

Emerging evidences indicate that blood platelets function in multiple biological processes including immune response, bone metastasis and liver regeneration in addition to their known roles in hemostasis and thrombosis. Global elucidation of platelet proteome will provide the molecular base of these platelet functions. Here, we set up a high throughput platform for maximum exploration of the rat/human platelet proteome using integrated proteomics technologies, and then applied to identify the largest number of the proteins expressed in both rat and human platelets. After stringent statistical filtration, a total of 837 unique proteins matched with at least two unique peptides were precisely identified, making it the first comprehensive protein database so far for rat platelets. Meanwhile, quantitative analyses of the thrombin-stimulated platelets offered great insights into the biological functions of platelet proteins and therefore confirmed our global profiling data. A comparative proteomic analysis between rat and human platelets was also conducted, which revealed not only a significant similarity, but also an across-species evolutionary link that the orthologous proteins representing ‘core proteome’, and the ‘evolutionary proteome’ is actually a relatively static proteome. PMID:20443191

Updated procedures for using drill cores and cuttings at the Lithologic Core Storage Library, Idaho National Laboratory, Idaho

USGS Publications Warehouse

Hodges, Mary K.V.; Davis, Linda C.; Bartholomay, Roy C.

2018-01-30

In 1990, the U.S. Geological Survey, in cooperation with the U.S. Department of Energy Idaho Operations Office, established the Lithologic Core Storage Library at the Idaho National Laboratory (INL). The facility was established to consolidate, catalog, and permanently store nonradioactive drill cores and cuttings from subsurface investigations conducted at the INL, and to provide a location for researchers to examine, sample, and test these materials.The facility is open by appointment to researchers for examination, sampling, and testing of cores and cuttings. This report describes the facility and cores and cuttings stored at the facility. Descriptions of cores and cuttings include the corehole names, corehole locations, and depth intervals available.Most cores and cuttings stored at the facility were drilled at or near the INL, on the eastern Snake River Plain; however, two cores drilled on the western Snake River Plain are stored for comparative studies. Basalt, rhyolite, sedimentary interbeds, and surficial sediments compose most cores and cuttings, most of which are continuous from land surface to their total depth. The deepest continuously drilled core stored at the facility was drilled to 5,000 feet below land surface. This report describes procedures and researchers' responsibilities for access to the facility and for examination, sampling, and return of materials.

The application of modular protein domains in proteomics

PubMed Central

Jadwin, Joshua A.; Ogiue-Ikeda, Mari; Machida, Kazuya

2012-01-01

The ability of modular protein domains to independently fold and bind short peptide ligands both in vivo and in vitro has allowed a significant number of protein-protein interaction studies to take advantage of them as affinity and detection reagents. Here, we refer to modular domain based proteomics as “domainomics” to draw attention to the potential of using domains and their motifs as tools in proteomics. In this review we describe core concepts of domainomics, established and emerging technologies, and recent studies by functional category. Accumulation of domain-motif binding data should ultimately provide the foundation for domain-specific interactomes, which will likely reveal the underlying substructure of protein networks as well as the selectivity and plasticity of signal transduction. PMID:22710164

Sex-Specific Biology of the Human Malaria Parasite Revealed from the Proteomes of Mature Male and Female Gametocytes.

PubMed

Miao, Jun; Chen, Zhao; Wang, Zenglei; Shrestha, Sony; Li, Xiaolian; Li, Runze; Cui, Liwang

2017-04-01

The gametocytes of the malaria parasites are obligate for perpetuating the parasite's life cycle through mosquitoes, but the sex-specific biology of gametocytes is poorly understood. We generated a transgenic line in the human malaria parasite Plasmodium falciparum , which allowed us to accurately separate male and female gametocytes by flow cytometry. In-depth analysis of the proteomes by liquid chromatography-tandem mass spectrometry identified 1244 and 1387 proteins in mature male and female gametocytes, respectively. GFP-tagging of nine selected proteins confirmed their sex-partitions to be agreeable with the results from the proteomic analysis. The sex-specific proteomes showed significant differences that are consistent with the divergent functions of the two sexes. Although the male-specific proteome (119 proteins) is enriched in proteins associated with the flagella and genome replication, the female-specific proteome (262 proteins) is more abundant in proteins involved in metabolism, translation and organellar functions. Compared with the Plasmodium berghei sex-specific proteomes, this study revealed both extensive conservation and considerable divergence between these two species, which reflect the disparities between the two species in proteins involved in cytoskeleton, lipid metabolism and protein degradation. Comparison with three sex-specific proteomes allowed us to obtain high-confidence lists of 73 and 89 core male- and female-specific/biased proteins conserved in Plasmodium The identification of sex-specific/biased proteomes in Plasmodium lays a solid foundation for understanding the molecular mechanisms underlying the unique sex-specific biology in this early-branching eukaryote. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Sex-Specific Biology of the Human Malaria Parasite Revealed from the Proteomes of Mature Male and Female Gametocytes *

PubMed Central

Miao, Jun; Chen, Zhao; Wang, Zenglei; Shrestha, Sony; Li, Xiaolian; Li, Runze; Cui, Liwang

2017-01-01

The gametocytes of the malaria parasites are obligate for perpetuating the parasite's life cycle through mosquitoes, but the sex-specific biology of gametocytes is poorly understood. We generated a transgenic line in the human malaria parasite Plasmodium falciparum, which allowed us to accurately separate male and female gametocytes by flow cytometry. In-depth analysis of the proteomes by liquid chromatography-tandem mass spectrometry identified 1244 and 1387 proteins in mature male and female gametocytes, respectively. GFP-tagging of nine selected proteins confirmed their sex-partitions to be agreeable with the results from the proteomic analysis. The sex-specific proteomes showed significant differences that are consistent with the divergent functions of the two sexes. Although the male-specific proteome (119 proteins) is enriched in proteins associated with the flagella and genome replication, the female-specific proteome (262 proteins) is more abundant in proteins involved in metabolism, translation and organellar functions. Compared with the Plasmodium berghei sex-specific proteomes, this study revealed both extensive conservation and considerable divergence between these two species, which reflect the disparities between the two species in proteins involved in cytoskeleton, lipid metabolism and protein degradation. Comparison with three sex-specific proteomes allowed us to obtain high-confidence lists of 73 and 89 core male- and female-specific/biased proteins conserved in Plasmodium. The identification of sex-specific/biased proteomes in Plasmodium lays a solid foundation for understanding the molecular mechanisms underlying the unique sex-specific biology in this early-branching eukaryote. PMID:28126901

Optic Atrophy 1 Is Epistatic to the Core MICOS Component MIC60 in Mitochondrial Cristae Shape Control.

PubMed

Glytsou, Christina; Calvo, Enrique; Cogliati, Sara; Mehrotra, Arpit; Anastasia, Irene; Rigoni, Giovanni; Raimondi, Andrea; Shintani, Norihito; Loureiro, Marta; Vazquez, Jesùs; Pellegrini, Luca; Enriquez, Jose Antonio; Scorrano, Luca; Soriano, Maria Eugenia

2016-12-13

The mitochondrial contact site and cristae organizing system (MICOS) and Optic atrophy 1 (OPA1) control cristae shape, thus affecting mitochondrial function and apoptosis. Whether and how they physically and functionally interact is unclear. Here, we provide evidence that OPA1 is epistatic to MICOS in the regulation of cristae shape. Proteomic analysis identifies multiple MICOS components in native OPA1-containing high molecular weight complexes disrupted during cristae remodeling. MIC60, a core MICOS protein, physically interacts with OPA1, and together, they control cristae junction number and stability, OPA1 being epistatic to MIC60. OPA1 defines cristae width and junction diameter independently of MIC60. Our combination of proteomics, biochemistry, genetics, and electron tomography provides a unifying model for mammalian cristae biogenesis by OPA1 and MICOS. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

MIMI: multimodality, multiresource, information integration environment for biomedical core facilities.

PubMed

Szymanski, Jacek; Wilson, David L; Zhang, Guo-Qiang

2009-10-01

The rapid expansion of biomedical research has brought substantial scientific and administrative data management challenges to modern core facilities. Scientifically, a core facility must be able to manage experimental workflow and the corresponding set of large and complex scientific data. It must also disseminate experimental data to relevant researchers in a secure and expedient manner that facilitates collaboration and provides support for data interpretation and analysis. Administratively, a core facility must be able to manage the scheduling of its equipment and to maintain a flexible and effective billing system to track material, resource, and personnel costs and charge for services to sustain its operation. It must also have the ability to regularly monitor the usage and performance of its equipment and to provide summary statistics on resources spent on different categories of research. To address these informatics challenges, we introduce a comprehensive system called MIMI (multimodality, multiresource, information integration environment) that integrates the administrative and scientific support of a core facility into a single web-based environment. We report the design, development, and deployment experience of a baseline MIMI system at an imaging core facility and discuss the general applicability of such a system in other types of core facilities. These initial results suggest that MIMI will be a unique, cost-effective approach to addressing the informatics infrastructure needs of core facilities and similar research laboratories.

A mass spectrometry proteomics data management platform.

PubMed

Sharma, Vagisha; Eng, Jimmy K; Maccoss, Michael J; Riffle, Michael

2012-09-01

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are "organically" distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/.

78 FR 33475 - Core Principles and Other Requirements for Swap Execution Facilities

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-04

... Core Principles and Other Requirements for Swap Execution Facilities; Final Rule #0;#0;Federal Register... FUTURES TRADING COMMISSION 17 CFR Part 37 RIN 3038-AD18 Core Principles and Other Requirements for Swap... Core Principles 1. Subpart B--Core Principle 1 (Compliance With Core Principles) 2. Subpart C--Core...

The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics.

PubMed

Mesuere, Bart; Van der Jeugt, Felix; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

2016-09-01

The Unique Peptide Finder (http://unipept.ugent.be/peptidefinder) is an interactive web application to quickly hunt for tryptic peptides that are unique to a particular species, genus, or any other taxon. Biodiversity within the target taxon is represented by a set of proteomes selected from a monthly updated list of complete and nonredundant UniProt proteomes, supplemented with proprietary proteomes loaded into persistent local browser storage. The software computes and visualizes pan and core peptidomes as unions and intersections of tryptic peptides occurring in the selected proteomes. In addition, it also computes and displays unique peptidomes as the set of all tryptic peptides that occur in all selected proteomes but not in any UniProt record not assigned to the target taxon. As a result, the unique peptides can serve as robust biomarkers for the target taxon, for example, in targeted metaproteomics studies. Computations are extremely fast since they are underpinned by the Unipept database, the lowest common ancestor algorithm implemented in Unipept and modern web technologies that facilitate in-browser data storage and parallel processing. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional proteomics within the genus Lactobacillus.

PubMed

De Angelis, Maria; Calasso, Maria; Cavallo, Noemi; Di Cagno, Raffaella; Gobbetti, Marco

2016-03-01

Lactobacillus are mainly used for the manufacture of fermented dairy, sourdough, meat, and vegetable foods or used as probiotics. Under optimal processing conditions, Lactobacillus strains contribute to food functionality through their enzyme portfolio and the release of metabolites. An extensive genomic diversity analysis was conducted to elucidate the core features of the genus Lactobacillus, and to provide a better comprehension of niche adaptation of the strains. However, proteomics is an indispensable "omics" science to elucidate the proteome diversity, and the mechanisms of regulation and adaptation of Lactobacillus strains. This review focuses on the novel and comprehensive knowledge of functional proteomics and metaproteomics of Lactobacillus species. A large list of proteomic case studies of different Lactobacillus species is provided to illustrate the adaptability of the main metabolic pathways (e.g., carbohydrate transport and metabolism, pyruvate metabolism, proteolytic system, amino acid metabolism, and protein synthesis) to various life conditions. These investigations have highlighted that lactobacilli modulate the level of a complex panel of proteins to growth/survive in different ecological niches. In addition to the general regulation and stress response, specific metabolic pathways can be switched on and off, modifying the behavior of the strains. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction.

PubMed

Thiele, Herbert; Glandorf, Jörg; Hufnagel, Peter

2010-05-27

With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScape bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists; current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specific questions about the biological condition or disease model of the analyzed sample. In this context, a new tool has been developed at the Spanish Centro Nacional de Biotecnologia Proteomics Facility termed PIKE (Protein information and Knowledge Extractor) that allows researchers to control, filter and access specific information from genomics and proteomic databases, to understand the role and relationships of the proteins identified in the experiments. Additionally, an EU funded project, ProDac, has coordinated systematic data collection in public standards-compliant repositories like PRIDE. This will cover all aspects from generating MS data in the laboratory, assembling the whole annotation information and storing it together with identifications in a standardised format.

Dr. Janie Merkel is interviewed by Ryan Blum and Janice Friend.

PubMed

Merkel, Janie

2007-12-01

Dr. Janie Merkel is the director of Yale's Chemical Genomics Screening Facility, a high-throughput screening laboratory that is part of the Yale University Center for Genomics and Proteomics. The Screening Facility connects Yale researchers with industry-quality robotic machinery and a diverse group of compound libraries, which have been used successfully to link therapeutic targets with potential therapies.

Exploring the human seminal plasma proteome: an unexplored gold mine of biomarker for male infertility and male reproduction disorder.

PubMed

Gilany, Kambiz; Minai-Tehrani, Arash; Savadi-Shiraz, Elham; Rezadoost, Hassan; Lakpour, Niknam

2015-01-01

The human seminal fluid is a complex body fluid. It is not known how many proteins are expressed in the seminal plasma; however in analog with the blood it is possible up to 10,000 proteins are expressed in the seminal plasma. The human seminal fluid is a rich source of potential biomarkers for male infertility and reproduction disorder. In this review, the ongoing list of proteins identified from the human seminal fluid was collected. To date, 4188 redundant proteins of the seminal fluid are identified using different proteomics technology, including 2-DE, SDS-PAGE-LC-MS/MS, MudPIT. However, this was reduced to a database of 2168 non-redundant protein using UniProtKB/Swiss-Prot reviewed database. The core concept of proteome were analyzed including pI, MW, Amino Acids, Chromosome and PTM distribution in the human seminal plasma proteome. Additionally, the biological process, molecular function and KEGG pathway were investigated using DAVID software. Finally, the biomarker identified in different male reproductive system disorder was investigated using proteomics platforms so far. In this study, an attempt was made to update the human seminal plasma proteome database. Our finding showed that human seminal plasma studies used to date seem to have converged on a set of proteins that are repeatedly identified in many studies and that represent only a small fraction of the entire human seminal plasma proteome.

U.S. National Institutes of Health core consolidation-investing in greater efficiency.

PubMed

Chang, Michael C; Birken, Steven; Grieder, Franziska; Anderson, James

2015-04-01

The U.S. National Institutes of Health (NIH) invests substantial resources in core research facilities (cores) that support research by providing advanced technologies and scientific and technical expertise as a shared resource. In 2010, the NIH issued an initiative to consolidate multiple core facilities into a single, more efficient core. Twenty-six institutions were awarded supplements to consolidate a number of similar core facilities. Although this approach may not work for all core settings, this effort resulted in consolidated cores that were more efficient and of greater benefit to investigators. The improvements in core operations resulted in both increased services and more core users through installation of advanced instrumentation, access to higher levels of management expertise; integration of information management and data systems; and consolidation of billing; purchasing, scheduling, and tracking services. Cost recovery to support core operations also benefitted from the consolidation effort, in some cases severalfold. In conclusion, this program of core consolidation resulted in improvements in the effective operation of core facilities, benefiting both investigators and their supporting institutions.

Institutional management of core facilities during challenging financial times.

PubMed

Haley, Rand

2011-12-01

The economic downturn is likely to have lasting effects on institutions of higher education, prioritizing proactive institutional leadership and planning. Although by design, core research facilities are more efficient and effective than supporting individual pieces of research equipment, cores can have significant underlying financial requirements and challenges. This paper explores several possible institutional approaches to managing core facilities during challenging financial times.

The Scottish Structural Proteomics Facility: targets, methods and outputs.

PubMed

Oke, Muse; Carter, Lester G; Johnson, Kenneth A; Liu, Huanting; McMahon, Stephen A; Yan, Xuan; Kerou, Melina; Weikart, Nadine D; Kadi, Nadia; Sheikh, Md Arif; Schmelz, Stefan; Dorward, Mark; Zawadzki, Michal; Cozens, Christopher; Falconer, Helen; Powers, Helen; Overton, Ian M; van Niekerk, C A Johannes; Peng, Xu; Patel, Prakash; Garrett, Roger A; Prangishvili, David; Botting, Catherine H; Coote, Peter J; Dryden, David T F; Barton, Geoffrey J; Schwarz-Linek, Ulrich; Challis, Gregory L; Taylor, Garry L; White, Malcolm F; Naismith, James H

2010-06-01

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.

A Sketch of the Taiwan Zebrafish Core Facility.

PubMed

You, May-Su; Jiang, Yun-Jin; Yuh, Chiou-Hwa; Wang, Chien-Ming; Tang, Chih-Hao; Chuang, Yung-Jen; Lin, Bo-Hung; Wu, Jen-Leih; Hwang, Sheng-Ping L

2016-07-01

In the past three decades, the number of zebrafish laboratories has significantly increased in Taiwan. The Taiwan Zebrafish Core Facility (TZCF), a government-funded core facility, was launched to serve this growing community. The Core Facility was built on two sites, one located at the National Health Research Institutes (NHRI, called Taiwan Zebrafish Core Facility at NHRI or TZeNH) and the other is located at the Academia Sinica (Taiwan Zebrafish Core Facility at AS a.k.a. TZCAS). The total surface area of the TZCF is about 180 m(2) encompassing 2880 fish tanks. Each site has a separate quarantine room and centralized water recirculating systems, monitoring key water parameters. To prevent diseases, three main strategies have been implemented: (1) imported fish must be quarantined; (2) only bleached embryos are introduced into the main facilities; and (3) working practices were implemented to minimize pathogen transfer between stocks and facilities. Currently, there is no health program in place; however, a fourth measure for the health program, specific regular pathogen tests, is being planned. In March 2015, the TZCF at NHRI has been AAALAC accredited. It is our goal to ensure that we provide "disease-free" fish and embryos to the Taiwanese research community.

STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eisenberg, David S.

2008-07-15

The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute hasmore » adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages. The development of publicly accessible, web-based servers, including the HOTPATCH server, the ProKnow Server and the SAVEs server. All of these are accessible from the home page of the Institute. Advancing the science of bioenergy, in the laboratories of the Principal Investigators of the Institute, including the laboratories of Shimon Weiss, James Liao, James Bowie, Todd Yeates, Rob Gunsalus.« less

Facilities Performance Indicators Report, 2004-05. Facilities Core Data Survey

ERIC Educational Resources Information Center

Glazner, Steve, Ed.

2006-01-01

The purpose of "Facilities Performance Indicators" is to provide a representative set of statistics about facilities in educational institutions. The second iteration of the web-based Facilities Core Data Survey was posted and available to facilities professionals at more than 3,000 institutions in the Fall of 2005. The website offered a printed…

Systems and Photosystems: Cellular Limits of Autotrophic Productivity in Cyanobacteria

PubMed Central

Burnap, Robert L.

2014-01-01

Recent advances in the modeling of microbial growth and metabolism have shown that growth rate critically depends upon the optimal allocation of finite proteomic resources among different cellular functions and that modeling growth rates becomes more realistic with the explicit accounting for the costs of macromolecular synthesis, most importantly, protein expression. The “proteomic constraint” is considered together with its application to understanding photosynthetic microbial growth. The central hypothesis is that physical limits of cellular space (and corresponding solvation capacity) in conjunction with cell surface-to-volume ratios represent the underlying constraints on the maximal rate of autotrophic microbial growth. The limitation of cellular space thus constrains the size the total complement of macromolecules, dissolved ions, and metabolites. To a first approximation, the upper limit in the cellular amount of the total proteome is bounded this space limit. This predicts that adaptation to osmotic stress will result in lower maximal growth rates due to decreased cellular concentrations of core metabolic proteins necessary for cell growth owing the accumulation of compatible osmolytes, as surmised previously. The finite capacity of membrane and cytoplasmic space also leads to the hypothesis that the species-specific differences in maximal growth rates likely reflect differences in the allocation of space to niche-specific proteins with the corresponding diminution of space devoted to other functions including proteins of core autotrophic metabolism, which drive cell reproduction. An optimization model for autotrophic microbial growth, the autotrophic replicator model, was developed based upon previous work investigating heterotrophic growth. The present model describes autotrophic growth in terms of the allocation protein resources among core functional groups including the photosynthetic electron transport chain, light-harvesting antennae, and the ribosome groups. PMID:25654078

A Mass Spectrometry Proteomics Data Management Platform*

PubMed Central

Sharma, Vagisha; Eng, Jimmy K.; MacCoss, Michael J.; Riffle, Michael

2012-01-01

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are “organically” distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/. PMID:22611296

76 FR 64355 - Science Advisory Board to the National Center for Toxicological Research; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-18

... commence during the next year. Next, the Chair of the Nanotechnology Core Facility Subcommittee will present an overview of the Nanotechnology Core Facility and subcommittee report. On August 16-17, 2011, the subcommittee convened to conduct an indepth review of the NCTR/ORA Nanotechnology Core Facility...

Proteomics Tracing the Footsteps of Infectious Disease*

PubMed Central

Greco, Todd M.; Cristea, Ileana M.

2017-01-01

Every year, a major cause of human disease and death worldwide is infection with the various pathogens—viruses, bacteria, fungi, and protozoa—that are intrinsic to our ecosystem. In efforts to control the prevalence of infectious disease and develop improved therapies, the scientific community has focused on building a molecular picture of pathogen infection and spread. These studies have been aimed at defining the cellular mechanisms that allow pathogen entry into hosts cells, their replication and transmission, as well as the core mechanisms of host defense against pathogens. The past two decades have demonstrated the valuable implementation of proteomic methods in all these areas of infectious disease research. Here, we provide a perspective on the contributions of mass spectrometry and other proteomics approaches to understanding the molecular details of pathogen infection. Specifically, we highlight methods used for defining the composition of viral and bacterial pathogens and the dynamic interaction with their hosts in space and time. We discuss the promise of MS-based proteomics in supporting the development of diagnostics and therapies, and the growing need for multiomics strategies for gaining a systems view of pathogen infection. PMID:28163258

Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer

NASA Astrophysics Data System (ADS)

Zhao, Xiaozheng; Huffman, Kenneth E.; Fujimoto, Junya; Canales, Jamie Rodriguez; Girard, Luc; Nie, Guangjun; Heymach, John V.; Wistuba, Igacio I.; Minna, John D.; Yu, Yonghao

2017-10-01

With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient's pathology based diagnosis of "poorly differentiated SqCC". Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic. [Figure not available: see fulltext.

CoreFlow: a computational platform for integration, analysis and modeling of complex biological data.

PubMed

Pasculescu, Adrian; Schoof, Erwin M; Creixell, Pau; Zheng, Yong; Olhovsky, Marina; Tian, Ruijun; So, Jonathan; Vanderlaan, Rachel D; Pawson, Tony; Linding, Rune; Colwill, Karen

2014-04-04

A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Python, or Perl for processing, correcting and modeling this data. CoreFlow organizes these scripts into project-specific pipelines, tracks interdependencies between related tasks, and enables the generation of summary reports as well as publication-quality images. As a result, the gap between experimental and computational components of a typical large-scale biology project is reduced, decreasing the time between data generation, analysis and manuscript writing. CoreFlow is being released to the scientific community as an open-sourced software package complete with proteomics-specific examples, which include corrections for incomplete isotopic labeling of peptides (SILAC) or arginine-to-proline conversion, and modeling of multiple/selected reaction monitoring (MRM/SRM) results. CoreFlow was purposely designed as an environment for programmers to rapidly perform data analysis. These analyses are assembled into project-specific workflows that are readily shared with biologists to guide the next stages of experimentation. Its simple yet powerful interface provides a structure where scripts can be written and tested virtually simultaneously to shorten the life cycle of code development for a particular task. The scripts are exposed at every step so that a user can quickly see the relationships between the data, the assumptions that have been made, and the manipulations that have been performed. Since the scripts use commonly available programming languages, they can easily be transferred to and from other computational environments for debugging or faster processing. This focus on 'on the fly' analysis sets CoreFlow apart from other workflow applications that require wrapping of scripts into particular formats and development of specific user interfaces. Importantly, current and future releases of data analysis scripts in CoreFlow format will be of widespread benefit to the proteomics community, not only for uptake and use in individual labs, but to enable full scrutiny of all analysis steps, thus increasing experimental reproducibility and decreasing errors. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes? Copyright © 2014 Elsevier B.V. All rights reserved.

Cardioproteomics: advancing the discovery of signaling mechanisms involved in cardiovascular diseases

PubMed Central

Cui, Ziyou; Dewey, Shannamar; Gomes, Aldrin V

2011-01-01

Cardioproteomics (Cardiovascular proteomics) is fast becoming an indispensible technique in deciphering changes in signaling pathways that occur in cardiovascular diseases (CVDs). The quality and availability of the instruments and bioinformatics software used for cardioproteomics continues to improve, and these techniques are now available to most cardiovascular researchers either directly or indirectly via university core centers. The heart and aorta are specialized tissues which present unique challenges to investigate. Currently, the diverse range of proteomic techniques available for cardiovascular research makes the choice of the best method or best combination of methods for the disease parameter(s) being investigated as important as the equipment used. This review focuses on proteomic techniques and their applications which have advanced our understanding of the signaling mechanisms involved in CVDs at the levels of protein complex/protein-protein interaction, post-translational modifications and signaling induced protein changes. PMID:22254205

Integration of Biosafety into Core Facility Management

PubMed Central

Fontes, Benjamin

2013-01-01

This presentation will discuss the implementation of biosafety policies for small, medium and large core laboratories with primary shared objectives of ensuring the control of biohazards to protect core facility operators and assure conformity with applicable state and federal policies, standards and guidelines. Of paramount importance is the educational process to inform core laboratories of biosafety principles and policies and to illustrate the technology and process pathways of the core laboratory for biosafety professionals. Elevating awareness of biohazards and the biosafety regulatory landscape among core facility operators is essential for the establishment of a framework for both project and material risk assessment. The goal of the biohazard risk assessment process is to identify the biohazard risk management parameters to conduct the procedure safely and in compliance with applicable regulations. An evaluation of the containment, protective equipment and work practices for the procedure for the level of risk identified is facilitated by the establishment of a core facility registration form for work with biohazards and other biological materials with potential risk. The final step in the biocontainment process is the assumption of Principal Investigator role with full responsibility for the structure of the site-specific biosafety program plan by core facility leadership. The presentation will provide example biohazard protocol reviews and accompanying containment measures for core laboratories at Yale University.

BRSCW Reference Set Application: Karen Abbott -University of Arkansas (2014) — EDRN Public Portal

Cancer.gov

Our earlier glycoproteomic studies have identified bisecting glycoslyation and core fucosylation changes on particular glycoproteins in endometrioid ovarian cancer tissues and plasma (Abbott et al, 2010, Proteomics). We have validated that these glycan changes occur on the same glycoproteins in serous ovarian cancer plasma using a lectin-pull down western blot assays. We would like to used pooled reference samples to develop a sensitive magnetic bead-based assay to detect these glycoproteins with bisecting and core fucosylation changes.

76 FR 1213 - Core Principles and Other Requirements for Swap Execution Facilities

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-07

... Part II Commodity Futures Trading Commission 17 CFR Part 37 Core Principles and Other Requirements... RIN Number 3038-AD18 Core Principles and Other Requirements for Swap Execution Facilities AGENCY... Compliance With the Core Principles III. Effective Date and Transition Period IV. Related Matters A...

17 CFR 37.6 - Compliance with core principles.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 17 Commodity and Securities Exchanges 1 2011-04-01 2011-04-01 false Compliance with core... DERIVATIVES TRANSACTION EXECUTION FACILITIES § 37.6 Compliance with core principles. (a) In general. To... transaction execution facility must have the capacity to be, and be, in compliance with the core principles of...

17 CFR 37.6 - Compliance with core principles.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 17 Commodity and Securities Exchanges 1 2010-04-01 2010-04-01 false Compliance with core... DERIVATIVES TRANSACTION EXECUTION FACILITIES § 37.6 Compliance with core principles. (a) In general. To... transaction execution facility must have the capacity to be, and be, in compliance with the core principles of...

Beyond the Natural Proteome: Nondegenerate Saturation Mutagenesis-Methodologies and Advantages.

PubMed

Ferreira Amaral, M M; Frigotto, L; Hine, A V

2017-01-01

Beyond the natural proteome, high-throughput mutagenesis offers the protein engineer an opportunity to "tweak" the wild-type activity of a protein to create a recombinant protein with required attributes. Of the various approaches available, saturation mutagenesis is one of the core techniques employed by protein engineers, and in recent times, nondegenerate saturation mutagenesis is emerging as the approach of choice. This review compares the current methodologies available for conducting nondegenerate saturation mutagenesis with traditional, degenerate saturation and briefly outlines the options available for screening the resulting libraries, to discover a novel protein with the required activity and/or specificity. © 2017 Elsevier Inc. All rights reserved.

Scheduler for multiprocessor system switch with selective pairing

DOEpatents

Gara, Alan; Gschwind, Michael Karl; Salapura, Valentina

2015-01-06

System, method and computer program product for scheduling threads in a multiprocessing system with selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). The method configures the selective pairing facility to use checking provide one highly reliable thread for high-reliability and allocate threads to corresponding processor cores indicating need for hardware checking. The method configures the selective pairing facility to provide multiple independent cores and allocate threads to corresponding processor cores indicating inherent resilience.

New Users | Center for Cancer Research

Cancer.gov

New Users Becoming a Core Facilities User The following steps are applicable to anyone who would like to become a user of the CCR SAXS Core facilities. All users are required to follow the Core Facilty User Polices.

Microgravity Science Glovebox (MSG)

NASA Technical Reports Server (NTRS)

1998-01-01

The Microgravity Science Glovebox is a facility for performing microgravity research in the areas of materials, combustion, fluids and biotechnology science. The facility occupies a full ISPR, consisting of: the ISPR rack and infrastructure for the rack, the glovebox core facility, data handling, rack stowage, outfitting equipment, and a video subsystem. MSG core facility provides the experiment developers a chamber with air filtering and recycling, up to two levels of containment, an airlock for transfer of payload equipment to/from the main volume, interface resources for the payload inside the core facility, resources inside the airlock, and storage drawers for MSG support equipment and consumables.

Microgravity

NASA Image and Video Library

1998-05-01

The Microgravity Science Glovebox is a facility for performing microgravity research in the areas of materials, combustion, fluids and biotechnology science. The facility occupies a full ISPR, consisting of: the ISPR rack and infrastructure for the rack, the glovebox core facility, data handling, rack stowage, outfitting equipment, and a video subsystem. MSG core facility provides the experiment developers a chamber with air filtering and recycling, up to two levels of containment, an airlock for transfer of payload equipment to/from the main volume, interface resources for the payload inside the core facility, resources inside the airlock, and storage drawers for MSG support equipment and consumables.

Characterization of the Low-Molecular-Weight Human Plasma Peptidome.

PubMed

Greening, David W; Simpson, Richard J

2017-01-01

The human plasma proteome represents an important secreted sub-proteome. Proteomic analysis of blood plasma with mass spectrometry is a challenging task. The high complexity and wide dynamic range of proteins as well as the presence of several proteins at very high concentrations complicate the profiling of the human plasma proteome. The peptidome (or low-molecular-weight fraction, LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based markers of disease. Peptides are generated by active synthesis and proteolytic processing, often yielding proteolytic fragments that mediate a variety of physiological and pathological functions. As such, degradomic studies, investigating cleavage products via peptidomics and top-down proteomics in particular, have warranted significant research interest. However, due to their molecular weight, abundance, and solubility, issues with identifying specific cleavage sites and coverage of peptide fragments remain challenging. Peptidomics is currently focused toward comprehensively studying peptides cleaved from precursor proteins by endogenous proteases. This protocol outlines a standardized rapid and reproducible procedure for peptidomic profiling of human plasma using centrifugal ultrafiltration and mass spectrometry. Ultrafiltration is a convective process that uses anisotropic semipermeable membranes to separate macromolecular species on the basis of size. We have optimized centrifugal ultrafiltration (cellulose triacetate membrane) for plasma fractionation with respect to buffer and solvent composition, centrifugal force, duration, and temperature to facilitate recovery >95% and enrichment of the human plasma peptidome. This method serves as a comprehensive and facile process to enrich and identify a key, underrepresented sub-proteome of human blood plasma.

Boosting the globalization of plant proteomics through INPPO: current developments and future prospects.

PubMed

Agrawal, Ganesh Kumar; Sarkar, Abhijit; Agrawal, Raj; Ndimba, Bongani Kaiser; Tanou, Georgia; Dunn, Michael J; Kieselbach, Thomas; Cramer, Rainer; Wienkoop, Stefanie; Chen, Sixue; Rafudeen, Mohammed Suhail; Deswal, Renu; Barkla, Bronwyn J; Weckwerth, Wolfram; Heazlewood, Joshua L; Renaut, Jenny; Job, Dominique; Chakraborty, Niranjan; Rakwal, Randeep

2012-02-01

The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO community, and also due to the wide encouragement and support from the communities (scientific and non-scientific). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conventional-Flow Liquid Chromatography-Mass Spectrometry for Exploratory Bottom-Up Proteomic Analyses.

PubMed

Lenčo, Juraj; Vajrychová, Marie; Pimková, Kristýna; Prokšová, Magdaléna; Benková, Markéta; Klimentová, Jana; Tambor, Vojtěch; Soukup, Ondřej

2018-04-17

Due to its sensitivity and productivity, bottom-up proteomics based on liquid chromatography-mass spectrometry (LC-MS) has become the core approach in the field. The de facto standard LC-MS platform for proteomics operates at sub-μL/min flow rates, and nanospray is required for efficiently introducing peptides into a mass spectrometer. Although this is almost a "dogma", this view is being reconsidered in light of developments in highly efficient chromatographic columns, and especially with the introduction of exceptionally sensitive MS instruments. Although conventional-flow LC-MS platforms have recently penetrated targeted proteomics successfully, their possibilities in discovery-oriented proteomics have not yet been thoroughly explored. Our objective was to determine what are the extra costs and what optimization and adjustments to a conventional-flow LC-MS system must be undertaken to identify a comparable number of proteins as can be identified on a nanoLC-MS system. We demonstrate that the amount of a complex tryptic digest needed for comparable proteome coverage can be roughly 5-fold greater, providing the column dimensions are properly chosen, extra-column peak dispersion is minimized, column temperature and flow rate are set to levels appropriate for peptide separation, and the composition of mobile phases is fine-tuned. Indeed, we identified 2 835 proteins from 2 μg of HeLa cells tryptic digest separated during a 60 min gradient at 68 μL/min on a 1.0 mm × 250 mm column held at 55 °C and using an aqua-acetonitrile mobile phases containing 0.1% formic acid, 0.4% acetic acid, and 3% dimethyl sulfoxide. Our results document that conventional-flow LC-MS is an attractive alternative for bottom-up exploratory proteomics.

Involvement of GABA Transporters in Atropine-Treated Myopic Retina As Revealed by iTRAQ Quantitative Proteomics

PubMed Central

2015-01-01

Atropine, a muscarinic antagonist, is known to inhibit myopia progression in several animal models and humans. However, the mode of action is not established yet. In this study, we compared quantitative iTRAQ proteomic analysis in the retinas collected from control and lens-induced myopic (LIM) mouse eyes treated with atropine. The myopic group received a (−15D) spectacle lens over the right eye on postnatal day 10 with or without atropine eye drops starting on postnatal day 24. Axial length was measured by optical low coherence interferometry (OLCI), AC-Master, and refraction was measured by automated infrared photorefractor at postnatal 24, 38, and 52 days. Retinal tissue samples were pooled from six eyes for each group. The experiments were repeated twice, and technical replicates were also performed for liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis. MetaCore was used to perform protein profiling for pathway analysis. We identified a total of 3882 unique proteins with <1% FDR by analyzing the samples in replicates for two independent experiments. This is the largest number of mouse retina proteome reported to date. Thirty proteins were found to be up-regulated (ratio for myopia/control > global mean ratio + 1 standard deviation), and 28 proteins were down-regulated (ratio for myopia/control < global mean ratio - 1 standard deviation) in myopic eyes as compared with control retinas. Pathway analysis using MetaCore revealed regulation of γ-aminobutyric acid (GABA) levels in the myopic eyes. Detailed analysis of the quantitative proteomics data showed that the levels of GABA transporter 1 (GAT-1) were elevated in myopic retina and significantly reduced after atropine treatment. These results were further validated with immunohistochemistry and Western blot analysis. In conclusion, this study provides a comprehensive quantitative proteomic analysis of atropine-treated mouse retina and suggests the involvement of GABAergic signaling in the antimyopic effects of atropine in mouse eyes. The GABAergic transmission in the neural retina plays a pivotal role in the maintenance of axial eye growth in mammals. PMID:25211393

Carbon assimilation in Eucalyptus urophylla grown under high atmospheric CO2 concentrations: A proteomics perspective.

PubMed

Santos, Bruna Marques Dos; Balbuena, Tiago Santana

2017-01-06

Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO 2 concentrations. Growth under a high concentration of CO 2 could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO 2 . Our strategy allowed the profiling of all Calvin-Benson cycle enzymes and associated protein species. Among the 816 isolated proteins, those involved in carbon fixation were found to be the most abundant ones. An increase in the abundance of six key enzymes out of the eleven core enzymes involved in carbon fixation was detected in plants grown at a high CO 2 concentration. Proteome changes were corroborated by the detection of a decrease in the stomatal aperture and in the vascular bundle area in Eucalyptus urophylla plantlets grown in an environment of high atmospheric CO 2 . Our proteomics approach indicates a positive metabolic response regarding carbon fixation in a CO 2 -enriched atmosphere. The slight but significant increase in the abundance of the Calvin enzymes suggests that stomatal closure did not prevent an increase in the carbon assimilation rates. The sample enrichment strategy and data analysis used here enabled the identification of all enzymes and most protein isoforms involved in the Calvin-Benson-Bessham cycle in Eucalyptus urophylla. Upon growth in CO 2 -enriched chambers, Eucalyptus urophylla plantlets responded by reducing the vascular bundle area and stomatal aperture size and by increasing the abundance of six of the eleven core enzymes involved in carbon fixation. Our proteome approach provides an estimate on how a commercially important C3-type plant would respond to an increase in CO 2 concentrations. Additionally, confirmation at the protein level of the predicted genes involved in carbon assimilation may be used in plant transformation strategies aiming to increase plant adaptability to climate changes or to increase plant productivity. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative proteomic profiling for clarification of the crucial roles of lysosomes in microbial infections.

PubMed

Xu, Benhong; Gao, Yanpan; Zhan, Shaohua; Ge, Wei

2017-07-01

Lysosomes play vital roles in both innate and adaptive immunity. It is widely accepted that lysosomes do not function exclusively as a digestive organelle. It is also involved in the process of immune cells against pathogens. However, the changes in the lysosomal proteome caused by infection with various microbes are still largely unknown, and our understanding of the proteome of the purified lysosome is another obstacle that needs to be resolved. Here, we performed a proteomic study on lysosomes enriched from THP1 cells after infection with Listeria monocytogenes (L.m), Herpes Simplex Virus 1 (HSV-1) and Vesicular Stomatitis Virus (VSV). In combination with the gene ontology (GO) analysis, we identified 284 lysosomal-related proteins from a total of 4560 proteins. We also constructed the protein-protein interaction networks for the differentially expressed proteins and revealed the core lysosomal proteins, including SRC in the L. m treated group, SRC, GLB1, HEXA and HEXB in the HSV-1 treated group and GLB1, CTSA, CTSB, HEXA and HEXB in the VSV treated group, which are involved in responding to diverse microbial infections. This study not only reveals variable lysosome responses depending on the bacterial or virus infection, but also provides the evidence based on which we propose a novel approach to proteome research for investigation of the function of the enriched organelles. Copyright © 2017 Elsevier Ltd. All rights reserved.

Global Analysis Reveals the Complexity of the Human Glomerular Extracellular Matrix

PubMed Central

Byron, Adam; Humphries, Jonathan D.; Randles, Michael J.; Carisey, Alex; Murphy, Stephanie; Knight, David; Brenchley, Paul E.; Zent, Roy; Humphries, Martin J.

2014-01-01

The glomerulus contains unique cellular and extracellular matrix (ECM) components, which are required for intact barrier function. Studies of the cellular components have helped to build understanding of glomerular disease; however, the full composition and regulation of glomerular ECM remains poorly understood. We used mass spectrometry-based proteomics of enriched ECM extracts for a global analysis of human glomerular ECM in vivo and identified a tissue-specific proteome of 144 structural and regulatory ECM proteins. This catalog includes all previously identified glomerular components plus many new and abundant components. Relative protein quantification showed a dominance of collagen IV, collagen I, and laminin isoforms in the glomerular ECM together with abundant collagen VI and TINAGL1. Protein network analysis enabled the creation of a glomerular ECM interactome, which revealed a core of highly connected structural components. More than one half of the glomerular ECM proteome was validated using colocalization studies and data from the Human Protein Atlas. This study yields the greatest number of ECM proteins relative to previous investigations of whole glomerular extracts, highlighting the importance of sample enrichment. It also shows that the composition of glomerular ECM is far more complex than previously appreciated and suggests that many more ECM components may contribute to glomerular development and disease processes. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000456. PMID:24436468

Comparative proteomics analysis of oral cancer cell lines: identification of cancer associated proteins

PubMed Central

2014-01-01

Background A limiting factor in performing proteomics analysis on cancerous cells is the difficulty in obtaining sufficient amounts of starting material. Cell lines can be used as a simplified model system for studying changes that accompany tumorigenesis. This study used two-dimensional gel electrophoresis (2DE) to compare the whole cell proteome of oral cancer cell lines vs normal cells in an attempt to identify cancer associated proteins. Results Three primary cell cultures of normal cells with a limited lifespan without hTERT immortalization have been successfully established. 2DE was used to compare the whole cell proteome of these cells with that of three oral cancer cell lines. Twenty four protein spots were found to have changed in abundance. MALDI TOF/TOF was then used to determine the identity of these proteins. Identified proteins were classified into seven functional categories – structural proteins, enzymes, regulatory proteins, chaperones and others. IPA core analysis predicted that 18 proteins were related to cancer with involvements in hyperplasia, metastasis, invasion, growth and tumorigenesis. The mRNA expressions of two proteins – 14-3-3 protein sigma and Stress-induced-phosphoprotein 1 – were found to correlate with the corresponding proteins’ abundance. Conclusions The outcome of this analysis demonstrated that a comparative study of whole cell proteome of cancer versus normal cell lines can be used to identify cancer associated proteins. PMID:24422745

Phosphorylation of plastoglobular proteins in Arabidopsis thaliana

PubMed Central

Lohscheider, Jens N.; Friso, Giulia; van Wijk, Klaas J.

2016-01-01

Plastoglobules (PGs) are plastid lipid–protein particles with a small specialized proteome and metabolome. Among the 30 core PG proteins are six proteins of the ancient ABC1 atypical kinase (ABC1K) family and their locations in an Arabidopsis mRNA-based co-expression network suggested central regulatory roles. To identify candidate ABC1K targets and a possible ABC1K hierarchical phosphorylation network within the chloroplast PG proteome, we searched Arabidopsis phosphoproteomics data from publicly available sources. Evaluation of underlying spectra and/or associated information was challenging for a variety of reasons, but supported pSer sites and a few pThr sites in nine PG proteins, including five FIBRILLINS. PG phosphorylation motifs are discussed in the context of possible responsible kinases. The challenges of collection and evaluation of published Arabidopsis phosphorylation data are discussed, illustrating the importance of deposition of all mass spectrometry data in well-organized repositories such as PRIDE and ProteomeXchange. This study provides a starting point for experimental testing of phosho-sites in PG proteins and also suggests that phosphoproteomics studies specifically designed toward the PG proteome and its ABC1K are needed to understand phosphorylation networks in these specialized particles. PMID:26962209

Proteomics Tracing the Footsteps of Infectious Disease.

PubMed

Greco, Todd M; Cristea, Ileana M

2017-04-01

Every year, a major cause of human disease and death worldwide is infection with the various pathogens-viruses, bacteria, fungi, and protozoa-that are intrinsic to our ecosystem. In efforts to control the prevalence of infectious disease and develop improved therapies, the scientific community has focused on building a molecular picture of pathogen infection and spread. These studies have been aimed at defining the cellular mechanisms that allow pathogen entry into hosts cells, their replication and transmission, as well as the core mechanisms of host defense against pathogens. The past two decades have demonstrated the valuable implementation of proteomic methods in all these areas of infectious disease research. Here, we provide a perspective on the contributions of mass spectrometry and other proteomics approaches to understanding the molecular details of pathogen infection. Specifically, we highlight methods used for defining the composition of viral and bacterial pathogens and the dynamic interaction with their hosts in space and time. We discuss the promise of MS-based proteomics in supporting the development of diagnostics and therapies, and the growing need for multiomics strategies for gaining a systems view of pathogen infection. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Space Station Furnace Facility. Volume 2: Appendix 1: Contract End Item specification (CEI), part 1

NASA Technical Reports Server (NTRS)

Seabrook, Craig

1992-01-01

This specification establishes the performance, design, development, and verification requirements for the Space Station Furnace Facility (SSFF) Core. The definition of the SSFF Core and its interfaces, specifies requirements for the SSFF Core performance, specifies requirements for the SSFF Core design, and construction are presented, and the verification requirements are established.

In-depth Proteomics Characterization of Embryogenesis of the Honey Bee Worker (Apis mellifera ligustica) *

PubMed Central

Fang, Yu; Feng, Mao; Han, Bin; Lu, Xiaoshan; Ramadan, Haitham; Li, Jianke

2014-01-01

Identifying proteome changes of honey bee embryogenesis is of prime importance for unraveling the molecular mechanisms that they underlie. However, many proteomic changes during the embryonic period are not well characterized. We analyzed the proteomic alterations over the complete time course of honey bee worker embryogenesis at 24, 48, and 72 h of age, using mass spectrometry-based proteomics, label-free quantitation, and bioinformatics. Of the 1460 proteins identified the embryo of all three ages, the core proteome (proteins shared by the embryos of all three ages, accounting for 40%) was mainly involved in protein synthesis, metabolic energy, development, and molecular transporter, which indicates their centrality in driving embryogenesis. However, embryos at different developmental stages have their own specific proteome and pathway signatures to coordinate and modulate developmental events. The young embryos (<24 h) stronger expression of proteins related to nutrition storage and nucleic acid metabolism may correlate with the cell proliferation occurring at this stage. The middle aged embryos (24–48 h) enhanced expression of proteins associated with cell cycle control, transporters, antioxidant activity, and the cytoskeleton suggest their roles to support rudimentary organogenesis. Among these proteins, the biological pathways of aminoacyl-tRNA biosynthesis, β-alanine metabolism, and protein export are intensively activated in the embryos of middle age. The old embryos (48–72 h) elevated expression of proteins implicated in fatty acid metabolism and morphogenesis indicate their functionality for the formation and development of organs and dorsal closure, in which the biological pathways of fatty acid metabolism and RNA transport are highly activated. These findings add novel understanding to the molecular details of honey bee embryogenesis, in which the programmed activation of the proteome matches with the physiological transition observed during embryogenesis. The identified biological pathways and key node proteins allow for further functional analysis and genetic manipulation for both the honey bee embryos and other eusocial insects. PMID:24895377

In-depth proteomics characterization of embryogenesis of the honey bee worker (Apis mellifera ligustica).

PubMed

Fang, Yu; Feng, Mao; Han, Bin; Lu, Xiaoshan; Ramadan, Haitham; Li, Jianke

2014-09-01

Identifying proteome changes of honey bee embryogenesis is of prime importance for unraveling the molecular mechanisms that they underlie. However, many proteomic changes during the embryonic period are not well characterized. We analyzed the proteomic alterations over the complete time course of honey bee worker embryogenesis at 24, 48, and 72 h of age, using mass spectrometry-based proteomics, label-free quantitation, and bioinformatics. Of the 1460 proteins identified the embryo of all three ages, the core proteome (proteins shared by the embryos of all three ages, accounting for 40%) was mainly involved in protein synthesis, metabolic energy, development, and molecular transporter, which indicates their centrality in driving embryogenesis. However, embryos at different developmental stages have their own specific proteome and pathway signatures to coordinate and modulate developmental events. The young embryos (<24 h) stronger expression of proteins related to nutrition storage and nucleic acid metabolism may correlate with the cell proliferation occurring at this stage. The middle aged embryos (24-48 h) enhanced expression of proteins associated with cell cycle control, transporters, antioxidant activity, and the cytoskeleton suggest their roles to support rudimentary organogenesis. Among these proteins, the biological pathways of aminoacyl-tRNA biosynthesis, β-alanine metabolism, and protein export are intensively activated in the embryos of middle age. The old embryos (48-72 h) elevated expression of proteins implicated in fatty acid metabolism and morphogenesis indicate their functionality for the formation and development of organs and dorsal closure, in which the biological pathways of fatty acid metabolism and RNA transport are highly activated. These findings add novel understanding to the molecular details of honey bee embryogenesis, in which the programmed activation of the proteome matches with the physiological transition observed during embryogenesis. The identified biological pathways and key node proteins allow for further functional analysis and genetic manipulation for both the honey bee embryos and other eusocial insects. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

A Novel Protective Vaccine Antigen from the Core Escherichia coli Genome

PubMed Central

Moriel, Danilo G.; Tan, Lendl; Goh, Kelvin G. K.; Ipe, Deepak S.; Lo, Alvin W.; Peters, Kate M.

2016-01-01

ABSTRACT Escherichia coli is a versatile pathogen capable of causing intestinal and extraintestinal infections that result in a huge burden of global human disease. The diversity of E. coli is reflected by its multiple different pathotypes and mosaic genome composition. E. coli strains are also a major driver of antibiotic resistance, emphasizing the urgent need for new treatment and prevention measures. Here, we used a large data set comprising 1,700 draft and complete genomes to define the core and accessory genome of E. coli and demonstrated the overlapping relationship between strains from different pathotypes. In combination with proteomic investigation, this analysis revealed core genes that encode surface-exposed or secreted proteins that represent potential broad-coverage vaccine antigens. One of these antigens, YncE, was characterized as a conserved immunogenic antigen able to protect against acute systemic infection in mice after vaccination. Overall, this work provides a genomic blueprint for future analyses of conserved and accessory E. coli genes. The work also identified YncE as a novel antigen that could be exploited in the development of a vaccine against all pathogenic E. coli strains—an important direction given the high global incidence of infections caused by multidrug-resistant strains for which there are few effective antibiotics. IMPORTANCE E. coli is a multifaceted pathogen of major significance to global human health and an important contributor to increasing antibiotic resistance. Given the paucity of therapies still effective against multidrug-resistant pathogenic E. coli strains, novel treatment and prevention strategies are urgently required. In this study, we defined the core and accessory components of the E. coli genome by examining a large collection of draft and completely sequenced strains available from public databases. This data set was mined by employing a reverse-vaccinology approach in combination with proteomics to identify putative broadly protective vaccine antigens. One such antigen was identified that was highly immunogenic and induced protection in a mouse model of bacteremia. Overall, our study provides a genomic and proteomic framework for the selection of novel vaccine antigens that could mediate broad protection against pathogenic E. coli. PMID:27904885

Chronic intermittent ethanol exposure and withdrawal leads to adaptations in nucleus accumbens core postsynaptic density proteome and dendritic spines.

PubMed

Uys, Joachim D; McGuier, Natalie S; Gass, Justin T; Griffin, William C; Ball, Lauren E; Mulholland, Patrick J

2016-05-01

Alcohol use disorder is a chronic relapsing brain disease characterized by the loss of ability to control alcohol (ethanol) intake despite knowledge of detrimental health or personal consequences. Clinical and pre-clinical models provide strong evidence for chronic ethanol-associated alterations in glutamatergic signaling and impaired synaptic plasticity in the nucleus accumbens (NAc). However, the neural mechanisms that contribute to aberrant glutamatergic signaling in ethanol-dependent individuals in this critical brain structure remain unknown. Using an unbiased proteomic approach, we investigated the effects of chronic intermittent ethanol (CIE) exposure on neuroadaptations in postsynaptic density (PSD)-enriched proteins in the NAc of ethanol-dependent mice. Compared with controls, CIE exposure significantly changed expression levels of 50 proteins in the PSD-enriched fraction. Systems biology and functional annotation analyses demonstrated that the dysregulated proteins are expressed at tetrapartite synapses and critically regulate cellular morphology. To confirm this latter finding, the density and morphology of dendritic spines were examined in the NAc core of ethanol-dependent mice. We found that CIE exposure and withdrawal differentially altered dendrite diameter and dendritic spine density and morphology. Through the use of quantitative proteomics and functional annotation, these series of experiments demonstrate that ethanol dependence produces neuroadaptations in proteins that modify dendritic spine morphology. In addition, these studies identified novel PSD-related proteins that contribute to the neurobiological mechanisms of ethanol dependence that drive maladaptive structural plasticity of NAc neurons. © 2015 Society for the Study of Addiction.

Proteoglycomics: Recent Progress and Future Challenges

PubMed Central

Ly, Mellisa; Laremore, Tatiana N.

2010-01-01

Abstract Proteoglycomics is a systematic study of structure, expression, and function of proteoglycans, a posttranslationally modified subset of a proteome. Although relying on the established technologies of proteomics and glycomics, proteoglycomics research requires unique approaches for elucidating structure–function relationships of both proteoglycan components, glycosaminoglycan chain, and core protein. This review discusses our current understanding of structure and function of proteoglycans, major players in the development, normal physiology, and disease. A brief outline of the proteoglycomic sample preparation and analysis is provided along with examples of several recent proteoglycomic studies. Unique challenges in the characterization of glycosaminoglycan component of proteoglycans are discussed, with emphasis on the many analytical tools used and the types of information they provide. PMID:20450439

The Scottish Structural Proteomics Facility: targets, methods and outputs

PubMed Central

Oke, Muse; Carter, Lester G.; Johnson, Kenneth A.; Liu, Huanting; McMahon, Stephen A.; Yan, Xuan; Kerou, Melina; Weikart, Nadine D.; Kadi, Nadia; Sheikh, Md. Arif; Schmelz, Stefan; Dorward, Mark; Zawadzki, Michal; Cozens, Christopher; Falconer, Helen; Powers, Helen; Overton, Ian M.; van Niekerk, C. A. Johannes; Peng, Xu; Patel, Prakash; Garrett, Roger A.; Prangishvili, David; Botting, Catherine H.; Coote, Peter J.; Dryden, David T. F.; Barton, Geoffrey J.; Schwarz-Linek, Ulrich; Challis, Gregory L.; Taylor, Garry L.; White, Malcolm F.

2010-01-01

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology. Electronic supplementary material The online version of this article (doi:10.1007/s10969-010-9090-y) contains supplementary material, which is available to authorized users. PMID:20419351

The proteomics of lipid droplets: structure, dynamics, and functions of the organelle conserved from bacteria to humans

PubMed Central

Yang, Li; Ding, Yunfeng; Chen, Yong; Zhang, Shuyan; Huo, Chaoxing; Wang, Yang; Yu, Jinhai; Zhang, Peng; Na, Huimin; Zhang, Huina; Ma, Yanbin; Liu, Pingsheng

2012-01-01

Lipid droplets are cellular organelles that consists of a neutral lipid core covered by a monolayer of phospholipids and many proteins. They are thought to function in the storage, transport, and metabolism of lipids, in signaling, and as a specialized microenvironment for metabolism in most types of cells from prokaryotic to eukaryotic organisms. Lipid droplets have received a lot of attention in the last 10 years as they are linked to the progression of many metabolic diseases and hold great potential for the development of neutral lipid-derived products, such as biofuels, food supplements, hormones, and medicines. Proteomic analysis of lipid droplets has yielded a comprehensive catalog of lipid droplet proteins, shedding light on the function of this organelle and providing evidence that its function is conserved from bacteria to man. This review summarizes many of the proteomic studies on lipid droplets from a wide range of organisms, providing an evolutionary perspective on this organelle. PMID:22534641

Proteomic analyses of ethanol tolerance in Lactobacillus buchneri NRRL B-30929

USDA-ARS?s Scientific Manuscript database

The Lactobacillus buchneri NRRL B-30929 strain, isolated from a fuel ethanol production facility, exhibits high tolerance to environmental ethanol concentrations. This study aimed to identify proteins produced by B-30929 in response to environmental ethanol. Cellular proteins expressed by B-30929 gr...

Data management integration for biomedical core facilities

NASA Astrophysics Data System (ADS)

Zhang, Guo-Qiang; Szymanski, Jacek; Wilson, David

2007-03-01

We present the design, development, and pilot-deployment experiences of MIMI, a web-based, Multi-modality Multi-Resource Information Integration environment for biomedical core facilities. This is an easily customizable, web-based software tool that integrates scientific and administrative support for a biomedical core facility involving a common set of entities: researchers; projects; equipments and devices; support staff; services; samples and materials; experimental workflow; large and complex data. With this software, one can: register users; manage projects; schedule resources; bill services; perform site-wide search; archive, back-up, and share data. With its customizable, expandable, and scalable characteristics, MIMI not only provides a cost-effective solution to the overarching data management problem of biomedical core facilities unavailable in the market place, but also lays a foundation for data federation to facilitate and support discovery-driven research.

Gains in efficiency and scientific potential of continental climate reconstruction provided by the LRC LacCore Facility, University of Minnesota

NASA Astrophysics Data System (ADS)

Noren, A.; Brady, K.; Myrbo, A.; Ito, E.

2007-12-01

Lacustrine sediment cores comprise an integral archive for the determination of continental paleoclimate, for their potentially high temporal resolution and for their ability to resolve spatial variability in climate across vast sections of the globe. Researchers studying these archives now have a large, nationally-funded, public facility dedicated to the support of their efforts. The LRC LacCore Facility, funded by NSF and the University of Minnesota, provides free or low-cost assistance to any portion of research projects, depending on the specific needs of the project. A large collection of field equipment (site survey equipment, coring devices, boats/platforms, water sampling devices) for nearly any lacustrine setting is available for rental, and Livingstone-type corers and drive rods may be purchased. LacCore staff can accompany field expeditions to operate these devices and curate samples, or provide training prior to device rental. The Facility maintains strong connections to experienced shipping agents and customs brokers, which vastly improves transport and importation of samples. In the lab, high-end instrumentation (e.g., multisensor loggers, high-resolution digital linescan cameras) provides a baseline of fundamental analyses before any sample material is consumed. LacCore staff provide support and training in lithological description, including smear-slide, XRD, and SEM analyses. The LRC botanical macrofossil reference collection is a valuable resource for both core description and detailed macrofossil analysis. Dedicated equipment and space for various subsample analyses streamlines these endeavors; subsamples for several analyses may be submitted for preparation or analysis by Facility technicians for a fee (e.g., carbon and sulfur coulometry, grain size, pollen sample preparation and analysis, charcoal, biogenic silica, LOI, freeze drying). The National Lacustrine Core Repository now curates ~9km of sediment cores from expeditions around the world, and stores metadata and analytical data for all cores processed at the facility. Any researcher may submit sample requests for material in archived cores. Supplies for field (e.g., polycarbonate pipe, endcaps), lab (e.g., sample containers, pollen sample spike), and curation (e.g., D-tubes) are sold at cost. In collaboration with facility users, staff continually develop new equipment, supplies, and procedures as needed in order to provide the best and most comprehensive set of services to the research community.

TRAC analyses for CCTF and SCTF tests and UPTF design/operation. [Cylindrical Core Test Facility; Slab Core Test Facility; Upper Plenum Test Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spore, J.W.; Cappiello, M.W.; Dotson, P.J.

The analytical support in 1985 for Cylindrical Core Test Facility (CCTF), Slab Core Test Facility (SCTF), and Upper Plenum Test Facility (UPTF) tests involves the posttest analysis of 16 tests that have already been run in the CCTF and the SCTF and the pretest analysis of 3 tests to be performed in the UPTF. Posttest analysis is used to provide insight into the detailed thermal-hydraulic phenomena occurring during the refill and reflood tests performed in CCTF and SCTF. Pretest analysis is used to ensure that the test facility is operated in a manner consistent with the expected behavior of anmore » operating full-scale plant during an accident. To obtain expected behavior of a plant during an accident, two plant loss-of-coolant-accident (LOCA) calculations were performed: a 200% cold-leg-break LOCA calculation for a 2772 MW(t) Babcock and Wilcox plant and a 200% cold-leg-break LOCA calculation for a 3315 MW(t) Westinghouse plant. Detailed results are presented for several CCTF UPI tests and the Westinghouse plant analysis.« less

The Common Core of a Child Care Center. Child Care Facility Design.

ERIC Educational Resources Information Center

Moore, Gary T.

1997-01-01

Examines the notion of an early childhood education center organized as a series of houses around a common core of shared facilities. Discusses examples of child-care centers in Sweden and explores ideas that can promote functional facilities. Suggestions include ideas about physical-motor activities areas, administration offices, centralized…

Identification of a regulation network in response to cadmium toxicity using blood clam Tegillarca granosa as model

PubMed Central

Bao, Yongbo; Liu, Xiao; Zhang, Weiwei; Cao, Jianping; Li, Wei; Li, Chenghua; Lin, Zhihua

2016-01-01

Clam, a filter-feeding lamellibranch mollusk, is capable to accumulate high levels of trace metals and has therefore become a model for investigation the mechanism of heavy metal toxification. In this study, the effects of cadmium were characterized in the gills of Tegillarca granosa during a 96-hour exposure course using integrated metabolomic and proteomic approaches. Neurotoxicity and disturbances in energy metabolism were implicated according to the metabolic responses after Cd exposure, and eventually affected the osmotic function of gill tissue. Proteomic analysis showed that oxidative stress, calcium-binding and sulfur-compound metabolism proteins were key factors responding to Cd challenge. A knowledge-based network regulation model was constructed with both metabolic and proteomic data. The model suggests that Cd stimulation mainly inhibits a core regulation network that is associated with histone function, ribosome processing and tight junctions, with the hub proteins actin, gamma 1 and Calmodulin 1. Moreover, myosin complex inhibition causes abnormal tight junctions and is linked to the irregular synthesis of amino acids. For the first time, this study provides insight into the proteomic and metabolomic changes caused by Cd in the blood clam T. granosa and suggests a potential toxicological pathway for Cd. PMID:27760991

A standardized framing for reporting protein identifications in mzIdentML 1.2

PubMed Central

Seymour, Sean L.; Farrah, Terry; Binz, Pierre-Alain; Chalkley, Robert J.; Cottrell, John S.; Searle, Brian C.; Tabb, David L.; Vizcaíno, Juan Antonio; Prieto, Gorka; Uszkoreit, Julian; Eisenacher, Martin; Martínez-Bartolomé, Salvador; Ghali, Fawaz; Jones, Andrew R.

2015-01-01

Inferring which protein species have been detected in bottom-up proteomics experiments has been a challenging problem for which solutions have been maturing over the past decade. While many inference approaches now function well in isolation, comparing and reconciling the results generated across different tools remains difficult. It presently stands as one of the greatest barriers in collaborative efforts such as the Human Proteome Project and public repositories like the PRoteomics IDEntifications (PRIDE) database. Here we present a framework for reporting protein identifications that seeks to improve capabilities for comparing results generated by different inference tools. This framework standardizes the terminology for describing protein identification results, associated with the HUPO-Proteomics Standards Initiative (PSI) mzIdentML standard, while still allowing for differing methodologies to reach that final state. It is proposed that developers of software for reporting identification results will adopt this terminology in their outputs. While the new terminology does not require any changes to the core mzIdentML model, it represents a significant change in practice, and, as such, the rules will be released via a new version of the mzIdentML specification (version 1.2) so that consumers of files are able to determine whether the new guidelines have been adopted by export software. PMID:25092112

Functional Proteomics-Based Ovarian Cancer Biomarkers

DTIC Science & Technology

2010-11-01

1765. 52  Garrido, Carmen, et al. " HSP27 and HSP70: potentially oncogenic apoptosis inhibitors." Cell Cycle 2.6 (2003): 578-583. 53  Greenman...group AT- hook 2 Use with caution 99 HNRNP hnRNP core protein A1 Use with caution 110 85 HSP27 heat shock 27kDa protein Validated 163

A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses.

PubMed

Hall, Neil; Karras, Marianna; Raine, J Dale; Carlton, Jane M; Kooij, Taco W A; Berriman, Matthew; Florens, Laurence; Janssen, Christoph S; Pain, Arnab; Christophides, Georges K; James, Keith; Rutherford, Kim; Harris, Barbara; Harris, David; Churcher, Carol; Quail, Michael A; Ormond, Doug; Doggett, Jon; Trueman, Holly E; Mendoza, Jacqui; Bidwell, Shelby L; Rajandream, Marie-Adele; Carucci, Daniel J; Yates, John R; Kafatos, Fotis C; Janse, Chris J; Barrell, Bart; Turner, C Michael R; Waters, Andrew P; Sinden, Robert E

2005-01-07

Plasmodium berghei and Plasmodium chabaudi are widely used model malaria species. Comparison of their genomes, integrated with proteomic and microarray data, with the genomes of Plasmodium falciparum and Plasmodium yoelii revealed a conserved core of 4500 Plasmodium genes in the central regions of the 14 chromosomes and highlighted genes evolving rapidly because of stage-specific selective pressures. Four strategies for gene expression are apparent during the parasites' life cycle: (i) housekeeping; (ii) host-related; (iii) strategy-specific related to invasion, asexual replication, and sexual development; and (iv) stage-specific. We observed posttranscriptional gene silencing through translational repression of messenger RNA during sexual development, and a 47-base 3' untranslated region motif is implicated in this process.

Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes.

PubMed

Wang, Guanghui; Wu, Wells W; Zeng, Weihua; Chou, Chung-Lin; Shen, Rong-Fong

2006-05-01

A critical step in protein biomarker discovery is the ability to contrast proteomes, a process referred generally as quantitative proteomics. While stable-isotope labeling (e.g., ICAT, 18O- or 15N-labeling, or AQUA) remains the core technology used in mass spectrometry-based proteomic quantification, increasing efforts have been directed to the label-free approach that relies on direct comparison of peptide peak areas between LC-MS runs. This latter approach is attractive to investigators for its simplicity as well as cost effectiveness. In the present study, the reproducibility and linearity of using a label-free approach to highly complex proteomes were evaluated. Various amounts of proteins from different proteomes were subjected to repeated LC-MS analyses using an ion trap or Fourier transform mass spectrometer. Highly reproducible data were obtained between replicated runs, as evidenced by nearly ideal Pearson's correlation coefficients (for ion's peak areas or retention time) and average peak area ratios. In general, more than 50% and nearly 90% of the peptide ion ratios deviated less than 10% and 20%, respectively, from the average in duplicate runs. In addition, the multiplicity ratios of the amounts of proteins used correlated nicely with the observed averaged ratios of peak areas calculated from detected peptides. Furthermore, the removal of abundant proteins from the samples led to an improvement in reproducibility and linearity. A computer program has been written to automate the processing of data sets from experiments with groups of multiple samples for statistical analysis. Algorithms for outlier-resistant mean estimation and for adjusting statistical significance threshold in multiplicity of testing were incorporated to minimize the rate of false positives. The program was applied to quantify changes in proteomes of parental and p53-deficient HCT-116 human cells and found to yield reproducible results. Overall, this study demonstrates an alternative approach that allows global quantification of differentially expressed proteins in complex proteomes. The utility of this method to biomarker discovery is likely to synergize with future improvements in the detecting sensitivity of mass spectrometers.

RADIATION FACILITY FOR NUCLEAR REACTORS

DOEpatents

Currier, E.L. Jr.; Nicklas, J.H.

1961-12-12

A radiation facility is designed for irradiating samples in close proximity to the core of a nuclear reactor. The facility comprises essentially a tubular member extending through the biological shield of the reactor and containing a manipulatable rod having the sample carrier at its inner end, the carrier being longitudinally movable from a position in close proximity to the reactor core to a position between the inner and outer faces of the shield. Shield plugs are provided within the tubular member to prevent direct radiation from the core emanating therethrough. In this device, samples may be inserted or removed during normal operation of the reactor without exposing personnel to direct radiation from the reactor core. A storage chamber is also provided within the radiation facility to contain an irradiated sample during the period of time required to reduce the radioactivity enough to permit removal of the sample for external handling. (AEC)

Best Practices for Core Facilities: Handling External Customers

PubMed Central

Hockberger, Philip; Meyn, Susan; Nicklin, Connie; Tabarini, Diane; Turpen, Paula; Auger, Julie

2013-01-01

This article addresses the growing interest among U.S. scientific organizations and federal funding agencies in strengthening research partnerships between American universities and the private sector. It outlines how core facilities at universities can contribute to this partnership by offering services and access to high-end instrumentation to both nonprofit organizations and commercial organizations. We describe institutional policies (best practices) and procedures (terms and conditions) that are essential for facilitating and enabling such partnerships. In addition, we provide an overview of the relevant federal regulations that apply to external use of academic core facilities and offer a set of guidelines for handling them. We conclude by encouraging directors and managers of core facilities to work with the relevant organizational offices to promote and nurture such partnerships. If handled appropriately, we believe such partnerships can be a win-win situation for both organizations that will support research and bolster the American economy. PMID:23814500

TIMMDC1/C3orf1 functions as a membrane-embedded mitochondrial complex I assembly factor through association with the MCIA complex.

PubMed

Guarani, Virginia; Paulo, Joao; Zhai, Bo; Huttlin, Edward L; Gygi, Steven P; Harper, J Wade

2014-03-01

Complex I (CI) of the electron transport chain, a large membrane-embedded NADH dehydrogenase, couples electron transfer to the release of protons into the mitochondrial inner membrane space to promote ATP production through ATP synthase. In addition to being a central conduit for ATP production, CI activity has been linked to neurodegenerative disorders, including Parkinson's disease. CI is built in a stepwise fashion through the actions of several assembly factors. We employed interaction proteomics to interrogate the molecular associations of 15 core subunits and assembly factors previously linked to human CI deficiency, resulting in a network of 101 proteins and 335 interactions (edges). TIMMDC1, a predicted 4-pass membrane protein, reciprocally associated with multiple members of the MCIA CI assembly factor complex and core CI subunits and was localized in the mitochondrial inner membrane, and its depletion resulted in reduced CI activity and cellular respiration. Quantitative proteomics demonstrated a role for TIMMDC1 in assembly of membrane-embedded and soluble arms of the complex. This study defines a new membrane-embedded CI assembly factor and provides a resource for further analysis of CI biology.

Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803

DOE PAGES

Liberton, Michelle; Chrisler, William B.; Nicora, Carrie D.; ...

2017-03-02

Here, cyanobacteria, such as Synechocystis sp. PCC 6803, utilize large antenna systems to optimize light harvesting and energy transfer to reaction centers. Understanding the structure and function of these complexes, particularly when altered, will help direct bio-design efforts to optimize biofuel production. Three specific phycobilisome (PBS) complex truncation mutants were studied, ranging from progressive truncation of phycocyanin rods in the CB and CK strains, to full removal of all phycocyanin and allophycocyanin cores in the PAL mutant. We applied comprehensive proteomic analyses to investigate both direct and downstream molecular systems implications of each truncation. Results showed that PBS truncation inmore » Synechocystis sp. PCC 6803 dramatically alters core cellular mechanisms beyond energy capture and electron transport, placing constraints upon cellular processes that dramatically altered phenotypes. This included primarily membrane associated functions and altered regulation of cellular resources (i.e., iron, nitrite/nitrate, bicarbonate). Additionally, each PBS truncation, though progressive in nature, exhibited unique phenotypes compare to WT, and hence we assert that in the current realm of extensive bioengineering and bio-design, there remains a continuing need to assess systems-wide protein based abundances to capture potential indirect phenotypic effects.« less

Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liberton, Michelle; Chrisler, William B.; Nicora, Carrie D.

Here, cyanobacteria, such as Synechocystis sp. PCC 6803, utilize large antenna systems to optimize light harvesting and energy transfer to reaction centers. Understanding the structure and function of these complexes, particularly when altered, will help direct bio-design efforts to optimize biofuel production. Three specific phycobilisome (PBS) complex truncation mutants were studied, ranging from progressive truncation of phycocyanin rods in the CB and CK strains, to full removal of all phycocyanin and allophycocyanin cores in the PAL mutant. We applied comprehensive proteomic analyses to investigate both direct and downstream molecular systems implications of each truncation. Results showed that PBS truncation inmore » Synechocystis sp. PCC 6803 dramatically alters core cellular mechanisms beyond energy capture and electron transport, placing constraints upon cellular processes that dramatically altered phenotypes. This included primarily membrane associated functions and altered regulation of cellular resources (i.e., iron, nitrite/nitrate, bicarbonate). Additionally, each PBS truncation, though progressive in nature, exhibited unique phenotypes compare to WT, and hence we assert that in the current realm of extensive bioengineering and bio-design, there remains a continuing need to assess systems-wide protein based abundances to capture potential indirect phenotypic effects.« less

Integrative Identification of Arabidopsis Mitochondrial Proteome and Its Function Exploitation through Protein Interaction Network

PubMed Central

Cui, Jian; Liu, Jinghua; Li, Yuhua; Shi, Tieliu

2011-01-01

Mitochondria are major players on the production of energy, and host several key reactions involved in basic metabolism and biosynthesis of essential molecules. Currently, the majority of nucleus-encoded mitochondrial proteins are unknown even for model plant Arabidopsis. We reported a computational framework for predicting Arabidopsis mitochondrial proteins based on a probabilistic model, called Naive Bayesian Network, which integrates disparate genomic data generated from eight bioinformatics tools, multiple orthologous mappings, protein domain properties and co-expression patterns using 1,027 microarray profiles. Through this approach, we predicted 2,311 candidate mitochondrial proteins with 84.67% accuracy and 2.53% FPR performances. Together with those experimental confirmed proteins, 2,585 mitochondria proteins (named CoreMitoP) were identified, we explored those proteins with unknown functions based on protein-protein interaction network (PIN) and annotated novel functions for 26.65% CoreMitoP proteins. Moreover, we found newly predicted mitochondrial proteins embedded in particular subnetworks of the PIN, mainly functioning in response to diverse environmental stresses, like salt, draught, cold, and wound etc. Candidate mitochondrial proteins involved in those physiological acitivites provide useful targets for further investigation. Assigned functions also provide comprehensive information for Arabidopsis mitochondrial proteome. PMID:21297957

Quantitative Proteomics of Sleep-Deprived Mouse Brains Reveals Global Changes in Mitochondrial Proteins

PubMed Central

Li, Tie-Mei; Zhang, Ju-en; Lin, Rui; Chen, She; Luo, Minmin; Dong, Meng-Qiu

2016-01-01

Sleep is a ubiquitous, tightly regulated, and evolutionarily conserved behavior observed in almost all animals. Prolonged sleep deprivation can be fatal, indicating that sleep is a physiological necessity. However, little is known about its core function. To gain insight into this mystery, we used advanced quantitative proteomics technology to survey the global changes in brain protein abundance. Aiming to gain a comprehensive profile, our proteomics workflow included filter-aided sample preparation (FASP), which increased the coverage of membrane proteins; tandem mass tag (TMT) labeling, for relative quantitation; and high resolution, high mass accuracy, high throughput mass spectrometry (MS). In total, we obtained the relative abundance ratios of 9888 proteins encoded by 6070 genes. Interestingly, we observed significant enrichment for mitochondrial proteins among the differentially expressed proteins. This finding suggests that sleep deprivation strongly affects signaling pathways that govern either energy metabolism or responses to mitochondrial stress. Additionally, the differentially-expressed proteins are enriched in pathways implicated in age-dependent neurodegenerative diseases, including Parkinson’s, Huntington’s, and Alzheimer’s, hinting at possible connections between sleep loss, mitochondrial stress, and neurodegeneration. PMID:27684481

A Combined Metabonomic and Proteomic Approach Identifies Frontal Cortex Changes in a Chronic Phencyclidine Rat Model in Relation to Human Schizophrenia Brain Pathology

PubMed Central

Wesseling, Hendrik; Chan, Man K; Tsang, T M; Ernst, Agnes; Peters, Fabian; Guest, Paul C; Holmes, Elaine; Bahn, Sabine

2013-01-01

Current schizophrenia (SCZ) treatments fail to treat the broad range of manifestations associated with this devastating disorder. Thus, new translational models that reproduce the core pathological features are urgently needed to facilitate novel drug discovery efforts. Here, we report findings from the first comprehensive label-free liquid-mass spectrometry proteomic- and proton nuclear magnetic resonance-based metabonomic profiling of the rat frontal cortex after chronic phencyclidine (PCP) intervention, which induces SCZ-like symptoms. The findings were compared with results from a proteomic profiling of post-mortem prefrontal cortex from SCZ patients and with relevant findings in the literature. Through this approach, we identified proteomic alterations in glutamate-mediated Ca2+ signaling (Ca2+/calmodulin-dependent protein kinase II, PPP3CA, and VISL1), mitochondrial function (GOT2 and PKLR), and cytoskeletal remodeling (ARP3). Metabonomic profiling revealed changes in the levels of glutamate, glutamine, glycine, pyruvate, and the Ca2+ regulator taurine. Effects on similar pathways were also identified in the prefrontal cortex tissue from human SCZ subjects. The discovery of similar but not identical proteomic and metabonomic alterations in the chronic PCP rat model and human brain indicates that this model recapitulates only some of the molecular alterations of the disease. This knowledge may be helpful in understanding mechanisms underlying psychosis, which, in turn, can facilitate improved therapy and drug discovery for SCZ and other psychiatric diseases. Most importantly, these molecular findings suggest that the combined use of multiple models may be required for more effective translation to studies of human SCZ. PMID:23942359

Virus-producing cells determine the host protein profiles of HIV-1 virion cores

PubMed Central

2012-01-01

Background Upon HIV entry into target cells, viral cores are released and rearranged into reverse transcription complexes (RTCs), which support reverse transcription and also protect and transport viral cDNA to the site of integration. RTCs are composed of viral and cellular proteins that originate from both target and producer cells, the latter entering the target cell within the viral core. However, the proteome of HIV-1 viral cores in the context of the type of producer cells has not yet been characterized. Results We examined the proteomic profiles of the cores purified from HIV-1 NL4-3 virions assembled in Sup-T1 cells (T lymphocytes), PMA and vitamin D3 activated THP1 (model of macrophages, mMΦ), and non-activated THP1 cells (model of monocytes, mMN) and assessed potential involvement of identified proteins in the early stages of infection using gene ontology information and data from genome-wide screens on proteins important for HIV-1 replication. We identified 202 cellular proteins incorporated in the viral cores (T cells: 125, mMΦ: 110, mMN: 90) with the overlap between these sets limited to 42 proteins. The groups of RNA binding (29), DNA binding (17), cytoskeleton (15), cytoskeleton regulation (21), chaperone (18), vesicular trafficking-associated (12) and ubiquitin-proteasome pathway-associated proteins (9) were most numerous. Cores of the virions from SupT1 cells contained twice as many RNA binding proteins as cores of THP1-derived virus, whereas cores of virions from mMΦ and mMN were enriched in components of cytoskeleton and vesicular transport machinery, most probably due to differences in virion assembly pathways between these cells. Spectra of chaperones, cytoskeletal proteins and ubiquitin-proteasome pathway components were similar between viral cores from different cell types, whereas DNA-binding and especially RNA-binding proteins were highly diverse. Western blot analysis showed that within the group of overlapping proteins, the level of incorporation of some RNA binding (RHA and HELIC2) and DNA binding proteins (MCM5 and Ku80) in the viral cores from T cells was higher than in the cores from both mMΦ and mMN and did not correlate with the abundance of these proteins in virus producing cells. Conclusions Profiles of host proteins packaged in the cores of HIV-1 virions depend on the type of virus producing cell. The pool of proteins present in the cores of all virions is likely to contain factors important for viral functions. Incorporation ratio of certain RNA- and DNA-binding proteins suggests their more efficient, non-random packaging into virions in T cells than in mMΦ and mMN. PMID:22889230

Cloud CPFP: a shotgun proteomics data analysis pipeline using cloud and high performance computing.

PubMed

Trudgian, David C; Mirzaei, Hamid

2012-12-07

We have extended the functionality of the Central Proteomics Facilities Pipeline (CPFP) to allow use of remote cloud and high performance computing (HPC) resources for shotgun proteomics data processing. CPFP has been modified to include modular local and remote scheduling for data processing jobs. The pipeline can now be run on a single PC or server, a local cluster, a remote HPC cluster, and/or the Amazon Web Services (AWS) cloud. We provide public images that allow easy deployment of CPFP in its entirety in the AWS cloud. This significantly reduces the effort necessary to use the software, and allows proteomics laboratories to pay for compute time ad hoc, rather than obtaining and maintaining expensive local server clusters. Alternatively the Amazon cloud can be used to increase the throughput of a local installation of CPFP as necessary. We demonstrate that cloud CPFP allows users to process data at higher speed than local installations but with similar cost and lower staff requirements. In addition to the computational improvements, the web interface to CPFP is simplified, and other functionalities are enhanced. The software is under active development at two leading institutions and continues to be released under an open-source license at http://cpfp.sourceforge.net.

BIOLOGICAL IRRADIATION FACILITY

DOEpatents

McCorkle, W.H.; Cern, H.S.

1962-04-24

A facility for irradiating biological specimens with neutrons is described. It includes a reactor wherein the core is off center in a reflector. A high-exposure room is located outside the reactor on the side nearest the core while a low-exposure room is located on the opposite side. Means for converting thermal neutrons to fast neutrons are movably disposed between the reactor core and the high and low-exposure rooms. (AEC)

Proteome Analysis of Borrelia burgdorferi Response to Environmental Change

DOE Office of Scientific and Technical Information (OSTI.GOV)

Angel, Thomas E.; Luft, Benjamin J.; Yang, Xiaohua

2010-11-02

We examined global changes in protein expression in the B31 strain of Borrelia burgdorferi, in response to two environmental cues (pH and temperature) chosen for their reported similarity to those encountered at different stages of the organism’s life cycle. Multidimensional nano-liquid chromatographic separations coupled with tandem mass spectrometry were used to examine the array of proteins (i.e., the proteome) of B. burgdorferi for different pH and temperature culture conditions. Changes in pH and temperature elicited in vitro adaptations of this spirochete known to cause Lyme disease and led to alterations in protein expression that are associated with increased microbial pathogenesis.more » We identified 1031 proteins that represent 59% of the annotated genome of B. burgdorferi and elucidated a core proteome of 414 proteins that were present in all environmental conditions investigated. Observed changes in protein abundances indicated varied replicon usage, as well as proteome functional distributions between the in vitro cell culture conditions. Surprisingly, the pH and temperature conditions that mimicked B. burgdorferi residing in the gut of a fed tick showed a marked reduction in protein diversity. Additionally, the results provide us with leading candidates for exploring how B. burgdorferi adapts to and is able to survive in a wide variety of environmental conditions and lay a foundation for planned in situ studies of B. burgdorferi isolated from the tick midgut and infected animals.« less

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.

PubMed

Tyanova, Stefka; Temu, Tikira; Cox, Juergen

2016-12-01

MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms. Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques. This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda. This protocol update describes an adaptation of an existing protocol that substantially modifies the technique. Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs). The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail. Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs. The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores. The software is written in C# and is freely available at http://www.maxquant.org.

Rapid Myeloid Cell Transcriptional and Proteomic Responses to Periodontopathogenic Porphyromonas gingivalis

PubMed Central

Nares, Salvador; Moutsopoulos, Niki M.; Angelov, Nikola; Rangel, Zoila G.; Munson, Peter J.; Sinha, Neha; Wahl, Sharon M.

2009-01-01

Long-lived monocytes, macrophages, and dendritic cells (DCs) are Toll-like receptor-expressing, antigen-presenting cells derived from a common myeloid lineage that play key roles in innate and adaptive immune responses. Based on immunohistochemical and molecular analyses of inflamed tissues from patients with chronic destructive periodontal disease, these cells, found in the inflammatory infiltrate, may drive the progressive periodontal pathogenesis. To investigate early transcriptional signatures and subsequent proteomic responses to the periodontal pathogen, Porphyromonas gingivalis, donor-matched human blood monocytes, differentiated DCs, and macrophages were exposed to P. gingivalis lipopolysaccharide (LPS) and gene expression levels were measured by oligonucleotide microarrays. In addition to striking differences in constitutive transcriptional profiles between these myeloid populations, we identify a P. gingivalis LPS-inducible convergent, transcriptional core response of more than 400 annotated genes/ESTs among these populations, reflected by a shared, but quantitatively distinct, proteomic response. Nonetheless, clear differences emerged between the monocytes, DCs, and macrophages. The finding that long-lived myeloid inflammatory cells, particularly DCs, rapidly and aggressively respond to P. gingivalis LPS by generating chemokines, proteases, and cytokines capable of driving T-helper cell lineage polarization without evidence of corresponding immunosuppressive pathways highlights their prominent role in host defense and progressive tissue pathogenesis. The shared, unique, and/or complementary transcriptional and proteomic profiles may frame the context of the host response to P. gingivalis, contributing to the destructive nature of periodontal inflammation. PMID:19264901

Proteomic identification of a potential sex biomarker for 2 fruit fly species at pupal stage

USDA-ARS?s Scientific Manuscript database

We collected brown and white pupae from rearing DTWP larvae on liquid diet and TSL strain from CDFA rearing facility respectively and daily and analyzed protein expression from pupal age 1-10 days old using 2D electrophoresis. In this report, two pupal color sexing strain [dorsalis translocation whi...

Differential proteomic analysis of mouse macrophages exposed to adsorbate-loaded heavy fuel oil derived combustion particles using an automated sample-preparation workflow.

PubMed

Kanashova, Tamara; Popp, Oliver; Orasche, Jürgen; Karg, Erwin; Harndorf, Horst; Stengel, Benjamin; Sklorz, Martin; Streibel, Thorsten; Zimmermann, Ralf; Dittmar, Gunnar

2015-08-01

Ship diesel combustion particles are known to cause broad cytotoxic effects and thereby strongly impact human health. Particles from heavy fuel oil (HFO) operated ships are considered as particularly dangerous. However, little is known about the relevant components of the ship emission particles. In particular, it is interesting to know if the particle cores, consisting of soot and metal oxides, or the adsorbate layers, consisting of semi- and low-volatile organic compounds and salts, are more relevant. We therefore sought to relate the adsorbates and the core composition of HFO combustion particles to the early cellular responses, allowing for the development of measures that counteract their detrimental effects. Hence, the semi-volatile coating of HFO-operated ship diesel engine particles was removed by stepwise thermal stripping using different temperatures. RAW 264.7 macrophages were exposed to native and thermally stripped particles in submersed culture. Proteomic changes were monitored by two different quantitative mass spectrometry approaches, stable isotope labeling by amino acids in cell culture (SILAC) and dimethyl labeling. Our data revealed that cells reacted differently to native or stripped HFO combustion particles. Cells exposed to thermally stripped particles showed a very differential reaction with respect to the composition of the individual chemical load of the particle. The cellular reactions of the HFO particles included reaction to oxidative stress, reorganization of the cytoskeleton and changes in endocytosis. Cells exposed to the 280 °C treated particles showed an induction of RNA-related processes, a number of mitochondria-associated processes as well as DNA damage response, while the exposure to 580 °C treated HFO particles mainly induced the regulation of intracellular transport. In summary, our analysis based on a highly reproducible automated proteomic sample-preparation procedure shows a diverse cellular response, depending on the soot particle composition. In particular, it was shown that both the molecules of the adsorbate layer as well as particle cores induced strong but different effects in the exposed cells.

State recovery and lockstep execution restart in a system with multiprocessor pairing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gara, Alan; Gschwind, Michael K; Salapura, Valentina

System, method and computer program product for a multiprocessing system to offer selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). Each paired microprocessor or processor cores that provide one highly reliable thread for high-reliability connect with a system components such as a memory "nest" (or memory hierarchy), an optional system controller, and optional interrupt controller, optional I/O or peripheral devices, etc. The memory nest is attached to a selective pairing facility via a switchmore » or a bus. Each selectively paired processor core is includes a transactional execution facility, whereing the system is configured to enable processor rollback to a previous state and reinitialize lockstep execution in order to recover from an incorrect execution when an incorrect execution has been detected by the selective pairing facility.« less

Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics: HIP BMD LOSS & FRACTURE RISK MARKERS BY POPULATION-BASED SERUM PROTEOMICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nielson, Carrie M.; Wiedrick, Jack; Shen, Jian

Accelerated bone loss significantly increases the risk of osteoporosis and fracture. The mechanisms underlying bone loss remain incompletely understood, and there are few available biomarkers. We utilized a novel proteomics approach to identify serum peptides and proteins associated with bone loss in 1967 older men who were randomly chosen from the Osteoporotic Fracture in Men Study (MrOS study) (age ≥ 65 yrs). Men had 2-3 measures of femoral neck BMD over an average follow-up of 4.6 years. Change in BMD was estimated and then categorized into three groups: maintained BMD (n=453), expected loss (n=1185) and accelerated loss (n=237). A liquidmore » chromatography–ion mobility separation-mass spectrometry (LC-IMS-MS) proteomics platform was used to identify and quantify peptides from serum proteins. The whole cohort was randomly divided into discovery (N= 960) and validation (N= 915) sub-cohorts. Linear regression models and a random forest approach were used to discover differentially abundant individual peptides and a proteomic signature that distinguished individuals with accelerated bone loss from those who maintained BMD. Network analyses were performed using the MetaCore knowledgebase. We identified 12 peptides that were associated with BMD loss in both discovery (P< 0.1 FDR) and replication sub-cohorts (P<0.05). Those 12 peptides mapped to the following proteins: ALS, LYVE1, RNAS1, C2, ICOSL, C163A, C7, HEMO, CD14, CERU, CRAC1 and CD59. Meta-analysis of peptidesassociated with bone loss identified 6 additional proteins including GRP78, IGF-2, SHBG, ENPP2, IBP2 and IBP6. We also identified a proteomic signature that was predictive of BMD loss with a discriminative value similar to serum bone marker carboxy-terminal collagen crosslink peptide (CTX). Interestingly, combining the proteomic signature with CTX significantly improved the ability to discriminate men with accelerated loss. In summary, we have identified potential new biomarkers for bone loss that provide a more in depth understanding of its pathophysiology.« less

Bringing the Pieces Together – Placing Core Facilities at the Core of Universities and Institutions: Lessons from Mergers, Acquisitions and Consolidations

PubMed Central

Mundoma, Claudius

2013-01-01

As organizations expand and grow, the core facilities have become more dispersed disconnected. This is happening at a time when collaborations within the organization is a driver to increased productivity. Stakeholders are looking at the best way to bring the pieces together. It is inevitable that core facilities at universities and research institutes have to be integrated in order to streamline services and facilitate ease of collaboration. The path to integration often goes through consolidation, merging and shedding of redundant services. Managing this process requires a delicate coordination of two critical factors: the human (lab managers) factor and the physical assets factor. Traditionally more emphasis has been placed on reorganizing the physical assets without paying enough attention to the professionals who have been managing the assets for years, if not decades. The presentation focuses on how a systems approach can be used to effect a smooth core facility integration process. Managing the human element requires strengthening existing channels of communication and if necessary, creating new ones throughout the organization to break cultural and structural barriers. Managing the physical assets requires a complete asset audit and this requires direct input from the administration as well as the facility managers. Organizations can harness the power of IT to create asset visibility. Successfully managing the physical assets and the human assets increases productivity and efficiency within the organization.

Evaluation of the Nicotinic Acetylcholine Receptor-Associated Proteome at Baseline and Following Nicotine Exposure in Human and Mouse Cortex.

PubMed

McClure-Begley, Tristan D; Esterlis, Irina; Stone, Kathryn L; Lam, TuKiet T; Grady, Sharon R; Colangelo, Christopher M; Lindstrom, Jon M; Marks, Michael J; Picciotto, Marina R

2016-01-01

Nicotinic acetylcholine receptors (nAChRs) support the initiation and maintenance of smoking, but the long-term changes occurring in the protein complex as a result of smoking and the nicotine in tobacco are not known. Human studies and animal models have also demonstrated that increasing cholinergic tone increases behaviors related to depression, suggesting that the nAChR-associated proteome could be altered in individuals with mood disorders. We therefore immunopurified nAChRs and associated proteins for quantitative proteomic assessment of changes in protein-protein interactions of high-affinity nAChRs containing the β2 subunit (β2*-nAChRs) from either cortex of mice treated with saline or nicotine, or postmortem human temporal cortex tissue from tobacco-exposed and nonexposed individuals, with a further comparison of diagnosed mood disorder to control subjects. We observed significant effects of nicotine exposure on the β2*-nAChR-associated proteome in human and mouse cortex, particularly in the abundance of the nAChR subunits themselves, as well as putative interacting proteins that make up core components of neuronal excitability (Na/K ATPase subunits), presynaptic neurotransmitter release (syntaxins, SNAP25, synaptotagmin), and a member of a known nAChR protein chaperone family (14-3-3ζ). These findings identify candidate-signaling proteins that could mediate changes in cholinergic signaling via nicotine or tobacco use. Further analysis of identified proteins will determine whether these interactions are essential for primary function of nAChRs at presynaptic terminals. The identification of differences in the nAChR-associated proteome and downstream signaling in subjects with various mood disorders may also identify novel etiological mechanisms and reveal new treatment targets.

Combining results of multiple search engines in proteomics.

PubMed

Shteynberg, David; Nesvizhskii, Alexey I; Moritz, Robert L; Deutsch, Eric W

2013-09-01

A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the parent molecular ion that produced each fragment ion spectrum in the dataset. There are many different search engines, both commercial and open source, each employing a somewhat different technique for spectrum identification. The set of high-scoring peptide-spectrum matches for a defined set of input spectra differs markedly among the various search engine results; individual engines each provide unique correct identifications among a core set of correlative identifications. This has led to the approach of combining the results from multiple search engines to achieve improved analysis of each dataset. Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques.

Combining Results of Multiple Search Engines in Proteomics*

PubMed Central

Shteynberg, David; Nesvizhskii, Alexey I.; Moritz, Robert L.; Deutsch, Eric W.

2013-01-01

A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the parent molecular ion that produced each fragment ion spectrum in the dataset. There are many different search engines, both commercial and open source, each employing a somewhat different technique for spectrum identification. The set of high-scoring peptide-spectrum matches for a defined set of input spectra differs markedly among the various search engine results; individual engines each provide unique correct identifications among a core set of correlative identifications. This has led to the approach of combining the results from multiple search engines to achieve improved analysis of each dataset. Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques. PMID:23720762

17 CFR 37.900 - Core Principle 9-Timely publication of trading information.

Code of Federal Regulations, 2014 CFR

2014-04-01

... publication of trading information. 37.900 Section 37.900 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION SWAP EXECUTION FACILITIES Timely Publication of Trading Information § 37.900 Core Principle 9—Timely publication of trading information. (a) In general. The swap execution facility shall...

The Pfam protein families database: towards a more sustainable future.

PubMed

Finn, Robert D; Coggill, Penelope; Eberhardt, Ruth Y; Eddy, Sean R; Mistry, Jaina; Mitchell, Alex L; Potter, Simon C; Punta, Marco; Qureshi, Matloob; Sangrador-Vegas, Amaia; Salazar, Gustavo A; Tate, John; Bateman, Alex

2016-01-04

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Lead Coolant Test Facility Systems Design, Thermal Hydraulic Analysis and Cost Estimate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soli Khericha; Edwin Harvego; John Svoboda

2012-01-01

The Idaho National Laboratory prepared a preliminary technical and functional requirements (T&FR), thermal hydraulic design and cost estimate for a lead coolant test facility. The purpose of this small scale facility is to simulate lead coolant fast reactor (LFR) coolant flow in an open lattice geometry core using seven electrical rods and liquid lead or lead-bismuth eutectic coolant. Based on review of current world lead or lead-bismuth test facilities and research needs listed in the Generation IV Roadmap, five broad areas of requirements were identified as listed: (1) Develop and Demonstrate Feasibility of Submerged Heat Exchanger; (2) Develop and Demonstratemore » Open-lattice Flow in Electrically Heated Core; (3) Develop and Demonstrate Chemistry Control; (4) Demonstrate Safe Operation; and (5) Provision for Future Testing. This paper discusses the preliminary design of systems, thermal hydraulic analysis, and simplified cost estimate. The facility thermal hydraulic design is based on the maximum simulated core power using seven electrical heater rods of 420 kW; average linear heat generation rate of 300 W/cm. The core inlet temperature for liquid lead or Pb/Bi eutectic is 4200 C. The design includes approximately seventy-five data measurements such as pressure, temperature, and flow rates. The preliminary estimated cost of construction of the facility is $3.7M (in 2006 $). It is also estimated that the facility will require two years to be constructed and ready for operation.« less

Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals

PubMed Central

Shabalina, Svetlana A.; Ogurtsov, Aleksey Y.; Spiridonov, Nikolay A.; Koonin, Eugene V.

2014-01-01

Alternative splicing (AS), alternative transcription initiation (ATI) and alternative transcription termination (ATT) create the extraordinary complexity of transcriptomes and make key contributions to the structural and functional diversity of mammalian proteomes. Analysis of mammalian genomic and transcriptomic data shows that contrary to the traditional view, the joint contribution of ATI and ATT to the transcriptome and proteome diversity is quantitatively greater than the contribution of AS. Although the mean numbers of protein-coding constitutive and alternative nucleotides in gene loci are nearly identical, their distribution along the transcripts is highly non-uniform. On average, coding exons in the variable 5′ and 3′ transcript ends that are created by ATI and ATT contain approximately four times more alternative nucleotides than core protein-coding regions that diversify exclusively via AS. Short upstream exons that encompass alternative 5′-untranslated regions and N-termini of proteins evolve under strong nucleotide-level selection whereas in 3′-terminal exons that encode protein C-termini, protein-level selection is significantly stronger. The groups of genes that are subject to ATI and ATT show major differences in biological roles, expression and selection patterns. PMID:24792168

Protein Changes in Macrophages Induced by Plasma from Rats Exposed to 35-GHz Millimeter Waves

DTIC Science & Technology

2010-12-01

HumanEffectiveness Directorate, Air Force Research Laboratory, Brooks City-Base,Texas A macrophage assay and proteomic screening were used to...mW/cm2 until core temperature reached 41.0 8C. Two-dimensional polyacrylamide gel electrophoresis, image analysis, and Western blotting were used to...stimulation. Proteins of interest were identified using peptide mass fingerprinting. Compared to plasma from sham- exposed rats, plasma from

Comparative proteomic assessment of matrisome enrichment methodologies

PubMed Central

Krasny, Lukas; Paul, Angela; Wai, Patty; Howard, Beatrice A.; Natrajan, Rachael C.; Huang, Paul H.

2016-01-01

The matrisome is a complex and heterogeneous collection of extracellular matrix (ECM) and ECM-associated proteins that play important roles in tissue development and homeostasis. While several strategies for matrisome enrichment have been developed, it is currently unknown how the performance of these different methodologies compares in the proteomic identification of matrisome components across multiple tissue types. In the present study, we perform a comparative proteomic assessment of two widely used decellularisation protocols and two extraction methods to characterise the matrisome in four murine organs (heart, mammary gland, lung and liver). We undertook a systematic evaluation of the performance of the individual methods on protein yield, matrisome enrichment capability and the ability to isolate core matrisome and matrisome-associated components. Our data find that sodium dodecyl sulphate (SDS) decellularisation leads to the highest matrisome enrichment efficiency, while the extraction protocol that comprises chemical and trypsin digestion of the ECM fraction consistently identifies the highest number of matrisomal proteins across all types of tissue examined. Matrisome enrichment had a clear benefit over non-enriched tissue for the comprehensive identification of matrisomal components in murine liver and heart. Strikingly, we find that all four matrisome enrichment methods led to significant losses in the soluble matrisome-associated proteins across all organs. Our findings highlight the multiple factors (including tissue type, matrisome class of interest and desired enrichment purity) that influence the choice of enrichment methodology, and we anticipate that these data will serve as a useful guide for the design of future proteomic studies of the matrisome. PMID:27589945

17 CFR 37.400 - Core Principle 4-Monitoring of trading and trade processing.

Code of Federal Regulations, 2014 CFR

2014-04-01

... trading and trade processing. 37.400 Section 37.400 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION SWAP EXECUTION FACILITIES Monitoring of Trading and Trade Processing § 37.400 Core Principle 4—Monitoring of trading and trade processing. The swap execution facility shall: (a) Establish and...

Biotechnology Protein Expression and Purification Facility

NASA Technical Reports Server (NTRS)

2003-01-01

The purpose of the Project Scientist Core Facility is to provide purified proteins, both recombinant and natural, to the Biotechnology Science Team Project Scientists and the NRA-Structural Biology Test Investigators. Having a core facility for this purpose obviates the need for each scientist to develop the necessary expertise and equipment for molecular biology, protein expression, and protein purification. Because of this, they are able to focus their energies as well as their funding on the crystallization and structure determination of their target proteins.

Metabolic drift in the aging brain.

PubMed

Ivanisevic, Julijana; Stauch, Kelly L; Petrascheck, Michael; Benton, H Paul; Epstein, Adrian A; Fang, Mingliang; Gorantla, Santhi; Tran, Minerva; Hoang, Linh; Kurczy, Michael E; Boska, Michael D; Gendelman, Howard E; Fox, Howard S; Siuzdak, Gary

2016-05-01

Brain function is highly dependent upon controlled energy metabolism whose loss heralds cognitive impairments. This is particularly notable in the aged individuals and in age-related neurodegenerative diseases. However, how metabolic homeostasis is disrupted in the aging brain is still poorly understood. Here we performed global, metabolomic and proteomic analyses across different anatomical regions of mouse brain at different stages of its adult lifespan. Interestingly, while severe proteomic imbalance was absent, global-untargeted metabolomics revealed an energymetabolic drift or significant imbalance in core metabolite levels in aged mouse brains. Metabolic imbalance was characterized by compromised cellular energy status (NAD decline, increased AMP/ATP, purine/pyrimidine accumulation) and significantly altered oxidative phosphorylation and nucleotide biosynthesis and degradation. The central energy metabolic drift suggests a failure of the cellular machinery to restore metabostasis (metabolite homeostasis) in the aged brain and therefore an inability to respond properly to external stimuli, likely driving the alterations in signaling activity and thus in neuronal function and communication.

Lewis and Clark Elementary School Riverview Gardens School District, St. Louis, Missouri. Profile of a Significant School.

ERIC Educational Resources Information Center

Gilliland, John W.

Development of a design for a new elementary school facility is traced through evaluation of various innovative facilities. Significant features include--(1) the spiral plan form, (2) centralized core levels including teacher work center, "perception" core, and interior stream aquariam, (3) the learning laboratory classroom suites, (4) a unique…

Efficient Site-Specific Labeling of Proteins via Cysteines

PubMed Central

Kim, Younggyu; Ho, Sam O.; Gassman, Natalie R.; Korlann, You; Landorf, Elizabeth V.; Collart, Frank R.; Weiss, Shimon

2011-01-01

Methods for chemical modifications of proteins have been crucial for the advancement of proteomics. In particular, site-specific covalent labeling of proteins with fluorophores and other moieties has permitted the development of a multitude of assays for proteome analysis. A common approach for such a modification is solvent-accessible cysteine labeling using thiol-reactive dyes. Cysteine is very attractive for site-specific conjugation due to its relative rarity throughout the proteome and the ease of its introduction into a specific site along the protein's amino acid chain. This is achieved by site-directed mutagenesis, most often without perturbing the protein's function. Bottlenecks in this reaction, however, include the maintenance of reactive thiol groups without oxidation before the reaction, and the effective removal of unreacted molecules prior to fluorescence studies. Here, we describe an efficient, specific, and rapid procedure for cysteine labeling starting from well-reduced proteins in the solid state. The efficacy and specificity of the improved procedure are estimated using a variety of single-cysteine proteins and thiol-reactive dyes. Based on UV/vis absorbance spectra, coupling efficiencies are typically in the range 70–90%, and specificities are better than ~95%. The labeled proteins are evaluated using fluorescence assays, proving that the covalent modification does not alter their function. In addition to maleimide-based conjugation, this improved procedure may be used for other thiol-reactive conjugations such as haloacetyl, alkyl halide, and disulfide interchange derivatives. This facile and rapid procedure is well suited for high throughput proteome analysis. PMID:18275130

Efficient site-specific labeling of proteins via cysteines.

PubMed

Kim, Younggyu; Ho, Sam O; Gassman, Natalie R; Korlann, You; Landorf, Elizabeth V; Collart, Frank R; Weiss, Shimon

2008-03-01

Methods for chemical modifications of proteins have been crucial for the advancement of proteomics. In particular, site-specific covalent labeling of proteins with fluorophores and other moieties has permitted the development of a multitude of assays for proteome analysis. A common approach for such a modification is solvent-accessible cysteine labeling using thiol-reactive dyes. Cysteine is very attractive for site-specific conjugation due to its relative rarity throughout the proteome and the ease of its introduction into a specific site along the protein's amino acid chain. This is achieved by site-directed mutagenesis, most often without perturbing the protein's function. Bottlenecks in this reaction, however, include the maintenance of reactive thiol groups without oxidation before the reaction, and the effective removal of unreacted molecules prior to fluorescence studies. Here, we describe an efficient, specific, and rapid procedure for cysteine labeling starting from well-reduced proteins in the solid state. The efficacy and specificity of the improved procedure are estimated using a variety of single-cysteine proteins and thiol-reactive dyes. Based on UV/vis absorbance spectra, coupling efficiencies are typically in the range 70-90%, and specificities are better than approximately 95%. The labeled proteins are evaluated using fluorescence assays, proving that the covalent modification does not alter their function. In addition to maleimide-based conjugation, this improved procedure may be used for other thiol-reactive conjugations such as haloacetyl, alkyl halide, and disulfide interchange derivatives. This facile and rapid procedure is well suited for high throughput proteome analysis.

The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles

PubMed Central

Topalidou, Irini; Cattin-Ortolá, Jérôme; MacCoss, Michael J.

2016-01-01

The dense-core vesicle is a secretory organelle that mediates the regulated release of peptide hormones, growth factors, and biogenic amines. Dense-core vesicles originate from the trans-Golgi of neurons and neuroendocrine cells, but it is unclear how this specialized organelle is formed and acquires its specific cargos. To identify proteins that act in dense-core vesicle biogenesis, we performed a forward genetic screen in Caenorhabditis elegans for mutants defective in dense-core vesicle function. We previously reported the identification of two conserved proteins that interact with the small GTPase RAB-2 to control normal dense-core vesicle cargo-sorting. Here we identify several additional conserved factors important for dense-core vesicle cargo sorting: the WD40 domain protein EIPR-1 and the endosome-associated recycling protein (EARP) complex. By assaying behavior and the trafficking of dense-core vesicle cargos, we show that mutants that lack EIPR-1 or EARP have defects in dense-core vesicle cargo-sorting similar to those of mutants in the RAB-2 pathway. Genetic epistasis data indicate that RAB-2, EIPR-1 and EARP function in a common pathway. In addition, using a proteomic approach in rat insulinoma cells, we show that EIPR-1 physically interacts with the EARP complex. Our data suggest that EIPR-1 is a new interactor of the EARP complex and that dense-core vesicle cargo sorting depends on the EARP-dependent trafficking of cargo through an endosomal sorting compartment. PMID:27191843

Trichloroethylene (TCE) in tree cores to complement a subsurface investigation on residential property near a former electroplating facility.

PubMed

Wilcox, Jeffrey D; Johnson, Kathy M

2016-10-01

Tree cores were collected and analyzed for trichloroethylene (TCE) on a private property between a former electroplating facility in Asheville, North Carolina (USA), and a contaminated wetland/spring complex. TCE was detected in 16 of 31 trees, the locations of which were largely consistent with a "plume core" delineated by a more detailed subsurface investigation nearly 2 years later. Concentrations in tree cores and nearby soil borings were not correlated, perhaps due to heterogeneities in both geologic and tree root structure, spatial and temporal variability in transpiration rates, or interferences caused by other contaminants at the site. Several tree cores without TCE provided evidence for significantly lower TCE concentrations in shallow groundwater along the margins of the contaminated spring complex in an area with limited accessibility. This study demonstrates that tree core analyses can complement a more extensive subsurface investigation, particularly in residential or ecologically sensitive areas.

Comparative proteomic assessment of matrisome enrichment methodologies.

PubMed

Krasny, Lukas; Paul, Angela; Wai, Patty; Howard, Beatrice A; Natrajan, Rachael C; Huang, Paul H

2016-11-01

The matrisome is a complex and heterogeneous collection of extracellular matrix (ECM) and ECM-associated proteins that play important roles in tissue development and homeostasis. While several strategies for matrisome enrichment have been developed, it is currently unknown how the performance of these different methodologies compares in the proteomic identification of matrisome components across multiple tissue types. In the present study, we perform a comparative proteomic assessment of two widely used decellularisation protocols and two extraction methods to characterise the matrisome in four murine organs (heart, mammary gland, lung and liver). We undertook a systematic evaluation of the performance of the individual methods on protein yield, matrisome enrichment capability and the ability to isolate core matrisome and matrisome-associated components. Our data find that sodium dodecyl sulphate (SDS) decellularisation leads to the highest matrisome enrichment efficiency, while the extraction protocol that comprises chemical and trypsin digestion of the ECM fraction consistently identifies the highest number of matrisomal proteins across all types of tissue examined. Matrisome enrichment had a clear benefit over non-enriched tissue for the comprehensive identification of matrisomal components in murine liver and heart. Strikingly, we find that all four matrisome enrichment methods led to significant losses in the soluble matrisome-associated proteins across all organs. Our findings highlight the multiple factors (including tissue type, matrisome class of interest and desired enrichment purity) that influence the choice of enrichment methodology, and we anticipate that these data will serve as a useful guide for the design of future proteomic studies of the matrisome. © 2016 The Author(s).

Proteomic analysis of isolated chlamydomonas centrioles reveals orthologs of ciliary-disease genes.

PubMed

Keller, Lani C; Romijn, Edwin P; Zamora, Ivan; Yates, John R; Marshall, Wallace F

2005-06-21

The centriole is one of the most enigmatic organelles in the cell. Centrioles are cylindrical, microtubule-based barrels found in the core of the centrosome. Centrioles also act as basal bodies during interphase to nucleate the assembly of cilia and flagella. There are currently only a handful of known centriole proteins. We used mass-spectrometry-based MudPIT (multidimensional protein identification technology) to identify the protein composition of basal bodies (centrioles) isolated from the green alga Chlamydomonas reinhardtii. This analysis detected the majority of known centriole proteins, including centrin, epsilon tubulin, and the cartwheel protein BLD10p. By combining proteomic data with information about gene expression and comparative genomics, we identified 45 cross-validated centriole candidate proteins in two classes. Members of the first class of proteins (BUG1-BUG27) are encoded by genes whose expression correlates with flagellar assembly and which therefore may play a role in ciliogenesis-related functions of basal bodies. Members of the second class (POC1-POC18) are implicated by comparative-genomics and -proteomics studies to be conserved components of the centriole. We confirmed centriolar localization for the human homologs of four candidate proteins. Three of the cross-validated centriole candidate proteins are encoded by orthologs of genes (OFD1, NPHP-4, and PACRG) implicated in mammalian ciliary function and disease, suggesting that oral-facial-digital syndrome and nephronophthisis may involve a dysfunction of centrioles and/or basal bodies. By analyzing isolated Chlamydomonas basal bodies, we have been able to obtain the first reported proteomic analysis of the centriole.

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Yufeng; Tolic, Nikola; Piehowski, Paul D.

We report development of an approach providing high-resolution RPLC of proteins and its utility for mass spectrometry-based top-down proteomics. A chromatographic peak capacity of ~450 was achieved for proteins and large polypeptides having MWs up to 43 kDa in the context of proteomics applications. RPLC column lengths from 20 to 200 cm, particle sizes from 1.5 to 5 m, bonding alkyl chains from C1 to C2, C4, C8, and C18, and particle surface structures that spanned porous, superficially porous (porous shell, core-shell), and nonporous were investigated at pressures up to14K psi. Column length was found as the most important factormore » for >20 kDa proteins in gradient RPLC, and shortening column length degraded RPLC resolution and sensitivity regardless of the size and surface structure of the packing particles used. The alkyl chains bonded to the silica particle surface significantly affected the RPLC recovery and efficiency, and short alkyl C1-C4 phases provided higher sensitivity and resolution than C8 and C18 phases. Long gradient separations (e.g., >10 hours) with long columns (e.g., 100 cm) were particularly effective in conjunction with use of high accuracy mass spectrometers (e.g., the Orbitrap Elite) for top-down proteomics with improved proteoform coverage by allowing multiple HCD, CID, and ETD dissociation modes. It was also found that HCD produced small fragments useful for proteoform identification, while low energy CID and ETD often complemented HCD by providing large fragments.« less

Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum

PubMed Central

2012-01-01

Background The post-genomic era of malaria research provided unprecedented insights into the biology of Plasmodium parasites. Due to the large evolutionary distance to model eukaryotes, however, we lack a profound understanding of many processes in Plasmodium biology. One example is the cell nucleus, which controls the parasite genome in a development- and cell cycle-specific manner through mostly unknown mechanisms. To study this important organelle in detail, we conducted an integrative analysis of the P. falciparum nuclear proteome. Results We combined high accuracy mass spectrometry and bioinformatic approaches to present for the first time an experimentally determined core nuclear proteome for P. falciparum. Besides a large number of factors implicated in known nuclear processes, one-third of all detected proteins carry no functional annotation, including many phylum- or genus-specific factors. Importantly, extensive experimental validation using 30 transgenic cell lines confirmed the high specificity of this inventory, and revealed distinct nuclear localization patterns of hitherto uncharacterized proteins. Further, our detailed analysis identified novel protein domains potentially implicated in gene transcription pathways, and sheds important new light on nuclear compartments and processes including regulatory complexes, the nucleolus, nuclear pores, and nuclear import pathways. Conclusion Our study provides comprehensive new insight into the biology of the Plasmodium nucleus and will serve as an important platform for dissecting general and parasite-specific nuclear processes in malaria parasites. Moreover, as the first nuclear proteome characterized in any protist organism, it will provide an important resource for studying evolutionary aspects of nuclear biology. PMID:23181666

A Miniaturized Chemical Proteomic Approach for Target Profiling of Clinical Kinase Inhibitors in Tumor Biopsies

PubMed Central

Chamrád, Ivo; Rix, Uwe; Stukalov, Alexey; Gridling, Manuela; Parapatics, Katja; Müller, André C.; Altiok, Soner; Colinge, Jacques; Superti-Furga, Giulio; Haura, Eric B.; Bennett, Keiryn L.

2014-01-01

While targeted therapy based on the idea of attenuating the activity of a preselected, therapeutically relevant protein has become one of the major trends in modern cancer therapy, no truly specific targeted drug has been developed and most clinical agents have displayed a degree of polypharmacology. Therefore, the specificity of anticancer therapeutics has emerged as a highly important but severely underestimated issue. Chemical proteomics is a powerful technique combining postgenomic drug-affinity chromatography with high-end mass spectrometry analysis and bioinformatic data processing to assemble a target profile of a desired therapeutic molecule. Due to high demands on the starting material, however, chemical proteomic studies have been mostly limited to cancer cell lines. Herein, we report a down-scaling of the technique to enable the analysis of very low abundance samples, as those obtained from needle biopsies. By a systematic investigation of several important parameters in pull-downs with the multikinase inhibitor bosutinib, the standard experimental protocol was optimized to 100 µg protein input. At this level, more than 30 well-known targets were detected per single pull-down replicate with high reproducibility. Moreover, as presented by the comprehensive target profile obtained from miniaturized pull-downs with another clinical drug, dasatinib, the optimized protocol seems to be extendable to other drugs of interest. Sixty distinct human and murine targets were finally identified for bosutinib and dasatinib in chemical proteomic experiments utilizing core needle biopsy samples from xenotransplants derived from patient tumor tissue. Altogether, the developed methodology proves robust and generic and holds many promises for the field of personalized health care. PMID:23901793

Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis.

PubMed

Poliakov, Anton; Russell, Calum W; Ponnala, Lalit; Hoops, Harold J; Sun, Qi; Douglas, Angela E; van Wijk, Klaas J

2011-06-01

Many insects are nutritionally dependent on symbiotic microorganisms that have tiny genomes and are housed in specialized host cells called bacteriocytes. The obligate symbiosis between the pea aphid Acyrthosiphon pisum and the γ-proteobacterium Buchnera aphidicola (only 584 predicted proteins) is particularly amenable for molecular analysis because the genomes of both partners have been sequenced. To better define the symbiotic relationship between this aphid and Buchnera, we used large-scale, high accuracy tandem mass spectrometry (nanoLC-LTQ-Orbtrap) to identify aphid and Buchnera proteins in the whole aphid body, purified bacteriocytes, isolated Buchnera cells and the residual bacteriocyte fraction. More than 1900 aphid and 400 Buchnera proteins were identified. All enzymes in amino acid metabolism annotated in the Buchnera genome were detected, reflecting the high (68%) coverage of the proteome and supporting the core function of Buchnera in the aphid symbiosis. Transporters mediating the transport of predicted metabolites were present in the bacteriocyte. Label-free spectral counting combined with hierarchical clustering, allowed to define the quantitative distribution of a subset of these proteins across both symbiotic partners, yielding no evidence for the selective transfer of protein among the partners in either direction. This is the first quantitative proteome analysis of bacteriocyte symbiosis, providing a wealth of information about molecular function of both the host cell and bacterial symbiont.

Genetically and Phenotypically Distinct Pseudomonas aeruginosa Cystic Fibrosis Isolates Share a Core Proteomic Signature

PubMed Central

Penesyan, Anahit; Kumar, Sheemal S.; Kamath, Karthik; Shathili, Abdulrahman M.; Venkatakrishnan, Vignesh; Krisp, Christoph; Packer, Nicolle H.; Molloy, Mark P.; Paulsen, Ian T.

2015-01-01

The opportunistic pathogen Pseudomonas aeruginosa is among the main colonizers of the lungs of cystic fibrosis (CF) patients. We have isolated and sequenced several P. aeruginosa isolates from the sputum of CF patients and compared them with each other and with the model strain PAO1. Phenotypic analysis of CF isolates showed significant variability in colonization and virulence-related traits suggesting different strategies for adaptation to the CF lung. Genomic analysis indicated these strains shared a large set of core genes with the standard laboratory strain PAO1, and identified the genetic basis for some of the observed phenotypic differences. Proteomics revealed that in a conventional laboratory medium PAO1 expressed 827 proteins that were absent in the CF isolates while the CF isolates shared a distinctive signature set of 703 proteins not detected in PAO1. PAO1 expressed many transporters for the uptake of organic nutrients and relatively few biosynthetic pathways. Conversely, the CF isolates expressed a narrower range of transporters and a broader set of metabolic pathways for the biosynthesis of amino acids, carbohydrates, nucleotides and polyamines. The proteomic data suggests that in a common laboratory medium PAO1 may transport a diverse set of “ready-made” nutrients from the rich medium, whereas the CF isolates may only utilize a limited number of nutrients from the medium relying mainly on their own metabolism for synthesis of essential nutrients. These variations indicate significant differences between the metabolism and physiology of P. aeruginosa CF isolates and PAO1 that cannot be detected at the genome level alone. The widening gap between the increasing genomic data and the lack of phenotypic data means that researchers are increasingly reliant on extrapolating from genomic comparisons using experimentally characterized model organisms such as PAO1. While comparative genomics can provide valuable information, our data suggests that such extrapolations may be fraught with peril. PMID:26431321

A large scale Plasmodium vivax- Saimiri boliviensis trophozoite-schizont transition proteome

PubMed Central

Lapp, Stacey A.; Barnwell, John W.; Galinski, Mary R.

2017-01-01

Plasmodium vivax is a complex protozoan parasite with over 6,500 genes and stage-specific differential expression. Much of the unique biology of this pathogen remains unknown, including how it modifies and restructures the host reticulocyte. Using a recently published P. vivax reference genome, we report the proteome from two biological replicates of infected Saimiri boliviensis host reticulocytes undergoing transition from the late trophozoite to early schizont stages. Using five database search engines, we identified a total of 2000 P. vivax and 3487 S. boliviensis proteins, making this the most comprehensive P. vivax proteome to date. PlasmoDB GO-term enrichment analysis of proteins identified at least twice by a search engine highlighted core metabolic processes and molecular functions such as glycolysis, translation and protein folding, cell components such as ribosomes, proteasomes and the Golgi apparatus, and a number of vesicle and trafficking related clusters. Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8 enriched functional annotation clusters of S. boliviensis proteins highlighted vesicle and trafficking-related clusters, elements of the cytoskeleton, oxidative processes and response to oxidative stress, macromolecular complexes such as the proteasome and ribosome, metabolism, translation, and cell death. Host and parasite proteins potentially involved in cell adhesion were also identified. Over 25% of the P. vivax proteins have no functional annotation; this group includes 45 VIR members of the large PIR family. A number of host and pathogen proteins contained highly oxidized or nitrated residues, extending prior trophozoite-enriched stage observations from S. boliviensis infections, and supporting the possibility of oxidative stress in relation to the disease. This proteome significantly expands the size and complexity of the known P. vivax and Saimiri host iRBC proteomes, and provides in-depth data that will be valuable for ongoing research on this parasite’s biology and pathogenesis. PMID:28829774

Proteomics and bioinformatics analysis of altered protein expression in the placental villous tissue from early recurrent miscarriage patients.

PubMed

Pan, Hai-Tao; Ding, Hai-Gang; Fang, Min; Yu, Bin; Cheng, Yi; Tan, Ya-Jing; Fu, Qi-Qin; Lu, Bo; Cai, Hong-Guang; Jin, Xin; Xia, Xian-Qing; Zhang, Tao

2018-01-01

Recurrent miscarriage (RM) affects 5% of women, it has an adverse emotional impact on women. Because of the complexities of early development, the mechanism of recurrent miscarriage is still unclear. We hypothesized that abnormal placenta leads to early recurrent miscarriage (ERM). The aim of this study was to identify ERM associated factors in human placenta villous tissue using proteomics. Investigation of these differences in protein expression in parallel profiling is essential to understand the comprehensive pathophysiological mechanism underlying recurrent miscarriage (RM). To gain more insight into mechanisms of recurrent miscarriage (RM), a comparative proteome profile of the human placenta villous tissue in normal and RM pregnancies was analyzed using iTRAQ technology and bioinformatics analysis used by Ingenuity Pathway Analysis (IPA) software. In this study, we employed an iTRAQ based proteomics analysis of four placental villous tissues from patients with early recurrent miscarriage (ERM) and four from normal pregnant women. Finally, we identified 2805 proteins and 79,998 peptides between patients with RM and normal matched group. Further analysis identified 314 differentially expressed proteins in placental villous tissue (≥1.3-fold, Student's t-test, p < 0.05); 209 proteins showed the increased expression while 105 proteins showed decreased expression. These 314 proteins were analyzed by Ingenuity Pathway Analysis (IPA) and were found to play important roles in the growth of embryo. Furthermore, network analysis show that Angiotensinogen (AGT), MAPK14 and Prothrombin (F2) are core factors in early embryonic development. We used another 8 independent samples (4 cases and 4 controls) to cross validation of the proteomic data. This study has identified several proteins that are associated with early development, these results may supply new insight into mechanisms behind recurrent miscarriage. Copyright © 2017 Elsevier Ltd. All rights reserved.

Experiment/facility requirements document for the Space Station Furnace Facility. Section 1: Integrated configuration

NASA Astrophysics Data System (ADS)

1992-05-01

The function of the Space Station Furnace Facility (SSFF) is to support materials research into the crystal growth and solidification processes of electronic and photonic materials, metals and alloys, and glasses and ceramics. To support this broad base of research requirements, the SSFF will employ a variety of furnace modules which will be operated, regulated, and supported by a core of common subsystems. Furnace modules may be reconfigured or specifically developed to provide unique solidification conditions for each set of experiments. The SSFF modular approach permits the addition of new or scaled-up furnace modules to support the evolution of the facility as new science requirements are identified. The SSFF Core is of modular design to permit augmentation for enhanced capabilities. The fully integrated configuration of the SSFF will consist of three racks with the capability of supporting up to two furnace modules per rack. The initial configuration of the SSFF will consist of two of the three racks and one furnace module. This Experiment/Facility Requirements Document (E/FRD) describes the integrated facility requirements for the Space Station Freedom (SSF) Integrated Configuration-1 (IC1) mission. The IC1 SSFF will consist of two racks: the Core Rack, with the centralized subsystem equipment; and the Experiment Rack-1, with Furnace Module-1 and the distributed subsystem equipment to support the furnace. The SSFF support functions are provided by the following Core subsystems: power conditioning and distribution subsystem (SSFF PCDS); data management subsystem (SSFF DMS); thermal control Subsystem (SSFF TCS); gas distribution subsystem (SSFF GDS); and mechanical structures subsystem (SSFF MSS).

Experiment/facility requirements document for the Space Station Furnace Facility. Section 1: Integrated configuration

NASA Technical Reports Server (NTRS)

1992-01-01

The function of the Space Station Furnace Facility (SSFF) is to support materials research into the crystal growth and solidification processes of electronic and photonic materials, metals and alloys, and glasses and ceramics. To support this broad base of research requirements, the SSFF will employ a variety of furnace modules which will be operated, regulated, and supported by a core of common subsystems. Furnace modules may be reconfigured or specifically developed to provide unique solidification conditions for each set of experiments. The SSFF modular approach permits the addition of new or scaled-up furnace modules to support the evolution of the facility as new science requirements are identified. The SSFF Core is of modular design to permit augmentation for enhanced capabilities. The fully integrated configuration of the SSFF will consist of three racks with the capability of supporting up to two furnace modules per rack. The initial configuration of the SSFF will consist of two of the three racks and one furnace module. This Experiment/Facility Requirements Document (E/FRD) describes the integrated facility requirements for the Space Station Freedom (SSF) Integrated Configuration-1 (IC1) mission. The IC1 SSFF will consist of two racks: the Core Rack, with the centralized subsystem equipment; and the Experiment Rack-1, with Furnace Module-1 and the distributed subsystem equipment to support the furnace. The SSFF support functions are provided by the following Core subsystems: power conditioning and distribution subsystem (SSFF PCDS); data management subsystem (SSFF DMS); thermal control Subsystem (SSFF TCS); gas distribution subsystem (SSFF GDS); and mechanical structures subsystem (SSFF MSS).

Vector production in an academic environment: a tool to assess production costs.

PubMed

Boeke, Aaron; Doumas, Patrick; Reeves, Lilith; McClurg, Kyle; Bischof, Daniela; Sego, Lina; Auberry, Alisha; Tatikonda, Mohan; Cornetta, Kenneth

2013-02-01

Generating gene and cell therapy products under good manufacturing practices is a complex process. When determining the cost of these products, researchers must consider the large number of supplies used for manufacturing and the personnel and facility costs to generate vector and maintain a cleanroom facility. To facilitate cost estimates, the Indiana University Vector Production Facility teamed with the Indiana University Kelley School of Business to develop a costing tool that, in turn, provides pricing. The tool is designed in Microsoft Excel and is customizable to meet the needs of other core facilities. It is available from the National Gene Vector Biorepository. The tool allows cost determinations using three different costing methods and was developed in an effort to meet the A21 circular requirements for U.S. core facilities performing work for federally funded projects. The costing tool analysis reveals that the cost of vector production does not have a linear relationship with batch size. For example, increasing the production from 9 to18 liters of a retroviral vector product increases total costs a modest 1.2-fold rather than doubling in total cost. The analysis discussed in this article will help core facilities and investigators plan a cost-effective strategy for gene and cell therapy production.

Vector Production in an Academic Environment: A Tool to Assess Production Costs

PubMed Central

Boeke, Aaron; Doumas, Patrick; Reeves, Lilith; McClurg, Kyle; Bischof, Daniela; Sego, Lina; Auberry, Alisha; Tatikonda, Mohan

2013-01-01

Abstract Generating gene and cell therapy products under good manufacturing practices is a complex process. When determining the cost of these products, researchers must consider the large number of supplies used for manufacturing and the personnel and facility costs to generate vector and maintain a cleanroom facility. To facilitate cost estimates, the Indiana University Vector Production Facility teamed with the Indiana University Kelley School of Business to develop a costing tool that, in turn, provides pricing. The tool is designed in Microsoft Excel and is customizable to meet the needs of other core facilities. It is available from the National Gene Vector Biorepository. The tool allows cost determinations using three different costing methods and was developed in an effort to meet the A21 circular requirements for U.S. core facilities performing work for federally funded projects. The costing tool analysis reveals that the cost of vector production does not have a linear relationship with batch size. For example, increasing the production from 9 to18 liters of a retroviral vector product increases total costs a modest 1.2-fold rather than doubling in total cost. The analysis discussed in this article will help core facilities and investigators plan a cost-effective strategy for gene and cell therapy production. PMID:23360377

78 FR 47154 - Core Principles and Other Requirements for Swap Execution Facilities; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-05

... COMMODITY FUTURES TRADING COMMISSION 17 CFR Part 37 RIN 3038-AD18 Core Principles and Other... this chapter. Appendix B to Part 37--Guidance on, and Acceptable Practices in, Compliance With Core Principles [Corrected] 2. On page 33600, in the second column, under the heading Core Principle 3 of Section...

Pricing the Services of Scientific Cores. Part I: Charging Subsidized and Unsubsidized Users.

ERIC Educational Resources Information Center

Fife, Jerry; Forrester, Robert

2002-01-01

Explaining that scientific cores at research institutions support shared resources and facilities, discusses devising a method of charging users for core services and controlling and managing the rates. Proposes the concept of program-based management to cover sources of core support that are funding similar work. (EV)

Facile synthesis of hierarchical Co3O4@MnO2 core-shell arrays on Ni foam for asymmetric supercapacitors

NASA Astrophysics Data System (ADS)

Huang, Ming; Zhang, Yuxin; Li, Fei; Zhang, Lili; Wen, Zhiyu; Liu, Qing

2014-04-01

Hierarchical Co3O4@MnO2 core-shell arrays on Ni foam have been fabricated by a facile hydrothermal approach and further investigated as the electrode for high-performance supercapacitors. Owing to the high conductivity of the well-defined mesoporous Co3O4 nanowire arrays in combination with the large surface area provided by the ultrathin MnO2 nanosheets, the unique designed Co3O4@MnO2 core-shell arrays on Ni foam have exhibited a high specific capacitance (560 F g-1 at a current density of 0.2 A g-1), good rate capability, and excellent cycling stability (95% capacitance retention after 5000 cycles). An asymmetric supercapacitor with Co3O4@MnO2 core-shell nanostructure as the positive electrode and activated microwave exfoliated graphite oxide activated graphene (MEGO) as the negative electrode yielded an energy density of 17.7 Wh kg-1 and a maximum power density of 158 kW kg-1. The rational design of the unique core-shell array architectures demonstrated in this work provides a new and facile approach to fabricate high-performance electrode for supercapacitors.

Multiprocessor switch with selective pairing

DOEpatents

Gara, Alan; Gschwind, Michael K; Salapura, Valentina

2014-03-11

System, method and computer program product for a multiprocessing system to offer selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). Each paired microprocessor or processor cores that provide one highly reliable thread for high-reliability connect with a system components such as a memory "nest" (or memory hierarchy), an optional system controller, and optional interrupt controller, optional I/O or peripheral devices, etc. The memory nest is attached to a selective pairing facility via a switch or a bus

A facile single-step synthesis of ternary multicore magneto-plasmonic nanoparticles.

PubMed

Benelmekki, Maria; Bohra, Murtaza; Kim, Jeong-Hwan; Diaz, Rosa E; Vernieres, Jerome; Grammatikopoulos, Panagiotis; Sowwan, Mukhles

2014-04-07

We report a facile single-step synthesis of ternary hybrid nanoparticles (NPs) composed of multiple dumbbell-like iron-silver (FeAg) cores encapsulated by a silicon (Si) shell using a versatile co-sputter gas-condensation technique. In comparison to previously reported binary magneto-plasmonic NPs, the advantage conferred by a Si shell is to bind the multiple magneto-plasmonic (FeAg) cores together and prevent them from aggregation at the same time. Further, we demonstrate that the size of the NPs and number of cores in each NP can be modulated over a wide range by tuning the experimental parameters.

Scientific Design of the New Neutron Radiography Facility (SANRAD) at SAFARI-1 for South Africa

NASA Astrophysics Data System (ADS)

de Beer, F. C.; Gruenauer, F.; Radebe, J. M.; Modise, T.; Schillinger, B.

The final scientific design for an upgraded neutron radiography/tomography facility at beam port no.2 of the SAFARI-1 nuclear research reactor has been performed through expert advice from Physics Consulting, FRMII in Germany and IPEN, Brazil. A need to upgrade the facility became apparent due to the identification of various deficiencies of the current SANRAD facility during an IAEA-sponsored expert mission of international scientists to Necsa, South Africa. A lack of adequate shielding that results in high neutron background on the beam port floor, a mismatch in the collimator aperture to the core that results in a high gradient in neutron flux on the imaging plane and due to a relative low L/D the quality of the radiographs are poor, are a number of deficiencies to name a few.The new design, based on results of Monte Carlo (MCNP-X) simulations of neutron- and gamma transport from the reactor core and through the new facility, is being outlined. The scientific design philosophy, neutron optics and imaging capabilities that include the utilization of fission neutrons, thermal neutrons, and gamma-rays emerging from the core of SAFARI-1 are discussed.

TNK2 Tyrosine Kinase as a Novel Therapeutic Target in Triple Negative Breast Cancer

DTIC Science & Technology

2016-10-01

Acknowledgement of federal support: Yes Books or other non-periodical, one-time publications. Nothing to Report. Other publications, conference papers...Majlis Amanah Rakyat (MARA) of Government of Malaysia for the research fellowship to M.S.Z. We thank the Mass Spectrometry and Proteomics Facility...Gyorffy B, Benke Z, Lanczky A, Balazs B, Szallasi Z, Timar J and Schafer R. RecurrenceOnline: an online analysis tool to determine breast cancer

Developing Breast Cancer Program at Xavier; Genomic and Proteomic Analysis of Signaling Pathways Involved in Xenohormone and MEK5 Regulation of Breast

DTIC Science & Technology

2008-05-01

will build a core of human talent that will address scientific problems such as drug resistance and the effect of environmental agents on breast...normal for Xavier University after the continuing effects of Hurricane Katrina. Xavier University of Louisiana did an amazing recovery from the...an increase in expression of ERβ . To determine the effects of MEK5 on ER signaling we used an ERE-luciferase reporter assay. Parental MCF-7 cells

Facile fabrication of core-in-shell particles by the slow removal of the core and its use in the encapsulation of metal nanoparticles.

PubMed

Choi, Won San; Koo, Hye Young; Kim, Dong-Yu

2008-05-06

Core-in-shell particles with controllable core size have been fabricated from core-shell particles by means of the controlled core-dissolution method. These cores in inorganic shells were employed as scaffolds for the synthesis of metal nanoparticles. After dissolution of the cores, metal nanoparticles embedded in cores were encapsulated into the interior of shell, without any damage or change. This article describes a very simple method for deriving core-in-shell particles with controllable core size and encapsulation of nanoparticles into the interior of shell.

Overview of Fuel Rod Simulator Usage at ORNL

NASA Astrophysics Data System (ADS)

Ott, Larry J.; McCulloch, Reg

2004-02-01

During the 1970s and early 1980s, the Oak Ridge National Laboratory (ORNL) operated large out-of-reactor experimental facilities to resolve thermal-hydraulic safety issues in nuclear reactors. The fundamental research ranged from material mechanical behavior of fuel cladding during the depressurization phase of a loss-of-coolant accident (LOCA) to basic heat transfer research in gas- or sodium-cooled cores. The largest facility simulated the initial phase (less than 1 min. of transient time) of a LOCA in a commercial pressurized-water reactor. The nonnuclear reactor cores of these facilities were mimicked via advanced, highly instrumented electric fuel rod simulators locally manufactured at ORNL. This paper provides an overview of these experimental facilities with an emphasis on the fuel rod simulators.

Titanium dioxide@polypyrrole core-shell nanowires for all solid-state flexible supercapacitors

NASA Astrophysics Data System (ADS)

Yu, Minghao; Zeng, Yinxiang; Zhang, Chong; Lu, Xihong; Zeng, Chenghui; Yao, Chenzhong; Yang, Yangyi; Tong, Yexiang

2013-10-01

Herein, we developed a facile two-step process to synthesize TiO2@PPy core-shell nanowires (NWs) on carbon cloth and reported their improved electrochemical performance for flexible supercapacitors (SCs). The fabricated solid-state SC device based on TiO2@PPy core-shell NWs not only has excellent flexibility, but also exhibits remarkable electrochemical performance.Herein, we developed a facile two-step process to synthesize TiO2@PPy core-shell nanowires (NWs) on carbon cloth and reported their improved electrochemical performance for flexible supercapacitors (SCs). The fabricated solid-state SC device based on TiO2@PPy core-shell NWs not only has excellent flexibility, but also exhibits remarkable electrochemical performance. Electronic supplementary information (ESI) available: Experimental details, XRD pattern, FT-IR absorption spectrum and CV curves of TiO2@PPy NWs, and SEM images of the PPy. See DOI: 10.1039/c3nr03578f

An accurate proteomic quantification method: fluorescence labeling absolute quantification (FLAQ) using multidimensional liquid chromatography and tandem mass spectrometry.

PubMed

Liu, Junyan; Liu, Yang; Gao, Mingxia; Zhang, Xiangmin

2012-08-01

A facile proteomic quantification method, fluorescent labeling absolute quantification (FLAQ), was developed. Instead of using MS for quantification, the FLAQ method is a chromatography-based quantification in combination with MS for identification. Multidimensional liquid chromatography (MDLC) with laser-induced fluorescence (LIF) detection with high accuracy and tandem MS system were employed for FLAQ. Several requirements should be met for fluorescent labeling in MS identification: Labeling completeness, minimum side-reactions, simple MS spectra, and no extra tandem MS fragmentations for structure elucidations. A fluorescence dye, 5-iodoacetamidofluorescein, was finally chosen to label proteins on all cysteine residues. The fluorescent dye was compatible with the process of the trypsin digestion and MALDI MS identification. Quantitative labeling was achieved with optimization of reacting conditions. A synthesized peptide and model proteins, BSA (35 cysteines), OVA (five cysteines), were used for verifying the completeness of labeling. Proteins were separated through MDLC and quantified based on fluorescent intensities, followed by MS identification. High accuracy (RSD% < 1.58) and wide linearity of quantification (1-10(5) ) were achieved by LIF detection. The limit of quantitation for the model protein was as low as 0.34 amol. Parts of proteins in human liver proteome were quantified and demonstrated using FLAQ. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs.

PubMed

Cuadrat, Rafael R C; da Serra Cruz, Sérgio Manuel; Tschoeke, Diogo Antônio; Silva, Edno; Tosta, Frederico; Jucá, Henrique; Jardim, Rodrigo; Campos, Maria Luiza M; Mattoso, Marta; Dávila, Alberto M R

2014-08-01

A key focus in 21(st) century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI's COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools.

An Orthology-Based Analysis of Pathogenic Protozoa Impacting Global Health: An Improved Comparative Genomics Approach with Prokaryotes and Model Eukaryote Orthologs

PubMed Central

Cuadrat, Rafael R. C.; da Serra Cruz, Sérgio Manuel; Tschoeke, Diogo Antônio; Silva, Edno; Tosta, Frederico; Jucá, Henrique; Jardim, Rodrigo; Campos, Maria Luiza M.; Mattoso, Marta

2014-01-01

Abstract A key focus in 21st century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI's COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools. PMID:24960463

Integrated redox proteomics and metabolomics of mitochondria to identify mechanisms of cd toxicity.

PubMed

Go, Young-Mi; Roede, James R; Orr, Michael; Liang, Yongliang; Jones, Dean P

2014-05-01

Cadmium (Cd) exposure contributes to human diseases affecting liver, kidney, lung, and other organ systems, but mechanisms underlying the pleotropic nature of these toxicities are poorly understood. Cd accumulates in humans from dietary, environmental (including cigarette smoke), and occupational sources, and has a twenty-year biologic half-life. Our previous mouse and cell studies showed that environmental low-dose Cd exposure altered protein redox states resulting in stimulation of inflammatory signaling and disruption of the actin cytoskeleton system, suggesting that Cd could impact multiple mechanisms of disease. In the current study, we investigated the effects of acute Cd exposure on the redox proteome and metabolome of mouse liver mitochondria to gain insight into associated toxicological mechanisms and functions. We analyzed redox states of liver mitochondrial proteins by redox proteomics using isotope coded affinity tag (ICAT) combined mass spectrometry. Redox ICAT identified 2687 cysteine-containing peptides (peptidyl Cys) of which 1667 peptidyl Cys (657 proteins) were detected in both control and Cd-exposed samples. Of these, 46% (1247 peptidyl Cys, 547 proteins) were oxidized by Cd more than 1.5-fold relative to controls. Bioinformatics analysis using MetaCore software showed that Cd affected 86 pathways, including 24 Cys in proteins functioning in branched chain amino acid (BCAA) and 14 Cys in proteins functioning in fatty acid (acylcarnitine/carnitine) metabolism. Consistently, high-resolution metabolomics data showed that Cd treatment altered levels of BCAA and carnitine metabolites. Together, these results show that mitochondrial protein redox and metabolites are targets in Cd-induced hepatotoxicity. The results further indicate that redox proteomics and metabolomics can be used in an integrated systems approach to investigate complex disease mechanisms.

Core characterization of the new CABRI Water Loop Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ritter, G.; Rodiac, F.; Beretz, D.

2011-07-01

The CABRI experimental reactor is located at the Cadarache nuclear research center, southern France. It is operated by the Atomic Energy Commission (CEA) and devoted to IRSN (Institut de Radioprotection et de Surete Nucleaire) safety programmes. It has been successfully operated during the last 30 years, enlightening the knowledge of FBR and LWR fuel behaviour during Reactivity Insertion Accident (RIA) and Loss Of Coolant Accident (LOCA) transients in the frame of IPSN (Institut de Protection et de Surete Nucleaire) and now IRSN programmes devoted to reactor safety. This operation was interrupted in 2003 to allow for a whole facility renewalmore » programme for the need of the CABRI International Programme (CIP) carried out by IRSN under the OECD umbrella. The principle of operation of the facility is based on the control of {sup 3}He, a major gaseous neutron absorber, in the core geometry. The purpose of this paper is to illustrate how several dosimetric devices have been set up to better characterize the core during the upcoming commissioning campaign. It presents the schemes and tools dedicated to core characterization. (authors)« less

AMPA-receptor specific biogenesis complexes control synaptic transmission and intellectual ability

PubMed Central

Brechet, Aline; Buchert, Rebecca; Schwenk, Jochen; Boudkkazi, Sami; Zolles, Gerd; Siquier-Pernet, Karine; Schaber, Irene; Bildl, Wolfgang; Saadi, Abdelkrim; Bole-Feysot, Christine; Nitschke, Patrick; Reis, Andre; Sticht, Heinrich; Al-Sanna’a, Nouriya; Rolfs, Arndt; Kulik, Akos; Schulte, Uwe; Colleaux, Laurence; Abou Jamra, Rami; Fakler, Bernd

2017-01-01

AMPA-type glutamate receptors (AMPARs), key elements in excitatory neurotransmission in the brain, are macromolecular complexes whose properties and cellular functions are determined by the co-assembled constituents of their proteome. Here we identify AMPAR complexes that transiently form in the endoplasmic reticulum (ER) and lack the core-subunits typical for AMPARs in the plasma membrane. Central components of these ER AMPARs are the proteome constituents FRRS1l (C9orf4) and CPT1c that specifically and cooperatively bind to the pore-forming GluA1-4 proteins of AMPARs. Bi-allelic mutations in the human FRRS1L gene are shown to cause severe intellectual disability with cognitive impairment, speech delay and epileptic activity. Virus-directed deletion or overexpression of FRRS1l strongly impact synaptic transmission in adult rat brain by decreasing or increasing the number of AMPARs in synapses and extra-synaptic sites. Our results provide insight into the early biogenesis of AMPARs and demonstrate its pronounced impact on synaptic transmission and brain function. PMID:28675162

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes

PubMed Central

Choi, Jaeyoung; Kim, Ki-Tae; Huh, Aram; Kwon, Seomun; Hong, Changyoung; Asiegbu, Fred O.; Jeon, Junhyun; Lee, Yong-Hwan

2015-01-01

Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11 576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies. Database URL: http://hme.riceblast.snu.ac.kr/ PMID:26055100

Identification of Autophagosome-associated Proteins and Regulators by Quantitative Proteomic Analysis and Genetic Screens*

PubMed Central

Dengjel, Jörn; Høyer-Hansen, Maria; Nielsen, Maria O.; Eisenberg, Tobias; Harder, Lea M.; Schandorff, Søren; Farkas, Thomas; Kirkegaard, Thomas; Becker, Andrea C.; Schroeder, Sabrina; Vanselow, Katja; Lundberg, Emma; Nielsen, Mogens M.; Kristensen, Anders R.; Akimov, Vyacheslav; Bunkenborg, Jakob; Madeo, Frank; Jäättelä, Marja; Andersen, Jens S.

2012-01-01

Autophagy is one of the major intracellular catabolic pathways, but little is known about the composition of autophagosomes. To study the associated proteins, we isolated autophagosomes from human breast cancer cells using two different biochemical methods and three stimulus types: amino acid deprivation or rapamycin or concanamycin A treatment. The autophagosome-associated proteins were dependent on stimulus, but a core set of proteins was stimulus-independent. Remarkably, proteasomal proteins were abundant among the stimulus-independent common autophagosome-associated proteins, and the activation of autophagy significantly decreased the cellular proteasome level and activity supporting interplay between the two degradation pathways. A screen of yeast strains defective in the orthologs of the human genes encoding for a common set of autophagosome-associated proteins revealed several regulators of autophagy, including subunits of the retromer complex. The combined spatiotemporal proteomic and genetic data sets presented here provide a basis for further characterization of autophagosome biogenesis and cargo selection. PMID:22311637

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes.

PubMed

Choi, Jaeyoung; Kim, Ki-Tae; Huh, Aram; Kwon, Seomun; Hong, Changyoung; Asiegbu, Fred O; Jeon, Junhyun; Lee, Yong-Hwan

2015-01-01

Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11,576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies. © The Author(s) 2015. Published by Oxford University Press.

Metabolic drift in the aging brain

PubMed Central

Ivanisevic, Julijana; Stauch, Kelly L.; Petrascheck, Michael; Benton, H. Paul; Epstein, Adrian A.; Fang, Mingliang; Gorantla, Santhi; Tran, Minerva; Hoang, Linh; Kurczy, Michael E.; Boska, Michael D.; Gendelman, Howard E.; Fox, Howard S.; Siuzdak, Gary

2016-01-01

Brain function is highly dependent upon controlled energy metabolism whose loss heralds cognitive impairments. This is particularly notable in the aged individuals and in age-related neurodegenerative diseases. However, how metabolic homeostasis is disrupted in the aging brain is still poorly understood. Here we performed global, metabolomic and proteomic analyses across different anatomical regions of mouse brain at different stages of its adult lifespan. Interestingly, while severe proteomic imbalance was absent, global-untargeted metabolomics revealed an energy metabolic drift or significant imbalance in core metabolite levels in aged mouse brains. Metabolic imbalance was characterized by compromised cellular energy status (NAD decline, increased AMP/ATP, purine/pyrimidine accumulation) and significantly altered oxidative phosphorylation and nucleotide biosynthesis and degradation. The central energy metabolic drift suggests a failure of the cellular machinery to restore metabostasis (metabolite homeostasis) in the aged brain and therefore an inability to respond properly to external stimuli, likely driving the alterations in signaling activity and thus in neuronal function and communication. PMID:27182841

Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in Oryza Sativa.

PubMed

Xue, Chao; Liu, Shuai; Chen, Chen; Zhu, Jun; Yang, Xibin; Zhou, Yong; Guo, Rui; Liu, Xiaoyu; Gong, Zhiyun

2018-01-01

Lysine acetylation (Kac) is an important protein post-translational modification in both eukaryotes and prokaryotes. Herein, we report the results of a global proteome analysis of Kac and its diverse functions in rice (Oryza sativa). We identified 1353 Kac sites in 866 proteins in rice seedlings. A total of 11 Kac motifs are conserved, and 45% of the identified proteins are localized to the chloroplast. Among all acetylated proteins, 38 Kac sites are combined in core histones. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Protein-protein interaction networks of the identified proteins provided further evidence that Kac contributes to a wide range of regulatory functions. Furthermore, we demonstrated that the acetylation level of histone H3 (lysine 27 and 36) is increased in response to cold stress. In summary, our approach comprehensively profiles the regulatory roles of Kac in the growth and development of rice. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Space Station Furnace Facility. Experiment/Facility Requirements Document (E/FRD), volume 2, appendix 5

NASA Technical Reports Server (NTRS)

Kephart, Nancy

1992-01-01

The function of the Space Station Furnace Facility (SSFF) is to support materials research into the crystal growth and solidification processes of electronic and photonic materials, metals and alloys, and glasses and ceramics. To support this broad base of research requirements, the SSFF will employ a variety of furnace modules operated, regulated, and supported by a core of common subsystems. Furnace modules may be reconfigured or specifically developed to provide unique solidifcation conditions for each set of experiments. The SSFF modular approach permits the addition of new or scaled-up furnace modules to support the evolution of the facility as new science requirements are identified. The SSFF Core is of modular design to permit augmentation for enhanced capabilities. The fully integrated configuration of the SSFF will consist of three racks with the capability of supporting up to two furnace modules per rack. The initial configuration of the SSFF will consist of two of the three racks and one furnace module. This Experiment/Facility Requirements Document (E/FRD) describes the integrated facility requirements for the Space Station Freedom (SSF) Integrated Configuration-1 (IC1) mission. The IC1 SSFF will consist of two racks: the Core Rack, with the centralized subsystem equipment, and the Experiment Rack-1, with Furnace Module-1 and the distributed subsystem equipment to support the furnace.

Evidence for a core gut microbiota in the zebrafish

PubMed Central

Roeselers, Guus; Mittge, Erika K; Stephens, W Zac; Parichy, David M; Cavanaugh, Colleen M; Guillemin, Karen; Rawls, John F

2011-01-01

Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status. PMID:21472014

Dose and Dose Risk Caused by Natural Phenomena - Proposed Powder Metallurgy Core Manufacturing Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holmes, W.G.

2001-08-16

The offsite radiological effects from high velocity straight winds, tornadoes, and earthquakes have been estimated for a proposed facility for manufacturing enriched uranium fuel cores by powder metallurgy. Projected doses range up to 30 mrem/event to the maximum offsite individual for high winds and up to 85 mrem/event for very severe earthquakes. Even under conservative assumptions on meteorological conditions, the maximum offsite dose would be about 20 per cent of the DOE limit for accidents involving enriched uranium storage facilities. The total dose risk is low and is dominated by the risk from earthquakes. This report discusses this test.

Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis.

PubMed

Finka, Andrija; Goloubinoff, Pierre

2013-09-01

In the crowded environment of human cells, folding of nascent polypeptides and refolding of stress-unfolded proteins is error prone. Accumulation of cytotoxic misfolded and aggregated species may cause cell death, tissue loss, degenerative conformational diseases, and aging. Nevertheless, young cells effectively express a network of molecular chaperones and folding enzymes, termed here "the chaperome," which can prevent formation of potentially harmful misfolded protein conformers and use the energy of adenosine triphosphate (ATP) to rehabilitate already formed toxic aggregates into native functional proteins. In an attempt to extend knowledge of chaperome mechanisms in cellular proteostasis, we performed a meta-analysis of human chaperome using high-throughput proteomic data from 11 immortalized human cell lines. Chaperome polypeptides were about 10% of total protein mass of human cells, half of which were Hsp90s and Hsp70s. Knowledge of cellular concentrations and ratios among chaperome polypeptides provided a novel basis to understand mechanisms by which the Hsp60, Hsp70, Hsp90, and small heat shock proteins (HSPs), in collaboration with cochaperones and folding enzymes, assist de novo protein folding, import polypeptides into organelles, unfold stress-destabilized toxic conformers, and control the conformal activity of native proteins in the crowded environment of the cell. Proteomic data also provided means to distinguish between stable components of chaperone core machineries and dynamic regulatory cochaperones.

A thiol probe for measuring unfolded protein load and proteostasis in cells.

PubMed

Chen, Moore Z; Moily, Nagaraj S; Bridgford, Jessica L; Wood, Rebecca J; Radwan, Mona; Smith, Trevor A; Song, Zhegang; Tang, Ben Zhong; Tilley, Leann; Xu, Xiaohong; Reid, Gavin E; Pouladi, Mahmoud A; Hong, Yuning; Hatters, Danny M

2017-09-07

When proteostasis becomes unbalanced, unfolded proteins can accumulate and aggregate. Here we report that the dye, tetraphenylethene maleimide (TPE-MI) can be used to measure cellular unfolded protein load. TPE-MI fluorescence is activated upon labelling free cysteine thiols, normally buried in the core of globular proteins that are exposed upon unfolding. Crucially TPE-MI does not become fluorescent when conjugated to soluble glutathione. We find that TPE-MI fluorescence is enhanced upon reaction with cellular proteomes under conditions promoting accumulation of unfolded proteins. TPE-MI reactivity can be used to track which proteins expose more cysteine residues under stress through proteomic analysis. We show that TPE-MI can report imbalances in proteostasis in induced pluripotent stem cell models of Huntington disease, as well as cells transfected with mutant Huntington exon 1 before the formation of visible aggregates. TPE-MI also detects protein damage following dihydroartemisinin treatment of the malaria parasites Plasmodium falciparum. TPE-MI therefore holds promise as a tool to probe proteostasis mechanisms in disease.Proteostasis is maintained through a number of molecular mechanisms, some of which function to protect the folded state of proteins. Here the authors demonstrate the use of TPE-MI in a fluorigenic dye assay for the quantitation of unfolded proteins that can be used to assess proteostasis on a cellular or proteome scale.

Integrating Proteomics and Enzyme Kinetics Reveals Tissue-Specific Types of the Glycolytic and Gluconeogenic Pathways.

PubMed

Wiśniewski, Jacek R; Gizak, Agnieszka; Rakus, Dariusz

2015-08-07

Glycolysis is the core metabolic pathway supplying energy to cells. Whereas the vast majority of studies focus on specific aspects of the process, global analyses characterizing simultaneously all enzymes involved in the process are scarce. Here, we demonstrate that quantitative label- and standard-free proteomics allows accurate determination of titers of metabolic enzymes and enables simultaneous measurements of titers and maximal enzymatic activities (Amax) of all glycolytic enzymes and the gluconeogenic fructose 1,6-bisphosphatase in mouse brain, liver and muscle. Despite occurrence of tissue-specific isoenzymes bearing different kinetic properties, the enzyme titers often correlated well with the Amax values. To provide a more general picture of energy metabolism, we analyzed titers of the enzymes in additional 7 mouse organs and in human cells. Across the analyzed samples, we identified two basic profiles: a "fast glucose uptake" one in brain and heart, and a "gluconeogenic rich" one occurring in liver. In skeletal muscles and other organs, we found intermediate profiles. Obtained data highlighted the glucose-flux-limiting role of hexokinase which activity was always 10- to 100-fold lower than the average activity of all other glycolytic enzymes. A parallel determination of enzyme titers and maximal enzymatic activities allowed determination of kcat values without enzyme purification. Results of our in-depth proteomic analysis of the mouse organs did not support the concepts of regulation of glycolysis by lysine acetylation.

LC–MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

PubMed Central

2015-01-01

The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity, and metabolism in Caenorhabditis elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including the expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass spectrometry (LC–MS)-based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2);daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the upregulation of many core intermediary metabolic pathways. These include glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complexes I, II, III, and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative of spatiotemporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. This restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves and possibly also shunting metabolites through alternative energy-generating pathways to sustain longevity. PMID:24555535

Structural proteomics: Topology and relative accessibility of plant lipid droplet associated proteins.

PubMed

Jolivet, Pascale; Aymé, Laure; Giuliani, Alexandre; Wien, Frank; Chardot, Thierry; Gohon, Yann

2017-10-03

Lipid droplets are the major stock of lipids in oleaginous plant seeds. Despite their economic importance for oil production and biotechnological issues (biofuels, lubricants and plasticizers), numerous questions about their formation, structure and regulation are still unresolved. To determine water accessible domains of protein coating at lipid droplets surface, a structural proteomic approach has been performed. This technique relies on the millisecond timescale production of hydroxyl radicals by the radiolysis of water using Synchrotron X-ray white beam. Thanks to the evolution of mass spectrometry analysis techniques this approach allows the creation of a map of the solvent accessibility for proteins difficult to study by other means. Using these results, a S3 oleosin water accessibility map is proposed. This is the first time that such a map on an oleosin co-purified with plant lipid droplets and other associated protein is presented. Lipid droplet associated proteins function is linked to stability, structure and probably formation and lipid mobilization of droplets. Structure of these proteins in their native environment, at the interface between bulk water and the lipidic core of these organelles is only based on hydrophobicity plot. Using hydroxyl radical footprinting and proteomics approaches we studied water accessibility of one major protein in these droplets: S3 oleosin of Arabidopsis thaliana seeds. Copyright © 2017 Elsevier B.V. All rights reserved.

Insights into temperature modulation of the Eucalyptus globulus and Eucalyptus grandis antioxidant and lignification subproteomes.

PubMed

de Santana Costa, Marília Gabriela; Mazzafera, Paulo; Balbuena, Tiago Santana

2017-05-01

Eucalyptus grandis and Eucalyptus globulus are among the most widely cultivated trees, differing in lignin composition and plantation areas, as E. grandis is mostly cultivated in tropical regions while E. globulus is preferred in temperate areas. As temperature is a key modulator in plant metabolism, a large-scale proteome analysis was carried out to investigate changes in the antioxidant system and the lignification metabolism in plantlets grown at different temperatures. Our strategy allowed the identification of 3111 stem proteins. A total of 103 antioxidant proteins were detected in the stems of both species. Hierarchical clustering revealed that alterations in the antioxidant proteins are more prominent when Eucalyptus seedlings were exposed to high temperature and that the superoxide isoforms coded by the gene Eucgr.B03930 are the most abundant antioxidant enzymes induced by thermal stimulus. Regarding the lignin biosynthesis, our proteomics approach resulted in the identification of 13 of the 17 core proteins involved in this metabolism, corroborating with gene predictions and the proposed lignin toolbox. Quantitative analyses revealed significant differences in 8 protein isoforms, including the ferulate 5-hydroxylase isoform F5H1, a key enzyme in catalyzing the synthesis of sinapyl alcohol, and the cinnamyl alcohol dehydrogenase isoform CAD2, the last enzyme in monolignol biosynthesis. Data are available via ProteomeXchange with identifier PXD005743. Copyright © 2017 Elsevier Ltd. All rights reserved.

17 CFR 37.1400 - Core Principle 14-System safeguards.

Code of Federal Regulations, 2014 CFR

2014-04-01

... procedures, and automated systems, that: (1) Are reliable and secure; and (2) Have adequate scalable capacity... 17 Commodity and Securities Exchanges 1 2014-04-01 2014-04-01 false Core Principle 14-System... SWAP EXECUTION FACILITIES System Safeguards § 37.1400 Core Principle 14—System safeguards. The swap...

Space Station Environmental Control and Life Support System Test Facility at Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

Springer, Darlene

1989-01-01

Different aspects of Space Station Environmental Control and Life Support System (ECLSS) testing are currently taking place at Marshall Space Flight Center (MSFC). Unique to this testing is the variety of test areas and the fact that all are located in one building. The north high bay of building 4755, the Core Module Integration Facility (CMIF), contains the following test areas: the Subsystem Test Area, the Comparative Test Area, the Process Material Management System (PMMS), the Core Module Simulator (CMS), the End-use Equipment Facility (EEF), and the Pre-development Operational System Test (POST) Area. This paper addresses the facility that supports these test areas and briefly describes the testing in each area. Future plans for the building and Space Station module configurations will also be discussed.

Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network.

PubMed

Shen, Xianjun; Yi, Li; Jiang, Xingpeng; He, Tingting; Yang, Jincai; Xie, Wei; Hu, Po; Hu, Xiaohua

2017-01-01

How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI) data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes. In order to achieve this goal, this paper proposes a novel algorithm DCA (Dynamic Core-Attachment). It detects protein-complex core comprising of continually expressed and highly connected proteins in dynamic PPI network, and then the protein complex is formed by including the attachments with high adhesion into the core. The integration of core-attachment feature into the dynamic PPI network is responsible for the superiority of our algorithm. DCA has been applied on two different yeast dynamic PPI networks and the experimental results show that it performs significantly better than the state-of-the-art techniques in terms of prediction accuracy, hF-measure and statistical significance in biology. In addition, the identified complexes with strong biological significance provide potential candidate complexes for biologists to validate.

Consensus-based approach to develop a measurement framework and identify a core set of indicators to track implementation and progress towards effective coverage of facility-based Kangaroo Mother Care.

PubMed

Guenther, Tanya; Moxon, Sarah; Valsangkar, Bina; Wetzel, Greta; Ruiz, Juan; Kerber, Kate; Blencowe, Hannah; Dube, Queen; Vani, Shashi N; Vivio, Donna; Magge, Hema; De Leon-Mendoza, Socorro; Patterson, Janna; Mazia, Goldy

2017-12-01

As efforts to scale up the delivery of Kangaroo Mother Care (KMC) in facilities are increasing, a standardized approach to measure implementation and progress towards effective coverage is needed. Here, we describe a consensus-based approach to develop a measurement framework and identify a core set of indicators for monitoring facility-based KMC that would be feasible to measure within existing systems. The KMC measurement framework and core list of indicators were developed through: 1) scoping exercise to identify potential indicators through literature review and requests from researchers and program implementers; and 2) face-to-face consultations with KMC and measurement experts working at country and global levels to review candidate indicators and finalize selection and definitions. The KMC measurement framework includes two main components: 1) service readiness, based on the WHO building blocks framework; and 2) service delivery action sequence covering identification, service initiation, continuation to discharge, and follow-up to graduation. Consensus was reached on 10 core indicators for KMC, which were organized according to the measurement framework. We identified 4 service readiness indicators, capturing national level policy for KMC, availability of KMC indicators in HMIS, costed operational plans for KMC and availability of KMC services at health facilities with inpatient maternity services. Six indicators were defined for service delivery, including weighing of babies at birth, identification of those ≤2000 g, initiation of facility-based KMC, monitoring the quality of KMC, status of babies at discharge from the facility and levels of follow-up (according to country-specific protocol). These core KMC indicators, identified with input from a wide range of global and country-level KMC and measurement experts, can aid efforts to strengthen monitoring systems and facilitate global tracking of KMC implementation. As data collection systems advance, we encourage program managers and evaluators to document their experiences using this framework to measure progress and allow indicator refinement, with the overall aim of working towards sustainable, country-led data systems.

Efficient tungsten oxide/bismuth oxyiodide core/shell photoanode for photoelectrochemical water splitting

NASA Astrophysics Data System (ADS)

Ma, Haipeng; Zhang, Jing; Liu, Zhifeng

2017-11-01

The novel WO3 nanorods (NRs)/BiOI core/shell structure composite is used as an efficient photoanode applied in photoelectrochemical (PEC) water splitting for the first time. It is synthesized via facile hydrothermal method and, successive ionic layer adsorption and reaction (SILAR) process. This facile synthesis route can achieve uniform WO3/BiOI core/shell composite nanostructures and obtain varied BiOI morphologies simultaneously. The WO3 NRs/BiOI-20 composite exhibits enhanced PEC activity compared to pristine WO3 with a photocurrent density of 0.79 mA cm-2 measured at 0.8 V vs. RHE under AM 1.5G. This excellent performance benefits from the broader absorption spectrum and suppressed electron-hole recombination. This novel core/shell composite may provide insight in developing more efficient solar driven photoelectrodes.

Facile in situ synthesis of wurtzite ZnS/ZnO core/shell heterostructure with highly efficient visible-light photocatalytic activity and photostability

NASA Astrophysics Data System (ADS)

Xiao, Jian-Hua; Huang, Wei-Qing; Hu, Yong-sheng; Zeng, Fan; Huang, Qin-Yi; Zhou, Bing-Xin; Pan, Anlian; Li, Kai; Huang, Gui-Fang

2018-02-01

High photocatalytic activity and photostability are the pursuit of the goal for designing promising photocatalysts. Herein, using ZnO to encapsulate ZnS nanoparticles is proposed as an effective strategy to enhance photocatalytic activity and anti-photocorrosion. The ZnS/ZnO core/shell heterostructures are obtained via an annealing treatment of ZnS nanoparticles produced by a facile wet chemical approach. Due to its small size, the nascent cubic sphalerite ZnS (s-ZnS) converts into a hexagonal wurtzite ZnS (w-ZnS)/ZnO core/shell structure after annealing treatment. In situ oxidation leads to increasing ZnO, simultaneously decreasing the w-ZnS content in the resultant w-ZnS/ZnO with thermal annealing time. The w-ZnS/ZnO core/shell heterostructures show high photocatalytic activity, demonstrated by the photodegradation rate of methylene blue being up to ten-fold and seven-fold higher than that of s-ZnS under UV and visible light irradiation, respectively, and the high capability of degrading rhodamine B. The enhanced photocatalytic activity may be attributed to the large specific surface and improved charge carrier separation at the core/shell interface. Moreover, it displays high photostability owing to the protection of the ZnO shell, greatly inhibiting the photocorrosion of ZnS. This facile in situ oxidation is effective and easily scalable, providing opportunities for developing novel core/shell structure photocatalysts with high activity and photostability.

Data Independent Acquisition analysis in ProHits 4.0.

PubMed

Liu, Guomin; Knight, James D R; Zhang, Jian Ping; Tsou, Chih-Chiang; Wang, Jian; Lambert, Jean-Philippe; Larsen, Brett; Tyers, Mike; Raught, Brian; Bandeira, Nuno; Nesvizhskii, Alexey I; Choi, Hyungwon; Gingras, Anne-Claude

2016-10-21

Affinity purification coupled with mass spectrometry (AP-MS) is a powerful technique for the identification and quantification of physical interactions. AP-MS requires careful experimental design, appropriate control selection and quantitative workflows to successfully identify bona fide interactors amongst a large background of contaminants. We previously introduced ProHits, a Laboratory Information Management System for interaction proteomics, which tracks all samples in a mass spectrometry facility, initiates database searches and provides visualization tools for spectral counting-based AP-MS approaches. More recently, we implemented Significance Analysis of INTeractome (SAINT) within ProHits to provide scoring of interactions based on spectral counts. Here, we provide an update to ProHits to support Data Independent Acquisition (DIA) with identification software (DIA-Umpire and MSPLIT-DIA), quantification tools (through DIA-Umpire, or externally via targeted extraction), and assessment of quantitative enrichment (through mapDIA) and scoring of interactions (through SAINT-intensity). With additional improvements, notably support of the iProphet pipeline, facilitated deposition into ProteomeXchange repositories and enhanced export and viewing functions, ProHits 4.0 offers a comprehensive suite of tools to facilitate affinity proteomics studies. It remains challenging to score, annotate and analyze proteomics data in a transparent manner. ProHits was previously introduced as a LIMS to enable storing, tracking and analysis of standard AP-MS data. In this revised version, we expand ProHits to include integration with a number of identification and quantification tools based on Data-Independent Acquisition (DIA). ProHits 4.0 also facilitates data deposition into public repositories, and the transfer of data to new visualization tools. Copyright © 2016 Elsevier B.V. All rights reserved.

Pricing the Services of Scientific Cores. Part II: Charging Outside Users.

ERIC Educational Resources Information Center

Fife, Jerry; Forrester, Robert

2002-01-01

Explaining that scientific cores at research institutions support shared resources and facilities, considers pricing of services to users from outside the institution. Proposes a method of allocating charges from the cores to projects with multiple funding sources through program-based management. Describes aspects of an example program: price of…

Geological Data Preservation Program Receives Bipartisan Support

NASA Astrophysics Data System (ADS)

Showstack, Randy

2014-09-01

More than 22 million vertical feet of geologic cores and cuttings fill the Kentucky Geological Survey's Well Sample and Core Library in Lexington. The materials are from at least 22,000 sites within Kentucky—including collections from oil and gas exploration operations, coal and other mining companies, highway construction projects, environmental studies, and federal facilities such as Fort Knox—and they are straining the 15-year-old facility to the point where there is no room to keep everything, according to geologist Patrick Gooding, the library manager.

Gamma-Radiation-Induced Degradation of Actively Pumped Single-Mode Ytterbium-Doped Optical Laser - Postprint

DTIC Science & Technology

2015-01-01

evaluated using the cobalt (Co)-60 gamma irradiation facility at The Ohio State University. A radiation dose rate of 43 krad(Si)/hr was used to expose the...Table 1. Description of the optical fibers used for in-situ analysis of the radiation damage Optical fiber Core Dopant Core/cladding diameters (μm...University is a pool-type gamma irradiation facility using a common cobalt cylindrical rod irradiator submerged 20 feet into a water tank. A

Alleviation of Facility/Engine Interactions in an Open-Jet Scramjet Test Facility

NASA Technical Reports Server (NTRS)

Albertson, Cindy W.; Emami, Saied

2001-01-01

Results of a series of shakedown tests to eliminate facility/engine interactions in an open-jet scramjet test facility are presented. The tests were conducted with the NASA DFX (Dual-Fuel eXperimental scramjet) engine in the NASA Langley Combustion Heated Scramjet Test Facility (CHSTF) in support of the Hyper-X program, The majority of the tests were conducted at a total enthalpy and pressure corresponding to Mach 5 flight at a dynamic pressure of 734 psf. The DFX is the largest engine ever tested in the CHSTF. Blockage, in terms of the projected engine area relative to the nozzle exit area, is 81% with the engine forebody leading edge aligned with the upper edge of the facility nozzle such that it ingests the nozzle boundary layer. The blockage increases to 95% with the engine forebody leading edge positioned 2 in. down in the core flow. Previous engines successfully tested in the CHSTF have had blockages of no more than 51%. Oil flow studies along with facility and engine pressure measurements were used to define flow behavior. These results guided modifications to existing aeroappliances and the design of new aeroappliances. These changes allowed fueled tests to be conducted without facility interaction effects in the data with the engine forebody leading edge positioned to ingest the facility nozzle boundary layer. Interaction effects were also reduced for tests with the engine forebody leading edge positioned 2 in. into the core flow, however some interaction effects were still evident in the engine data. A new shroud and diffuser have been designed with the goal of allowing fueled tests to be conducted with the engine forebody leading edge positioned in the core without facility interaction effects in the data. Evaluation tests of the new shroud and diffuser will be conducted once ongoing fueled engine tests have been completed.

Experimental and code simulation of a station blackout scenario for APR1400 with test facility ATLAS and MARS code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, X. G.; Kim, Y. S.; Choi, K. Y.

2012-07-01

A SBO (station blackout) experiment named SBO-01 was performed at full-pressure IET (Integral Effect Test) facility ATLAS (Advanced Test Loop for Accident Simulation) which is scaled down from the APR1400 (Advanced Power Reactor 1400 MWe). In this study, the transient of SBO-01 is discussed and is subdivided into three phases: the SG fluid loss phase, the RCS fluid loss phase, and the core coolant depletion and core heatup phase. In addition, the typical phenomena in SBO-01 test - SG dryout, natural circulation, core coolant boiling, the PRZ full, core heat-up - are identified. Furthermore, the SBO-01 test is reproduced bymore » the MARS code calculation with the ATLAS model which represents the ATLAS test facility. The experimental and calculated transients are then compared and discussed. The comparison reveals there was malfunction of equipments: the SG leakage through SG MSSV and the measurement error of loop flow meter. As the ATLAS model is validated against the experimental results, it can be further employed to investigate the other possible SBO scenarios and to study the scaling distortions in the ATLAS. (authors)« less

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

PubMed

Peterson, Elena S; McCue, Lee Ann; Schrimpe-Rutledge, Alexandra C; Jensen, Jeffrey L; Walker, Hyunjoo; Kobold, Markus A; Webb, Samantha R; Payne, Samuel H; Ansong, Charles; Adkins, Joshua N; Cannon, William R; Webb-Robertson, Bobbie-Jo M

2012-04-05

The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

Comparative analysis of Staphylococcus epidermidis strains utilizing quantitative and cell surface shaving proteomics.

PubMed

Solis, Nestor; Cain, Joel A; Cordwell, Stuart J

2016-01-01

Staphylococcus epidermidis is an opportunistic pathogen that is an emerging risk factor in hospitals worldwide and is often difficult to eradicate as virulent strains produce a protective biofilm matrix. We utilized cell shaving proteomics to profile surface-exposed proteins from two fully genome sequenced S. epidermidis strains: the avirulent, non-biofilm forming ATCC12228 and the virulent, strongly adherent biofilm forming ATCC35984 (RP62A). A false positive control strategy was employed to calculate the probabilities of proteins being truly surface-exposed. A total of 78 surface-exposed proteins were identified, of which only 19 proteins were common to ATCC12228 and RP62A, and which thus represents the core surfaceome. S. epidermidis RP62A displayed additional proteins involved in biofilm formation (cell wall-associated Bhp and intercellular adhesion protein IcaB), surface antigenicity, peptidoglycan biosynthesis and antibiotic resistance. We concurrently profiled whole cell proteomes of the two strains using iTRAQ quantitation and LC-MS/MS. A total of 1610 proteins were confidently identified (representing 64% of the theoretical S. epidermidis proteome). One hundred and ninety one proteins were differentially abundant between strains. Proteins associated with RP62A were clustered into functions including Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-mediated defense, sulfate assimilation, antibiotic resistance and biofilm formation. Validation of the sulfate assimilation and cysteine/methionine biosynthesis pathways showed RP62A contained elevated levels (~25% increase) of methionine that are likely linked to biofilm formation. Cell shaving and quantitative proteomics identified proteins associated with a biofilm-forming, virulent strain of S. epidermidis (RP62A). These proteins show RP62A maintains an active CRISPR-mediated defense, as well as heightened antibiotic resistance in comparison to a non-virulent, non-biofilm forming strain. Increased abundances of sulfate assimilation proteins lead to elevated intracellular methionine. Proteins and their exposed peptides identified on the surface of S. epidermidis RP62A may be useful vaccine antigens in clinical settings if administered in at-risk patients prior to surgical implantations. Copyright © 2015 Elsevier B.V. All rights reserved.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

PubMed Central

2012-01-01

Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php. PMID:22480257

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

DOE Office of Scientific and Technical Information (OSTI.GOV)

Omenn, Gilbert; States, David J.; Adamski, Marcin

2005-08-13

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasetsmore » had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.« less

Highly efficient enrichment of low-abundance intact proteins by core-shell structured Fe3O4-chitosan@graphene composites.

PubMed

Zhang, Peng; Fang, Xiaoni; Yan, Guoquan; Gao, Mingxia; Zhang, Xiangmin

2017-11-01

In proteomics research, the screening and monitoring of disease biomarkers is still a major challenge, mainly due to their low concentration in biological samples. However, the universal enrichment of intact proteins has not been further studied. In this work, we developed a Fe 3 O 4 -chitosan@graphene (Fe 3 O 4 -CS@G) core-shell composite to enrich low-abundance proteins from biological samples. Fe 3 O 4 -CS@G composite holds chitosan layer decorated Fe 3 O 4 core, which improves the hydrophilicity of materials greatly. Meanwhile, the graphene nanosheets shell formed via electrostatic assembly endows the composite with huge surface area (178m 2 /g). The good water dispersibility ensures the sufficient contact opportunities between graphene composites and proteins, and the large surface area provides enough adsorption sites for the enrichment of proteins. Using Fe 3 O 4 -CS@G, four standard proteins Cyt-c, BSA, Myo and OVA were enriched with better adsorption capacity and recovery rate, compared with previously reported magnetic graphene composites. Additionally, the mechanism of compared to" is corrected into "compared with". proteins adsorption on Fe 3 O 4 -CS@G was further studied, which indicates that hydrophobic and electrostatic interaction work together to facilitate the universal and efficient enrichment of proteins. Human plasma sample was employed to further evaluate the enrichment performance of Fe 3 O 4 -CS@G. Eventually, 123 proteins were identified from one of SAX fractions of human plasma, which is much better than commercial Sep-pak C18 enrichment column (39 proteins). All these outstanding performances suggest that Fe 3 O 4 -CS@G is an ideal platform for the enrichment of low-abundance intact proteins and thus holds great potential to facilitate the identification of biomarkers from biological samples in proteomics research. Copyright © 2017 Elsevier B.V. All rights reserved.

Stability Estimation of ABWR on the Basis of Noise Analysis

NASA Astrophysics Data System (ADS)

Furuya, Masahiro; Fukahori, Takanori; Mizokami, Shinya; Yokoya, Jun

In order to investigate the stability of a nuclear reactor core with an oxide mixture of uranium and plutonium (MOX) fuel installed, channel stability and regional stability tests were conducted with the SIRIUS-F facility. The SIRIUS-F facility was designed and constructed to provide a highly accurate simulation of thermal-hydraulic (channel) instabilities and coupled thermalhydraulics-neutronics instabilities of the Advanced Boiling Water Reactors (ABWRs). A real-time simulation was performed by modal point kinetics of reactor neutronics and fuel-rod thermal conduction on the basis of a measured void fraction in a reactor core section of the facility. A time series analysis was performed to calculate decay ratio and resonance frequency from a dominant pole of a transfer function by applying auto regressive (AR) methods to the time-series of the core inlet flow rate. Experiments were conducted with the SIRIUS-F facility, which simulates ABWR with MOX fuel installed. The variations in the decay ratio and resonance frequency among the five common AR methods are within 0.03 and 0.01 Hz, respectively. In this system, the appropriate decay ratio and resonance frequency can be estimated on the basis of the Yule-Walker method with the model order of 30.

Static and Wind Tunnel Aero-Performance Tests of NASA AST Separate Flow Nozzle Noise Reduction Configurations

NASA Technical Reports Server (NTRS)

Mikkelsen, Kevin L.; McDonald, Timothy J.; Saiyed, Naseem (Technical Monitor)

2001-01-01

This report presents the results of cold flow model tests to determine the static and wind tunnel performance of several NASA AST separate flow nozzle noise reduction configurations. The tests were conducted by Aero Systems Engineering, Inc., for NASA Glenn Research Center. The tests were performed in the Channels 14 and 6 static thrust stands and the Channel 10 transonic wind tunnel at the FluiDyne Aerodynamics Laboratory in Plymouth, Minnesota. Facility checkout tests were made using standard ASME long-radius metering nozzles. These tests demonstrated facility data accuracy at flow conditions similar to the model tests. Channel 14 static tests reported here consisted of 21 ASME nozzle facility checkout tests and 57 static model performance tests (including 22 at no charge). Fan nozzle pressure ratio varied from 1.4 to 2.0, and fan to core total pressure ratio varied from 1.0 to 1.19. Core to fan total temperature ratio was 1.0. Channel 10 wind tunnel tests consisted of 15 tests at Mach number 0.28 and 31 tests at Mach 0.8. The sting was checked out statically in Channel 6 before the wind tunnel tests. In the Channel 6 facility, 12 ASME nozzle data points were taken and 7 model data points were taken. In the wind tunnel, fan nozzle pressure ratio varied from 1.73 to 2.8, and fan to core total pressure ratio varied from 1.0 to 1.19. Core to fan total temperature ratio was 1.0. Test results include thrust coefficients, thrust vector angle, core and fan nozzle discharge coefficients, total pressure and temperature charging station profiles, and boat-tail static pressure distributions in the wind tunnel.

Access to Core Facilities and Other Research Resources Provided by the Clinical and Translational Science Awards

PubMed Central

2012-01-01

Abstract  Principal investigators who received Clinical and Translational Science Awards created academic homes for biomedical research. They developed program‐supported websites to offer coordinated access to a range of core facilities and other research resources. Visitors to the 60 websites will find at least 170 generic services, which this review has categorized in the following seven areas: (1) core facilities, (2) biomedical informatics, (3) funding, (4) regulatory knowledge and support, (5) biostatistics, epidemiology, research design, and ethics, (6) participant and clinical interaction resources, and (7) community engagement. In addition, many websites facilitate access to resources with search engines, navigators, studios, project development teams, collaboration tools, communication systems, and teaching tools. Each of these websites may be accessed from a single site, http://www.CTSAcentral.org. The ability to access the research resources from 60 of the nation's academic health centers presents a novel opportunity for investigators engaged in clinical and translational research. Clin Trans Sci 2012; Volume #: 1–5 PMID:22376262

Access to core facilities and other research resources provided by the Clinical and Translational Science Awards.

PubMed

Rosenblum, Daniel

2012-02-01

Principal investigators who received Clinical and Translational Science Awards created academic homes for biomedical research. They developed program-supported websites to offer coordinated access to a range of core facilities and other research resources. Visitors to the 60 websites will find at least 170 generic services, which this review has categorized in the following seven areas: (1) core facilities, (2) biomedical informatics, (3) funding, (4) regulatory knowledge and support, (5) biostatistics, epidemiology, research design, and ethics, (6) participant and clinical interaction resources, and (7) community engagement. In addition, many websites facilitate access to resources with search engines, navigators, studios, project development teams, collaboration tools, communication systems, and teaching tools. Each of these websites may be accessed from a single site, http://www.CTSAcentral.org. The ability to access the research resources from 60 of the nation's academic health centers presents a novel opportunity for investigators engaged in clinical and translational research. © 2012 Wiley Periodicals, Inc.

Core commands across airway facilities systems.

DOT National Transportation Integrated Search

2003-05-01

This study takes a high-level approach to evaluate computer systems without regard to the specific method of : interaction. This document analyzes the commands that Airway Facilities (AF) use across different systems and : the meanings attributed to ...

LUMA: A many-core, Fluid-Structure Interaction solver based on the Lattice-Boltzmann Method

NASA Astrophysics Data System (ADS)

Harwood, Adrian R. G.; O'Connor, Joseph; Sanchez Muñoz, Jonathan; Camps Santasmasas, Marta; Revell, Alistair J.

2018-01-01

The Lattice-Boltzmann Method at the University of Manchester (LUMA) project was commissioned to build a collaborative research environment in which researchers of all abilities can study fluid-structure interaction (FSI) problems in engineering applications from aerodynamics to medicine. It is built on the principles of accessibility, simplicity and flexibility. The LUMA software at the core of the project is a capable FSI solver with turbulence modelling and many-core scalability as well as a wealth of input/output and pre- and post-processing facilities. The software has been validated and several major releases benchmarked on supercomputing facilities internationally. The software architecture is modular and arranged logically using a minimal amount of object-orientation to maintain a simple and accessible software.

User Policies | Center for Cancer Research

Cancer.gov

User Policies 1. Authorship and Acknowledgement: The SAXS Core facility is a CCR resource dedicated to the CCR researchers. But we also make this resource accessible to non-CCR users free of charge. There are three ways to make use the SAXS Core resource. Asking the SAXS Core staff to collect, process and analyze data, and jointly interpret data with your teams. Asking the core staff to collect data and send it to you.

LC-MS Proteomics Analysis of the Insulin/IGF-1 Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Depuydt, Geert G.; Xie, Fang; Petyuk, Vladislav A.

2014-02-20

The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity and metabolism in C. elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass-spectrometry (LC-MS) based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2); daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the up-regulation of many core intermediarymore » metabolic pathways. These include, glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complex I, II, III and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative for spatio-temporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. This restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves, possibly also shunting metabolites through alternative energy-generating pathways, in order to sustain longevity.« less

LC–MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Depuydt, Geert; Xie, Fang; Petyuk, Vladislav A.

2014-04-04

The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity, and metabolism in Caenorhabditis elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including the expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass spectrometry (LC–MS)-based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2);daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the upregulation of many core intermediarymore » metabolic pathways. These include glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complexes I, II, III, and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative of spatiotemporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. Finally, this restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves and possibly also shunting metabolites through alternative energy-generating pathways to sustain longevity.« less

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics.

PubMed

Joyce, Brendan; Lee, Danny; Rubio, Alex; Ogurtsov, Aleksey; Alves, Gelio; Yu, Yi-Kuo

2018-03-15

RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId's core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. We have constructed a graphical user interface to facilitate the use of RAId on users' local machines. Written in Java, RAId_GUI not only makes easy executions of RAId but also provides tools for data/spectra visualization, MS-product analysis, molecular isotopic distribution analysis, and graphing the retrieval versus the proportion of false discoveries. The results viewer displays and allows the users to download the analyses results. Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html .

Proteomic analysis of laser capture microscopy purified myotendinous junction regions from muscle sections

PubMed Central

2014-01-01

The myotendinous junction is a specialized structure of the muscle fibre enriched in mechanosensing complexes, including costameric proteins and core elements of the z-disc. Here, laser capture microdissection was applied to purify membrane regions from the myotendinous junctions of mouse skeletal muscles, which were then processed for proteomic analysis. Sarcolemma sections from the longitudinal axis of the muscle fibre were used as control for the specificity of the junctional preparation. Gene ontology term analysis of the combined lists indicated a statistically significant enrichment in membrane-associated proteins. The myotendinous junction preparation contained previously uncharacterized proteins, a number of z-disc costameric ligands (e.g., actinins, capZ, αB cristallin, filamin C, cypher, calsarcin, desmin, FHL1, telethonin, nebulin, titin and an enigma-like protein) and other proposed players of sarcomeric stretch sensing and signalling, such as myotilin and the three myomesin homologs. A subset were confirmed by immunofluorescence analysis as enriched at the myotendinous junction, suggesting that laser capture microdissection from muscle sections is a valid approach to identify novel myotendinous junction players potentially involved in mechanotransduction pathways. PMID:25071420

SIRT3 mediates multi-tissue coupling for metabolic fuel switching.

PubMed

Dittenhafer-Reed, Kristin E; Richards, Alicia L; Fan, Jing; Smallegan, Michael J; Fotuhi Siahpirani, Alireza; Kemmerer, Zachary A; Prolla, Tomas A; Roy, Sushmita; Coon, Joshua J; Denu, John M

2015-04-07

SIRT3 is a member of the Sirtuin family of NAD(+)-dependent deacylases and plays a critical role in metabolic regulation. Organism-wide SIRT3 loss manifests in metabolic alterations; however, the coordinating role of SIRT3 among metabolically distinct tissues is unknown. Using multi-tissue quantitative proteomics comparing fasted wild-type mice to mice lacking SIRT3, innovative bioinformatic analysis, and biochemical validation, we provide a comprehensive view of mitochondrial acetylation and SIRT3 function. We find SIRT3 regulates the acetyl-proteome in core mitochondrial processes common to brain, heart, kidney, liver, and skeletal muscle, but differentially regulates metabolic pathways in fuel-producing and fuel-utilizing tissues. We propose an additional maintenance function for SIRT3 in liver and kidney where SIRT3 expression is elevated to reduce the acetate load on mitochondrial proteins. We provide evidence that SIRT3 impacts ketone body utilization in the brain and reveal a pivotal role for SIRT3 in the coordination between tissues required for metabolic homeostasis. Copyright © 2015 Elsevier Inc. All rights reserved.

Vice President Pence Visits SLS Engineering Test Facility

NASA Image and Video Library

2017-09-25

The Vice President toured the SLS engineering facility where the engine section of the rocket’s massive core stage is undergoing a major stress test. The rocket’s four RS-25 engines and the two solid rocket boosters that attach to the SLS engine section will produce more than 8 million pounds of thrust to launch the Orion spacecraft beyond low-Earth orbit. More than 3,000 measurements using sensors installed on the test section will help ensure the core stage for all SLS missions can withstand the extreme forces of flight.

Offshore Installations and Their Relevance to the Coast Guard through the Next Twenty-Five Years. Volume III. Appendices.

DTIC Science & Technology

1980-11-01

facility common to all facilities as well as a separate municipal waste treatment plant . The crude refinery and petrochemicals plant produces high...offshore: refinery L M H I power plant I L L M I industrial complex I L L L I II Extensive use of sub-sea production systems I M H I up to 5,000 ft. I... petrochemicals factory or a refinery acting as the core around which an in- dustrial complex is built. The type of core industry selected would depend

Titanium dioxide@polypyrrole core-shell nanowires for all solid-state flexible supercapacitors.

PubMed

Yu, Minghao; Zeng, Yinxiang; Zhang, Chong; Lu, Xihong; Zeng, Chenghui; Yao, Chenzhong; Yang, Yangyi; Tong, Yexiang

2013-11-21

Herein, we developed a facile two-step process to synthesize TiO2@PPy core-shell nanowires (NWs) on carbon cloth and reported their improved electrochemical performance for flexible supercapacitors (SCs). The fabricated solid-state SC device based on TiO2@PPy core-shell NWs not only has excellent flexibility, but also exhibits remarkable electrochemical performance.

User Policies | Center for Cancer Research

Cancer.gov

User Policies 1. Authorship and Acknowledgement: The SAXS Core facility is a CCR resource dedicated to the CCR researchers. But we also make this resource accessible to non-CCR users free of charge. There are three ways to make use the SAXS Core resource. Asking the SAXS Core staff to collect, process and analyze data, and jointly interpret data with your teams. Asking the

Systems Check: Community Colleges Turn to Facilities Assessments to Plan Capital Projects and Avoid Expensive Emergency Repairs

ERIC Educational Resources Information Center

Joch, Alan

2014-01-01

With an emphasis on planning and cutting costs to make better use of resources, facilities managers at community colleges across the nation have undertaken facilities audits usually with the help of outside engineers. Such assessments analyze the history and structural integrity of buildings and core components on campus, including heating…

The Thiamin Pyrophosphate-Motif

NASA Technical Reports Server (NTRS)

Dominiak, P.; Ciszak, E.

2003-01-01

Using databases the authors have identified a common thiamin pyrophosphate (TPP)-motif in the family of functionally diverse TPP-dependent enzymes. This common motif consists of multimeric organization of subunits and two catalytic centers. Each catalytic center (PP:PYR) is formed at the interface of the PP-domain binding the magnesium ion, pyrophosphate and amhopyrimidine ring of TPP, and the PYR-domain binding the aminopyrimidine ring of that cofactor. A pair of these catalytic centers constitutes the catalytic core (PP:PYR)(sub 2) within these enzymes. Analysis of the structural elements of this catalytic core reveals novel definition of the common amino acid sequences, which are GXPhiX(sub 4)(G)PhiXXGQ and GDGX(sub 25-30)NN in the PP-domain, and the EX(sub 4)(G)PhiXXGPhi in the PYR-domain, where Phi corresponds to a hydrophobic amino acid. This TPP-motif provides a novel tool for annotation of TPP-dependent enzymes useful in advancing functional proteomics.

Mir Training Facility

NASA Technical Reports Server (NTRS)

1995-01-01

A full-scale mockup of Russia's Space Station with the core module called Mir in the center. Other modules connected to the core include Kvant, Kvant II and Kristall. The mockup at the Gagarin Cosmonaut Training Center in Star City, Russia is used for cos

Proteomics approach combined with biochemical attributes to elucidate compatible and incompatible plant-virus interactions between Vigna mungo and Mungbean Yellow Mosaic India Virus.

PubMed

Kundu, Subrata; Chakraborty, Dipjyoti; Kundu, Anirban; Pal, Amita

2013-01-01

Vigna mungo, a tropical leguminous plant, highly susceptible to yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus (MYMIV) resulting in high yield penalty. The molecular events occurring during compatible and incompatible interactions between V. mungo and MYMIV pathosystem are yet to be explored. In this study biochemical analyses in conjunction with proteomics of MYMIV-susceptible and -resistant V. mungo genotypes were executed to get an insight in the molecular events during compatible and incompatible plant-virus interactions. Biochemical analysis revealed an increase in phenolics, hydrogen peroxide and carbohydrate contents in both compatible and incompatible interactions; but the magnitudes were higher during incompatible interaction. In the resistant genotype the activities of superoxide dismutase and ascorbate peroxidase increased significantly, while catalase activity decreased. Comparative proteome analyses using two-dimensional gel electrophoresis coupled with mass spectrometry identified 109 differentially abundant proteins at 3, 7 and 14 days post MYMIV-inoculation. Proteins of several functional categories were differentially changed in abundance during both compatible and incompatible interactions. Among these, photosynthesis related proteins were mostly affected in the susceptible genotype resulting in reduced photosynthesis rate under MYMIV-stress. Differential intensities of chlorophyll fluorescence and chlorophyll contents are in congruence with proteomics data. It was revealed that Photosystem II electron transports are the primary targets of MYMIV during pathogenesis. Quantitative real time PCR analyses of selected genes corroborates with respective protein abundance during incompatible interaction. The network of various cellular pathways that are involved in inducing defense response contains several conglomerated cores of nodal proteins, of which ascorbate peroxidase, rubisco activase and serine/glycine hydroxymethyl transferase are the three major hubs with high connectivity. These nodal proteins play the crucial role of key regulators in bringing about a coordinated defense response in highly orchestrated manner. Biochemical and proteomic analyses revealed early accumulation of the defense/stress related proteins involved in ROS metabolism during incompatible interaction. The robustness in induction of defense/stress and signal transduction related proteins is the key factor in inducing resistance. The mechanism of MYMIV-resistance in V. mungo involves redirection of carbohydrate flux towards pentose phosphate pathway. Some of these identified, differentially regulated proteins are also conferring abiotic stress responses illustrating harmony amongst different stress responses. To the best of our knowledge, this is the lone study deciphering differential regulations of V. mungo leaf proteome upon MYMIV infection elucidating the mode of resistance response at the biochemical level.

Indoor Air Quality Design Tools for Schools

EPA Pesticide Factsheets

The information available here is presented as a tool to help school districts and facility planners design the next generation of learning environments so that the school facility will help, rather than hinder, schools in achieving their core mission

Space Launch System, Core Stage, Structural Test Design and Implementation

NASA Technical Reports Server (NTRS)

Shaughnessy, Ray

2017-01-01

As part of the National Aeronautics and Space Administration's (NASA) Space Launch System (SLS) Program, engineers at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama are working to design, develop and implement the SLS Core Stage structural testing. The SLS will have the capability to return humans to the Moon and beyond and its first launch is scheduled for December of 2017. The SLS Core Stage consist of five major elements; Forward Skirt, Liquid Oxygen (LOX) tank, Intertank (IT), Liquid Hydrogen (LH2) tank and the Engine Section (ES). Structural Test Articles (STA) for each of these elements are being designed and produced by Boeing at Michoud Assembly Facility located in New Orleans, La. The structural test for the Core Stage STAs (LH2, LOX, IT and ES) are to be conducted by the MSFC Test Laboratory. Additionally, the MSFC Test Laboratory manages the Structural Test Equipment (STE) design and development to support the STAs. It was decided early (April 2012) in the project life that the LH2 and LOX tank STAs would require new test stands and the Engine Section and Intertank would be tested in existing facilities. This decision impacted schedules immediately because the new facilities would require Construction of Facilities (C of F) funds that require congressional approval and long lead times. The Engine Section and Intertank structural test are to be conducted in existing facilities which will limit lead times required to support the first launch of SLS. With a SLS launch date of December, 2017 Boeing had a need date for testing to be complete by September of 2017 to support flight certification requirements. The test facilities were required to be ready by October of 2016 to support test article delivery. The race was on to get the stands ready before Test Article delivery and meet the test complete date of September 2017. This paper documents the past and current design and development phases and the supporting processes, tools, and methodology for supporting the SLS Core Stage STA test stands and related STE. The paper will address key requirements, system development activities and project challenges. Additionally, the interrelationships as well as interdependencies within the SLS project will be discussed.

Protein kinases responsible for the phosphorylation of the nuclear egress core complex of human cytomegalovirus.

PubMed

Sonntag, Eric; Milbradt, Jens; Svrlanska, Adriana; Strojan, Hanife; Häge, Sigrun; Kraut, Alexandra; Hesse, Anne-Marie; Amin, Bushra; Sonnewald, Uwe; Couté, Yohann; Marschall, Manfred

2017-10-01

Nuclear egress of herpesvirus capsids is mediated by a multi-component nuclear egress complex (NEC) assembled by a heterodimer of two essential viral core egress proteins. In the case of human cytomegalovirus (HCMV), this core NEC is defined by the interaction between the membrane-anchored pUL50 and its nuclear cofactor, pUL53. NEC protein phosphorylation is considered to be an important regulatory step, so this study focused on the respective role of viral and cellular protein kinases. Multiply phosphorylated pUL50 varieties were detected by Western blot and Phos-tag analyses as resulting from both viral and cellular kinase activities. In vitro kinase analyses demonstrated that pUL50 is a substrate of both PKCα and CDK1, while pUL53 can also be moderately phosphorylated by CDK1. The use of kinase inhibitors further illustrated the importance of distinct kinases for core NEC phosphorylation. Importantly, mass spectrometry-based proteomic analyses identified five major and nine minor sites of pUL50 phosphorylation. The functional relevance of core NEC phosphorylation was confirmed by various experimental settings, including kinase knock-down/knock-out and confocal imaging, in which it was found that (i) HCMV core NEC proteins are not phosphorylated solely by viral pUL97, but also by cellular kinases; (ii) both PKC and CDK1 phosphorylation are detectable for pUL50; (iii) no impact of PKC phosphorylation on NEC functionality has been identified so far; (iv) nonetheless, CDK1-specific phosphorylation appears to be required for functional core NEC interaction. In summary, our findings provide the first evidence that the HCMV core NEC is phosphorylated by cellular kinases, and that the complex pattern of NEC phosphorylation has functional relevance.

Nasal mucus proteomic changes reflect altered immune responses and epithelial permeability in patients with allergic rhinitis.

PubMed

Tomazic, Peter Valentin; Birner-Gruenberger, Ruth; Leitner, Anita; Obrist, Britta; Spoerk, Stefan; Lang-Loidolt, Doris

2014-03-01

Nasal mucus is the first-line defense barrier against (aero-) allergens. However, its proteome and function have not been clearly investigated. The role of nasal mucus in the pathophysiology of allergic rhinitis was investigated by analyzing its proteome in patients with allergic rhinitis (n = 29) and healthy control subjects (n = 29). Nasal mucus was collected with a suction device, tryptically digested, and analyzed by using liquid chromatography-tandem mass spectrometry. Proteins were identified by searching the SwissProt database and annotated by collecting gene ontology data from databases and existing literature. Gene enrichment analysis was performed by using Cytoscape/BINGO software tools. Proteins were quantified with spectral counting, and selected proteins were confirmed by means of Western blotting. In total, 267 proteins were identified, with 20 (7.5%) found exclusively in patients with allergic rhinitis and 25 (9.5%) found exclusively in healthy control subjects. Five proteins were found to be significantly upregulated in patients with allergic rhinitis (apolipoprotein A-2 [APOA2], 9.7-fold; α2-macroglobulin [A2M], 4.5-fold; apolipoprotein A-1 [APOA1], 3.2-fold; α1-antitrypsin [SERPINA1], 2.5-fold; and complement C3 [C3], 2.3-fold) and 5 were found to be downregulated (antileukoproteinase [SLPI], 0.6-fold; WAP 4-disulfide core domain protein [WFDC2], 0.5-fold; haptoglobin [HP], 0.7-fold; IgJ chain [IGJ], 0.7-fold; and Ig hc V-III region BRO, 0.8-fold) compared with levels seen in healthy control subjects. The allergic rhinitis mucus proteome shows an enhanced immune response in which apolipoproteins might play an important role. Furthermore, an imbalance between cysteine proteases and antiproteases could be seen, which negatively affects epithelial integrity on exposure to pollen protease activity. This reflects the important role of mucus as the first-line defense barrier against allergens. Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

Anticoagulants and the propagation phase of thrombin generation.

PubMed

Orfeo, Thomas; Gissel, Matthew; Butenas, Saulius; Undas, Anetta; Brummel-Ziedins, Kathleen E; Mann, Kenneth G

2011-01-01

The view that clot time-based assays do not provide a sufficient assessment of an individual's hemostatic competence, especially in the context of anticoagulant therapy, has provoked a search for new metrics, with significant focus directed at techniques that define the propagation phase of thrombin generation. Here we use our deterministic mathematical model of tissue-factor initiated thrombin generation in combination with reconstructions using purified protein components to characterize how the interplay between anticoagulant mechanisms and variable composition of the coagulation proteome result in differential regulation of the propagation phase of thrombin generation. Thrombin parameters were extracted from computationally derived thrombin generation profiles generated using coagulation proteome factor data from warfarin-treated individuals (N = 54) and matching groups of control individuals (N = 37). A computational clot time prolongation value (cINR) was devised that correlated with their actual International Normalized Ratio (INR) values, with differences between individual INR and cINR values shown to derive from the insensitivity of the INR to tissue factor pathway inhibitor (TFPI). The analysis suggests that normal range variation in TFPI levels could be an important contributor to the failure of the INR to adequately reflect the anticoagulated state in some individuals. Warfarin-induced changes in thrombin propagation phase parameters were then compared to those induced by unfractionated heparin, fondaparinux, rivaroxaban, and a reversible thrombin inhibitor. Anticoagulants were assessed at concentrations yielding equivalent cINR values, with each anticoagulant evaluated using 32 unique coagulation proteome compositions. The analyses showed that no anticoagulant recapitulated all features of warfarin propagation phase dynamics; differences in propagation phase effects suggest that anticoagulants that selectively target fXa or thrombin may provoke fewer bleeding episodes. More generally, the study shows that computational modeling of the response of core elements of the coagulation proteome to a physiologically relevant tissue factor stimulus may improve the monitoring of a broad range of anticoagulants.

Nuclear thermal propulsion test facility requirements and development strategy

NASA Technical Reports Server (NTRS)

Allen, George C.; Warren, John; Clark, J. S.

1991-01-01

The Nuclear Thermal Propulsion (NTP) subpanel of the Space Nuclear Propulsion Test Facilities Panel evaluated facility requirements and strategies for nuclear thermal propulsion systems development. High pressure, solid core concepts were considered as the baseline for the evaluation, with low pressure concepts an alternative. The work of the NTP subpanel revealed that a wealth of facilities already exists to support NTP development, and that only a few new facilities must be constructed. Some modifications to existing facilities will be required. Present funding emphasis should be on long-lead-time items for the major new ground test facility complex and on facilities supporting nuclear fuel development, hot hydrogen flow test facilities, and low power critical facilities.

Critical need for MFE: the Alcator DX advanced divertor test facility

NASA Astrophysics Data System (ADS)

Vieira, R.; Labombard, B.; Marmar, E.; Irby, J.; Wolf, S.; Bonoli, P.; Fiore, C.; Granetz, R.; Greenwald, M.; Hutchinson, I.; Hubbard, A.; Hughes, J.; Lin, Y.; Lipschultz, B.; Parker, R.; Porkolab, M.; Reinke, M.; Rice, J.; Shiraiwa, S.; Terry, J.; Theiler, C.; Wallace, G.; White, A.; Whyte, D.; Wukitch, S.

2013-10-01

Three critical challenges must be met before a steady-state, power-producing fusion reactor can be realized: how to (1) safely handle extreme plasma exhaust power, (2) completely suppress material erosion at divertor targets and (3) do this while maintaining a burning plasma core. Advanced divertors such as ``Super X'' and ``X-point target'' may allow a fully detached, low temperature plasma to be produced in the divertor while maintaining a hot boundary layer around a clean plasma core - a potential game-changer for magnetic fusion. No facility currently exists to test these ideas at the required parallel heat flux densities. Alcator DX will be a national facility, employing the high magnetic field technology of Alcator combined with high-power ICRH and LHCD to test advanced divertor concepts at FNSF/DEMO power exhaust densities and plasma pressures. Its extended vacuum vessel contains divertor cassettes with poloidal field coils for conventional, snowflake, super-X and X-point target geometries. Divertor and core plasma performance will be explored in regimes inaccessible in conventional devices. Reactor relevant ICRF and LH drivers will be developed, utilizing high-field side launch platforms for low PMI. Alcator DX will inform the conceptual development and accelerate the readiness-for-deployment of next-step fusion facilities.

Resources for Indoor Air Quality Design Tools for Schools

EPA Pesticide Factsheets

The information available here is presented as a tool to help school districts and facility planners design the next generation of learning environments so that the school facility will help schools in achieving their core mission of educating children.

A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility.

PubMed

Yennawar, Neela H; Fecko, Julia A; Showalter, Scott A; Bevilacqua, Philip C

2016-01-01

Many labs have conventional calorimeters where denaturation and binding experiments are setup and run one at a time. While these systems are highly informative to biopolymer folding and ligand interaction, they require considerable manual intervention for cleaning and setup. As such, the throughput for such setups is limited typically to a few runs a day. With a large number of experimental parameters to explore including different buffers, macromolecule concentrations, temperatures, ligands, mutants, controls, replicates, and instrument tests, the need for high-throughput automated calorimeters is on the rise. Lower sample volume requirements and reduced user intervention time compared to the manual instruments have improved turnover of calorimetry experiments in a high-throughput format where 25 or more runs can be conducted per day. The cost and efforts to maintain high-throughput equipment typically demands that these instruments be housed in a multiuser core facility. We describe here the steps taken to successfully start and run an automated biological calorimetry facility at Pennsylvania State University. Scientists from various departments at Penn State including Chemistry, Biochemistry and Molecular Biology, Bioengineering, Biology, Food Science, and Chemical Engineering are benefiting from this core facility. Samples studied include proteins, nucleic acids, sugars, lipids, synthetic polymers, small molecules, natural products, and virus capsids. This facility has led to higher throughput of data, which has been leveraged into grant support, attracting new faculty hire and has led to some exciting publications. © 2016 Elsevier Inc. All rights reserved.

NCI Core Open House Shines Spotlight on Supportive Science and Basic Research | Poster

Cancer.gov

The lobby of Building 549 at NCI at Frederick bustled with activity for two hours on Tuesday, May 1, as several dozen scientists and staff gathered for the NCI Core Open House. The event aimed to encourage discussion and educate visitors about the capabilities of the cores, laboratories, and facilities that offer support to NCI’s Center for Cancer Research.

POWER-BURST FACILITY (PBF) CONCEPTUAL DESIGN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wasserman, A.A.; Johnson, S.O.; Heffner, R.E.

1963-06-21

A description is presented of the conceptual design of a high- performance, pulsed reactor called the Power Burst Facility (PBF). This reactor is designed to generate power bursts with initial asymptotic periods as short as 1 msec, producing energy releases large enough to destroy entire fuel subassemblies placed in a capsule or flow loop mounted in the reactor, all without damage to the reactor itself. It will be used primarily to evaluate the consequences and hazards of very rapid destructive accidents in reactors representing the entire range of current nuclear technology as applied to power generation, propulsion, and testing. Itmore » will also be used to carry out detailed studies of nondestructive reactivity feedback mechanisms in the shortperiod domain. The facility was designed to be sufficiently flexible to accommodate future cores of even more advanced design. The design for the first reactor core is based upon proven technology; hence, completion of the final design of this core will involve no significant development delays. Construction of the PBF is proposed to begin in September 1984, and is expected to take approximately 20 months to complete. (auth)« less

Oak Ridge National Laboratory Core Competencies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberto, J.B.; Anderson, T.D.; Berven, B.A.

1994-12-01

A core competency is a distinguishing integration of capabilities which enables an organization to deliver mission results. Core competencies represent the collective learning of an organization and provide the capacity to perform present and future missions. Core competencies are distinguishing characteristics which offer comparative advantage and are difficult to reproduce. They exhibit customer focus, mission relevance, and vertical integration from research through applications. They are demonstrable by metrics such as level of investment, uniqueness of facilities and expertise, and national impact. The Oak Ridge National Laboratory (ORNL) has identified four core competencies which satisfy the above criteria. Each core competencymore » represents an annual investment of at least $100M and is characterized by an integration of Laboratory technical foundations in physical, chemical, and materials sciences; biological, environmental, and social sciences; engineering sciences; and computational sciences and informatics. The ability to integrate broad technical foundations to develop and sustain core competencies in support of national R&D goals is a distinguishing strength of the national laboratories. The ORNL core competencies are: 9 Energy Production and End-Use Technologies o Biological and Environmental Sciences and Technology o Advanced Materials Synthesis, Processing, and Characterization & Neutron-Based Science and Technology. The distinguishing characteristics of each ORNL core competency are described. In addition, written material is provided for two emerging competencies: Manufacturing Technologies and Computational Science and Advanced Computing. Distinguishing institutional competencies in the Development and Operation of National Research Facilities, R&D Integration and Partnerships, Technology Transfer, and Science Education are also described. Finally, financial data for the ORNL core competencies are summarized in the appendices.« less

Integrating cell biology and proteomic approaches in plants.

PubMed

Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

2017-10-03

Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of representative studies combining proteomic and cell biology methods for various purposes. Integrating cell biology approaches with proteomic ones allow validation and better interpretation of proteomic data. Moreover, cell biology methods remarkably extend the knowledge provided by proteomic studies and might be fundamental for the functional complementation of proteomic data. This review article summarizes current literature linking proteomics with cell biology. Copyright © 2017 Elsevier B.V. All rights reserved.

Partnership between CTSI and Business Schools Can Promote Best Practices for Core Facilities and Resources

PubMed Central

Reeves, Lilith; Dunn‐Jensen, Linda M.; Baldwin, Timothy T.; Tatikonda, Mohan V.

2013-01-01

Abstract Biomedical research enterprises require a large number of core facilities and resources to supply the infrastructure necessary for translational research. Maintaining the financial viability and promoting efficiency in an academic environment can be particularly challenging for medical schools and universities. The Indiana Clinical and Translational Sciences Institute sought to improve core and service programs through a partnership with the Indiana University Kelley School of Business. The program paired teams of Masters of Business Administration students with cores and programs that self‐identified the need for assistance in project management, financial management, marketing, or resource efficiency. The projects were developed by CTSI project managers and business school faculty using service‐learning principles to ensure learning for students who also received course credit for their participation. With three years of experience, the program demonstrates a successful partnership that improves clinical research infrastructure by promoting business best practices and providing a valued learning experience for business students. PMID:23919365

Partnership between CTSI and business schools can promote best practices for core facilities and resources.

PubMed

Reeves, Lilith; Dunn-Jensen, Linda M; Baldwin, Timothy T; Tatikonda, Mohan V; Cornetta, Kenneth

2013-08-01

Biomedical research enterprises require a large number of core facilities and resources to supply the infrastructure necessary for translational research. Maintaining the financial viability and promoting efficiency in an academic environment can be particularly challenging for medical schools and universities. The Indiana Clinical and Translational Sciences Institute sought to improve core and service programs through a partnership with the Indiana University Kelley School of Business. The program paired teams of Masters of Business Administration students with cores and programs that self-identified the need for assistance in project management, financial management, marketing, or resource efficiency. The projects were developed by CTSI project managers and business school faculty using service-learning principles to ensure learning for students who also received course credit for their participation. With three years of experience, the program demonstrates a successful partnership that improves clinical research infrastructure by promoting business best practices and providing a valued learning experience for business students. © 2013 Wiley Periodicals, Inc.

A Strategy for Fabricating Porous PdNi@Pt Core-shell Nanostructures and Their Enhanced Activity and Durability for the Methanol Electrooxidation

PubMed Central

Liu, Xinyu; Xu, Guangrui; Chen, Yu; Lu, Tianhong; Tang, Yawen; Xing, Wei

2015-01-01

Three-dimensionally (3D) porous morphology of nanostructures can effectively improve their electrocatalytic activity and durability for various electrochemical reactions owing to big surface area and interconnected structure. Cyanogel, a jelly-like inorganic polymer, can be used to synthesize various three-dimensionally (3D) porous alloy nanomaterials owing to its double-metal property and particular 3D backbone. Here, 3D porous PdNi@Pt core-shell nanostructures (CSNSs) are facilely synthesized by first preparing the Pd-Ni alloy networks (Pd-Ni ANWs) core via cyanogel-reduction method followed by a galvanic displacement reaction to generate the Pt-rich shell. The as-synthesized PdNi@Pt CSNSs exhibit a much improved catalytic activity and durability for the methanol oxidation reaction (MOR) in the acidic media compared to the commercial used Pt black because of their specific structural characteristics. The facile and mild method described herein is highly attractive for the synthisis of 3D porous core-shell nanostructures. PMID:25557190

HTR-PROTEUS Pebble Bed Experimental Program Cores 1, 1A, 2, and 3: Hexagonal Close Packing with a 1:2 Moderator-to-Fuel Pebble Ratio

DOE Office of Scientific and Technical Information (OSTI.GOV)

John D. Bess; Barbara H. Dolphin; James W. Sterbentz

2013-03-01

In its deployment as a pebble bed reactor (PBR) critical facility from 1992 to 1996, the PROTEUS facility was designated as HTR-PROTEUS. This experimental program was performed as part of an International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on the Validation of Safety Related Physics Calculations for Low Enriched HTGRs. Within this project, critical experiments were conducted for graphite moderated LEU systems to determine core reactivity, flux and power profiles, reaction-rate ratios, the worth of control rods, both in-core and reflector based, the worth of burnable poisons, kinetic parameters, and the effects of moisture ingress on these parameters.more » Four benchmark experiments were evaluated in this report: Cores 1, 1A, 2, and 3. These core configurations represent the hexagonal close packing (HCP) configurations of the HTR-PROTEUS experiment with a moderator-to-fuel pebble ratio of 1:2. Core 1 represents the only configuration utilizing ZEBRA control rods. Cores 1A, 2, and 3 use withdrawable, hollow, stainless steel control rods. Cores 1 and 1A are similar except for the use of different control rods; Core 1A also has one less layer of pebbles (21 layers instead of 22). Core 2 retains the first 16 layers of pebbles from Cores 1 and 1A and has 16 layers of moderator pebbles stacked above the fueled layers. Core 3 retains the first 17 layers of pebbles but has polyethylene rods inserted between pebbles to simulate water ingress. The additional partial pebble layer (layer 18) for Core 3 was not included as it was used for core operations and not the reported critical configuration. Cores 1, 1A, 2, and 3 were determined to be acceptable benchmark experiments.« less

HTR-PROTEUS Pebble Bed Experimental Program Cores 1, 1A, 2, and 3: Hexagonal Close Packing with a 1:2 Moderator-to-Fuel Pebble Ratio

DOE Office of Scientific and Technical Information (OSTI.GOV)

John D. Bess; Barbara H. Dolphin; James W. Sterbentz

2012-03-01

In its deployment as a pebble bed reactor (PBR) critical facility from 1992 to 1996, the PROTEUS facility was designated as HTR-PROTEUS. This experimental program was performed as part of an International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on the Validation of Safety Related Physics Calculations for Low Enriched HTGRs. Within this project, critical experiments were conducted for graphite moderated LEU systems to determine core reactivity, flux and power profiles, reaction-rate ratios, the worth of control rods, both in-core and reflector based, the worth of burnable poisons, kinetic parameters, and the effects of moisture ingress on these parameters.more » Four benchmark experiments were evaluated in this report: Cores 1, 1A, 2, and 3. These core configurations represent the hexagonal close packing (HCP) configurations of the HTR-PROTEUS experiment with a moderator-to-fuel pebble ratio of 1:2. Core 1 represents the only configuration utilizing ZEBRA control rods. Cores 1A, 2, and 3 use withdrawable, hollow, stainless steel control rods. Cores 1 and 1A are similar except for the use of different control rods; Core 1A also has one less layer of pebbles (21 layers instead of 22). Core 2 retains the first 16 layers of pebbles from Cores 1 and 1A and has 16 layers of moderator pebbles stacked above the fueled layers. Core 3 retains the first 17 layers of pebbles but has polyethylene rods inserted between pebbles to simulate water ingress. The additional partial pebble layer (layer 18) for Core 3 was not included as it was used for core operations and not the reported critical configuration. Cores 1, 1A, 2, and 3 were determined to be acceptable benchmark experiments.« less

Pacific Northwest Laboratory Institutional Plan FY 1995-2000

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1994-12-01

This report serves as a document to describe the role PNL is positioned to take in the Department of Energy`s plans for its national centers in the period 1995-2000. It highlights the strengths of the facilities and personnel present at the laboratory, touches on the accomplishments and projects they have contributed to, and the direction being taken to prepare for the demands to be placed on DOE facilities in the near and far term. It consists of sections titled: director`s statement; laboratory mission and core competencies; laboratory strategic plan; laboratory initiatives; core business areas; critical success factors.

TREE Simulation Facilities, Second Edition, Revision 2

DTIC Science & Technology

1979-01-01

included radiation effects on propellants , ordnance, electronics and chemicals, vehicle shielding, neutron radiography , dosimetry, and health physics...Special Capabilities 2.11.10.1 Radiography Facility 2.11.10.2 Flexo-Rabbit System Support Capabilities 2.11.11.1 Staff 2.11.11.2 Electronics...5,400-MW pulsing operation (experimental dosimetry values for a typical core loading of 94 fuel elements). 2-156 2-46 ACPR radiography facility

Completed | Office of Cancer Clinical Proteomics Research

Cancer.gov

Prior to the current Clinical Proteomic Tumor Analysis Consortium (CPTAC), previously funded initiatives associated with clinical proteomics research included: Clinical Proteomic Tumor Analysis Consortium (CPTAC 2.0) Clinical Proteomic Technologies for Cancer Initiative (CPTC) Mouse Proteomic Technologies Initiative

Proteomic Analysis of the Multimeric Nuclear Egress Complex of Human Cytomegalovirus*

PubMed Central

Milbradt, Jens; Kraut, Alexandra; Hutterer, Corina; Sonntag, Eric; Schmeiser, Cathrin; Ferro, Myriam; Wagner, Sabrina; Lenac, Tihana; Claus, Claudia; Pinkert, Sandra; Hamilton, Stuart T.; Rawlinson, William D.; Sticht, Heinrich; Couté, Yohann; Marschall, Manfred

2014-01-01

Herpesviral capsids are assembled in the host cell nucleus before being translocated into the cytoplasm for further maturation. The crossing of the nuclear envelope represents a major event that requires the formation of the nuclear egress complex (NEC). Previous studies demonstrated that human cytomegalovirus (HCMV) proteins pUL50 and pUL53, as well as their homologs in all members of Herpesviridae, interact with each other at the nuclear envelope and form the heterodimeric core of the NEC. In order to characterize further the viral and cellular protein content of the multimeric NEC, the native complex was isolated from HCMV-infected human primary fibroblasts at various time points and analyzed using quantitative proteomics. Previously postulated components of the HCMV-specific NEC, as well as novel potential NEC-associated proteins such as emerin, were identified. In this regard, interaction and colocalization between emerin and pUL50 were confirmed by coimmunoprecipitation and confocal microscopy analyses, respectively. A functional validation of viral and cellular NEC constituents was achieved through siRNA-mediated knockdown experiments. The important role of emerin in NEC functionality was demonstrated by a reduction of viral replication when emerin expression was down-regulated. Moreover, under such conditions, reduced production of viral proteins and deregulation of viral late cytoplasmic maturation were observed. Combined, these data prove the functional importance of emerin as an NEC component, associated with pUL50, pUL53, pUL97, p32/gC1qR, and further regulatory proteins. Summarized, our findings provide the first proteomics-based characterization and functional validation of the HCMV-specific multimeric NEC. PMID:24969177

An Anti-proteome Nanobody Library Approach Yields a Specific Immunoassay for Trypanosoma congolense Diagnosis Targeting Glycosomal Aldolase.

PubMed

Odongo, Steven; Sterckx, Yann G J; Stijlemans, Benoît; Pillay, Davita; Baltz, Théo; Muyldermans, Serge; Magez, Stefan

2016-02-01

Infectious diseases pose a severe worldwide threat to human and livestock health. While early diagnosis could enable prompt preventive interventions, the majority of diseases are found in rural settings where basic laboratory facilities are scarce. Under such field conditions, point-of-care immunoassays provide an appropriate solution for rapid and reliable diagnosis. The limiting steps in the development of the assay are the identification of a suitable target antigen and the selection of appropriate high affinity capture and detection antibodies. To meet these challenges, we describe the development of a Nanobody (Nb)-based antigen detection assay generated from a Nb library directed against the soluble proteome of an infectious agent. In this study, Trypanosoma congolense was chosen as a model system. An alpaca was vaccinated with whole-parasite soluble proteome to generate a Nb library from which the most potent T. congolense specific Nb sandwich immunoassay (Nb474H-Nb474B) was selected. First, the Nb474-homologous sandwich ELISA (Nb474-ELISA) was shown to detect experimental infections with high Positive Predictive Value (98%), Sensitivity (87%) and Specificity (94%). Second, it was demonstrated under experimental conditions that the assay serves as test-of-cure after Berenil treatment. Finally, this assay allowed target antigen identification. The latter was independently purified through immuno-capturing from (i) T. congolense soluble proteome, (ii) T. congolense secretome preparation and (iii) sera of T. congolense infected mice. Subsequent mass spectrometry analysis identified the target as T. congolense glycosomal aldolase. The results show that glycosomal aldolase is a candidate biomarker for active T. congolense infections. In addition, and by proof-of-principle, the data demonstrate that the Nb strategy devised here offers a unique approach to both diagnostic development and target discovery that could be widely applied to other infectious diseases.

Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation.

PubMed

Barallobre-Barreiro, Javier; Gupta, Shashi K; Zoccarato, Anna; Kitazume-Taneike, Rika; Fava, Marika; Yin, Xiaoke; Werner, Tessa; Hirt, Marc N; Zampetaki, Anna; Viviano, Alessandro; Chong, Mei; Bern, Marshall; Kourliouros, Antonios; Domenech, Nieves; Willeit, Peter; Shah, Ajay M; Jahangiri, Marjan; Schaefer, Liliana; Fischer, Jens W; Iozzo, Renato V; Viner, Rosa; Thum, Thomas; Heineke, Joerg; Kichler, Antoine; Otsu, Kinya; Mayr, Manuel

2016-09-13

Myocardial fibrosis is a feature of many cardiac diseases. We used proteomics to profile glycoproteins in the human cardiac extracellular matrix (ECM). Atrial specimens were analyzed by mass spectrometry after extraction of ECM proteins and enrichment for glycoproteins or glycopeptides. ECM-related glycoproteins were identified in left and right atrial appendages from the same patients. Several known glycosylation sites were confirmed. In addition, putative and novel glycosylation sites were detected. On enrichment for glycoproteins, peptides of the small leucine-rich proteoglycan decorin were identified consistently in the flowthrough. Of all ECM proteins identified, decorin was found to be the most fragmented. Within its protein core, 18 different cleavage sites were identified. In contrast, less cleavage was observed for biglycan, the most closely related proteoglycan. Decorin processing differed between human ventricles and atria and was altered in disease. The C-terminus of decorin, important for the interaction with connective tissue growth factor, was detected predominantly in ventricles in comparison with atria. In contrast, atrial appendages from patients in persistent atrial fibrillation had greater levels of full-length decorin but also harbored a cleavage site that was not found in atrial appendages from patients in sinus rhythm. This cleavage site preceded the N-terminal domain of decorin that controls muscle growth by altering the binding capacity for myostatin. Myostatin expression was decreased in atrial appendages of patients with persistent atrial fibrillation and hearts of decorin null mice. A synthetic peptide corresponding to this decorin region dose-dependently inhibited the response to myostatin in cardiomyocytes and in perfused mouse hearts. This proteomics study is the first to analyze the human cardiac ECM. Novel processed forms of decorin protein core, uncovered in human atrial appendages, can regulate the local bioavailability of antihypertrophic and profibrotic growth factors. © 2016 American Heart Association, Inc.

Chemical data for bottom sediment in Mountain Creek Lake, Dallas, Texas, 1999-2000

USGS Publications Warehouse

Wilson, Jennifer T.

2002-01-01

Mountain Creek Lake is a reservoir adjacent to the Naval Weapons Industrial Reserve Plant and the former Naval Air Station in Dallas, Texas. The U.S. Geological Survey began studies of water, sediment, and biota in the reservoir in 1994 after a Resource Conservation and Recovery Act Facility Investigation detected concentrations of organic chemicals on both facilities. Additional reservoir bottom sediment samples were collected during December 1999–January 2000 at the request of the Southern Division Naval Facilities Engineering Command to further define the occurrence and distribution of selected constituents and to supplement available data. The U.S. Geological Survey National Water Quality Laboratory analyzed bottom-sediment samples from 16 box cores and 5 gravity cores for major and trace elements, organochlorine pesticides, polychlorinated biphenyls, polycyclic aromatic hydrocarbons, grain size, and cesium-137.

20 CFR 672.110 - What definitions apply to this part?

Code of Federal Regulations, 2014 CFR

2014-04-01

... limited to, construction skills that may be required by green building and weatherization industries but... a YouthBuild program. Community or other public facility. The term “community or other public... publicly owned and publicly used for the benefit of the community. Core construction. The term “core...

20 CFR 672.110 - What definitions apply to this part?

Code of Federal Regulations, 2012 CFR

2012-04-01

... limited to, construction skills that may be required by green building and weatherization industries but... a YouthBuild program. Community or other public facility. The term “community or other public... publicly owned and publicly used for the benefit of the community. Core construction. The term “core...

20 CFR 672.110 - What definitions apply to this part?

Code of Federal Regulations, 2013 CFR

2013-04-01

... limited to, construction skills that may be required by green building and weatherization industries but... a YouthBuild program. Community or other public facility. The term “community or other public... publicly owned and publicly used for the benefit of the community. Core construction. The term “core...

Humidity effects on soluble core mechanical and thermal properties (polyvinyl alcohol/microballoon composite) type CG extendospheres, volume 2

NASA Technical Reports Server (NTRS)

1993-01-01

This document constitutes the final report for the study of humidity effects and loading rate on soluble core (PVA/MB composite material) mechanical and thermal properties under Contract No. 100345. This report describes test results procedures employed, and any unusual occurrences or specific observations associated with this test program. The primary objective of this work was to determine if cured soluble core filler material regains its tensile and compressive strength after exposure to high humidity conditions and following a drying cycle. Secondary objectives include measurements of tensile and compressive modulus, and Poisson's ratio, and coefficient of thermal expansion (CTE) for various moisture exposure states. A third objective was to compare the mechanical and thermal properties of the composite using 'SG' and 'CG' type extendospheres. The proposed facility for the manufacture of soluble cores at the Yellow Creek site incorporates no capability for the control of humidity. Recent physical property tests performed with the soluble core filler material showed that prolonged exposure to high humidity significantly degradates in strength. The purpose of these tests is to determine if the product, process or facility designs require modification to avoid imparting a high risk condition to the ASRM.

Facile green in situ synthesis of Mg/CuO core/shell nanoenergetic arrays with a superior heat-release property and long-term storage stability.

PubMed

Zhou, Xiang; Xu, Daguo; Zhang, Qiaobao; Lu, Jian; Zhang, Kaili

2013-08-14

We report a facile green method for the in situ synthesis of Mg/CuO core/shell nanoenergetic arrays on silicon, with Mg nanorods as the core and CuO as the shell. Mg nanorods are first prepared by glancing angle deposition. CuO is then deposited around the Mg nanorods by reactive magnetron sputtering to realize the core/shell structure. Various characterization techniques are used to investigate the prepared Mg/CuO core/shell nanoenergetic arrays, including scanning electron microscopy, transmission electron microscopy, X-ray energy dispersive spectroscopy, X-ray diffraction, and thermal analysis. Uniform mixing and intimate contact between the Mg nanorods and CuO are confirmed from both visual inspection of the morphological images and analyses of the heat-release curves. The nanoenergetic arrays exhibit a low-onset reaction temperature (∼300 °C) and high heat of reaction (∼3400 J/g). Most importantly, the nanoenergetic arrays possess long-term storage stability resulting from the stable CuO shell. This study provides a potential general strategy for the synthesis of various Mg nanorod-based stable nanoenergetic arrays.

PACAP38 Differentially Effects Genes and CRMP2 Protein Expression in Ischemic Core and Penumbra Regions of Permanent Middle Cerebral Artery Occlusion Model Mice Brain

PubMed Central

Hori, Motohide; Nakamachi, Tomoya; Shibato, Junko; Rakwal, Randeep; Tsuchida, Masachi; Shioda, Seiji; Numazawa, Satoshi

2014-01-01

Pituitary adenylate-cyclase activating polypeptide (PACAP) has neuroprotective and axonal guidance functions, but the mechanisms behind such actions remain unclear. Previously we examined effects of PACAP (PACAP38, 1 pmol) injection intracerebroventrically in a mouse model of permanent middle cerebral artery occlusion (PMCAO) along with control saline (0.9% NaCl) injection. Transcriptomic and proteomic approaches using ischemic (ipsilateral) brain hemisphere revealed differentially regulated genes and proteins by PACAP38 at 6 and 24 h post-treatment. However, as the ischemic hemisphere consisted of infarct core, penumbra, and non-ischemic regions, specificity of expression and localization of these identified molecular factors remained incomplete. This led us to devise a new experimental strategy wherein, ischemic core and penumbra were carefully sampled and compared to the corresponding contralateral (healthy) core and penumbra regions at 6 and 24 h post PACAP38 or saline injections. Both reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting were used to examine targeted gene expressions and the collapsin response mediator protein 2 (CRMP2) protein profiles, respectively. Clear differences in expression of genes and CRMP2 protein abundance and degradation product/short isoform was observed between ischemic core and penumbra and also compared to the contralateral healthy tissues after PACAP38 or saline treatment. Results indicate the importance of region-specific analyses to further identify, localize and functionally analyse target molecular factors for clarifying the neuroprotective function of PACAP38. PMID:25257527

10 CFR 140.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... atomic weapon, designed or used to sustain nuclear fission in a self-supporting chain reaction. (g... experiments; or (ii) A liquid fuel loading; or (iii) An experimental facility in the core in excess of 16... in the isotope 235, except laboratory scale facilities designed or used for experimental or...

10 CFR 140.3 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... in the isotope 235, except laboratory scale facilities designed or used for experimental or... atomic weapon, designed or used to sustain nuclear fission in a self-supporting chain reaction. (g... experiments; or (ii) A liquid fuel loading; or (iii) An experimental facility in the core in excess of 16...

10 CFR 140.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... in the isotope 235, except laboratory scale facilities designed or used for experimental or... atomic weapon, designed or used to sustain nuclear fission in a self-supporting chain reaction. (g... experiments; or (ii) A liquid fuel loading; or (iii) An experimental facility in the core in excess of 16...

Removal of the Plutonium Recycle Test Reactor - 13031

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herzog, C. Brad; Guercia, Rudolph; LaCome, Matt

2013-07-01

The 309 Facility housed the Plutonium Recycle Test Reactor (PRTR), an operating test reactor in the 300 Area at Hanford, Washington. The reactor first went critical in 1960 and was originally used for experiments under the Hanford Site Plutonium Fuels Utilization Program. The facility was decontaminated and decommissioned in 1988-1989, and the facility was deactivated in 1994. The 309 facility was added to Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) response actions as established in an Interim Record of Decision (IROD) and Action Memorandum (AM). The IROD directs a remedial action for the 309 facility, associated waste sites, associatedmore » underground piping and contaminated soils resulting from past unplanned releases. The AM directs a removal action through physical demolition of the facility, including removal of the reactor. Both CERCLA actions are implemented in accordance with U.S. EPA approved Remedial Action Work Plan, and the Remedial Design Report / Remedial Action Report associated with the Hanford 300-FF-2 Operable Unit. The selected method for remedy was to conventionally demolish above grade structures including the easily distinguished containment vessel dome, remove the PRTR and a minimum of 300 mm (12 in) of shielding as a single 560 Ton unit, and conventionally demolish the below grade structure. Initial sample core drilling in the Bio-Shield for radiological surveys showed evidence that the Bio-Shield was of sound structure. Core drills for the separation process of the PRTR from the 309 structure began at the deck level and revealed substantial thermal degradation of at least the top 1.2 m (4LF) of Bio-Shield structure. The degraded structure combined with the original materials used in the Bio-Shield would not allow for a stable structure to be extracted. The water used in the core drilling process proved to erode the sand mixture of the Bio-Shield leaving the steel aggregate to act as ball bearings against the core drill bit. A redesign is being completed to extract the 309 PRTR and entire Bio-Shield structure together as one monolith weighing 1100 Ton by cutting structural concrete supports. In addition, the PRTR has hundreds of contaminated process tubes and pipes that have to be severed to allow for a uniformly flush fit with a lower lifting frame. Thirty-two 50 mm (2 in) core drills must be connected with thirty-two wire saw cuts to allow for lifting columns to be inserted. Then eight primary saw cuts must be completed to severe the PRTR from the 309 Facility. Once the weight of the PRTR is transferred to the lifting frame, then the PRTR may be lifted out of the facility. The critical lift will be executed using four 450 Ton strand jacks mounted on a 9 m (30 LF) tall mobile lifting frame that will allow the PRTR to be transported by eight 600 mm (24 in) Slide Shoes. The PRTR will then be placed on a twenty-four line, double wide, self powered Goldhofer for transfer to the onsite CERCLA Disposal Cell (ERDF Facility), approximately 33 km (20 miles) away. (authors)« less

TRAC-PD2 posttest analysis of CCTF Test C1-16 (Run 025). [Cylindrical Core Test Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugimoto, J.

The TRAC-PD2 code version was used to analyze CCTF Test C1-16 (Run 025). The results indicate that the core heater rod temperatures, the liquid mass in the vessel, and differential pressures in the primary loop are predicted well, but the void fraction distribution in the core and water accumulation in the upper plenum are not in good agreement with the data.

Using Firn Air for Facility Cooling at the WAIS Divide Site

DTIC Science & Technology

2014-09-17

reduce logistics costs at remote field camps where it is critical to maintain proper temperatures to preserve sensitive deep ice cores. We assessed the...feasibility of using firn air for cooling at the West Antarc- tic Ice Sheet (WAIS) Divide ice core drilling site as a means to adequately and...efficiently refrigerate ice cores during storage and processing. We used estimates of mean annual temperature, temperature variations, and firn

CT Scanning and Geophysical Measurements of the Marcellus Formation from the Tippens 6HS Well

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crandall, Dustin; Paronish, Thomas; Brown, Sarah

The computed tomography (CT) facilities and the Multi-Sensor Core Logger (MSCL) at the National Energy Technology Laboratory (NETL) Morgantown, West Virginia site were used to characterize core of the Marcellus Shale from a vertical well drilled in Eastern Ohio. The core is from the Tippens 6HS Well in Monroe County, Ohio and is comprised primarily of the Marcellus Shale from depths of 5550 to 5663 ft.

Extensible byssus of Pinctada fucata: Ca2+-stabilized nanocavities and a thrombospondin-1 protein

NASA Astrophysics Data System (ADS)

Liu, Chuang; Li, Shiguo; Huang, Jingliang; Liu, Yangjia; Jia, Ganchu; Xie, Liping; Zhang, Rongqing

2015-10-01

The extensible byssus is produced by the foot of bivalve animals, including the pearl oyster Pinctada fucata, and enables them to attach to hard underwater surfaces. However, the mechanism of their extensibility is not well understood. To understand this mechanism, we analyzed the ultrastructure, composition and mechanical properties of the P. fucata byssus using electron microscopy, elemental analysis, proteomics and mechanical testing. In contrast to the microstructures of Mytilus sp. byssus, the P. fucata byssus has an exterior cuticle without granules and an inner core with nanocavities. The removal of Ca2+ by ethylenediaminetetraacetic acid (EDTA) treatment expands the nanocavities and reduces the extensibility of the byssus, which is accompanied by a decrease in the β-sheet conformation of byssal proteins. Through proteomic methods, several proteins with antioxidant and anti-corrosive properties were identified as the main components of the distal byssus regions. Specifically, a protein containing thrombospondin-1 (TSP-1), which is highly expressed in the foot, is hypothesized to be responsible for byssus extensibility. Together, our findings demonstrate the importance of inorganic ions and multiple proteins for bivalve byssus extension, which could guide the future design of biomaterials for use in seawater.

High-throughput proteomics : optical approaches.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davidson, George S.

2008-09-01

Realistic cell models could greatly accelerate our ability to engineer biochemical pathways and the production of valuable organic products, which would be of great use in the development of biofuels, pharmaceuticals, and the crops for the next green revolution. However, this level of engineering will require a great deal more knowledge about the mechanisms of life than is currently available. In particular, we need to understand the interactome (which proteins interact) as it is situated in the three dimensional geometry of the cell (i.e., a situated interactome), and the regulation/dynamics of these interactions. Methods for optical proteomics have become availablemore » that allow the monitoring and even disruption/control of interacting proteins in living cells. Here, a range of these methods is reviewed with respect to their role in elucidating the interactome and the relevant spatial localizations. Development of these technologies and their integration into the core competencies of research organizations can position whole institutions and teams of researchers to lead in both the fundamental science and the engineering applications of cellular biology. That leadership could be particularly important with respect to problems of national urgency centered around security, biofuels, and healthcare.« less

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.

PubMed

Mauvoisin, Daniel; Wang, Jingkui; Jouffe, Céline; Martin, Eva; Atger, Florian; Waridel, Patrice; Quadroni, Manfredo; Gachon, Frédéric; Naef, Felix

2014-01-07

Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known about the accumulation patterns of proteins. Here, we quantified temporal profiles in the murine hepatic proteome under physiological light-dark conditions using stable isotope labeling by amino acids quantitative MS. Our analysis identified over 5,000 proteins, of which several hundred showed robust diurnal oscillations with peak phases enriched in the morning and during the night and related to core hepatic physiological functions. Combined mathematical modeling of temporal protein and mRNA profiles indicated that proteins accumulate with reduced amplitudes and significant delays, consistent with protein half-life data. Moreover, a group comprising about one-half of the rhythmic proteins showed no corresponding rhythmic mRNAs, indicating significant translational or posttranslational diurnal control. Such rhythms were highly enriched in secreted proteins accumulating tightly during the night. Also, these rhythms persisted in clock-deficient animals subjected to rhythmic feeding, suggesting that food-related entrainment signals influence rhythms in circulating plasma factors.

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

PubMed Central

Mauvoisin, Daniel; Wang, Jingkui; Jouffe, Céline; Martin, Eva; Atger, Florian; Waridel, Patrice; Quadroni, Manfredo; Gachon, Frédéric; Naef, Felix

2014-01-01

Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known about the accumulation patterns of proteins. Here, we quantified temporal profiles in the murine hepatic proteome under physiological light–dark conditions using stable isotope labeling by amino acids quantitative MS. Our analysis identified over 5,000 proteins, of which several hundred showed robust diurnal oscillations with peak phases enriched in the morning and during the night and related to core hepatic physiological functions. Combined mathematical modeling of temporal protein and mRNA profiles indicated that proteins accumulate with reduced amplitudes and significant delays, consistent with protein half-life data. Moreover, a group comprising about one-half of the rhythmic proteins showed no corresponding rhythmic mRNAs, indicating significant translational or posttranslational diurnal control. Such rhythms were highly enriched in secreted proteins accumulating tightly during the night. Also, these rhythms persisted in clock-deficient animals subjected to rhythmic feeding, suggesting that food-related entrainment signals influence rhythms in circulating plasma factors. PMID:24344304

Extensible byssus of Pinctada fucata: Ca2+-stabilized nanocavities and a thrombospondin-1 protein

PubMed Central

Liu, Chuang; Li, Shiguo; Huang, Jingliang; Liu, Yangjia; Jia, Ganchu; Xie, Liping; Zhang, Rongqing

2015-01-01

The extensible byssus is produced by the foot of bivalve animals, including the pearl oyster Pinctada fucata, and enables them to attach to hard underwater surfaces. However, the mechanism of their extensibility is not well understood. To understand this mechanism, we analyzed the ultrastructure, composition and mechanical properties of the P. fucata byssus using electron microscopy, elemental analysis, proteomics and mechanical testing. In contrast to the microstructures of Mytilus sp. byssus, the P. fucata byssus has an exterior cuticle without granules and an inner core with nanocavities. The removal of Ca2+ by ethylenediaminetetraacetic acid (EDTA) treatment expands the nanocavities and reduces the extensibility of the byssus, which is accompanied by a decrease in the β-sheet conformation of byssal proteins. Through proteomic methods, several proteins with antioxidant and anti-corrosive properties were identified as the main components of the distal byssus regions. Specifically, a protein containing thrombospondin-1 (TSP-1), which is highly expressed in the foot, is hypothesized to be responsible for byssus extensibility. Together, our findings demonstrate the importance of inorganic ions and multiple proteins for bivalve byssus extension, which could guide the future design of biomaterials for use in seawater. PMID:26446436

Reengineering of waste management at the Oak Ridge National Laboratory. Volume 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Myrick, T.E.

1997-08-01

A reengineering evaluation of the waste management program at the Oak Ridge National Laboratory (ORNL) was conducted during the months of February through July 1997. The goal of the reengineering was to identify ways in which the waste management process could be streamlined and improved to reduce costs while maintaining full compliance and customer satisfaction. A Core Team conducted preliminary evaluations and determined that eight particular aspects of the ORNL waste management program warranted focused investigations during the reengineering. The eight areas included Pollution Prevention, Waste Characterization, Waste Certification/Verification, Hazardous/Mixed Waste Stream, Generator/WM Teaming, Reporting/Records, Disposal End Points, and On-Sitemore » Treatment/Storage. The Core Team commissioned and assembled Process Teams to conduct in-depth evaluations of each of these eight areas. The Core Team then evaluated the Process Team results and consolidated the 80 process-specific recommendations into 15 overall recommendations. Benchmarking of a commercial nuclear facility, a commercial research facility, and a DOE research facility was conducted to both validate the efficacy of these findings and seek additional ideas for improvement. The outcome of this evaluation is represented by the 15 final recommendations that are described in this report.« less

Space Station Furnace Facility Core. Requirements definition and conceptual design study. Volume 2: Technical report. Appendix 6: Technical summary reports

NASA Technical Reports Server (NTRS)

1992-01-01

The Space Station Furnace Facility (SSFF) is a modular facility for materials research in the microgravity environment of the Space Station Freedom (SSF). The SSFF is designed for crystal growth and solidification research in the fields of electronic and photonic materials, metals and alloys, and glasses and ceramics and will allow for experimental determination of the role of gravitational forces in the solidification process. The facility will provide a capability for basic scientific research and will evaluate the commercial viability of low-gravity processing of selected technologically important materials. The facility is designed to support a complement of furnace modules as outlined in the Science Capabilities Requirements Document (SCRD). The SSFF is a three rack facility that provides the functions, interfaces, and equipment necessary for the processing of the furnaces and consists of two main parts: the SSFF Core Rack and the two Experiment Racks. The facility is designed to accommodate two experimenter-provided furnace modules housed within the two experiment racks, and is designed to operate these two furnace modules simultaneously. The SCRD specifies a wide range of furnace requirements and serves as the basis for the SSFF conceptual design. SSFF will support automated processing during the man-tended operations and is also designed for crew interface during the permanently manned configuration. The facility is modular in design and facilitates changes as required, so the SSFF is adept to modifications, maintenance, reconfiguration, and technology evolution.

Crew Member Interface with Space Station Furnace Facility

NASA Technical Reports Server (NTRS)

Cash, Martha B.

1997-01-01

The Space Station Furnace Facility (SSFF) is a facility located in the International Space Station United States Laboratory (ISS US Lab) for materials research in the microgravity environment. The SSFF will accommodate basic research, commercial applications, and studies of phenomena of metals and alloys, electronic and photonic materials, and glasses and ceramics. To support this broad base of research requirements, the SSFF will operate, regulate, and support a variety of Experiment Modules (EMs). To meet station requirements concerning the microgravity level needed for experiments, station is providing an active vibration isolation system, and SSFF provides the interface. SSFF physically consists of a Core Rack and two instrument racks (IRs) that occupy three adjacent ISS US Lab rack locations within the International Space Station (ISS). All SSFF racks are modified International Standard Payload Racks (ISPR). SSFF racks will have a 50% larger pass through area on the lower sides than ISPRs to accommodate the many rack to rack interconnections. The Instrument Racks are further modified with lowered floors and an additional removable panel (15" x 22") on top of the rack for access if needed. The Core Rack shall contain all centralized Core subsystems and ISS subsystem equipment. The two Instrument Racks shall contain the distributed Core subsystem equipment, ISS subsystem equipment, and the EMs. The Core System, which includes the Core Rack, the IR structures, and subsystem components located in the IRs serves as the central control and management for the IRs and the EMs. The Core System receives the resources provided by the International Space Station (ISS) and modifies, allocates, and distributes these resources to meet the operational requirements of the furnace. The Core System is able to support a total of four EMs and can control, support, and activate/deactivate the operations of two EMs, simultaneously. The IRs can be configured to house two small EMs or one tall vertical EM, and serve as the interface between the Core and the respective EM. The Core Rack and an adjacent Instrument Rack (containing one or more furnaces) will be delivered to the ISS in one launch. This is Integrated Configuration One (ICI). The Core Rack and IRI will be passive during transport in the Mini Pressurized Logistics Module (MPLM): Any subsequent EMs to operate within IRI are installed on-orbit. The second IR (containing one or more furnaces) is delivered to ISS on a subsequent launch which will establish Integrated Configuration Two (IC2). Additional integrated configurations will be established with the replacement of EMs or Instrument Racks.

Interface engineered ferrite@ferroelectric core-shell nanostructures: A facile approach to impart superior magneto-electric coupling

NASA Astrophysics Data System (ADS)

Abraham, Ann Rose; Raneesh, B.; Das, Dipankar; Oluwafemi, Oluwatobi Samuel; Thomas, Sabu; Kalarikkal, Nandakumar

2018-04-01

The electric field control of magnetism in multiferroics is attractive for the realization of ultra-fast and miniaturized low power device applications like nonvolatile memories. Room temperature hybrid multiferroic heterostructures with core-shell (0-0) architecture (ferrite core and ferroelectric shell) were developed via a two-step method. High-Resolution Transmission Electron Microscopy (HRTEM) images confirm the core-shell structure. The temperature dependant magnetization measurements and Mossbauer spectra reveal superparamagnetic nature of the core-shell sample. The ferroelectric hysteresis loops reveal leaky nature of the samples. The results indicate the promising applications of the samples for magneto-electric memories and spintronics.

One-pot facile synthesis of reusable tremella-like M1@M2@M1(OH)2 (M1 = Co, Ni, M2 = Pt/Pd, Pt, Pd and Au) three layers core-shell nanostructures as highly efficient catalysts

NASA Astrophysics Data System (ADS)

Liu, Yadong; Fang, Zhen; Kuai, Long; Geng, Baoyou

2014-07-01

In this work, a general, facile, successive and eco-friendly method for multilayer nanostructures has been established for the first time. We take full advantage of the structural and compositional character of M1@M2 (M1 = Co, Ni, M2 = Pt/Pd, Pt, Pd and Au) core-shell nanostructures to prepare a series of reusable tremella-like M1@M2@M1(OH)2 three layer core-shell or yolk-shell nanocomposites with a magnetic core, a porous noble metal shell, and an ultrathin cobalt or nickel hydroxide shell. We evaluated their catalytic performance using a model reaction based on the reduction of 4-nitrophenol. These novel M1@M2@M1(OH)2 nanomaterials with a unique internal micro environment promoted the efficiency of the catalytic reaction, prolonged the service life of the catalyst and enhanced the overall activity of the catalyst in the catalytic process. The novel three layer core-shell nanocomposites can be extended to other applications such as biomedical detection, energy conversion and storage systems.In this work, a general, facile, successive and eco-friendly method for multilayer nanostructures has been established for the first time. We take full advantage of the structural and compositional character of M1@M2 (M1 = Co, Ni, M2 = Pt/Pd, Pt, Pd and Au) core-shell nanostructures to prepare a series of reusable tremella-like M1@M2@M1(OH)2 three layer core-shell or yolk-shell nanocomposites with a magnetic core, a porous noble metal shell, and an ultrathin cobalt or nickel hydroxide shell. We evaluated their catalytic performance using a model reaction based on the reduction of 4-nitrophenol. These novel M1@M2@M1(OH)2 nanomaterials with a unique internal micro environment promoted the efficiency of the catalytic reaction, prolonged the service life of the catalyst and enhanced the overall activity of the catalyst in the catalytic process. The novel three layer core-shell nanocomposites can be extended to other applications such as biomedical detection, energy conversion and storage systems. Electronic supplementary information (ESI) available: Fig. S1-S6. See DOI: 10.1039/c4nr01470g

Tory II-A: a nuclear ramjet test reactor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadley, J.W.

Declassified 28 Nov 1973. The first test reactor in the Pluto program, leading to development of a nuclear ramjet engine, is called Tory II-A. While it is not an actual prototype engine, this reactor embodies a core design which is considered feasible for an engine, and operation of the reactor will provide a test of that core type as well as more generalized values in reactor design and testing. The design of Tory II-A and construction of the reactor and of its test facility are described. Operation of the Tory II-A core at a total power of 160 megawatts, withmore » 800 pounds of air per second passing through the core and emerging at a temperature of 2000 deg F, is the central objective of the test program. All other reactor and facility components exist to support operation of the core, and preliminary steps in the test program itself will be directed primarily toward ensuring attalnment of full-power operation and collection of meaningful data on core behavior during that operation. The core, 3 feet in diameter and 41/2 feet long, will be composed of bundled ceramic tubes whose central holes will provide continuous air passages from end to end of the reactor. These tubes are to be composed of a homogeneous mixture of UO/sub 2/ fuel and BeO moderator, compacted and sintered to achieve high strength and density. (30 references) (auth)« less

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.

PubMed

Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

2010-08-10

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)-cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK-cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants.

Approaches to N-Methylwelwitindolinone C Isothiocyanate: Facile Synthesis of the Tetracyclic Core

PubMed Central

Heidebrecht, Richard W.; Gulledge, Brian; Martin, Stephen F.

2010-01-01

The synthesis of a functionalized, tetracyclic core of N-methylwelwitindolinone C isothiocyanate is reported. The approach features a convergent coupling between an indole iminium ion and a highly functionalized vinylogous silyl ketene acetal followed by an intramolecular palladium-catalyzed cyclization that proceeds via an enolate arylation. PMID:20446675

Facile consecutive solvothermal growth of highly fluorescent InP/ZnS core/shell quantum dots using a safer phosphorus source.

PubMed

Byun, Ho-June; Song, Woo-Seuk; Yang, Heesun

2011-06-10

The work presents a facile, stepwise synthetic approach for the production of highly fluorescent InP/ZnS core/shell quantum dots (QDs) by using a safer phosphorus (P) precursor. First, InP quantum dots (QDs) were solvothermally prepared at 180 °C for 24 h by using a P source of P(N(CH(3))(2))(3). The as-grown InP QDs were consecutively placed in another solvothermal condition for ZnS shell overcoating. In contrast to the almost non-fluorescent InP QDs, due to their highly defective surface states, the ZnS-coated InP QDs were highly fluorescent as a result of effective surface passivation. After the shell growth, the resulting InP/ZnS core/shell QDs were subjected to a size-sorting processing, by which red- to green-emitting QDs with quantum yields (QYs) of 24-60% were produced. Solvothermal shell growth parameters such as the reaction time and Zn/In solution concentration ratio were varied and optimized toward the highest QYs of core/shell QDs.

Facile consecutive solvothermal growth of highly fluorescent InP/ZnS core/shell quantum dots using a safer phosphorus source

NASA Astrophysics Data System (ADS)

Byun, Ho-June; Song, Woo-Seuk; Yang, Heesun

2011-06-01

The work presents a facile, stepwise synthetic approach for the production of highly fluorescent InP/ZnS core/shell quantum dots (QDs) by using a safer phosphorus (P) precursor. First, InP quantum dots (QDs) were solvothermally prepared at 180 °C for 24 h by using a P source of P(N(CH3)2)3. The as-grown InP QDs were consecutively placed in another solvothermal condition for ZnS shell overcoating. In contrast to the almost non-fluorescent InP QDs, due to their highly defective surface states, the ZnS-coated InP QDs were highly fluorescent as a result of effective surface passivation. After the shell growth, the resulting InP/ZnS core/shell QDs were subjected to a size-sorting processing, by which red- to green-emitting QDs with quantum yields (QYs) of 24-60% were produced. Solvothermal shell growth parameters such as the reaction time and Zn/In solution concentration ratio were varied and optimized toward the highest QYs of core/shell QDs.

genenames.org: the HGNC resources in 2011

PubMed Central

Seal, Ruth L.; Gordon, Susan M.; Lush, Michael J.; Wright, Mathew W.; Bruford, Elspeth A.

2011-01-01

The HUGO Gene Nomenclature Committee (HGNC) aims to assign a unique gene symbol and name to every human gene. The HGNC database currently contains almost 30 000 approved gene symbols, over 19 000 of which represent protein-coding genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC editors and links to related genomic, phenotypic and proteomic information. Here we describe improvements to our resources, including a new Quick Gene Search, a new List Search, an integrated HGNC BioMart and a new Statistics and Downloads facility. PMID:20929869

Evaluation of a Systems Analysis and Improvement Approach to Optimize Prevention of Mother-To-Child Transmission of HIV Using the Consolidated Framework for Implementation Research.

PubMed

Gimbel, Sarah; Rustagi, Alison S; Robinson, Julia; Kouyate, Seydou; Coutinho, Joana; Nduati, Ruth; Pfeiffer, James; Gloyd, Stephen; Sherr, Kenneth; Granato, S Adam; Kone, Ahoua; Cruz, Emilia; Manuel, Joao Luis; Zucule, Justina; Napua, Manuel; Mbatia, Grace; Wariua, Grace; Maina, Martin

2016-08-01

Despite large investments to prevent mother-to-child-transmission (PMTCT), pediatric HIV elimination goals are not on track in many countries. The Systems Analysis and Improvement Approach (SAIA) study was a cluster randomized trial to test whether a package of systems engineering tools could strengthen PMTCT programs. We sought to (1) define core and adaptable components of the SAIA intervention, and (2) explain the heterogeneity in SAIA's success between facilities. The Consolidated Framework for Implementation Research (CFIR) guided all data collection efforts. CFIR constructs were assessed in focus group discussions and interviews with study and facility staff in 6 health facilities (1 high-performing and 1 low-performing site per country, identified by study staff) in December 2014 at the end of the intervention period. SAIA staff identified the intervention's core and adaptable components at an end-of-study meeting in August 2015. Two independent analysts used CFIR constructs to code transcripts before reaching consensus. Flow mapping and continuous quality improvement were the core to the SAIA in all settings, whereas the PMTCT cascade analysis tool was the core in high HIV prevalence settings. Five CFIR constructs distinguished strongly between high and low performers: 2 in inner setting (networks and communication, available resources) and 3 in process (external change agents, executing, reflecting and evaluating). The CFIR is a valuable tool to categorize elements of an intervention as core versus adaptable, and to understand heterogeneity in study implementation. Future intervention studies should apply evidence-based implementation science frameworks, like the CFIR, to provide salient data to expand implementation to other settings.

Evaluation of a Systems Analysis and Improvement Approach to Optimize Prevention of Mother-To-Child Transmission of HIV Using the Consolidated Framework for Implementation Research

PubMed Central

Rustagi, Alison S.; Robinson, Julia; Kouyate, Seydou; Coutinho, Joana; Nduati, Ruth; Pfeiffer, James; Gloyd, Stephen; Sherr, Kenneth; Granato, S. Adam; Kone, Ahoua; Cruz, Emilia; Manuel, Joao Luis; Zucule, Justina; Napua, Manuel; Mbatia, Grace; Wariua, Grace; Maina, Martin

2016-01-01

Background: Despite large investments to prevent mother-to-child-transmission (PMTCT), pediatric HIV elimination goals are not on track in many countries. The Systems Analysis and Improvement Approach (SAIA) study was a cluster randomized trial to test whether a package of systems engineering tools could strengthen PMTCT programs. We sought to (1) define core and adaptable components of the SAIA intervention, and (2) explain the heterogeneity in SAIA's success between facilities. Methods: The Consolidated Framework for Implementation Research (CFIR) guided all data collection efforts. CFIR constructs were assessed in focus group discussions and interviews with study and facility staff in 6 health facilities (1 high-performing and 1 low-performing site per country, identified by study staff) in December 2014 at the end of the intervention period. SAIA staff identified the intervention's core and adaptable components at an end-of-study meeting in August 2015. Two independent analysts used CFIR constructs to code transcripts before reaching consensus. Results: Flow mapping and continuous quality improvement were the core to the SAIA in all settings, whereas the PMTCT cascade analysis tool was the core in high HIV prevalence settings. Five CFIR constructs distinguished strongly between high and low performers: 2 in inner setting (networks and communication, available resources) and 3 in process (external change agents, executing, reflecting and evaluating). Discussion: The CFIR is a valuable tool to categorize elements of an intervention as core versus adaptable, and to understand heterogeneity in study implementation. Future intervention studies should apply evidence-based implementation science frameworks, like the CFIR, to provide salient data to expand implementation to other settings. PMID:27355497

Top-Down Proteomics and Farm Animal and Aquatic Sciences.

PubMed

Campos, Alexandre M O; de Almeida, André M

2016-12-21

Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.

Williams working on the JAXA MS (Marangoni Surface) Experiment

NASA Image and Video Library

2009-11-05

ISS021-E-020304 (5 Nov. 2009) --- NASA astronaut Jeffrey Williams, Expedition 21 flight engineer, works with Fluid Physics Experiment Facility/Marangoni Surface (FPEF MS) Core hardware in the Kibo laboratory of the International Space Station. Williams first inserted the Marangoni Inside (MI) cassette in the MI Core for a leak check, and then installed the MI Core into the FPEF MI Body. The Marangoni convection experiment in the FPEF examines fluid tension flow in micro-G.

The Thiamin Pyrophosphate-Motif

NASA Technical Reports Server (NTRS)

Dominiak, Paulina M.; Ciszak, Ewa M.

2003-01-01

Using databases the authors have identified a common thiamin pyrophosphate (TPP)-motif in the family of functionally diverse TPP-dependent enzymes. This common motif consists of multimeric organization of subunits, two catalytic centers, common amino acid sequence, and specific contacts to provide a flip-flop, or alternate site, mechanism of action. Each catalytic center [PP:PYR] is formed at the interface of the PP-domain binding the magnesium ion, pyrophosphate and aminopyrimidine ring of TPP, and the PYR-domain binding the aminopyrimidine ring of that cofactor. A pair of these catalytic centers constitutes the catalytic core [PP:PYR]* within these enzymes. Analysis of the structural elements of this catalytic core reveals novel definition of the common amino acid sequences, which are GX@&(G)@XXGQ, and GDGX25-30 within the PP- domain, and the E&(G)@XXG@ within the PYR-domain, where Q, corresponds to a hydrophobic amino acid. This TPP-motif provides a novel tool for annotation of TPP-dependent enzymes useful in advancing functional proteomics.

SPS' Digest: the Swiss Proteomics Society selection of proteomics articles.

PubMed

Hoogland, Christine; Lion, Niels; Palagi, Patricia M; Sanchez, Jean-Charles; Tissot, Jean-Daniel

2005-08-01

Despite the consolidation of the specialized proteomics literature around a few established journals, such as Proteomics, Molecular and Cellular Proteomics, and the Journal of Proteome Research, a lot of information is still spread in many different publications from different fields, such as analytical sciences, MS, bioinformatics, etc. The purpose of SPS' Digest is to gather a selection of proteomics articles, to categorize them, and to make the list available on a periodic basis through a web page and email alerts.

17 CFR Appendix B to Part 36 - Guidance on, and Acceptable Practices in, Compliance With Core Principles

Code of Federal Regulations, 2012 CFR

2012-04-01

... spot-month positions. Spot-month limits should be adopted for significant price discovery contracts to... market or derivatives transaction execution facility should set the spot-month limit for its significant... designated contract market or derivatives transaction execution facility. In this case, the spot-month...

Preliminary risk assessment for nuclear waste disposal in space, volume 2

NASA Technical Reports Server (NTRS)

Rice, E. E.; Denning, R. S.; Friedlander, A. L.

1982-01-01

Safety guidelines are presented. Waste form, waste processing and payload fabrication facilities, shipping casks and ground transport vehicles, payload primary container/core, radiation shield, reentry systems, launch site facilities, uprooted space shuttle launch vehicle, Earth packing orbits, orbit transfer systems, and space destination are discussed. Disposed concepts and risks are then discussed.

Integration of the SSPM and STAGE with the MPACT Virtual Facility Distributed Test Bed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cipiti, Benjamin B.; Shoman, Nathan

The Material Protection Accounting and Control Technologies (MPACT) program within DOE NE is working toward a 2020 milestone to demonstrate a Virtual Facility Distributed Test Bed. The goal of the Virtual Test Bed is to link all MPACT modeling tools, technology development, and experimental work to create a Safeguards and Security by Design capability for fuel cycle facilities. The Separation and Safeguards Performance Model (SSPM) forms the core safeguards analysis tool, and the Scenario Toolkit and Generation Environment (STAGE) code forms the core physical security tool. These models are used to design and analyze safeguards and security systems and generatemore » performance metrics. Work over the past year has focused on how these models will integrate with the other capabilities in the MPACT program and specific model changes to enable more streamlined integration in the future. This report describes the model changes and plans for how the models will be used more collaboratively. The Virtual Facility is not designed to integrate all capabilities into one master code, but rather to maintain stand-alone capabilities that communicate results between codes more effectively.« less

Large-scale testing of in-vessel debris cooling through external flooding of the reactor pressure vessel in the CYBL facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chu, T.Y.; Bentz, J.H.; Bergeron, K.D.

1994-04-01

The possibility of achieving in-vessel core retention by flooding the reactor cavity, or the ``flooded cavity``, is an accident management concept currently under consideration for advanced light water reactors (ALWR), as well as for existing light water reactors (LWR). The CYBL (CYlindrical BoiLing) facility is a facility specifically designed to perform large-scale confirmatory testing of the flooded cavity concept. CYBL has a tank-within-a-tank design; the inner 3.7 m diameter tank simulates the reactor vessel, and the outer tank simulates the reactor cavity. The energy deposition on the bottom head is simulated with an array of radiant heaters. The array canmore » deliver a tailored heat flux distribution corresponding to that resulting from core melt convection. The present paper provides a detailed description of the capabilities of the facility, as well as results of recent experiments with heat flux in the range of interest to those required for in-vessel retention in typical ALWRs. The paper concludes with a discussion of other experiments for the flooded cavity applications.« less

Interior of the Plum Brook Reactor Facility

NASA Image and Video Library

1961-02-21

A view inside the 55-foot high containment vessel of the National Aeronautics and Space Administration (NASA) Plum Brook Reactor Facility in Sandusky, Ohio. The 60-megawatt test reactor went critical for the first time in 1961 and began its full-power research operations in 1963. From 1961 to 1973, this reactor performed some of the nation’s most advanced nuclear research. The reactor was designed to determine the behavior of metals and other materials after long durations of irradiation. The materials would be used to construct a nuclear-powered rocket. The reactor core, where the chain reaction occurred, sat at the bottom of the tubular pressure vessel, seen here at the center of the shielding pool. The core contained fuel rods with uranium isotopes. A cooling system was needed to reduce the heat levels during the reaction. A neutron-impervious reflector was also employed to send many of the neutrons back to the core. The Plum Brook Reactor Facility was constructed from high-density concrete and steel to prevent the excess neutrons from escaping the facility, but the water in the pool shielded most of the radiation. The water, found in three of the four quadrants served as a reflector, moderator, and coolant. In this photograph, the three 20-ton protective shrapnel shields and hatch have been removed from the top of the pressure tank revealing the reactor tank. An overhead crane could be manipulated to reach any section of this room. It was used to remove the shrapnel shields and transfer equipment.

Protein complex prediction for large protein protein interaction networks with the Core&Peel method.

PubMed

Pellegrini, Marco; Baglioni, Miriam; Geraci, Filippo

2016-11-08

Biological networks play an increasingly important role in the exploration of functional modularity and cellular organization at a systemic level. Quite often the first tools used to analyze these networks are clustering algorithms. We concentrate here on the specific task of predicting protein complexes (PC) in large protein-protein interaction networks (PPIN). Currently, many state-of-the-art algorithms work well for networks of small or moderate size. However, their performance on much larger networks, which are becoming increasingly common in modern proteome-wise studies, needs to be re-assessed. We present a new fast algorithm for clustering large sparse networks: Core&Peel, which runs essentially in time and storage O(a(G)m+n) for a network G of n nodes and m arcs, where a(G) is the arboricity of G (which is roughly proportional to the maximum average degree of any induced subgraph in G). We evaluated Core&Peel on five PPI networks of large size and one of medium size from both yeast and homo sapiens, comparing its performance against those of ten state-of-the-art methods. We demonstrate that Core&Peel consistently outperforms the ten competitors in its ability to identify known protein complexes and in the functional coherence of its predictions. Our method is remarkably robust, being quite insensible to the injection of random interactions. Core&Peel is also empirically efficient attaining the second best running time over large networks among the tested algorithms. Our algorithm Core&Peel pushes forward the state-of the-art in PPIN clustering providing an algorithmic solution with polynomial running time that attains experimentally demonstrable good output quality and speed on challenging large real networks.

CPTAC Releases Cancer Proteome Confirmatory Colon Study Data | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) announces the release of the cancer proteome confirmatory colon study data. The goal of the study is to analyze the proteomes of approximately 100 confirmatory colon tumor patients, which includes tumor and adjacent normal samples, with liquid chromatography-tandem mass spectrometry (LC-MS/MS) global proteomic and phosphoproteomic profiling.

Outreach, Diversity, and Education Supported by NSF Facilities LacCore and the Continental Scientific Drilling Coordination Office (CSDCO), University of Minnesota

NASA Astrophysics Data System (ADS)

Myrbo, A.

2015-12-01

Climatic and environmental change are a powerful hook to engage students and the public with geoscience. Recent lake sediments often feature visual and compositional evidence of anthropogenic changes, which can pique curiosity and serve as a gateway for interest in more remote past changes. Cores provide an integrative, place-based geoscience education/outreach platform: lake dynamics incorporate principles of chemistry, physics, and biology; lake basin formation and sedimentary signals trace back to numerous geoscience subdisciplines. Lakes reflect local changes, and so are inherently place-based and relevant to both rural and urban populations. The esthetics of lakes in the landscape and sediments under the microscope spark the artistic sensibilities of those who do not consider themselves scientists: lakes are readymade for STEAM education. LacCore has exploited the magic of lake sediment cores in its 15 years as an NSF Facility, and now expands to additional environments as the NSF Continental Scientific Drilling Coordination Office. Part of scaling up is the formalization of major support for the Broader Impacts (BI) activities of Facility users. LacCore/CSDCO now musters its collaborative experiences in site REUs and other undergrad research projects, in-depth training of students, teachers, and faculty, a long list of informal education experiences, and common-good software development, to provide assistance to researchers seeking meaningful broader impacts and educators seeking extra- or co-curricular field and laboratory research experiences for their students. Outreach, diversity, and education support includes dissemination of best practices, as well as coordination, administration, and basic capacity for such activities in collaboration with project PIs and students, through no-cost support, or collaborative proposals or supplements from NSF where necessary for project scale. Community-driven research and broadening participation are central to the vision. In the same way that LacCore/CSDCO nurtures drilling and coring project concepts through to fruition, it can foster the BI activities critical to project success in 21st century geoscience, where the challenges are profound, the answers are depressing, and real impacts may occur on the scale of only a few individuals.

Differential Expression of In Vivo and In Vitro Protein Profile of Outer Membrane of Acidovorax avenae Subsp. avenae

PubMed Central

Qiu, Hui; Li, Bin; Jabeen, Amara; Li, Liping; Liu, He; Kube, Michael; Xie, Guanlin; Wang, Yanli; Sun, Guochang

2012-01-01

Outer membrane (OM) proteins play a significant role in bacterial pathogenesis. In this work, we examined and compared the expression of the OM proteins of the rice pathogen Acidovorax avenae subsp. avenae strain RS-1, a Gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. Global proteomic profiling of A. avenae subsp. avenae strain RS-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenicity of the rice pathogen in host plants. The shotgun proteomics analysis of OM proteins resulted in the identification of 97 proteins in vitro and 62 proteins in vivo by mass spectrometry. Among these OM proteins, there is a high number of porins, TonB-dependent receptors, lipoproteins of the NodT family, ABC transporters, flagellins, and proteins of unknown function expressed under both conditions. However, the major proteins such as phospholipase and OmpA domain containing proteins were expressed in vitro, while the proteins such as the surface anchored protein F, ATP-dependent Clp protease, OmpA and MotB domain containing proteins were expressed in vivo. This may indicate that these in vivo OM proteins have roles in the pathogenicity of A. avenae subsp. avenae strain RS-1. In addition, the LC-MS/MS identification of OmpA and MotB validated the in silico prediction of the existance of Type VI secretion system core components. To the best of our knowledge, this is the first study to reveal the in vitro and in vivo protein profiles, in combination with LC-MS/MS mass spectra, in silico OM proteome and in silico genome wide analysis, of pathogenicity or plant host required proteins of a plant pathogenic bacterium. PMID:23166741

Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles.

PubMed

Deeb, Sally J; Tyanova, Stefka; Hummel, Michael; Schmidt-Supprian, Marc; Cox, Juergen; Mann, Matthias

2015-11-01

Characterization of tumors at the molecular level has improved our knowledge of cancer causation and progression. Proteomic analysis of their signaling pathways promises to enhance our understanding of cancer aberrations at the functional level, but this requires accurate and robust tools. Here, we develop a state of the art quantitative mass spectrometric pipeline to characterize formalin-fixed paraffin-embedded tissues of patients with closely related subtypes of diffuse large B-cell lymphoma. We combined a super-SILAC approach with label-free quantification (hybrid LFQ) to address situations where the protein is absent in the super-SILAC standard but present in the patient samples. Shotgun proteomic analysis on a quadrupole Orbitrap quantified almost 9,000 tumor proteins in 20 patients. The quantitative accuracy of our approach allowed the segregation of diffuse large B-cell lymphoma patients according to their cell of origin using both their global protein expression patterns and the 55-protein signature obtained previously from patient-derived cell lines (Deeb, S. J., D'Souza, R. C., Cox, J., Schmidt-Supprian, M., and Mann, M. (2012) Mol. Cell. Proteomics 11, 77-89). Expression levels of individual segregation-driving proteins as well as categories such as extracellular matrix proteins behaved consistently with known trends between the subtypes. We used machine learning (support vector machines) to extract candidate proteins with the highest segregating power. A panel of four proteins (PALD1, MME, TNFAIP8, and TBC1D4) is predicted to classify patients with low error rates. Highly ranked proteins from the support vector analysis revealed differential expression of core signaling molecules between the subtypes, elucidating aspects of their pathobiology. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Transcriptomic and proteomic analysis reveals wall-associated and glucan-degrading proteins with potential roles in Phytophthora infestans sexual spore development.

PubMed

Niu, Xiaofan; Ah-Fong, Audrey M V; Lopez, Lilianna A; Judelson, Howard S

2018-01-01

Sexual reproduction remains an understudied feature of oomycete biology. To expand our knowledge of this process, we used RNA-seq and quantitative proteomics to examine matings in Phytophthora infestans. Exhibiting significant changes in mRNA abundance in three matings between different A1 and A2 strains compared to nonmating controls were 1170 genes, most being mating-induced. Rising by >10-fold in at least one cross were 455 genes, and 182 in all three crosses. Most genes had elevated expression in a self-fertile strain. Many mating-induced genes were associated with cell wall biosynthesis, which may relate to forming the thick-walled sexual spore (oospore). Several gene families were induced during mating including one encoding histidine, serine, and tyrosine-rich putative wall proteins, and another encoding prolyl hydroxylases which may strengthen the extracellular matrix. The sizes of these families vary >10-fold between Phytophthora species and one exhibits concerted evolution, highlighting two features of genome dynamics within the genus. Proteomic analyses of mature oospores and nonmating hyphae using isobaric tags for quantification identified 835 shared proteins, with 5% showing >2-fold changes in abundance between the tissues. Enriched in oospores were β-glucanases potentially involved in digesting the oospore wall during germination. Despite being dormant, oospores contained a mostly normal complement of proteins required for core cellular functions. The RNA-seq data generated here and in prior studies were used to identify new housekeeping controls for gene expression studies that are more stable than existing normalization standards. We also observed >2-fold variation in the fraction of polyA+ RNA between life stages, which should be considered when quantifying transcripts and may also be relevant to understanding translational control during development.

Proteomic endorsed transcriptomic profiles of venom glands from Tityus obscurus and T. serrulatus scorpions

PubMed Central

Nishiyama, Milton Yutaka; dos Santos, Maria Beatriz Viana; Santos-da-Silva, Andria de Paula; Chalkidis, Hipócrates de Menezes; Souza-Imberg, Andreia; Candido, Denise Maria; Yamanouye, Norma; Dorce, Valquíria Abrão Coronado; Junqueira-de-Azevedo, Inácio de Loiola Meirelles

2018-01-01

Background Except for the northern region, where the Amazonian black scorpion, T. obscurus, represents the predominant and most medically relevant scorpion species, Tityus serrulatus, the Brazilian yellow scorpion, is widely distributed throughout Brazil, causing most envenoming and fatalities due to scorpion sting. In order to evaluate and compare the diversity of venom components of Tityus obscurus and T. serrulatus, we performed a transcriptomic investigation of the telsons (venom glands) corroborated by a shotgun proteomic analysis of the venom from the two species. Results The putative venom components represented 11.4% and 16.7% of the total gene expression for T. obscurus and T. serrulatus, respectively. Transcriptome and proteome data revealed high abundance of metalloproteinases sequences followed by sodium and potassium channel toxins, making the toxin core of the venom. The phylogenetic analysis of metalloproteinases from T. obscurus and T. serrulatus suggested an intraspecific gene expansion, as we previously observed for T. bahiensis, indicating that this enzyme may be under evolutionary pressure for diversification. We also identified several putative venom components such as anionic peptides, antimicrobial peptides, bradykinin-potentiating peptide, cysteine rich protein, serine proteinases, cathepsins, angiotensin-converting enzyme, endothelin-converting enzyme and chymotrypsin like protein, proteinases inhibitors, phospholipases and hyaluronidases. Conclusion The present work shows that the venom composition of these two allopatric species of Tityus are considerably similar in terms of the major classes of proteins produced and secreted, although their individual toxin sequences are considerably divergent. These differences at amino acid level may reflect in different epitopes for the same protein classes in each species, explaining the basis for the poor recognition of T. obscurus venom by the antiserum raised against other species. PMID:29561852

Discovery of Colorectal Cancer Biomarker Candidates by Membrane Proteomic Analysis and Subsequent Verification using Selected Reaction Monitoring (SRM) and Tissue Microarray (TMA) Analysis*

PubMed Central

Kume, Hideaki; Muraoka, Satoshi; Kuga, Takahisa; Adachi, Jun; Narumi, Ryohei; Watanabe, Shio; Kuwano, Masayoshi; Kodera, Yoshio; Matsushita, Kazuyuki; Fukuoka, Junya; Masuda, Takeshi; Ishihama, Yasushi; Matsubara, Hisahiro; Nomura, Fumio; Tomonaga, Takeshi

2014-01-01

Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851. PMID:24687888

Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis.

PubMed

Kume, Hideaki; Muraoka, Satoshi; Kuga, Takahisa; Adachi, Jun; Narumi, Ryohei; Watanabe, Shio; Kuwano, Masayoshi; Kodera, Yoshio; Matsushita, Kazuyuki; Fukuoka, Junya; Masuda, Takeshi; Ishihama, Yasushi; Matsubara, Hisahiro; Nomura, Fumio; Tomonaga, Takeshi

2014-06-01

Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Functional proteomic analysis reveals the involvement of KIAA1199 in breast cancer growth, motility and invasiveness

PubMed Central

2014-01-01

Background KIAA1199 is a recently identified novel gene that is up-regulated in human cancer with poor survival. Our proteomic study on signaling polarity in chemotactic cells revealed KIAA1199 as a novel protein target that may be involved in cellular chemotaxis and motility. In the present study, we examined the functional significance of KIAA1199 expression in breast cancer growth, motility and invasiveness. Methods We validated the previous microarray observation by tissue microarray immunohistochemistry using a TMA slide containing 12 breast tumor tissue cores and 12 corresponding normal tissues. We performed the shRNA-mediated knockdown of KIAA1199 in MDA-MB-231 and HS578T cells to study the role of this protein in cell proliferation, migration and apoptosis in vitro. We studied the effects of KIAA1199 knockdown in vivo in two groups of mice (n = 5). We carried out the SILAC LC-MS/MS based proteomic studies on the involvement of KIAA1199 in breast cancer. Results KIAA1199 mRNA and protein was significantly overexpressed in breast tumor specimens and cell lines as compared with non-neoplastic breast tissues from large-scale microarray and studies of breast cancer cell lines and tumors. To gain deeper insights into the novel role of KIAA1199 in breast cancer, we modulated KIAA1199 expression using shRNA-mediated knockdown in two breast cancer cell lines (MDA-MB-231 and HS578T), expressing higher levels of KIAA1199. The KIAA1199 knockdown cells showed reduced motility and cell proliferation in vitro. Moreover, when the knockdown cells were injected into the mammary fat pads of female athymic nude mice, there was a significant decrease in tumor incidence and growth. In addition, quantitative proteomic analysis revealed that knockdown of KIAA1199 in breast cancer (MDA-MB-231) cells affected a broad range of cellular functions including apoptosis, metabolism and cell motility. Conclusions Our findings indicate that KIAA1199 may play an important role in breast tumor growth and invasiveness, and that it may represent a novel target for biomarker development and a novel therapeutic target for breast cancer. PMID:24628760

[Progress in stable isotope labeled quantitative proteomics methods].

PubMed

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

Detection of Zn2+ release in nitric oxide treated cells and proteome: dependence on fluorescent sensor and proteomic sulfhydryl groups.

PubMed

Karim, Mohammad R; Petering, David H

2017-04-19

Nitric oxide (NO) is both an important regulatory molecule in biological systems and a toxic xenobiotic. Its oxidation products react with sulfhydryl groups and either nitrosylate or oxidize them. The aerobic reaction of NO supplied by diethylamine NONOate (DEA-NO) with pig kidney LLC-PK 1 cells and Zn-proteins within the isolated proteome was examined with three fluorescent zinc sensors, zinquin (ZQ), TSQ, and FluoZin-3 (FZ-3). Observations of Zn 2+ labilization from Zn-proteins depended on the specific sensor used. Upon cellular exposure to DEA-NO, ZQ sequestered about 13% of the proteomic Zn 2+ as Zn(ZQ) 2 and additional Zn 2+ as proteome·Zn-ZQ ternary complexes. TSQ, a sensor structurally related to ZQ with lower affinity for Zn 2+ , did not form Zn(TSQ) 2 . Instead, Zn 2+ mobilized by DEA-NO was exclusively bound as proteome·Zn-TSQ adducts. Analogous reactions of proteome with ZQ or TSQ in vitro displayed qualitatively similar products. Titration of native proteome with Zn 2+ in the presence of ZQ resulted in the sole formation of proteome·Zn-ZQ species. This result suggested that sulfhydryl groups are involved in non-specific proteomic binding of mobile Zn 2+ and that the appearance of Zn(ZQ) 2 after exposure of cells and proteome to DEA-NO resulted from a reduction in proteomic sulfhydryl ligands, favoring the formation of Zn(ZQ) 2 instead of proteome·Zn-ZQ. With the third sensor, FluoZin-3, neither Zn-FZ-3 nor proteome·Zn-FZ-3 was detected during the reaction of proteome with DEA-NO. Instead, it reacted independently with DEA-NO with a modest enhancement of fluorescence.

A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary.

PubMed

Gadher, Suresh Jivan; Drahos, László; Vékey, Károly; Kovarova, Hana

2017-07-01

The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine. To this end, proteomics may enable diverse intertwining research fields to reach their end goals. CEEPC will endeavor to facilitate these goals.

17 CFR Appendix B to Part 37 - Guidance on Compliance With Core Principles

Code of Federal Regulations, 2012 CFR

2012-04-01

..., resources and authority to detect and deter abuses by effectively and affirmatively enforcing its rules... privileges but having no, or only nominal equity, in the facility and non-member market participants or, in... transparent to the member or market participant. Core Principle 3 of section 5a(d) of the Act: MONITORING OF...

Impulse Flashover Tests at Edgar Beauchamp High Voltage Test Facility, Dixon, California, in Support of Cutler Insulator Failure Investigation

DTIC Science & Technology

2006-07-01

sites. The strength member of the safety core insulators is a fiberglass belt wrapped around pins in the end fittings. Porcelain tubes cover the belt... porcelain tube and heavily tracked the fiberglass belt but left the belt intact structurally (Figure 1). Figure 1. Cutler safety core insulator ...fail-safe insulators . For these tests, the porcelain tube of the safety core insulator was replaced with a plastic see-through tube. The test report [5

The quest of the human proteome and the missing proteins: digging deeper.

PubMed

Reddy, Panga Jaipal; Ray, Sandipan; Srivastava, Sanjeeva

2015-05-01

Given the diverse range of transcriptional and post-transcriptional mechanisms of gene regulation, the estimates of the human proteome is likely subject to scientific surprises as the field of proteomics has gained momentum worldwide. In this regard, the establishment of the "Human Proteome Draft" using high-resolution mass spectrometry (MS), tissue microarrays, and immunohistochemistry by three independent research groups (laboratories of Pandey, Kuster, and Uhlen) accelerated the pace of proteomics research. The Chromosome Centric Human Proteome Project (C-HPP) has taken initiative towards the completion of the Human Proteome Project (HPP) so as to understand the proteomics correlates of common complex human diseases and biological diversity, not to mention person-to-person and population differences in response to drugs, nutrition, vaccines, and other health interventions and host-environment interactions. Although high-resolution MS-based and antibody microarray approaches have shown enormous promises, we are still unable to map the whole human proteome due to the presence of numerous "missing proteins." In December 2014, at the Indian Institute of Technology Bombay, Mumbai the 6(th) Annual Meeting of the Proteomics Society, India (PSI) and the International Proteomics Conference was held. As part of this interdisciplinary summit, a panel discussion session on "The Quest of the Human Proteome and Missing Proteins" was organized. Eminent scientists in the field of proteomics and systems biology, including Akhilesh Pandey, Gilbert S. Omenn, Mark S. Baker, and Robert L. Mortiz, shed light on different aspects of the human proteome drafts and missing proteins. Importantly, the possible reasons for the "missing proteins" in shotgun MS workflow were identified and debated by experts as low tissue expression, lack of enzymatic digestion site, or protein lost during extraction, among other contributing factors. To capture the missing proteins, the experts' collective view was to study the wider tissue range with multiple digesting enzymes and follow targeted proteomics workflow in particular. On the innovation trajectory from the proteomics laboratory to novel proteomics diagnostics and therapeutics in society, we will also need new conceptual frames for translation science and innovation strategy in proteomics. These will embody both technical as well as rigorous social science and humanities considerations to understand the correlates of the proteome from cell to society.

The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms

PubMed Central

Kiraga, Joanna; Mackiewicz, Pawel; Mackiewicz, Dorota; Kowalczuk, Maria; Biecek, Przemysław; Polak, Natalia; Smolarczyk, Kamila; Dudek, Miroslaw R; Cebrat, Stanislaw

2007-01-01

Background The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size. Results We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes – positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution. Conclusion The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms. PMID:17565672

Post-test analysis of dryout test 7B' of the W-1 Sodium Loop Safety Facility Experiment with the SABRE-2P code. [LMFBR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rose, S.D.; Dearing, J.F.

An understanding of conditions that may cause sodium boiling and boiling propagation that may lead to dryout and fuel failure is crucial in liquid-metal fast-breeder reactor safety. In this study, the SABRE-2P subchannel analysis code has been used to analyze the ultimate transient of the in-core W-1 Sodium Loop Safety Facility experiment. This code has a 3-D simple nondynamic boiling model which is able to predict the flow instability which caused dryout. In other analyses dryout has been predicted for out-of-core test bundles and so this study provides additional confirmation of the model.

Role of Proteomics in the Development of Personalized Medicine.

PubMed

Jain, Kewal K

2016-01-01

Advances in proteomic technologies have made import contribution to the development of personalized medicine by facilitating detection of protein biomarkers, proteomics-based molecular diagnostics, as well as protein biochips and pharmacoproteomics. Application of nanobiotechnology in proteomics, nanoproteomics, has further enhanced applications in personalized medicine. Proteomics-based molecular diagnostics will have an important role in the diagnosis of certain conditions and understanding the pathomechanism of disease. Proteomics will be a good bridge between diagnostics and therapeutics; the integration of these will be important for advancing personalized medicine. Use of proteomic biomarkers and combination of pharmacoproteomics with pharmacogenomics will enable stratification of clinical trials and improve monitoring of patients for development of personalized therapies. Proteomics is an important component of several interacting technologies used for development of personalized medicine, which is depicted graphically. Finally, cancer is a good example of applications of proteomic technologies for personalized management of cancer. © 2016 Elsevier Inc. All rights reserved.

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes

PubMed Central

Zhang, Yanling; Zhang, Yong; Adachi, Jun; Olsen, Jesper V.; Shi, Rong; de Souza, Gustavo; Pasini, Erica; Foster, Leonard J.; Macek, Boris; Zougman, Alexandre; Kumar, Chanchal; Wiśniewski, Jacek R.; Jun, Wang; Mann, Matthias

2007-01-01

Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities and is freely available at using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools. PMID:17090601

Linking the proteins--elucidation of proteome-scale networks using mass spectrometry.

PubMed

Pflieger, Delphine; Gonnet, Florence; de la Fuente van Bentem, Sergio; Hirt, Heribert; de la Fuente, Alberto

2011-01-01

Proteomes are intricate. Typically, thousands of proteins interact through physical association and post-translational modifications (PTMs) to give rise to the emergent functions of cells. Understanding these functions requires one to study proteomes as "systems" rather than collections of individual protein molecules. The abstraction of the interacting proteome to "protein networks" has recently gained much attention, as networks are effective representations, that lose specific molecular details, but provide the ability to see the proteome as a whole. Mostly two aspects of the proteome have been represented by network models: proteome-wide physical protein-protein-binding interactions organized into Protein Interaction Networks (PINs), and proteome-wide PTM relations organized into Protein Signaling Networks (PSNs). Mass spectrometry (MS) techniques have been shown to be essential to reveal both of these aspects on a proteome-wide scale. Techniques such as affinity purification followed by MS have been used to elucidate protein-protein interactions, and MS-based quantitative phosphoproteomics is critical to understand the structure and dynamics of signaling through the proteome. We here review the current state-of-the-art MS-based analytical pipelines for the purpose to characterize proteome-scale networks. Copyright © 2010 Wiley Periodicals, Inc.

PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information.

PubMed

Yu, Kebing; Salomon, Arthur R

2009-12-01

Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to various experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker-driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end-users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our high throughput autonomous proteomic pipeline used in the automated acquisition and post-acquisition analysis of proteomic data.

Influence of Diet on the Proteome of Drosophila Melanogaster as Assessed by Two-Dimensional Gel Electrophoresis and Capillary Liquid Chromatography–Mass Spectrometry: The Hamburger Effect Revisited

PubMed Central

Culwell, Thomas F.; Thulin, Craig D.; Merrell, Karen J.; Graves, Steven W.

2008-01-01

Proteomic biomarker discovery has been called into question. Diamandis hypothesized that seemingly trivial factors, such as eating a hamburger, may cause sufficient proteomic change as to confound proteomic differences. This has been termed the hamburger effect. Little is known about the variability of complex proteomes in response to the environment. Two methods—two-dimensional gel electrophoresis (2DGE) and capillary liquid chromatography–electrospray ionization time-of-flight mass spectrometry (LCMS)—were used to study the hamburger effect in two cross-sections of the soluble fruit fly proteome. 2DGE measured abundant proteins, whereas LCMS measured small proteins and peptides. Proteomic differences between males and females were first evaluated to assess the discriminatory capability of the methods. Likewise, wild-type and white-eyed flies were analyzed as a further demonstration that genetically based proteomic differences could be observed above the background analytical variation. Then dietary interventions were imposed. Ethanol was added to the diet of some populations without significant proteomic effect. However, after a 24-h fast, proteomic differences were found using LCMS but not 2DGE. Even so, only three of ~1000 molecular species were altered significantly, suggesting that the influence of even an extreme diet change produced only modest proteomic variability, and that much of the fruit fly proteome remains relatively constant in response to diet. These experiments suggest that proteomics can be a viable approach to biomarker discovery. PMID:19137114

Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopez-Ferrer, Daniel; Petritis, Konstantinos; Robinson, Errol W.

2011-02-01

Integrated top-down bottom-up proteomics combined with online digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to highthroughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications (PTMs). Herein, we describe recent efforts towards efficient integration of bottom-up and top-down LCMS based proteomic strategies. Since most proteomic platforms (i.e. LC systems) operate in acidic environments, we exploited themore » compatibility of the pepsin (i.e. the enzyme’s natural acidic activity) for the integration of bottom-up and top-down proteomics. Pressure enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an offline mode using a Barocycler or an online mode using a modified high pressure LC system referred to as a fast online digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultra-rapid integrated bottom-up top-down proteomic strategy employing a standard mixture of proteins and a monkey pox virus proteome.« less

HTR-PROTEUS PEBBLE BED EXPERIMENTAL PROGRAM CORE 4: RANDOM PACKING WITH A 1:1 MODERATOR-TO-FUEL PEBBLE RATIO

DOE Office of Scientific and Technical Information (OSTI.GOV)

John D. Bess; Leland M. Montierth

2013-03-01

In its deployment as a pebble bed reactor (PBR) critical facility from 1992 to 1996, the PROTEUS facility was designated as HTR-PROTEUS. This experimental program was performed as part of an International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on the Validation of Safety Related Physics Calculations for Low Enriched HTGRs. Within this project, critical experiments were conducted for graphite moderated LEU systems to determine core reactivity, flux and power profiles, reaction-rate ratios, the worth of control rods, both in-core and reflector based, the worth of burnable poisons, kinetic parameters, and the effects of moisture ingress on these parameters.more » One benchmark experiment was evaluated in this report: Core 4. Core 4 represents the only configuration with random pebble packing in the HTR-PROTEUS series of experiments, and has a moderator-to-fuel pebble ratio of 1:1. Three random configurations were performed. The initial configuration, Core 4.1, was rejected because the method for pebble loading, separate delivery tubes for the moderator and fuel pebbles, may not have been completely random; this core loading was rejected by the experimenters. Cores 4.2 and 4.3 were loaded using a single delivery tube, eliminating the possibility for systematic ordering effects. The second and third cores differed slightly in the quantity of pebbles loaded (40 each of moderator and fuel pebbles), stacked height of the pebbles in the core cavity (0.02 m), withdrawn distance of the stainless steel control rods (20 mm), and withdrawn distance of the autorod (30 mm). The 34 coolant channels in the upper axial reflector and the 33 coolant channels in the lower axial reflector were open. Additionally, the axial graphite fillers used in all other HTR-PROTEUS configurations to create a 12-sided core cavity were not used in the randomly packed cores. Instead, graphite fillers were placed on the cavity floor, creating a funnel-like base, to discourage ordering effects during pebble loading. Core 4 was determined to be acceptable benchmark experiment.« less

HTR-proteus pebble bed experimental program core 4: random packing with a 1:1 moderator-to-fuel pebble ratio

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bess, John D.; Montierth, Leland M.; Sterbentz, James W.

2014-03-01

In its deployment as a pebble bed reactor (PBR) critical facility from 1992 to 1996, the PROTEUS facility was designated as HTR-PROTEUS. This experimental program was performed as part of an International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on the Validation of Safety Related Physics Calculations for Low Enriched HTGRs. Within this project, critical experiments were conducted for graphite moderated LEU systems to determine core reactivity, flux and power profiles, reaction-rate ratios, the worth of control rods, both in-core and reflector based, the worth of burnable poisons, kinetic parameters, and the effects of moisture ingress on these parameters.more » One benchmark experiment was evaluated in this report: Core 4. Core 4 represents the only configuration with random pebble packing in the HTR-PROTEUS series of experiments, and has a moderator-to-fuel pebble ratio of 1:1. Three random configurations were performed. The initial configuration, Core 4.1, was rejected because the method for pebble loading, separate delivery tubes for the moderator and fuel pebbles, may not have been completely random; this core loading was rejected by the experimenters. Cores 4.2 and 4.3 were loaded using a single delivery tube, eliminating the possibility for systematic ordering effects. The second and third cores differed slightly in the quantity of pebbles loaded (40 each of moderator and fuel pebbles), stacked height of the pebbles in the core cavity (0.02 m), withdrawn distance of the stainless steel control rods (20 mm), and withdrawn distance of the autorod (30 mm). The 34 coolant channels in the upper axial reflector and the 33 coolant channels in the lower axial reflector were open. Additionally, the axial graphite fillers used in all other HTR-PROTEUS configurations to create a 12-sided core cavity were not used in the randomly packed cores. Instead, graphite fillers were placed on the cavity floor, creating a funnel-like base, to discourage ordering effects during pebble loading. Core 4 was determined to be acceptable benchmark experiment.« less

76 FR 23848 - Carolina Power And Light Company; Notice of Withdrawal of Application for Amendment to Renewed...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-28

...; Notice of Withdrawal of Application for Amendment to Renewed Facility Operating License The U.S. Nuclear... December 9, 2010, for a proposed amendment to Renewed Facility Operating License No. NPF-63 for the Shearon... Pressurized Water Reactors,'' to the Core Operating Limits Report methodologies list. This change would have...

Furnace and support equipment for space processing. [space manufacturing - Czochralski method

NASA Technical Reports Server (NTRS)

Mazelsky, R.; Duncan, C. S.; Seidensticker, R. G.; Johnson, R. A.; Hopkins, R. H.; Roland, G. W.

1975-01-01

A core facility capable of performing a majority of materials processing experiments is discussed. Experiment classes are described, the needs peculiar to each experiment type are outlined, and projected facility requirements to perform the experiments are treated. Control equipment (automatic control) and variations of the Czochralski method for use in space are discussed.

STATE OF NEW YORK STANDARD PLAN TYPE A-1, ONE-STORY 14-21 CLASSROOM ELEMENTARY SCHOOL.

ERIC Educational Resources Information Center

King and King, Syracuse, NY.

THE PROGRAM FOR AN ELEMENTARY SCHOOL FACILITY REQUIRED 14 CLASSROOMS WITH THE POTENTIAL FOR ACCOMMODATING AN INCREASE OF SEVEN CLASSROOMS. THE EXPANSION POTENTIAL ALSO INVOLVED ADDITION OF A CONSIDERABLE NUMBER OF NON-TEACHING AREAS. THE DESIGN FEATURED A CENTRAL CORE CONTAINING ADMINISTRATION, PLAYROOM, CAFETERIA, AND KITCHEN FACILITIES WITH TWO…

Birth of plant proteomics in India: a new horizon.

PubMed

Narula, Kanika; Pandey, Aarti; Gayali, Saurabh; Chakraborty, Niranjan; Chakraborty, Subhra

2015-09-08

In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Melamine-assisted one-pot synthesis of hierarchical nitrogen-doped carbon@MoS2 nanowalled core-shell microspheres and their enhanced Li-storage performances

NASA Astrophysics Data System (ADS)

Sun, Fugen; Wei, Yanju; Chen, Jianzhuang; Long, Donghui; Ling, Licheng; Li, Yongsheng; Shi, Jianlin

2015-07-01

A facile and scalable one-pot approach has been developed to synthesize carbon@MoS2 core-shell microspheres by a hydrothermal method, which involves the fast formation of melamine-resorcinol-formaldehyde polymeric microspheres in situ, followed by direct growth of the MoS2 nanowalls on them. The results give unequivocal proof that melamine could be the key to forming the core-shell microspherical morphology, and the contents of MoS2 shells can be easily tuned by initial ratios of the precursors. After a simple heat treatment, the obtained carbon@MoS2 microspheres simultaneously integrate the nitrogen-doped carbon cores and the hierarchical shells which consist of few-layered MoS2 nanowalls with an expanded interlayer spacing. Their unique architectures are favourable for high electronic/ionic conductivity and accommodate volume strain during the electrochemical reaction of the MoS2 anodes in lithium-ion batteries. Thus, a very high reversibility capacity of 771 mA h g-1 at 100 mA g-1 after 100 cycles, and a rate capacity of 598 mA h g-1 at 2000 mA g-1 could be achieved for the carbon@MoS2 core-shell microspheres with the optimal composition. Furthermore, a thin carbon coating on the carbon@MoS2 microspheres could further increase the reversible capacity to 856 mA h g-1 after 100 cycles at 100 mA g-1. These encouraging results suggest that such a facile and efficient protocol can provide a new pathway to produce hierarchical core-shell microspheres which integrate the structural, morphological and compositional design rationales for advanced lithium-ion batteries.A facile and scalable one-pot approach has been developed to synthesize carbon@MoS2 core-shell microspheres by a hydrothermal method, which involves the fast formation of melamine-resorcinol-formaldehyde polymeric microspheres in situ, followed by direct growth of the MoS2 nanowalls on them. The results give unequivocal proof that melamine could be the key to forming the core-shell microspherical morphology, and the contents of MoS2 shells can be easily tuned by initial ratios of the precursors. After a simple heat treatment, the obtained carbon@MoS2 microspheres simultaneously integrate the nitrogen-doped carbon cores and the hierarchical shells which consist of few-layered MoS2 nanowalls with an expanded interlayer spacing. Their unique architectures are favourable for high electronic/ionic conductivity and accommodate volume strain during the electrochemical reaction of the MoS2 anodes in lithium-ion batteries. Thus, a very high reversibility capacity of 771 mA h g-1 at 100 mA g-1 after 100 cycles, and a rate capacity of 598 mA h g-1 at 2000 mA g-1 could be achieved for the carbon@MoS2 core-shell microspheres with the optimal composition. Furthermore, a thin carbon coating on the carbon@MoS2 microspheres could further increase the reversible capacity to 856 mA h g-1 after 100 cycles at 100 mA g-1. These encouraging results suggest that such a facile and efficient protocol can provide a new pathway to produce hierarchical core-shell microspheres which integrate the structural, morphological and compositional design rationales for advanced lithium-ion batteries. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03708e

Building ProteomeTools based on a complete synthetic human proteome

PubMed Central

Zolg, Daniel P.; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J.; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard

2018-01-01

The ProteomeTools project builds molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we report the generation and multimodal LC-MS/MS analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products and exemplify the utility of this data. The resource will be extended to >1 million peptides and all data will be shared with the community via ProteomicsDB and proteomeXchange. PMID:28135259

Pressurized Pepsin Digestion in Proteomics

PubMed Central

López-Ferrer, Daniel; Petritis, Konstantinos; Robinson, Errol W.; Hixson, Kim K.; Tian, Zhixin; Lee, Jung Hwa; Lee, Sang-Won; Tolić, Nikola; Weitz, Karl K.; Belov, Mikhail E.; Smith, Richard D.; Paša-Tolić, Ljiljana

2011-01-01

Integrated top-down bottom-up proteomics combined with on-line digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to high throughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications. Herein, we describe recent efforts toward efficient integration of bottom-up and top-down LC-MS-based proteomics strategies. Since most proteomics separations utilize acidic conditions, we exploited the compatibility of pepsin (where the optimal digestion conditions are at low pH) for integration into bottom-up and top-down proteomics work flows. Pressure-enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an off-line mode using a Barocycler or an on-line mode using a modified high pressure LC system referred to as a fast on-line digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results were compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultrarapid integrated bottom-up top-down proteomics strategy using a standard mixture of proteins and a monkey pox virus proteome. PMID:20627868

SILAC-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers.

PubMed

Zanivan, Sara; Maione, Federica; Hein, Marco Y; Hernández-Fernaud, Juan Ramon; Ostasiewicz, Pawel; Giraudo, Enrico; Mann, Matthias

2013-12-01

Proteomics has been successfully used for cell culture on dishes, but more complex cellular systems have proven to be challenging and so far poorly approached with proteomics. Because of the complexity of the angiogenic program, we still do not have a complete understanding of the molecular mechanisms involved in this process, and there have been no in depth quantitative proteomic studies. Plating endothelial cells on matrigel recapitulates aspects of vessel growth, and here we investigate this mechanism by using a spike-in SILAC quantitative proteomic approach. By comparing proteomic changes in primary human endothelial cells morphogenesis on matrigel to general adhesion mechanisms in cells spreading on culture dish, we pinpoint pathways and proteins modulated by endothelial cells. The cell-extracellular matrix adhesion proteome depends on the adhesion substrate, and a detailed proteomic profile of the extracellular matrix secreted by endothelial cells identified CLEC14A as a matrix component, which binds to MMRN2. We verify deregulated levels of these proteins during tumor angiogenesis in models of multistage carcinogenesis. This is the most in depth quantitative proteomic study of endothelial cell morphogenesis, which shows the potential of applying high accuracy quantitative proteomics to in vitro models of vessel growth to shed new light on mechanisms that accompany pathological angiogenesis. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000359.

Clinical veterinary proteomics: Techniques and approaches to decipher the animal plasma proteome.

PubMed

Ghodasara, P; Sadowski, P; Satake, N; Kopp, S; Mills, P C

2017-12-01

Over the last two decades, technological advancements in the field of proteomics have advanced our understanding of the complex biological systems of living organisms. Techniques based on mass spectrometry (MS) have emerged as powerful tools to contextualise existing genomic information and to create quantitative protein profiles from plasma, tissues or cell lines of various species. Proteomic approaches have been used increasingly in veterinary science to investigate biological processes responsible for growth, reproduction and pathological events. However, the adoption of proteomic approaches by veterinary investigators lags behind that of researchers in the human medical field. Furthermore, in contrast to human proteomics studies, interpretation of veterinary proteomic data is difficult due to the limited protein databases available for many animal species. This review article examines the current use of advanced proteomics techniques for evaluation of animal health and welfare and covers the current status of clinical veterinary proteomics research, including successful protein identification and data interpretation studies. It includes a description of an emerging tool, sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS), available on selected mass spectrometry instruments. This newly developed data acquisition technique combines advantages of discovery and targeted proteomics approaches, and thus has the potential to advance the veterinary proteomics field by enhancing identification and reproducibility of proteomics data. Copyright © 2017 Elsevier Ltd. All rights reserved.

Proteome | Office of Cancer Clinical Proteomics Research

Cancer.gov

A proteome is the entire complement of proteins, including modifications made to a particular set of proteins, produced by an organism or a cellular system. This will vary with time and distinct requirements such as growth conditions and stresses, and thus is highly dynamic and spatial. Proteomics is the study of the proteome.

University of Victoria Genome British Columbia Proteomics Centre Partners with CPTAC | Office of Cancer Clinical Proteomics Research

Cancer.gov

University of Victoria Genome British Columbia Proteomics Centre, a leader in proteomic technology development, has partnered with the U.S. National Cancer Institute (NCI) to make targeted proteomic assays accessible to the community through NCI’s CPTAC Assay Portal (https://assays.cancer.gov).

A Review: Proteomics in Retinal Artery Occlusion, Retinal Vein Occlusion, Diabetic Retinopathy and Acquired Macular Disorders.

PubMed

Cehofski, Lasse Jørgensen; Honoré, Bent; Vorum, Henrik

2017-04-28

Retinal artery occlusion (RAO), retinal vein occlusion (RVO), diabetic retinopathy (DR) and age-related macular degeneration (AMD) are frequent ocular diseases with potentially sight-threatening outcomes. In the present review we discuss major findings of proteomic studies of RAO, RVO, DR and AMD, including an overview of ocular proteome changes associated with anti-vascular endothelial growth factor (VEGF) treatments. Despite the severe outcomes of RAO, the proteome of the disease remains largely unstudied. There is also limited knowledge about the proteome of RVO, but proteomic studies suggest that RVO is associated with remodeling of the extracellular matrix and adhesion processes. Proteomic studies of DR have resulted in the identification of potential therapeutic targets such as carbonic anhydrase-I. Proliferative diabetic retinopathy is the most intensively studied stage of DR. Proteomic studies have established VEGF, pigment epithelium-derived factor (PEDF) and complement components as key factors associated with AMD. The aim of this review is to highlight the major milestones in proteomics in RAO, RVO, DR and AMD. Through large-scale protein analyses, proteomics is bringing new important insights into these complex pathological conditions.

Personalized medicine beyond genomics: alternative futures in big data-proteomics, environtome and the social proteome.

PubMed

Özdemir, Vural; Dove, Edward S; Gürsoy, Ulvi K; Şardaş, Semra; Yıldırım, Arif; Yılmaz, Şenay Görücü; Ömer Barlas, I; Güngör, Kıvanç; Mete, Alper; Srivastava, Sanjeeva

2017-01-01

No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble. Yet the proteome is critical for life-it ensures the daily functioning of cells and whole organisms. In short, proteins are the blue-collar workers of biology, the down-to-earth molecules that we cannot live without. Since 2010, proteomics has found renewed meaning and international attention with the launch of the Human Proteome Project and the growing interest in Big Data technologies such as proteomics. This article presents an interdisciplinary technology foresight analysis and conceptualizes the terms "environtome" and "social proteome". We define "environtome" as the entire complement of elements external to the human host, from microbiome, ambient temperature and weather conditions to government innovation policies, stock market dynamics, human values, political power and social norms that collectively shape the human host spatially and temporally. The "social proteome" is the subset of the environtome that influences the transition of proteomics technology to innovative applications in society. The social proteome encompasses, for example, new reimbursement schemes and business innovation models for proteomics diagnostics that depart from the "once-a-life-time" genotypic tests and the anticipated hype attendant to context and time sensitive proteomics tests. Building on the "nesting principle" for governance of complex systems as discussed by Elinor Ostrom, we propose here a 3-tiered organizational architecture for Big Data science such as proteomics. The proposed nested governance structure is comprised of (a) scientists, (b) ethicists, and (c) scholars in the nascent field of "ethics-of-ethics", and aims to cultivate a robust social proteome for personalized medicine. Ostrom often noted that such nested governance designs offer assurance that political power embedded in innovation processes is distributed evenly and is not concentrated disproportionately in a single overbearing stakeholder or person. We agree with this assessment and conclude by underscoring the synergistic value of social and biological proteomes to realize the full potentials of proteomics science for personalized medicine in psychiatry in the present era of Big Data.

Plant proteome analysis: a 2006 update.

PubMed

Jorrín, Jesús V; Maldonado, Ana M; Castillejo, Ma Angeles

2007-08-01

This 2006 'Plant Proteomics Update' is a continuation of the two previously published in 'Proteomics' by 2004 (Canovas et al., Proteomics 2004, 4, 285-298) and 2006 (Rossignol et al., Proteomics 2006, 6, 5529-5548) and it aims to bring up-to-date the contribution of proteomics to plant biology on the basis of the original research papers published throughout 2006, with references to those appearing last year. According to the published papers and topics addressed, we can conclude that, as observed for the three previous years, there has been a quantitative, but not qualitative leap in plant proteomics. The full potential of proteomics is far from being exploited in plant biology research, especially if compared to other organisms, mainly yeast and humans, and a number of challenges, mainly technological, remain to be tackled. The original papers published last year numbered nearly 100 and deal with the proteome of at least 26 plant species, with a high percentage for Arabidopsis thaliana (28) and rice (11). Scientific objectives ranged from proteomic analysis of organs/tissues/cell suspensions (57) or subcellular fractions (29), to the study of plant development (12), the effect of hormones and signalling molecules (8) and response to symbionts (4) and stresses (27). A small number of contributions have covered PTMs (8) and protein interactions (4). 2-DE (specifically IEF-SDS-PAGE) coupled to MS still constitutes the almost unique platform utilized in plant proteome analysis. The application of gel-free protein separation methods and 'second generation' proteomic techniques such as multidimensional protein identification technology (MudPIT), and those for quantitative proteomics including DIGE, isotope-coded affinity tags (ICAT), iTRAQ and stable isotope labelling by amino acids in cell culture (SILAC) still remains anecdotal. This review is divided into seven sections: Introduction, Methodology, Subcellular proteomes, Development, Responses to biotic and abiotic stresses, PTMs and Protein interactions. Section 8 summarizes the major pitfalls and challenges of plant proteomics.

St. Petersburg Coastal and Marine Science Center's Core Archive Portal

USGS Publications Warehouse

Reich, Chris; Streubert, Matt; Dwyer, Brendan; Godbout, Meg; Muslic, Adis; Umberger, Dan

2012-01-01

This Web site contains information on rock cores archived at the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center (SPCMSC). Archived cores consist of 3- to 4-inch-diameter coral cores, 1- to 2-inch-diameter rock cores, and a few unlabeled loose coral and rock samples. This document - and specifically the archive Web site portal - is intended to be a 'living' document that will be updated continually as additional cores are collected and archived. This document may also contain future references and links to a catalog of sediment cores. Sediment cores will include vibracores, pushcores, and other loose sediment samples collected for research purposes. This document will: (1) serve as a database for locating core material currently archived at the USGS SPCMSC facility; (2) provide a protocol for entry of new core material into the archive system; and, (3) set the procedures necessary for checking out core material for scientific purposes. Core material may be loaned to other governmental agencies, academia, or non-governmental organizations at the discretion of the USGS SPCMSC curator.

The NASA Lewis Research Center Water Tunnel Facility

NASA Technical Reports Server (NTRS)

Wasserbauer, Charles A.

1997-01-01

A water tunnel facility specifically designed to investigate internal fluid duct flows has been built at the NASA Research Center. It is built in a modular fashion so that a variety of internal flow test hardware can be installed in the facility with minimal facility reconfiguration. The facility and test hardware interfaces are discussed along with design constraints for future test hardware. The inlet chamber flow conditioning approach is also detailed. Instrumentation and data acquisition capabilities are discussed. The incoming flow quality has been documented for about one quarter of the current facility operating range. At that range, there is some scatter in the data in the turbulent boundary layer which approaches 10 percent of the duct radius leading to a uniform core.

Astrophysics at RIA (ARIA) Working Group

NASA Astrophysics Data System (ADS)

Smith, Michael S.; Schatz, Hendrik; Timmes, Frank X.; Wiescher, Michael; Greife, Uwe

2006-07-01

The Astrophysics at RIA (ARIA) Working Group has been established to develop and promote the nuclear astrophysics research anticipated at the Rare Isotope Accelerator (RIA). RIA is a proposed next-generation nuclear science facility in the U.S. that will enable significant progress in studies of core collapse supernovae, thermonuclear supernovae, X-ray bursts, novae, and other astrophysical sites. Many of the topics addressed by the Working Group are relevant for the RIKEN RI Beam Factory, the planned GSI-Fair facility, and other advanced radioactive beam facilities.

Evolution of Clinical Proteomics and its Role in Medicine | Office of Cancer Clinical Proteomics Research

Cancer.gov

NCI's Office of Cancer Clinical Proteomics Research authored a review of the current state of clinical proteomics in the peer-reviewed Journal of Proteome Research. The review highlights outcomes from the CPTC program and also provides a thorough overview of the different technologies that have pushed the field forward. Additionally, the review provides a vision for moving the field forward through linking advances in genomic and proteomic analysis to develop new, molecularly targeted interventions.

Posttest TRAC-PD2/MOD1 predictions for FLECHT SEASET test 31504. [PWR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Booker, C.P.

TRAC-PD2/MOD1 is a publicly released version of TRAC that is used primarily to analyze large-break loss-of-coolant accidents in pressurized-water reactors (PWRs). TRAC-PD2 can calculate, among other things, reflood phenomena. TRAC posttest predictions are compared with test 31504 reflood data from the Full-Length Emergency Core Heat Transfer (FLECHT) System Effects and Separate Effects Tests (SEASET) facility. A false top-down quench is predicted near the top of the core and the subcooling is underpredicted at the bottom of the core. However, the overall TRAC predictions are good, especially near the center of the core.

Video Intertank for the Core Stage for the first SLS Flight

NASA Image and Video Library

2017-06-29

This video shows the Space Launch System interank, which recently completed assembly at NASA's Michoud Assembly Facility in New Orleans. This tank was bolted together with more than 7,000 bolts. It is the only part of the SLS core stage assembly with bolts rather than by welding. The rocket's interank is located between the core stage liquid oxygen and liquid hydrogen fuel tanks. It has to be strong because the two SLS solid rocket boosters attache to the sides of it. This flight article will be connected to four other parts to form the core stage for the first integrated flight of SLS and Orion.

Scaling up Planetary Dynamo Modeling to Massively Parallel Computing Systems: The Rayleigh Code at ALCF

NASA Astrophysics Data System (ADS)

Featherstone, N. A.; Aurnou, J. M.; Yadav, R. K.; Heimpel, M. H.; Soderlund, K. M.; Matsui, H.; Stanley, S.; Brown, B. P.; Glatzmaier, G.; Olson, P.; Buffett, B. A.; Hwang, L.; Kellogg, L. H.

2017-12-01

In the past three years, CIG's Dynamo Working Group has successfully ported the Rayleigh Code to the Argonne Leadership Computer Facility's Mira BG/Q device. In this poster, we present some our first results, showing simulations of 1) convection in the solar convection zone; 2) dynamo action in Earth's core and 3) convection in the jovian deep atmosphere. These simulations have made efficient use of 131 thousand cores, 131 thousand cores and 232 thousand cores, respectively, on Mira. In addition to our novel results, the joys and logistical challenges of carrying out such large runs will also be discussed.

Nac1 promotes self-renewal of embryonic stem cells through direct transcriptional regulation of c-Myc.

PubMed

Ruan, Yan; He, Jianrong; Wu, Wei; He, Ping; Tian, Yanping; Xiao, Lan; Liu, Gaoke; Wang, Jiali; Cheng, Yuda; Zhang, Shuo; Yang, Yi; Xiong, Jiaxiang; Zhao, Ke; Wan, Ying; Huang, He; Zhang, Junlei; Jian, Rui

2017-07-18

The pluripotency transcriptional network in embryonic stem cells (ESCs) is composed of distinct functional units including the core and Myc units. It is hoped that dissection of the cellular functions and interconnections of network factors will aid our understanding of ESC and cancer biology. Proteomic and genomic approaches have identified Nac1 as a member of the core pluripotency network. However, previous studies have predominantly focused on the role of Nac1 in psychomotor stimulant response and cancer pathogenesis. In this study, we report that Nac1 is a self-renewal promoting factor, but is not required for maintaining pluripotency of ESCs. Loss of function of Nac1 in ESCs results in a reduced proliferation rate and an enhanced differentiation propensity. Nac1 overexpression promotes ESC proliferation and delays ESC differentiation in the absence of leukemia inhibitory factor (LIF). Furthermore, we demonstrated that Nac1 directly binds to the c-Myc promoter and regulates c-Myc transcription. The study also revealed that the function of Nac1 in promoting ESC self-renewal appears to be partially mediated by c-Myc. These findings establish a functional link between the core and c-Myc-centered networks and provide new insights into mechanisms of stemness regulation in ESCs and cancer.

Caldicellulosiruptor Core and Pangenomes Reveal Determinants for Noncellulosomal Thermophilic Deconstruction of Plant Biomass

PubMed Central

Blumer-Schuette, Sara E.; Giannone, Richard J.; Zurawski, Jeffrey V.; Ozdemir, Inci; Ma, Qin; Yin, Yanbin; Xu, Ying; Kataeva, Irina; Poole, Farris L.; Adams, Michael W. W.; Hamilton-Brehm, Scott D.; Elkins, James G.; Larimer, Frank W.; Land, Miriam L.; Hauser, Loren J.; Cottingham, Robert W.; Hettich, Robert L.

2012-01-01

Extremely thermophilic bacteria of the genus Caldicellulosiruptor utilize carbohydrate components of plant cell walls, including cellulose and hemicellulose, facilitated by a diverse set of glycoside hydrolases (GHs). From a biofuel perspective, this capability is crucial for deconstruction of plant biomass into fermentable sugars. While all species from the genus grow on xylan and acid-pretreated switchgrass, growth on crystalline cellulose is variable. The basis for this variability was examined using microbiological, genomic, and proteomic analyses of eight globally diverse Caldicellulosiruptor species. The open Caldicellulosiruptor pangenome (4,009 open reading frames [ORFs]) encodes 106 GHs, representing 43 GH families, but only 26 GHs from 17 families are included in the core (noncellulosic) genome (1,543 ORFs). Differentiating the strongly cellulolytic Caldicellulosiruptor species from the others is a specific genomic locus that encodes multidomain cellulases from GH families 9 and 48, which are associated with cellulose-binding modules. This locus also encodes a novel adhesin associated with type IV pili, which was identified in the exoproteome bound to crystalline cellulose. Taking into account the core genomes, pangenomes, and individual genomes, the ancestral Caldicellulosiruptor was likely cellulolytic and evolved, in some cases, into species that lost the ability to degrade crystalline cellulose while maintaining the capacity to hydrolyze amorphous cellulose and hemicellulose. PMID:22636774

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.

PubMed

Zhang, Yanling; Zhang, Yong; Adachi, Jun; Olsen, Jesper V; Shi, Rong; de Souza, Gustavo; Pasini, Erica; Foster, Leonard J; Macek, Boris; Zougman, Alexandre; Kumar, Chanchal; Wisniewski, Jacek R; Jun, Wang; Mann, Matthias

2007-01-01

Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities and is freely available at http://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools.

PeptideDepot: Flexible Relational Database for Visual Analysis of Quantitative Proteomic Data and Integration of Existing Protein Information

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2010-01-01

Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through tandem mass spectrometry (MS/MS). Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to a variety of experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker-driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end-users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our High Throughput Autonomous Proteomic Pipeline (HTAPP) used in the automated acquisition and post-acquisition analysis of proteomic data. PMID:19834895

PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets.

PubMed

Martínez-Bartolomé, Salvador; Medina-Aunon, J Alberto; López-García, Miguel Ángel; González-Tejedo, Carmen; Prieto, Gorka; Navajas, Rosana; Salazar-Donate, Emilio; Fernández-Costa, Carolina; Yates, John R; Albar, Juan Pablo

2018-04-06

Mass-spectrometry-based proteomics has evolved into a high-throughput technology in which numerous large-scale data sets are generated from diverse analytical platforms. Furthermore, several scientific journals and funding agencies have emphasized the storage of proteomics data in public repositories to facilitate its evaluation, inspection, and reanalysis. (1) As a consequence, public proteomics data repositories are growing rapidly. However, tools are needed to integrate multiple proteomics data sets to compare different experimental features or to perform quality control analysis. Here, we present a new Java stand-alone tool, Proteomics Assay COMparator (PACOM), that is able to import, combine, and simultaneously compare numerous proteomics experiments to check the integrity of the proteomic data as well as verify data quality. With PACOM, the user can detect source of errors that may have been introduced in any step of a proteomics workflow and that influence the final results. Data sets can be easily compared and integrated, and data quality and reproducibility can be visually assessed through a rich set of graphical representations of proteomics data features as well as a wide variety of data filters. Its flexibility and easy-to-use interface make PACOM a unique tool for daily use in a proteomics laboratory. PACOM is available at https://github.com/smdb21/pacom .

Platinum-nanoparticle-supported core-shell polymer nanospheres with unexpected water stability and facile further modification

NASA Astrophysics Data System (ADS)

Yuan, Conghui; Xu, Yiting; Luo, Weiang; Zeng, Birong; Qiu, Wuhui; Liu, Jie; Huang, Huiling; Dai, Lizong

2012-05-01

Core-shell nanospheres (CSNSs) with hydrophobic cores and hydrophilic shells were fabricated via a simple mini-emulsion polymerization for the stabilization of platinum nanoparticles (Pt-NPs). The CSNSs showed extremely high loading capacity of Pt-NPs (the largest loading amount of the Pt-NPs was about 49.2 wt%). Importantly, the Pt-NPs/CSNSs nanocomposites had unexpected stability in aqueous solution. DLS results revealed that the CSNSs loaded with Pt-NPs exhibited almost no aggregation after standing for a long time . However, the Pt-NPs immobilized on the CSNSs were not straitlaced: they could transport and redistribute between CSNSs freely when the environmental temperature was higher than the melting point of the CSNS shell. Owing to their excellent stability in aqueous solution, the surface of the Pt-NPs/CSNSs nanocomposites could be further decorated easily. For example, polyaniline (PANI)-coated Pt-NPs/CSNSs, nickel (Ni)-coated Pt-NPs/CSNSs and PANI/Pt-NPs dual-layer hollow nanospheres were facilely fabricated from the Pt-NPs/CSNS nanocomposites.

Neutronics and Transient Calculations for the Conversion of the Transient Reactor Rest Facility (TREAT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kontogeorgakos, Dimitrios C.; Connaway, Heather M.; Papadias, Dionissios D.

2015-01-01

The Transient Reactor Test Facility (TREAT) is a graphite-reflected, graphitemoderated, and air-cooled reactor fueled with 93.1% enriched UO2 particles dispersed in graphite, with a carbon-to-235U ratio of ~10000:1. TREAT was used to simulate accident conditions by subjecting fuel test samples placed at the center of the core to high energy transient pulses. The transient pulse production is based on the core’s selflimiting nature due to the negative reactivity feedback provided by the fuel graphite as the core temperature rises. The analysis of the conversion of TREAT to low enriched uranium (LEU) is currently underway. This paper presents the analytical methodsmore » used to calculate the transient performance of TREAT in terms of power pulse production and resulting peak core temperatures. The validation of the HEU neutronics TREAT model, the calculation of the temperature distribution and the temperature reactivity feedback as well as the number of fissions generated inside fuel test samples are discussed.« less

Facile deposition of gold nanoparticles on core-shell Fe3O4@polydopamine as recyclable nanocatalyst

NASA Astrophysics Data System (ADS)

Zhao, Yan; Yeh, Yaowen; Liu, Rui; You, Jinmao; Qu, Fengli

2015-07-01

A simple and green method for the controllable synthesis of core-shell Fe3O4 polydopamine nanoparticles (Fe3O4@PDA NPs) with tunable shell thickness and their application as a recyclable nanocatalyst support is presented. Magnetite Fe3O4 NPs formed in a one-pot process by the hydrothermal approach with a diameter of ˜240 nm were coated with a polydopamine shell layer with a tunable thickness of 15-45 nm. The facile deposition of Au NPs atop Fe3O4@PDA NPs was achieved by utilizing PDA as both the reducing agent and the coupling agent. The satellite nanocatalysts exhibited high catalytic performance for the reduction of p-nitrophenol. Furthermore, the recovery and reuse of the catalyst was demonstrated 8 times without detectible loss in activity. The synergistic combination of unique features of PDA and magnetic nanoparticles establishes these core-shell NPs as a versatile platform for potential applications.

Potential Conservation of Circadian Clock Proteins in the phylum Nematoda as Revealed by Bioinformatic Searches

PubMed Central

Romanowski, Andrés; Garavaglia, Matías Javier; Goya, María Eugenia; Ghiringhelli, Pablo Daniel; Golombek, Diego Andrés

2014-01-01

Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive. In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda. With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system. PMID:25396739

Potential conservation of circadian clock proteins in the phylum Nematoda as revealed by bioinformatic searches.

PubMed

Romanowski, Andrés; Garavaglia, Matías Javier; Goya, María Eugenia; Ghiringhelli, Pablo Daniel; Golombek, Diego Andrés

2014-01-01

Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive. In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda. With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system.

Glioblastoma, a brief review of history, molecular genetics, animal models and novel therapeutic strategies.

PubMed

Agnihotri, Sameer; Burrell, Kelly E; Wolf, Amparo; Jalali, Sharzhad; Hawkins, Cynthia; Rutka, James T; Zadeh, Gelareh

2013-02-01

Glioblastoma (GBM) is the most common and lethal primary brain tumor. Over the past few years tremendous genomic and proteomic characterization along with robust animal models of GBM have provided invaluable data that show that "GBM", although histologically indistinguishable from one another, are comprised of molecularly heterogenous diseases. In addition, robust pre-clinical models and a better understanding of the core pathways disrupted in GBM are providing a renewed optimism for novel strategies targeting these devastating tumors. Here, we summarize a brief history of the disease, our current molecular knowledge, lessons from animal models and emerging concepts of angiogenesis, invasion, and metabolism in GBM that may lend themselves to therapeutic targeting.

The developmental proteome of Drosophila melanogaster

PubMed Central

Casas-Vila, Nuria; Bluhm, Alina; Sayols, Sergi; Dinges, Nadja; Dejung, Mario; Altenhein, Tina; Kappei, Dennis; Altenhein, Benjamin; Roignant, Jean-Yves; Butter, Falk

2017-01-01

Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive proteomic study covering the complete life cycle is still missing. Here, we apply label-free quantitative proteomics to explore proteome remodeling across Drosophila’s life cycle, resulting in 7952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5458 proteins. Our proteome data enabled us to monitor isoform-specific expression of 34 genes during development, to identify the pseudogene Cyp9f3Ψ as a protein-coding gene, and to obtain evidence of 268 small proteins. Moreover, the comparison with available transcriptomic data uncovered examples of poor correlation between mRNA and protein, underscoring the importance of proteomics to study developmental progression. Data integration of our embryogenesis proteome with tissue-specific data revealed spatial and temporal information for further functional studies of yet uncharacterized proteins. Overall, our high resolution proteomes provide a powerful resource and can be explored in detail in our interactive web interface. PMID:28381612

INFN-Pisa scientific computation environment (GRID, HPC and Interactive Analysis)

NASA Astrophysics Data System (ADS)

Arezzini, S.; Carboni, A.; Caruso, G.; Ciampa, A.; Coscetti, S.; Mazzoni, E.; Piras, S.

2014-06-01

The INFN-Pisa Tier2 infrastructure is described, optimized not only for GRID CPU and Storage access, but also for a more interactive use of the resources in order to provide good solutions for the final data analysis step. The Data Center, equipped with about 6700 production cores, permits the use of modern analysis techniques realized via advanced statistical tools (like RooFit and RooStat) implemented in multicore systems. In particular a POSIX file storage access integrated with standard SRM access is provided. Therefore the unified storage infrastructure is described, based on GPFS and Xrootd, used both for SRM data repository and interactive POSIX access. Such a common infrastructure allows a transparent access to the Tier2 data to the users for their interactive analysis. The organization of a specialized many cores CPU facility devoted to interactive analysis is also described along with the login mechanism integrated with the INFN-AAI (National INFN Infrastructure) to extend the site access and use to a geographical distributed community. Such infrastructure is used also for a national computing facility in use to the INFN theoretical community, it enables a synergic use of computing and storage resources. Our Center initially developed for the HEP community is now growing and includes also HPC resources fully integrated. In recent years has been installed and managed a cluster facility (1000 cores, parallel use via InfiniBand connection) and we are now updating this facility that will provide resources for all the intermediate level HPC computing needs of the INFN theoretical national community.

Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation

PubMed Central

González, Carolina; Lazcano, Marcelo; Valdés, Jorge; Holmes, David S.

2016-01-01

Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e−5. None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD). PMID:28082953

Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation.

PubMed

González, Carolina; Lazcano, Marcelo; Valdés, Jorge; Holmes, David S

2016-01-01

Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia . These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e -5 . None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus , making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

PubMed Central

Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

2010-01-01

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)–cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK–cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants. PMID:20706207

Knowledge Translation: Moving Proteomics Science to Innovation in Society.

PubMed

Holmes, Christina; McDonald, Fiona; Jones, Mavis; Graham, Janice

2016-06-01

Proteomics is one of the pivotal next-generation biotechnologies in the current "postgenomics" era. Little is known about the ways in which innovative proteomics science is navigating the complex socio-political space between laboratory and society. It cannot be assumed that the trajectory between proteomics laboratory and society is linear and unidirectional. Concerned about public accountability and hopes for knowledge-based innovations, funding agencies and citizens increasingly expect that emerging science and technologies, such as proteomics, are effectively translated and disseminated as innovation in society. Here, we describe translation strategies promoted in the knowledge translation (KT) and science communication literatures and examine the use of these strategies within the field of proteomics. Drawing on data generated from qualitative interviews with proteomics scientists and ethnographic observation of international proteomics conferences over a 5-year period, we found that proteomics science incorporates a variety of KT strategies to reach knowledge users outside the field. To attain the full benefit of KT, however, proteomics scientists must challenge their own normative assumptions and approaches to innovation dissemination-beyond the current paradigm relying primarily on publication for one's scientific peers within one's field-and embrace the value of broader (interdisciplinary) KT strategies in promoting the uptake of their research. Notably, the Human Proteome Organization (HUPO) is paying increasing attention to a broader range of KT strategies, including targeted dissemination, integrated KT, and public outreach. We suggest that increasing the variety of KT strategies employed by proteomics scientists is timely and would serve well the omics system sciences community.

Introducing the CPL/MUW proteome database: interpretation of human liver and liver cancer proteome profiles by referring to isolated primary cells.

PubMed

Wimmer, Helge; Gundacker, Nina C; Griss, Johannes; Haudek, Verena J; Stättner, Stefan; Mohr, Thomas; Zwickl, Hannes; Paulitschke, Verena; Baron, David M; Trittner, Wolfgang; Kubicek, Markus; Bayer, Editha; Slany, Astrid; Gerner, Christopher

2009-06-01

Interpretation of proteome data with a focus on biomarker discovery largely relies on comparative proteome analyses. Here, we introduce a database-assisted interpretation strategy based on proteome profiles of primary cells. Both 2-D-PAGE and shotgun proteomics are applied. We obtain high data concordance with these two different techniques. When applying mass analysis of tryptic spot digests from 2-D gels of cytoplasmic fractions, we typically identify several hundred proteins. Using the same protein fractions, we usually identify more than thousand proteins by shotgun proteomics. The data consistency obtained when comparing these independent data sets exceeds 99% of the proteins identified in the 2-D gels. Many characteristic differences in protein expression of different cells can thus be independently confirmed. Our self-designed SQL database (CPL/MUW - database of the Clinical Proteomics Laboratories at the Medical University of Vienna accessible via www.meduniwien.ac.at/proteomics/database) facilitates (i) quality management of protein identification data, which are based on MS, (ii) the detection of cell type-specific proteins and (iii) of molecular signatures of specific functional cell states. Here, we demonstrate, how the interpretation of proteome profiles obtained from human liver tissue and hepatocellular carcinoma tissue is assisted by the Clinical Proteomics Laboratories at the Medical University of Vienna-database. Therefore, we suggest that the use of reference experiments supported by a tailored database may substantially facilitate data interpretation of proteome profiling experiments.

Imaging of High-Z doped, Imploded Capsule Cores

NASA Astrophysics Data System (ADS)

Prisbrey, Shon T.; Edwards, M. John; Suter, Larry J.

2006-10-01

The ability to correctly ascertain the shape of imploded fusion capsules is critical to be able to achieve the spherical symmetry needed to maximize the energy yield of proposed fusion experiments for the National Ignition Facility. Implosion of the capsule creates a hot, dense core. The introduction of a high-Z dopant into the gas-filled core of the capsule increases the amount of bremsstrahlung radiation produced in the core and should make the imaging of the imploded core easier. Images of the imploded core can then be analyzed to ascertain the symmetry of the implosion. We calculate that the addition of Ne gas into a deuterium gas core will increase the amount of radiation emission while preserving the surrogacy of the radiation and hydrodynamics in the indirect drive NIF hohlraum in the proposed cryogenic hohlraums. The increased emission will more easily enable measurement of asymmetries and tuning of the implosion.

A Targeted Quantitative Proteomics Strategy for Global Kinome Profiling of Cancer Cells and Tissues*

PubMed Central

Xiao, Yongsheng; Guo, Lei; Wang, Yinsheng

2014-01-01

Kinases are among the most intensively pursued enzyme superfamilies as targets for anti-cancer drugs. Large data sets on inhibitor potency and selectivity for more than 400 human kinases became available recently, offering the opportunity to design rationally novel kinase-based anti-cancer therapies. However, the expression levels and activities of kinases are highly heterogeneous among different types of cancer and even among different stages of the same cancer. The lack of effective strategy for profiling the global kinome hampers the development of kinase-targeted cancer chemotherapy. Here, we introduced a novel global kinome profiling method, based on our recently developed isotope-coded ATP-affinity probe and a targeted proteomic method using multiple-reaction monitoring (MRM), for assessing simultaneously the expression of more than 300 kinases in human cells and tissues. This MRM-based assay displayed much better sensitivity, reproducibility, and accuracy than the discovery-based shotgun proteomic method. Approximately 250 kinases could be routinely detected in the lysate of a single cell line. Additionally, the incorporation of iRT into MRM kinome library rendered our MRM kinome assay easily transferrable across different instrument platforms and laboratories. We further employed this approach for profiling kinase expression in two melanoma cell lines, which revealed substantial kinome reprogramming during cancer progression and demonstrated an excellent correlation between the anti-proliferative effects of kinase inhibitors and the expression levels of their target kinases. Therefore, this facile and accurate kinome profiling assay, together with the kinome-inhibitor interaction map, could provide invaluable knowledge to predict the effectiveness of kinase inhibitor drugs and offer the opportunity for individualized cancer chemotherapy. PMID:24520089

Successive bacterial colonisation of pork and its implications for forensic investigations.

PubMed

Handke, Jessica; Procopio, Noemi; Buckley, Michael; van der Meer, Dieudonne; Williams, Graham; Carr, Martin; Williams, Anna

2017-12-01

Bacteria are considered one of the major driving forces of the mammalian decomposition process and have only recently been recognised as forensic tools. At this point, little is known about their potential use as 'post-mortem clocks'. This study aimed to establish the proof of concept for using bacterial identification as post-mortem interval (PMI) indicators, using a multi-omics approach. Pieces of pork were placed in the University's outdoor facility and surface swabs were taken at regular intervals up to 60 days. Terminal restriction fragment length polymorphism (T-RFLP) of the 16S rDNA was used to identify bacterial taxa. It succeeded in detecting two out of three key contributors involved in decomposition and represents the first study to reveal Vibrionaceae as abundant on decomposing pork. However, a high fraction of present bacterial taxa could not be identified by T-RFLP. Proteomic analyses were also performed at selected time points, and they partially succeeded in the identification of precise strains, subspecies and species of bacteria that colonized the body after different PMIs. T-RFLP is incapable of reliably and fully identifying bacterial taxa, whereas proteomics could help in the identification of specific strains of bacteria. Nevertheless, microbial identification by next generation sequencing might be used as PMI clock in future investigations and in conjunction with information provided by forensic entomologists. To the best of our knowledge, this work represents the first attempt to find a cheaper and easily accessible, culture-independent alternative to high-throughput techniques to establish a 'microbial clock', in combination with proteomic strategies to address this issue. Copyright © 2017 Elsevier B.V. All rights reserved.

Reduced Insulin/Insulin-like Growth Factor-1 Signaling and Dietary Restriction Inhibit Translation but Preserve Muscle Mass in Caenorhabditis elegans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Depuydt, Geert; Xie, Fang; Petyuk, Vladislav A.

Reduced signaling through the C. elegans insulin/IGF1 like tyrosine kinase receptor daf2 and dietary restriction via bacterial dilution are two well-characterized lifespan-extending interventions that operate in parallel or through (partially) independent mechanisms. Using accurate mass and time tag LCMS/MS quantitative proteomics we detected that the abundance of a large number of ribosomal subunits is decreased in response to dietary restriction as well as in the daf2(e1370) insulin/IGF1 receptor mutant. In addition, general protein synthesis levels in these long-lived worms are repressed. Surprisingly, ribosomal transcript levels were not correlated to actual protein abundance, suggesting that posttranscriptional regulation determines ribosome content. Proteomicsmore » also revealed increased presence of many structural muscle cell components in long-lived worms, which appears to result from prioritized preservation of muscle cell volume in nutrient-poor conditions or low insulin-like signaling. Activation of DAF16, but not diet-restriction, stimulates mRNA expression of muscle-related genes to prevent muscle atrophy. Important daf2 specific proteome changes include overexpression of aerobic metabolism enzymes and a general activation of stress responsive and immune defense systems, while increased abundance of many protein subunits of the proteasome core complex is a DR-specific characteristic.« less

Integrative FourD omics approach profiles the target network of the carbon storage regulatory system

PubMed Central

Sowa, Steven W.; Gelderman, Grant; Leistra, Abigail N.; Buvanendiran, Aishwarya; Lipp, Sarah; Pitaktong, Areen; Vakulskas, Christopher A.; Romeo, Tony; Baldea, Michael

2017-01-01

Abstract Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets. PMID:28126921

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

PubMed

Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

2016-01-04

Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

Identification of proteomic biomarkers predicting prostate cancer aggressiveness and lethality despite biopsy-sampling error.

PubMed

Shipitsin, M; Small, C; Choudhury, S; Giladi, E; Friedlander, S; Nardone, J; Hussain, S; Hurley, A D; Ernst, C; Huang, Y E; Chang, H; Nifong, T P; Rimm, D L; Dunyak, J; Loda, M; Berman, D M; Blume-Jensen, P

2014-09-09

Key challenges of biopsy-based determination of prostate cancer aggressiveness include tumour heterogeneity, biopsy-sampling error, and variations in biopsy interpretation. The resulting uncertainty in risk assessment leads to significant overtreatment, with associated costs and morbidity. We developed a performance-based strategy to identify protein biomarkers predictive of prostate cancer aggressiveness and lethality regardless of biopsy-sampling variation. Prostatectomy samples from a large patient cohort with long follow-up were blindly assessed by expert pathologists who identified the tissue regions with the highest and lowest Gleason grade from each patient. To simulate biopsy-sampling error, a core from a high- and a low-Gleason area from each patient sample was used to generate a 'high' and a 'low' tumour microarray, respectively. Using a quantitative proteomics approach, we identified from 160 candidates 12 biomarkers that predicted prostate cancer aggressiveness (surgical Gleason and TNM stage) and lethal outcome robustly in both high- and low-Gleason areas. Conversely, a previously reported lethal outcome-predictive marker signature for prostatectomy tissue was unable to perform under circumstances of maximal sampling error. Our results have important implications for cancer biomarker discovery in general and development of a sampling error-resistant clinical biopsy test for prediction of prostate cancer aggressiveness.

Facile preparation of core-shell magnetic metal-organic framework nanospheres for the selective enrichment of endogenous peptides.

PubMed

Xiong, Zhichao; Ji, Yongsheng; Fang, Chunli; Zhang, Quanqing; Zhang, Lingyi; Ye, Mingliang; Zhang, Weibing; Zou, Hanfa

2014-06-10

Facile preparation of core-shell magnetic metal-organic framework nanospheres by a layer-by-layer approach is presented. The nanospheres have high surface area (285.89 cm(2)  g(-1)), large pore volume (0.18 cm(3)  g(-1)), two kinds of mesopores (2.50 and 4.72 nm), excellent magnetic responsivity (55.65 emu g(-1)), structural stability, and good dispersibility. The combination of porosity, hydrophobicity, and uniform magnetism was exploited for effective enrichment of peptides with simultaneous exclusion of high molecular weight proteins. The nanospheres were successfully applied in the selective enrichment of endogenous peptides in human serum. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Review: Proteomics in Retinal Artery Occlusion, Retinal Vein Occlusion, Diabetic Retinopathy and Acquired Macular Disorders

PubMed Central

Cehofski, Lasse Jørgensen; Honoré, Bent; Vorum, Henrik

2017-01-01

Retinal artery occlusion (RAO), retinal vein occlusion (RVO), diabetic retinopathy (DR) and age-related macular degeneration (AMD) are frequent ocular diseases with potentially sight-threatening outcomes. In the present review we discuss major findings of proteomic studies of RAO, RVO, DR and AMD, including an overview of ocular proteome changes associated with anti-vascular endothelial growth factor (VEGF) treatments. Despite the severe outcomes of RAO, the proteome of the disease remains largely unstudied. There is also limited knowledge about the proteome of RVO, but proteomic studies suggest that RVO is associated with remodeling of the extracellular matrix and adhesion processes. Proteomic studies of DR have resulted in the identification of potential therapeutic targets such as carbonic anhydrase-I. Proliferative diabetic retinopathy is the most intensively studied stage of DR. Proteomic studies have established VEGF, pigment epithelium-derived factor (PEDF) and complement components as key factors associated with AMD. The aim of this review is to highlight the major milestones in proteomics in RAO, RVO, DR and AMD. Through large-scale protein analyses, proteomics is bringing new important insights into these complex pathological conditions. PMID:28452939

Health Occupations Curriculum. Skills and Theory for Health Assistant. Volume I, Units 1-4.

ERIC Educational Resources Information Center

Arizona State Dept. of Education, Phoenix.

This volume consists of the first four units of a basic core curriculum that is intended for all health workers. The units deal with the following topics: (1) the health care facility, the long-term care facility, the health team, and the nursing team; (2) verbal and nonverbal communication, written communication, human behavior, ethical behavior,…

30 CFR 254.23 - What information must I include in the “Emergency response action plan” section?

Code of Federal Regulations, 2011 CFR

2011-07-01

... FOR FACILITIES LOCATED SEAWARD OF THE COAST LINE Oil-Spill Response Plans for Outer Continental Shelf Facilities § 254.23 What information must I include in the “Emergency response action plan” section? The “Emergency response action plan”section is the core of the response plan. Put information in easy-to-use...

The WPI reactor-readying for the next generation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bobek, L.M.

1993-01-01

Built in 1959, the 10-kW open-pool nuclear training reactor at Worcester Polytechnic Institute (WPI) was one of the first such facilities in the nation located on a university campus. Since then, the reactor and its related facilities have been used to train two generations of nuclear engineers and scientists for the nuclear industry. With the use of nuclear technology playing an increasing role in many segments of the economy, WPI with its nuclear reactor facility is committed to continuing its mission of training future nuclear engineers and scientists. The WPI reactor includes a 6-in. beam port, graphite thermal column, andmore » in-core sample facility. The reactor, housed in an open 8000-gal tank of water, is designed so that the core is readily accessible. Both the control console and the peripheral counting equipment used for student projects and laboratory exercises are located in the reactor room. This arrangement provides convenience and flexibility in using the reactor for foil activations in neutron flux measurements, diffusion measurements, radioactive decay measurements, and the neutron activation of samples for analysis. In 1988, the reactor was successfully converted to low-enriched uranium fuel.« less

Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level.

PubMed

Bensaddek, Dalila; Narayan, Vikram; Nicolas, Armel; Murillo, Alejandro Brenes; Gartner, Anton; Kenyon, Cynthia J; Lamond, Angus I

2016-02-01

Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Translational plant proteomics: a perspective.

PubMed

Agrawal, Ganesh Kumar; Pedreschi, Romina; Barkla, Bronwyn J; Bindschedler, Laurence Veronique; Cramer, Rainer; Sarkar, Abhijit; Renaut, Jenny; Job, Dominique; Rakwal, Randeep

2012-08-03

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics. Copyright © 2012 Elsevier B.V. All rights reserved.

The strategy, organization, and progress of the HUPO Human Proteome Project.

PubMed

Omenn, Gilbert S

2014-04-04

The Human Proteome Project is a major, comprehensive initiative of the Human Proteome Organization. This global collaborative effort aims to identify and characterize at least one protein product and many PTM, SAP, and splice variant isoforms from the 20,300 human protein-coding genes. The deliverables are an extensive parts list and an array of technology platforms, reagents, spectral libraries, and linked knowledge bases that advance the field and facilitate the use of proteomics by a much wider community of life scientists. Such enablement will help address the Grand Challenge of using proteomics to bridge major gaps between evidence of genomic variation and diverse phenotypes. The HUPO Human Proteome Project (HPP) has made an outstanding launch, including a special issue of the Journal of Proteome Research on the Chromosome-centric HPP with a total of 48 articles. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes? © 2013.

The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weckwerth, Wolfram; Baginsky, Sacha; Van Wijk, Klass

2009-12-01

In the past 10 years, we have witnessed remarkable advances in the field of plant molecular biology. The rapid development of proteomic technologies and the speed with which these techniques have been applied to the field have altered our perception of how we can analyze proteins in complex systems. At nearly the same time, the availability of the complete genome for the model plant Arabidopsis thaliana was released; this effort provides an unsurpassed resource for the identification of proteins when researchers use MS to analyze plant samples. Recognizing the growth in this area, the Multinational Arabidopsis Steering Committee (MASC) establishedmore » a subcommittee for A. thaliana proteomics in 2006 with the objective of consolidating databases, technique standards, and experimentally validated candidate genes and functions. Since the establishment of the Multinational Arabidopsis Steering Subcommittee for Proteomics (MASCP), many new approaches and resources have become available. Recently, the subcommittee established a webpage to consolidate this information (www.masc-proteomics.org). It includes links to plant proteomic databases, general information about proteomic techniques, meeting information, a summary of proteomic standards, and other relevant resources. Altogether, this website provides a useful resource for the Arabidopsis proteomics community. In the future, the website will host discussions and investigate the cross-linking of databases. The subcommittee members have extensive experience in arabidopsis proteomics and collectively have produced some of the most extensive proteomics data sets for this model plant (Table S1 in the Supporting Information has a list of resources). The largest collection of proteomics data from a single study in A. thaliana was assembled into an accessible database (AtProteome; http://fgcz-atproteome.unizh.ch/index.php) and was recently published by the Baginsky lab.1 The database provides links to major Arabidopsis online resources, and raw data have been deposited in PRIDE and PRIDE BioMart. Included in this database is an Arabidopsis proteome map that provides evidence for the expression of {approx}50% of all predicted gene models, including several alternative gene models that are not represented in The Arabidopsis Information Resource (TAIR) protein database. A set of organ-specific biomarkers is provided, as well as organ-specific proteotypic peptides for 4105 proteins that can be used to facilitate targeted quantitative proteomic surveys. In the future, the AtProteome database will be linked to additional existing resources developed by MASCP members, such as PPDB, ProMEX, and SUBA. The most comprehensive study on the Arabidopsis chloroplast proteome, which includes information on chloroplast sorting signals, posttranslational modifications (PTMs), and protein abundances (analyzed by high-accuracy MS [Orbitrap]), was recently published by the van Wijk lab.2 These and previous data are available via the plant proteome database (PPDB; http://ppdb.tc.cornell.edu) for A. thaliana and maize. PPDB provides genome-wide experimental and functional characterization of the A. thaliana and maize proteomes, including PTMs and subcellular localization information, with an emphasis on leaf and plastid proteins. Maize and Arabidopsis proteome entries are directly linked via internal BLAST alignments within PPDB. Direct links for each protein to TAIR, SUBA, ProMEX, and other resources are also provided.« less

Advancing Proteomics Research through Collaboration | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute (NCI), through the Office of Cancer Clinical Proteomics Research (OCCPR), has signed two Memorandums of Understanding (MOUs) in the areas of sharing proteomics reagents and protocols and also in regulatory science.

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

PubMed

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-06-23

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from genome sequences, though there are over lapped proteins. Based on the demonstrated application of data stored in the database for functional analyses, it is suggested that these data will be useful for analyses of biological mechanisms in soybean. Furthermore, coupled with recent advances in information and communication technology, the usefulness of this database would increase in the analyses of biological mechanisms. Copyright © 2017 Elsevier B.V. All rights reserved.

The Escherichia coli Proteome: Past, Present, and Future Prospects†

PubMed Central

Han, Mee-Jung; Lee, Sang Yup

2006-01-01

Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects. PMID:16760308

Sys-BodyFluid: a systematical database for human body fluid proteome research

PubMed Central

Li, Su-Jun; Peng, Mao; Li, Hong; Liu, Bo-Shu; Wang, Chuan; Wu, Jia-Rui; Li, Yi-Xue; Zeng, Rong

2009-01-01

Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10 000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/. PMID:18978022

Sys-BodyFluid: a systematical database for human body fluid proteome research.

PubMed

Li, Su-Jun; Peng, Mao; Li, Hong; Liu, Bo-Shu; Wang, Chuan; Wu, Jia-Rui; Li, Yi-Xue; Zeng, Rong

2009-01-01

Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10,000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/.

The Challenge of Human Spermatozoa Proteome: A Systematic Review.

PubMed

Gilany, Kambiz; Minai-Tehrani, Arash; Amini, Mehdi; Agharezaee, Niloofar; Arjmand, Babak

2017-01-01

Currently, there are 20,197 human protein-coding genes in the most expertly curated database (UniProtKB/Swiss-Pro). Big efforts have been made by the international consortium, the Chromosome-Centric Human Proteome Project (C-HPP) and independent researchers, to map human proteome. In brief, anno 2017 the human proteome was outlined. The male factor contributes to 50% of infertility in couples. However, there are limited human spermatozoa proteomic studies. Firstly, the development of the mapping of the human spermatozoa was analyzed. The human spermatozoa have been used as a model for missing proteins. It has been shown that human spermatozoa are excellent sources for finding missing proteins. Y chromosome proteome mapping is led by Iran. However, it seems that it is extremely challenging to map the human spermatozoa Y chromosome proteins based on current mass spectrometry-based proteomics technology. Post-translation modifications (PTMs) of human spermatozoa proteome are the most unexplored area and currently the exact role of PTMs in male infertility is unknown. Additionally, the clinical human spermatozoa proteomic analysis, anno 2017 was done in this study.

A proteomics performance standard to support measurement quality in proteomics.

PubMed

Beasley-Green, Ashley; Bunk, David; Rudnick, Paul; Kilpatrick, Lisa; Phinney, Karen

2012-04-01

The emergence of MS-based proteomic platforms as a prominent technology utilized in biochemical and biomedical research has increased the need for high-quality MS measurements. To address this need, National Institute of Standards and Technology (NIST) reference material (RM) 8323 yeast protein extract is introduced as a proteomics quality control material for benchmarking the preanalytical and analytical performance of proteomics-based experimental workflows. RM 8323 yeast protein extract is based upon the well-characterized eukaryote Saccharomyces cerevisiae and can be utilized in the design and optimization of proteomics-based methodologies from sample preparation to data analysis. To demonstrate its utility as a proteomics quality control material, we coupled LC-MS/MS measurements of RM 8323 with the NIST MS Quality Control (MSQC) performance metrics to quantitatively assess the LC-MS/MS instrumentation parameters that influence measurement accuracy, repeatability, and reproducibility. Due to the complexity of the yeast proteome, we also demonstrate how NIST RM 8323, along with the NIST MSQC performance metrics, can be used in the evaluation and optimization of proteomics-based sample preparation methods. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The NASA Lewis Research Center Internal Fluid Mechanics Facility

NASA Technical Reports Server (NTRS)

Porro, A. R.; Hingst, W. R.; Wasserbauer, C. A.; Andrews, T. B.

1991-01-01

An experimental facility specifically designed to investigate internal fluid duct flows is described. It is built in a modular fashion so that a variety of internal flow test hardware can be installed in the facility with minimal facility reconfiguration. The facility and test hardware interfaces are discussed along with design constraints of future test hardware. The plenum flow conditioning approach is also detailed. Available instrumentation and data acquisition capabilities are discussed. The incoming flow quality was documented over the current facility operating range. The incoming flow produces well behaved turbulent boundary layers with a uniform core. For the calibration duct used, the boundary layers approached 10 percent of the duct radius. Freestream turbulence levels at the various operating conditions varied from 0.64 to 0.69 percent of the average freestream velocity.

Advances of Proteomic Sciences in Dentistry.

PubMed

Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

2016-05-13

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study

DOE PAGES

Sun, Su; Xie, Shangxian; Cheng, Yanbing; ...

2017-09-12

Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass, is discovered to promote the degradation of Azo dye by white-rot fungus Irpex lacteus CD2 in the lignin/dye/fungus system. Shotgun proteomics technique was used to understand degradation mechanism at the protein level formore » the lignin/dye/fungus system. Our proteomics study can identify about two thousand proteins (one third of the predicted white-rot fungal proteome) in a single experiment, as one of the most powerful proteomics platforms to study the fungal system to date. The study shows a significant enrichment of oxidoreduction functional category under the dye/lignin combined treatment. An in vitro validation is performed and supports our hypothesis that the synergy of Fenton reaction and manganese peroxidase might play an important role in DR5B dye degradation. The results could guide the development of effective bioremediation strategies and efficient lignocellulosic biomass conversion.« less

Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study.

PubMed

Sun, Su; Xie, Shangxian; Cheng, Yanbing; Yu, Hongbo; Zhao, Honglu; Li, Muzi; Li, Xiaotong; Zhang, Xiaoyu; Yuan, Joshua S; Dai, Susie Y

2017-09-12

Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass, is discovered to promote the degradation of Azo dye by white-rot fungus Irpex lacteus CD2 in the lignin/dye/fungus system. Shotgun proteomics technique was used to understand degradation mechanism at the protein level for the lignin/dye/fungus system. Our proteomics study can identify about two thousand proteins (one third of the predicted white-rot fungal proteome) in a single experiment, as one of the most powerful proteomics platforms to study the fungal system to date. The study shows a significant enrichment of oxidoreduction functional category under the dye/lignin combined treatment. An in vitro validation is performed and supports our hypothesis that the synergy of Fenton reaction and manganese peroxidase might play an important role in DR5B dye degradation. The results could guide the development of effective bioremediation strategies and efficient lignocellulosic biomass conversion.

Proteomic and Bioinformatic Profile of Primary Human Oral Epithelial Cells

PubMed Central

Ghosh, Santosh K.; Yohannes, Elizabeth; Bebek, Gurkan; Weinberg, Aaron; Jiang, Bin; Willard, Belinda; Chance, Mark R.; Kinter, Michael T.; McCormick, Thomas S.

2012-01-01

Wounding of the oral mucosa occurs frequently in a highly septic environment. Remarkably, these wounds heal quickly and the oral cavity, for the most part, remains healthy. Deciphering the normal human oral epithelial cell (NHOEC) proteome is critical for understanding the mechanism(s) of protection elicited when the mucosal barrier is intact, as well as when it is breached. Combining 2D gel electrophoresis with shotgun proteomics resulted in identification of 1662 NHOEC proteins. Proteome annotations were performed based on protein classes, molecular functions, disease association and membership in canonical and metabolic signaling pathways. Comparing the NHOEC proteome with a database of innate immunity-relevant interactions (InnateDB) identified 64 common proteins associated with innate immunity. Comparison with published salivary proteomes revealed that 738/1662 NHOEC proteins were common, suggesting that significant numbers of salivary proteins are of epithelial origin. Gene ontology analysis showed similarities in the distributions of NHOEC and saliva proteomes with regard to biological processes, and molecular functions. We also assessed the inter-individual variability of the NHOEC proteome and observed it to be comparable with other primary cells. The baseline proteome described in this study should serve as a resource for proteome studies of the oral mucosa, especially in relation to disease processes. PMID:23035736

The application of proteomics in different aspects of hepatocellular carcinoma research.

PubMed

Xing, Xiaohua; Liang, Dong; Huang, Yao; Zeng, Yongyi; Han, Xiao; Liu, Xiaolong; Liu, Jingfeng

2016-08-11

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors, which is causing the second leading cancer-related death worldwide. With the significant advances of high-throughput protein analysis techniques, the proteomics offered an extremely useful and versatile analytical platform for biomedical researches. In recent years, different proteomic strategies have been widely applied in the various aspects of HCC studies, ranging from screening the early diagnostic and prognostic biomarkers to in-depth investigating the underlying molecular mechanisms. In this review, we would like to systematically summarize the current applications of proteomics in hepatocellular carcinoma study, and discuss the challenges of applying proteomics in study clinical samples, as well as discuss the possible application of proteomics in precision medicine. In this review, we have systematically summarized the current applications of proteomics in hepatocellular carcinoma study, ranging from screening biomarkers to in-depth investigating the underlying molecular mechanisms. In addition, we have discussed the challenges of applying proteomics in study clinical samples, as well as the possible applications of proteomics in precision medicine. We believe that this review would help readers to be better familiar with the recent progresses of clinical proteomics, especially in the field of hepatocellular carcinoma research. Copyright © 2016 Elsevier B.V. All rights reserved.

Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Su; Xie, Shangxian; Cheng, Yanbing

Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass, is discovered to promote the degradation of Azo dye by white-rot fungus Irpex lacteus CD2 in the lignin/dye/fungus system. Shotgun proteomics technique was used to understand degradation mechanism at the protein level formore » the lignin/dye/fungus system. Our proteomics study can identify about two thousand proteins (one third of the predicted white-rot fungal proteome) in a single experiment, as one of the most powerful proteomics platforms to study the fungal system to date. The study shows a significant enrichment of oxidoreduction functional category under the dye/lignin combined treatment. An in vitro validation is performed and supports our hypothesis that the synergy of Fenton reaction and manganese peroxidase might play an important role in DR5B dye degradation. The results could guide the development of effective bioremediation strategies and efficient lignocellulosic biomass conversion.« less

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

PubMed

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.

Marine proteomics: a critical assessment of an emerging technology.

PubMed

Slattery, Marc; Ankisetty, Sridevi; Corrales, Jone; Marsh-Hunkin, K Erica; Gochfeld, Deborah J; Willett, Kristine L; Rimoldi, John M

2012-10-26

The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.

Proteomic Assessment of Poultry Spermatozoa

USDA-ARS?s Scientific Manuscript database

Fully characterizing the protein composition of spermatozoa is the first step in utilizing proteomics to delineate the function of sperm proteins. To date, sperm proteome maps have been partially developed for the human, mouse, rat, bull and several invertebrates. Here we report the first proteomic...

NETL CT Imaging Facility

ScienceCinema

None

2018-02-13

NETL's CT Scanner laboratory is equipped with three CT scanners and a mobile core logging unit that work together to provide characteristic geologic and geophysical information at different scales, non-destructively.

Assessment of the core and support functions of the Integrated Disease Surveillance system in Maharashtra, India

PubMed Central

2013-01-01

Background Monitoring the progress of the Integrated Disease Surveillance (IDS) strategy is an important component to ensure its sustainability in the state of Maharashtra in India. The purpose of the study was to document the baseline performance of the system on its core and support functions and to understand the challenges for its transition from an externally funded “project” to a state owned surveillance “program”. Methods Multi-centre, retrospective cross-sectional evaluation study to assess the structure, core and support surveillance functions using modified WHO generic questionnaires. All 34 districts in the state and randomly identified 46 facilities and 25 labs were included in the study. Results Case definitions were rarely used at the periphery. Limited laboratory capacity at all levels compromised case and outbreak confirmation. Only 53% districts could confirm all priority diseases. Stool sample processing was the weakest at the periphery. Availability of transport media, trained staff, and rapid diagnostic tests were main challenges at the periphery. Data analysis was weak at both district and facility levels. Outbreak thresholds were better understood at facility level (59%) than at the district (18%). None of the outbreak indicator targets were met and submission of final outbreak report was the weakest. Feedback and training was significantly better (p < 0.0001) at district level (65%; 76%) than at facility level (15%; 37%). Supervision was better at the facility level (37%) than at district (18%) and so were coordination, communication and logistic resources. Contractual part time positions, administrative delays in recruitment, and vacancies (30%) were main human resource issues that hampered system performance. Conclusions Significant progress has been made in the core and support surveillance functions in Maharashtra, however some challenges exist. Support functions (laboratory, transport and communication equipment, training, supervision, human and other resources) are particularly weak at the district level. Structural integration and establishing permanent state and district surveillance officer positions will ensure leadership; improve performance; support continuity; and offer sustainability to the program. Institutionalizing the integrated disease surveillance strategy through skills based personnel development and infrastructure strengthening at district levels is the only way to avoid it from ending up isolated! Improving surveillance quality should be the next on agenda for the state. PMID:23764137

Design and characterization of an irradiation facility with real-time monitoring

NASA Astrophysics Data System (ADS)

Braisted, Jonathan David

Radiation causes performance degradation in electronics by inducing atomic displacements and ionizations. While radiation hardened components are available, non-radiation hardened electronics can be preferable because they are generally more compact, require less power, and less expensive than radiation tolerant equivalents. It is therefore important to characterize the performance of electronics, both hardened and non-hardened, to prevent costly system or mission failures. Radiation effects tests for electronics generally involve a handful of step irradiations, leading to poorly-resolved data. Step irradiations also introduce uncertainties in electrical measurements due to temperature annealing effects. This effect may be intensified if the time between exposure and measurement is significant. Induced activity in test samples also complicates data collection of step irradiated test samples. The University of Texas at Austin operates a 1.1 MW Mark II TRIGA research reactor. An in-core irradiation facility for radiation effects testing with a real-time monitoring capability has been designed for the UT TRIGA reactor. The facility is larger than any currently available non-central location in a TRIGA, supporting testing of larger electronic components as well as other in-core irradiation applications requiring significant volume such as isotope production or neutron transmutation doping of silicon. This dissertation describes the design and testing of the large in-core irradiation facility and the experimental campaign developed to test the real-time monitoring capability. This irradiation campaign was performed to test the real-time monitoring capability at various reactor power levels. The device chosen for characterization was the 4N25 general-purpose optocoupler. The current transfer ratio, which is an important electrical parameter for optocouplers, was calculated as a function of neutron fluence and gamma dose from the real-time voltage measurements. The resultant radiation effects data was seen to be repeatable and exceptionally finely-resolved. Therefore, the capability at UT TRIGA has been proven competitive with world-class effects characterization facilities.

Optimizing Algorithm Choice for Metaproteomics: Comparing X!Tandem and Proteome Discoverer for Soil Proteomes

NASA Astrophysics Data System (ADS)

Diaz, K. S.; Kim, E. H.; Jones, R. M.; de Leon, K. C.; Woodcroft, B. J.; Tyson, G. W.; Rich, V. I.

2014-12-01

The growing field of metaproteomics links microbial communities to their expressed functions by using mass spectrometry methods to characterize community proteins. Comparison of mass spectrometry protein search algorithms and their biases is crucial for maximizing the quality and amount of protein identifications in mass spectral data. Available algorithms employ different approaches when mapping mass spectra to peptides against a database. We compared mass spectra from four microbial proteomes derived from high-organic content soils searched with two search algorithms: 1) Sequest HT as packaged within Proteome Discoverer (v.1.4) and 2) X!Tandem as packaged in TransProteomicPipeline (v.4.7.1). Searches used matched metagenomes, and results were filtered to allow identification of high probability proteins. There was little overlap in proteins identified by both algorithms, on average just ~24% of the total. However, when adjusted for spectral abundance, the overlap improved to ~70%. Proteome Discoverer generally outperformed X!Tandem, identifying an average of 12.5% more proteins than X!Tandem, with X!Tandem identifying more proteins only in the first two proteomes. For spectrally-adjusted results, the algorithms were similar, with X!Tandem marginally outperforming Proteome Discoverer by an average of ~4%. We then assessed differences in heat shock proteins (HSP) identification by the two algorithms by BLASTing identified proteins against the Heat Shock Protein Information Resource, because HSP hits typically account for the majority signal in proteomes, due to extraction protocols. Total HSP identifications for each of the 4 proteomes were approximately ~15%, ~11%, ~17%, and ~19%, with ~14% for total HSPs with redundancies removed. Of the ~15% average of proteins from the 4 proteomes identified as HSPs, ~10% of proteins and spectra were identified by both algorithms. On average, Proteome Discoverer identified ~9% more HSPs than X!Tandem.

Construction of a high-performance magnetic enzyme nanosystem for rapid tryptic digestion

NASA Astrophysics Data System (ADS)

Cheng, Gong; Zheng, Si-Yang

2014-11-01

A magnetic enzyme nanosystem have been designed and constructed by a polydopamine (PDA)-modification strategy. The magnetic enzyme nanosystem has well defined core-shell structure and a relatively high saturation magnetization (Ms) value of 48.3 emu g-1. The magnetic enzyme system can realize rapid, efficient and reusable tryptic digestion of proteins by taking advantage of its magnetic core and biofunctional shell. Various standard proteins (e.g. cytochrome C (Cyt-C), myoglobin (MYO) and bovine serum albumin (BSA)) have been used to evaluate the effectiveness of the magnetic enzyme nanosystem. The results show that the magnetic enzyme nanosystem can digest the proteins in 30 minutes, and the results are comparable to conventional 12 hours in-solution digestion. Furthermore, the magnetic enzyme nanosystem is also effective in the digestion of low-concentration proteins, even at as low as 5 ng μL-1 substrate concentration. Importantly, the system can be reused several times, and has excellent stability for storage. Therefore, this work will be highly beneficial for the rapid digestion and identification of proteins in future proteomics.

NCI Launches Proteomics Assay Portal | Office of Cancer Clinical Proteomics Research

Cancer.gov

In a paper recently published by the journal Nature Methods, Investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) announced the launch of a proteomics Assay Portal for multiple reaction monitoring-mass spectrometry (MRM-MS) assays.  This community web-based repository for well-characterized quantitative proteomic assays currently consists of 456 unique peptide assays to 282 unique proteins and ser

CPTAC Releases Largest-Ever Colorectal Cancer Proteome Dataset from Previously Genome Characterized Tumors | Office of Cancer Clinical Proteomics Research

Cancer.gov

On September 4, 2013, NCI’s Clinical Proteomics Tumor Analysis Consortium (CPTAC) publicly released proteomic data produced from colorectal tumor samples previously analyzed by The Cancer Genome Atlas (TCGA).  This is the initial release of proteomic tumor data designed to complement genomic data on the same tumors. The data is publicly available at the CPTAC data portal.

CPTAC Releases Largest-Ever Ovarian Cancer Proteome Dataset from Previously Genome Characterized Tumors | Office of Cancer Clinical Proteomics Research

Cancer.gov

National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have just released a comprehensive dataset of the proteomic analysis of high grade serous ovarian tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).  This is one of the largest public datasets covering the proteome, phosphoproteome and glycoproteome with complementary deep genomic sequencing data on the same tumor.

Harnessing Data to Assess Equity of Care by Race, Ethnicity and Language

PubMed Central

Gracia, Amber; Cheirif, Jorge; Veliz, Juana; Reyna, Melissa; Vecchio, Mara; Aryal, Subhash

2015-01-01

Objective: Determine any disparities in care based on race, ethnicity and language (REaL) by utilizing inpatient (IP) core measures at Texas Health Resources, a large, faith-based, non-profit health care delivery system located in a large, ethnically diverse metropolitan area in Texas. These measures, which were established by the U.S. Centers for Medicare and Medicaid Services (CMS) and The Joint Commission (TJC), help to ensure better accountability for patient outcomes throughout the U.S. health care system. Methods: Sample analysis to understand the architecture of race, ethnicity and language (REaL) variables within the Texas Health clinical database, followed by development of the logic, method and framework for isolating populations and evaluating disparities by race (non-Hispanic White, non-Hispanic Black, Native American/Native Hawaiian/Pacific Islander, Asian and Other); ethnicity (Hispanic and non-Hispanic); and preferred language (English and Spanish). The study is based on use of existing clinical data for four inpatient (IP) core measures: Acute Myocardial Infarction (AMI), Congestive Heart Failure (CHF), Pneumonia (PN) and Surgical Care (SCIP), representing 100% of the sample population. These comprise a high number of cases presenting in our acute care facilities. Findings are based on a sample of clinical data (N = 19,873 cases) for the four inpatient (IP) core measures derived from 13 of Texas Health’s wholly-owned facilities, formulating a set of baseline data. Results: Based on applied method, Texas Health facilities consistently scored high with no discernable race, ethnicity and language (REaL) disparities as evidenced by a low percentage difference to the reference point (non-Hispanic White) on IP core measures, including: AMI (0.3%–1.2%), CHF (0.7%–3.0%), PN (0.5%–3.7%), and SCIP (0–0.7%). PMID:26703665

Tumor Cold Ischemia | Office of Cancer Clinical Proteomics Research

Cancer.gov

In a recently published manuscript in the journal of Molecular and Cellular Proteomics, researchers from the National Cancer Institutes (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigated the effect of cold ischemia on the proteome of fresh frozen tumors.

PatternLab for proteomics 4.0: A one-stop shop for analyzing shotgun proteomic data

PubMed Central

Carvalho, Paulo C; Lima, Diogo B; Leprevost, Felipe V; Santos, Marlon D M; Fischer, Juliana S G; Aquino, Priscila F; Moresco, James J; Yates, John R; Barbosa, Valmir C

2017-01-01

PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for analyzing shotgun proteomic data. PatternLab contains modules for formatting sequence databases, performing peptide spectrum matching, statistically filtering and organizing shotgun proteomic data, extracting quantitative information from label-free and chemically labeled data, performing statistics for differential proteomics, displaying results in a variety of graphical formats, performing similarity-driven studies with de novo sequencing data, analyzing time-course experiments, and helping with the understanding of the biological significance of data in the light of the Gene Ontology. Here we describe PatternLab for proteomics 4.0, which closely knits together all of these modules in a self-contained environment, covering the principal aspects of proteomic data analysis as a freely available and easily installable software package. All updates to PatternLab, as well as all new features added to it, have been tested over the years on millions of mass spectra. PMID:26658470

Computational clustering for viral reference proteomes

PubMed Central

Chen, Chuming; Huang, Hongzhan; Mazumder, Raja; Natale, Darren A.; McGarvey, Peter B.; Zhang, Jian; Polson, Shawn W.; Wang, Yuqi; Wu, Cathy H.

2016-01-01

Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies. Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt’s curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs. Availability and implementation: http://proteininformationresource.org/rps/viruses/ Contact: chenc@udel.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153712

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, D. H.; Reigel, M. M.

A full-scale formed core sampler was designed and functionally tested for use in the Saltstone Disposal Facility (SDF). Savannah River National Laboratory (SRNL) was requested to compare properties of the formed core samples and core drilled samples taken from adjacent areas in the full-scale sampler. While several physical properties were evaluated, the primary property of interest was hydraulic conductivity. Differences in hydraulic conductivity between the samples from the formed core sampler and those representing the bulk material were noted with respect to the initial handling and storage of the samples. Due to testing conditions, the site port samples were exposedmore » to uncontrolled temperature and humidity conditions prior to testing whereas the formed core samples were kept in sealed containers with minimal exposure to an uncontrolled environment prior to testing. Based on the results of the testing, no significant differences in porosity or density were found between the formed core samples and those representing the bulk material in the test stand.« less

Advances of Proteomic Sciences in Dentistry

PubMed Central

Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

2016-01-01

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed. PMID:27187379

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

PubMed Central

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

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. PMID:25158685

Current advances in esophageal cancer proteomics.

PubMed

Uemura, Norihisa; Kondo, Tadashi

2015-06-01

We review the current status of proteomics for esophageal cancer (EC) from a clinician's viewpoint. The ultimate goal of cancer proteomics is the improvement of clinical outcome. The proteome as a functional translation of the genome is a straightforward representation of genomic mechanisms that trigger carcinogenesis. Cancer proteomics has identified the mechanisms of carcinogenesis and tumor progression, detected biomarker candidates for early diagnosis, and provided novel therapeutic targets for personalized treatments. Our review focuses on three major topics in EC proteomics: diagnostics, treatment, and molecular mechanisms. We discuss the major histological differences between EC types, i.e., esophageal squamous cell carcinoma and adenocarcinoma, and evaluate the clinical significance of published proteomics studies, including promising diagnostic biomarkers and novel therapeutic targets, which should be further validated prior to launching clinical trials. Multi-disciplinary collaborations between basic scientists, clinicians, and pathologists should be established for inter-institutional validation. In conclusion, EC proteomics has provided significant results, which after thorough validation, should lead to the development of novel clinical tools and improvement of the clinical outcome for esophageal cancer patients. This article is part of a Special Issue entitled: Medical Proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

Proteomics reveals the effects of sustained weight loss on the human plasma proteome.

PubMed

Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka; Grassl, Niklas; Iepsen, Eva W; Lundgren, Julie; Madsbad, Sten; Holst, Jens J; Torekov, Signe S; Mann, Matthias

2016-12-22

Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly affected proteins. The adipocyte-secreted SERPINF1 and apolipoprotein APOF1 were most significantly regulated with fold changes of -16% and +37%, respectively (P < 10 -13 ), and the entire apolipoprotein family showed characteristic differential regulation. Clinical laboratory parameters are reflected in the plasma proteome, and eight plasma proteins correlated better with insulin resistance than the known marker adiponectin. Nearly all study participants benefited from weight loss regarding a ten-protein inflammation panel defined from the proteomics data. We conclude that plasma proteome profiling broadly evaluates and monitors intervention in metabolic diseases. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment.

PubMed

Welker, F

2018-02-20

The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized between moderately divergent proteomes, as indicated by almost complete recovery of informative positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications for the study of fast-evolving proteins in hominins, non-hominin animals, and ancient bacterial proteins in evolutionary contexts.

The Deferred Maintenance Dilemma.

ERIC Educational Resources Information Center

Medlin, E. Lander

2003-01-01

Discusses the hazards of the trend toward accumulated deferred maintenance in higher education and offers advice on tying facilities needs and issues to the core strategies and goals of the institution. (EV)

Preliminary control system design and analysis for the Space Station Furnace Facility thermal control system

NASA Technical Reports Server (NTRS)

Jackson, M. E.

1995-01-01

This report presents the Space Station Furnace Facility (SSFF) thermal control system (TCS) preliminary control system design and analysis. The SSFF provides the necessary core systems to operate various materials processing furnaces. The TCS is defined as one of the core systems, and its function is to collect excess heat from furnaces and to provide precise cold temperature control of components and of certain furnace zones. Physical interconnection of parallel thermal control subsystems through a common pump implies the description of the TCS by coupled nonlinear differential equations in pressure and flow. This report formulates the system equations and develops the controllers that cause the interconnected subsystems to satisfy flow rate tracking requirements. Extensive digital simulation results are presented to show the flow rate tracking performance.

Transient analysis for the tajoura critical facility with IRT-2M HEU fuel and IRT-4M leu fuel : ANL independent verification results.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garner, P. L.; Hanan, N. A.

2005-12-02

Calculations have been performed for postulated transients in the Critical Facility at the Tajoura Nuclear Research Center (TNRC) in Libya. These calculations have been performed at the request of staff of the Renewable Energy and Water Desalinization Research Center (REWDRC) who are performing similar calculations. The transients considered were established during a working meeting between ANL and REWDRC staff on October 1-2, 2005 and subsequent email correspondence. Calculations were performed for the current high-enriched uranium (HEU) core and the proposed low-enriched uranium (LEU) core. These calculations have been performed independently from those being performed by REWDRC and serve as onemore » step in the verification process.« less

STEADY STATE MODELING OF THE MINIMUM CRITICAL CORE OF THE TRANSIENT REACTOR TEST FACILITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anthony L. Alberti; Todd S. Palmer; Javier Ortensi

2016-05-01

With the advent of next generation reactor systems and new fuel designs, the U.S. Department of Energy (DOE) has identified the need for the resumption of transient testing of nuclear fuels. The DOE has decided that the Transient Reactor Test Facility (TREAT) at Idaho National Laboratory (INL) is best suited for future testing. TREAT is a thermal neutron spectrum, air-cooled, nuclear test facility that is designed to test nuclear fuels in transient scenarios. These specific scenarios range from simple temperature transients to full fuel melt accidents. DOE has expressed a desire to develop a simulation capability that will accurately modelmore » the experiments before they are irradiated at the facility. It is the aim for this capability to have an emphasis on effective and safe operation while minimizing experimental time and cost. The multi physics platform MOOSE has been selected as the framework for this project. The goals for this work are to identify the fundamental neutronics properties of TREAT and to develop an accurate steady state model for future multiphysics transient simulations. In order to minimize computational cost, the effect of spatial homogenization and angular discretization are investigated. It was found that significant anisotropy is present in TREAT assemblies and to capture this effect, explicit modeling of cooling channels and inter-element gaps is necessary. For this modeling scheme, single element calculations at 293 K gave power distributions with a root mean square difference of 0.076% from those of reference SERPENT calculations. The minimum critical core configuration with identical gap and channel treatment at 293 K resulted in a root mean square, total core, radial power distribution 2.423% different than those of reference SERPENT solutions.« less

OPERATION OF A PUBLIC GEOLOGIC CORE AND SAMPLE REPOSITORY IN HOUSTON, TEXAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scott W. Tinker; Beverly Blakeney DeJarnett; Laura C. Zahm

2005-04-01

The Bureau of Economic Geology's Houston Research Center (HRC) is well established as a premier regional research center for geologic research serving not only Houston, but geoscientists from around Texas, the U. S., and even the world. As reported in the 2003-2004 technical progress report to the DOE, the HRC provides a state-of-the-art core viewing facility, two fully equipped conference rooms, and a comprehensive technical library, all available for public use. In addition, the HRC currently houses over 500,000 boxes of rock material, and has space to hold approximately 400,000 more boxes. Use of the facility has continued to increasemore » during this third year of operation; over the past twelve months the HRC has averaged approximately 200 patrons per month. This usage is a combination of individuals describing core, groups of geoscientists holding seminars and workshops, and various industry and government-funded groups holding short courses, workshops, and seminars. The BEG/HRC secured several substantial donations of rock materials and/or cash during this operating period. All of these funds went directly into the endowment. Outreach during 2004 and 2005 included many technical presentations and several publications on the HRC. Several field trips to the facility were held for geoscience professionals and grade school students alike. Goals for the upcoming year involve securing more donations of rock material and cash in order to fully fund the HRC endowment. BEG will also continue to increase the number of patrons using the facility, and we will strive to raise awareness of the HRC's 100,000-volume geoscience technical library.« less

TREAT Modeling and Simulation Strategy

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeHart, Mark David

2015-09-01

This report summarizes a four-phase process used to describe the strategy in developing modeling and simulation software for the Transient Reactor Test Facility. The four phases of this research and development task are identified as (1) full core transient calculations with feedback, (2) experiment modeling, (3) full core plus experiment simulation and (4) quality assurance. The document describes the four phases, the relationship between these research phases, and anticipated needs within each phase.

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic datasets is critically important. The high-throughput autonomous proteomic pipeline (HTAPP) described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is comprised of software that controls the acquisition of mass spectral data along with automation of post-acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user-configurable lab-based relational database. The software design of HTAPP focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples. PMID:20336676

ProCon - PROteomics CONversion tool.

PubMed

Mayer, Gerhard; Stephan, Christian; Meyer, Helmut E; Kohl, Michael; Marcus, Katrin; Eisenacher, Martin

2015-11-03

With the growing amount of experimental data produced in proteomics experiments and the requirements/recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics data in public repositories arises. For such an upload one needs proteomics data in a standardized format. Therefore, it is desirable, that the proprietary vendor's software will integrate in the future such an export functionality using the standard formats for proteomics results defined by the HUPO-PSI group. Currently not all search engines and analysis tools support these standard formats. In the meantime there is a need to provide user-friendly free-to-use conversion tools that can convert the data into such standard formats in order to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. ProCon is such a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML. It allows the conversion of Sequest™/Comet .out files, of search results from the popular and often used ProteomeDiscoverer® 1.x (x=versions 1.1 to1.4) software and search results stored in the LIMS systems ProteinScape® 1.3 and 2.1 into mzIdentML and PRIDE XML. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015. Published by Elsevier B.V.

Virtual Labs in proteomics: new E-learning tools.

PubMed

Ray, Sandipan; Koshy, Nicole Rachel; Reddy, Panga Jaipal; Srivastava, Sanjeeva

2012-05-17

Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/. Copyright © 2012 Elsevier B.V. All rights reserved.

Application of proteomics to ecology and population biology.

PubMed

Karr, T L

2008-02-01

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

PubMed

Li, Feng; Li, Maoyu; Xiao, Zhiqiang; Zhang, Pengfei; Li, Jianling; Chen, Zhuchu

2006-01-11

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

Ultrathin TiO2 layer coated-CdS spheres core-shell nanocomposite with enhanced visible-light photoactivity.

PubMed

Chen, Zhang; Xu, Yi-Jun

2013-12-26

Development of various strategies for controllable fabrication of core-shell nanocomposites (CSNs) with highly active photocatalytic performance has been attracting ever-increasing research attention. In particular, control of the ultrathin layer TiO2 shell in constructing CSNs in an aqueous phase is a significant but technologically challenging issue. Here, this paper demonstrates the interface assembly synthesis of CdS nanospheres@TiO2 core-shell photocatalyst via the electrostatic interaction of negatively charged water-stable titania precursor with positively charged CdS nanospheres (CdS NSPs), followed by the formation of the ultrathin-layer TiO2 shell through a facile refluxing process in aqueous phase. The as-formed CdS NSPs@TiO2 core-shell nanohybrid exhibits a high visible-light-driven photoactivity for selective transformation and reduction of heavy metal ions. The ultrathin TiO2 layer coated on CdS NSPs results in excellent light transmission property, enhanced adsorption capacity, and improved transfer of charge carriers and lifespan of photoinduced electron-hole pairs, which would prominently contribute to the significant photoactivity enhancement. It is anticipated that this facile aqueous-phase synthesis strategy could be extended to design a variety of more efficient CSN photocatalysts with controllable morphology toward target applications in diverse photoredox processes.

Facile preparation of magnetic metal organic frameworks core-shell nanoparticles for stimuli-responsive drug carrier

NASA Astrophysics Data System (ADS)

Li, Sheng; Bi, Ke; Xiao, Ling; Shi, Xiaowen

2017-12-01

Facile synthesis of core-shell magnetic MOFs for drug delivery is of significance due to the advantages of high drug load and easy separation. In this work, magnetic metal organic frameworks (MOFs, Fe3O4-NH2@MIL101-NH2) core-shell nanoparticles were synthesized rapidly in water phase by microwave irradiation using Fe3+ and 2-amino-1,4-benzenedicarboxylate (BDC-NH2) as metal ions and ligands respectively. The resulting magnetic MOFs exhibit large surface areas (96.04 m2 g-1), excellent magnetic response (20.47 emu g-1) and large mesopore volume (22.07 cm3 g-1) along with spherical morphologies with the diameters ranging from 140-330 nm. Using doxorubicin (DOX) as a model drug, the drug loading capacity of Fe3O4-NH2@MIL101-NH2 could reach 36.02%, substantially higher than pristine MIL101-NH2. Importantly, the release of DOX could be controlled by pH as well as the meso pore size of MOFs. The cytotoxicity assay showed that the magnetic MOFs have low cytotoxicity and good biocompatibility. The results suggest great potential of the magnetic MOFs core-shell nanoparticles fabricated in this study on controlled drug release of DOX.

Facile preparation of magnetic metal organic frameworks core-shell nanoparticles for stimuli-responsive drug carrier.

PubMed

Li, Sheng; Bi, Ke; Xiao, Ling; Shi, Xiaowen

2017-12-08

Facile synthesis of core-shell magnetic MOFs for drug delivery is of significance due to the advantages of high drug load and easy separation. In this work, magnetic metal organic frameworks (MOFs, Fe 3 O 4 -NH 2 @MIL101-NH 2 ) core-shell nanoparticles were synthesized rapidly in water phase by microwave irradiation using Fe 3+ and 2-amino-1,4-benzenedicarboxylate (BDC-NH 2 ) as metal ions and ligands respectively. The resulting magnetic MOFs exhibit large surface areas (96.04 m 2 g -1 ), excellent magnetic response (20.47 emu g -1 ) and large mesopore volume (22.07 cm 3 g -1 ) along with spherical morphologies with the diameters ranging from 140-330 nm. Using doxorubicin (DOX) as a model drug, the drug loading capacity of Fe 3 O 4 -NH 2 @MIL101-NH 2 could reach 36.02%, substantially higher than pristine MIL101-NH 2 . Importantly, the release of DOX could be controlled by pH as well as the meso pore size of MOFs. The cytotoxicity assay showed that the magnetic MOFs have low cytotoxicity and good biocompatibility. The results suggest great potential of the magnetic MOFs core-shell nanoparticles fabricated in this study on controlled drug release of DOX.

Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference, Poznań, Poland.

PubMed

Gadher, Suresh Jivan; Marczak, Łukasz; Łuczak, Magdalena; Stobiecki, Maciej; Widlak, Piotr; Kovarova, Hana

2016-01-01

Every year since 2007, the Central and Eastern European Proteomic Conference (CEEPC) has excelled in representing state-of-the-art proteomics in and around Central and Eastern Europe, and linking it to international institutions worldwide. Its mission remains to contribute to all approaches of proteomics including traditional and often-revisited methodologies as well as the latest technological achievements in clinical, quantitative and structural proteomics with a view to systems biology of a variety of processes. The 9th CEEPC was held from June 15th to 18th, 2015, at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznań, Poland. The scientific program stimulated exchange of proteomic knowledge whilst the spectacular venue of the conference allowed participants to enjoy the cobblestoned historical city of Poznań.

Recent Advance in Applications of Proteomics Technologies on Traditional Chinese Medicine Research

PubMed Central

Zhu, Fangshi; Liu, Xuan; Li, Qi; Su, Shi-bing

2015-01-01

Proteomics technology, a major component of system biology, has gained comprehensive attention in the area of medical diagnosis, drug development, and mechanism research. On the holistic and systemic theory, proteomics has a convergence with traditional Chinese medicine (TCM). In this review, we discussed the applications of proteomic technologies in diseases-TCM syndrome combination researches. We also introduced the proteomic studies on the in vivo and in vitro effects and underlying mechanisms of TCM treatments using Chinese herbal medicine (CHM), Chinese herbal formula (CHF), and acupuncture. Furthermore, the combined studies of proteomics with other “-omics” technologies in TCM were also discussed. In summary, this report presents an overview of the recent advances in the application of proteomic technologies in TCM studies and sheds a light on the future global and further research on TCM. PMID:26557869

The path to enlightenment: making sense of genomic and proteomic information.

PubMed

Maurer, Martin H

2004-05-01

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.

Sound velocity measurements of dhcp-FeHx up to 70 GPa using inelastic X-ray scattering: Implications for the abundance of hydrogen in the Earth's core

NASA Astrophysics Data System (ADS)

Shibazaki, Y.; Ohtani, E.; Fukui, H.; Sakai, T.; Kamada, S.; Baron, A. Q.; Nishitani, N.; Hirao, N.; Takemura, K.

2011-12-01

The Earth's interior has been directly investigated by seismic wave propagation and normal mode oscillation. In particular, the distributions of density and sound velocity are available to study the Earth's core (e.g. PREM). The inner core, which is solid state, is approximately 3 % less dense than pure iron (a core density deficit), and it is considered that the core consists of iron and light elements, such as hydrogen, carbon, oxygen, silicon, and sulfur. In this work, in order to constrain the abundance of hydrogen in the Earth's core by matching the density and sound velocity of FeHx to those of PREM, we determined the compressional sound velocity of iron hydride at high pressure using inelastic X-ray scattering (IXS). The IXS experiments and in situ X-ray diffraction (XRD) experiments were conducted up to 70 GPa and room temperature. High-pressure conditions were generated using a symmetric diamond anvil cell (DAC) with tungsten gaskets. Hydrogen initially pressurized to 0.18 GPa was loaded to the sample chamber. The IXS experiments were performed at BL35XU of the SPring-8 facility in Japan. The XRD experiments at high pressure were carried out by the angle dispersive method at BL10XU of the SPring-8 facility in Japan. The each XRD pattern of FeHx was collected after each IXS measurement in order to obtain directly the density of FeHx. Over the range of pressure studied, the diffraction lines of double-hexagonal close-packed (dhcp)-FeHx were observed and there were no diffraction lines of iron. We show that FeHx follows Birch's law for Vp above 37 GPa, namely a linear dependence between velocity and density. The estimated Vp, extrapolated to core conditions, is compared with PREM. Our results provide that the Earth's inner core could contain about 0.2 wt% hydrogen.

SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments.

PubMed

Pichler, Peter; Mazanek, Michael; Dusberger, Frederico; Weilnböck, Lisa; Huber, Christian G; Stingl, Christoph; Luider, Theo M; Straube, Werner L; Köcher, Thomas; Mechtler, Karl

2012-11-02

While the performance of liquid chromatography (LC) and mass spectrometry (MS) instrumentation continues to increase, applications such as analyses of complete or near-complete proteomes and quantitative studies require constant and optimal system performance. For this reason, research laboratories and core facilities alike are recommended to implement quality control (QC) measures as part of their routine workflows. Many laboratories perform sporadic quality control checks. However, successive and systematic longitudinal monitoring of system performance would be facilitated by dedicated automatic or semiautomatic software solutions that aid an effortless analysis and display of QC metrics over time. We present the software package SIMPATIQCO (SIMPle AuTomatIc Quality COntrol) designed for evaluation of data from LTQ Orbitrap, Q-Exactive, LTQ FT, and LTQ instruments. A centralized SIMPATIQCO server can process QC data from multiple instruments. The software calculates QC metrics supervising every step of data acquisition from LC and electrospray to MS. For each QC metric the software learns the range indicating adequate system performance from the uploaded data using robust statistics. Results are stored in a database and can be displayed in a comfortable manner from any computer in the laboratory via a web browser. QC data can be monitored for individual LC runs as well as plotted over time. SIMPATIQCO thus assists the longitudinal monitoring of important QC metrics such as peptide elution times, peak widths, intensities, total ion current (TIC) as well as sensitivity, and overall LC-MS system performance; in this way the software also helps identify potential problems. The SIMPATIQCO software package is available free of charge.

SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC–MS Performance Metrics on Orbitrap Instruments

PubMed Central

2012-01-01

While the performance of liquid chromatography (LC) and mass spectrometry (MS) instrumentation continues to increase, applications such as analyses of complete or near-complete proteomes and quantitative studies require constant and optimal system performance. For this reason, research laboratories and core facilities alike are recommended to implement quality control (QC) measures as part of their routine workflows. Many laboratories perform sporadic quality control checks. However, successive and systematic longitudinal monitoring of system performance would be facilitated by dedicated automatic or semiautomatic software solutions that aid an effortless analysis and display of QC metrics over time. We present the software package SIMPATIQCO (SIMPle AuTomatIc Quality COntrol) designed for evaluation of data from LTQ Orbitrap, Q-Exactive, LTQ FT, and LTQ instruments. A centralized SIMPATIQCO server can process QC data from multiple instruments. The software calculates QC metrics supervising every step of data acquisition from LC and electrospray to MS. For each QC metric the software learns the range indicating adequate system performance from the uploaded data using robust statistics. Results are stored in a database and can be displayed in a comfortable manner from any computer in the laboratory via a web browser. QC data can be monitored for individual LC runs as well as plotted over time. SIMPATIQCO thus assists the longitudinal monitoring of important QC metrics such as peptide elution times, peak widths, intensities, total ion current (TIC) as well as sensitivity, and overall LC–MS system performance; in this way the software also helps identify potential problems. The SIMPATIQCO software package is available free of charge. PMID:23088386

Hypervelocity Impact Evaluation of Metal Foam Core Sandwich Structures

NASA Technical Reports Server (NTRS)

Yasensky, John; Christiansen, Eric L.

2007-01-01

A series of hypervelocity impact (HVI) tests were conducted by the NASA Johnson Space Center (JSC) Hypervelocity Impact Technology Facility (HITF) [1], building 267 (Houston, Texas) between January 2003 and December 2005 to test the HVI performance of metal foams, as compared to the metal honeycomb panels currently in service. The HITF testing was conducted at the NASA JSC White Sands Testing Facility (WSTF) at Las Cruces, New Mexico. Eric L. Christiansen, Ph.D., and NASA Lead for Micro-Meteoroid Orbital Debris (MMOD) Protection requested these hypervelocity impact tests as part of shielding research conducted for the JSC Center Director Discretionary Fund (CDDF) project. The structure tested is a metal foam sandwich structure; a metal foam core between two metal facesheets. Aluminum and Titanium metals were tested for foam sandwich and honeycomb sandwich structures. Aluminum honeycomb core material is currently used in Orbiter Vehicle (OV) radiator panels and in other places in space structures. It has many desirable characteristics and performs well by many measures, especially when normalized by density. Aluminum honeycomb does not perform well in Hypervelocity Impact (HVI) Testing. This is a concern, as honeycomb panels are often exposed to space environments, and take on the role of Micrometeoroid / Orbital Debris (MMOD) shielding. Therefore, information on possible replacement core materials which perform adequately in all necessary functions of the material would be useful. In this report, HVI data is gathered for these two core materials in certain configurations and compared to gain understanding of the metal foam HVI performance.

CPTAC Collaborates with Molecular & Cellular Proteomics to Address Reproducibility in Targeted Assay Development | Office of Cancer Clinical Proteomics Research

Cancer.gov

The journal Molecular & Cellular Proteomics (MCP), in collaboration with the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI), part of the National Institutes of Health, announce new guidelines and requirements for papers describing the development and application of targeted mass spectrometry measurements of peptides, modified peptides and proteins (Mol Cell Proteomics 2017; PMID: 28183812).  NCI’s participation is part of NIH’s overall effort to address the r

High-resolution proteomic profiling of spider venom: expanding the toxin diversity of Phoneutria nigriventer venom.

PubMed

Liberato, Tarcísio; Troncone, Lanfranco Ranieri Paolo; Yamashiro, Edson T; Serrano, Solange M T; Zelanis, André

2016-03-01

Here we present a proteomic characterization of Phoneutria nigriventer venom. A shotgun proteomic approach allowed the identification, for the first time, of O-glycosyl hydrolases (chitinases) in P. nigriventer venom. The electrophoretic profiles under nonreducing and reducing conditions, and protein identification by mass spectrometry, indicated the presence of oligomeric toxin structures in the venom. Complementary proteomic approaches allowed for a qualitative and semi-quantitative profiling of P. nigriventer venom complexity, expanding its known venom proteome diversity.

NIH Common Fund - Disruptive Proteomics Technologies - Challenges and Opportunities | Office of Cancer Clinical Proteomics Research

Cancer.gov

This Request for Information (RFI) is directed toward determining how best to accelerate research in disruptive proteomics technologies. The Disruptive Proteomics Technologies (DPT) Working Group of the NIH Common Fund wishes to identify gaps and opportunities in current technologies and methodologies related to proteome-wide measurements.  For the purposes of this RFI, “disruptive” is defined as very rapid, very significant gains, similar to the "disruptive" technology development that occurred in DNA sequencing technology.

CPTAC Releases Cancer Proteome Confirmatory Breast Study Data | Office of Cancer Clinical Proteomics Research

Cancer.gov

An estimated 252,710 new cases of female breast cancer, accounting for 15% of all new cancer cases, occurred in 2017. To better understand proteogenomic abnormalities in breast cancer, the National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) announces the release of the cancer proteome confirmatory breast study data. The goal of the study was to comprehensively characterize the proteome and phosphoproteome on approximately 100 prospectively collected breast tumor and adjacent normal tissues.

BluePen Biomarkers LLC: integrated biomarker solutions

PubMed Central

Blair, Ian A; Mesaros, Clementina; Lilley, Patrick; Nunez, Matthew

2016-01-01

BluePen Biomarkers provides a unique comprehensive multi-omics biomarker discovery and validation platform. We can quantify, integrate and analyze genomics, proteomics, metabolomics and lipidomics biomarkers, alongside clinical data, demographics and other phenotypic data. A unique bio-inspired signal processing analytic approach is used that has the proven ability to identify biomarkers in a wide variety of diseases. The resulting biomarkers can be used for diagnosis, prognosis, mechanistic studies and predicting treatment response, in contexts from core research through clinical trials. BluePen Biomarkers provides an additional groundbreaking research goal: identifying surrogate biomarkers from different modalities. This not only provides new biological insights, but enables least invasive, least-cost tests that meet or exceed the predictive quality of current tests. PMID:28031971

Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle.

PubMed

Patyshakuliyeva, Aleksandrina; Post, Harm; Zhou, Miaomiao; Jurak, Edita; Heck, Albert J R; Hildén, Kristiina S; Kabel, Mirjam A; Mäkelä, Miia R; Altelaar, Maarten A F; de Vries, Ronald P

2015-08-01

The economically important edible basidiomycete mushroom Agaricus bisporus thrives on decaying plant material in forests and grasslands of North America and Europe. It degrades forest litter and contributes to global carbon recycling, depolymerizing (hemi-)cellulose and lignin in plant biomass. Relatively little is known about how A. bisporus grows in the controlled environment in commercial production facilities and utilizes its substrate. Using transcriptomics and proteomics, we showed that changes in plant biomass degradation by A. bisporus occur throughout its life cycle. Ligninolytic genes were only highly expressed during the spawning stage day 16. In contrast, (hemi-)cellulolytic genes were highly expressed at the first flush, whereas low expression was observed at the second flush. The essential role for many highly expressed plant biomass degrading genes was supported by exo-proteome analysis. Our data also support a model of sequential lignocellulose degradation by wood-decaying fungi proposed in previous studies, concluding that lignin is degraded at the initial stage of growth in compost and is not modified after the spawning stage. The observed differences in gene expression involved in (hemi-)cellulose degradation between the first and second flushes could partially explain the reduction in the number of mushrooms during the second flush. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Radiative shocks produced from spherical cryogenic implosions at the National Ignition Facility

DOE PAGES

Pak, A.; Divol, L.; Gregori, G.; ...

2013-05-20

Spherically expanding radiative shock waves have been observed from inertially confined implosion experiments at the National Ignition Facility. In these experiments, a spherical fusion target, initially 2 mm in diameter, is compressed via the pressure induced from the ablation of the outer target surface. At the peak compression of the capsule, x-ray and nuclear diagnostics indicate the formation of a central core, with a radius and ion temperature of ~20 μm and ~ 2 keV, respectively. This central core is surrounded by a cooler compressed shell of deuterium-tritium fuel that has an outer radius of ~40 μm and a densitymore » of >500 g/cm 3. Using inputs from multiple diagnostics, the peak pressure of the compressed core has been inferred to be of order 100 Gbar for the implosions discussed here. Furthermore, the shock front, initially located at the interface between the high pressure compressed fuel shell and surrounding in-falling low pressure ablator plasma, begins to propagate outwards after peak compression has been reached.« less

Facile one-step synthesis of Ag@Fe3O4 core-shell nanospheres for reproducible SERS substrates

NASA Astrophysics Data System (ADS)

Sun, Lijuan; He, Jiang; An, Songsong; Zhang, Junwei; Ren, Dong

2013-08-01

A facile approach has been developed to synthesize Ag@Fe3O4 core-shell nanospheres, in which the Ag nanoparticle core was well wrapped by a permeable Fe3O4 shell. An in situ reduction of AgNO3 and Fe(NO3)3 was the basis of this one-step method with ethylene glycol as the reducing agent. The as-obtained Ag@Fe3O4 nanospheres were a highly efficient surface-enhanced Raman scattering (SERS) substrate; high reproducibility, stability, and reusability were obtained by employing 4-aminothiophenol (4-ATP) and rhodamine 6G (R6G) as the Raman probe molecules. It was revealed that the SERS signals of 4-ATP and R6G on the Ag@Fe3O4 nanospheres were much stronger than those on the pure Ag nanoparticles, demonstrating that the magnetic enrichment procedures can improve SERS detection sensitivity efficiently. A highly efficient and recyclable SERS substrate was produced by the new model system that has potential applications in chemical and biomolecular assays.

Facile synthesis of 3D few-layered MoS2 coated TiO2 nanosheet core-shell nanostructures for stable and high-performance lithium-ion batteries

NASA Astrophysics Data System (ADS)

Chen, Biao; Zhao, Naiqin; Guo, Lichao; He, Fang; Shi, Chunsheng; He, Chunnian; Li, Jiajun; Liu, Enzuo

2015-07-01

Uniform transition metal sulfide deposition on a smooth TiO2 surface to form a coating structure is a well-known challenge, caused mainly due to their poor affinities. Herein, we report a facile strategy for fabricating mesoporous 3D few-layered (<4 layers) MoS2 coated TiO2 nanosheet core-shell nanocomposites (denoted as 3D FL-MoS2@TiO2) by a novel two-step method using a smooth TiO2 nanosheet as a template and glucose as a binder. The core-shell structure has been systematically examined and corroborated by transmission electron microscopy, scanning transmission electron microscopy, and X-ray photoelectron spectroscopy analyses. It is found that the resultant 3D FL-MoS2@TiO2 as a lithium-ion battery anode delivers an outstanding high-rate capability with an excellent cycling performance, relating to the unique structure of 3D FL-MoS2@TiO2. The 3D uniform coverage of few-layered (<4 layers) MoS2 onto the TiO2 can remarkably enhance the structure stability and effectively shortens the transfer paths of both lithium ions and electrons, while the strong synergistic effect between MoS2 and TiO2 can significantly facilitate the transport of ions and electrons across the interfaces, especially in the high-rate charge-discharge process. Moreover, the facile fabrication strategy can be easily extended to design other oxide/carbon-sulfide/oxide core-shell materials for extensive applications.Uniform transition metal sulfide deposition on a smooth TiO2 surface to form a coating structure is a well-known challenge, caused mainly due to their poor affinities. Herein, we report a facile strategy for fabricating mesoporous 3D few-layered (<4 layers) MoS2 coated TiO2 nanosheet core-shell nanocomposites (denoted as 3D FL-MoS2@TiO2) by a novel two-step method using a smooth TiO2 nanosheet as a template and glucose as a binder. The core-shell structure has been systematically examined and corroborated by transmission electron microscopy, scanning transmission electron microscopy, and X-ray photoelectron spectroscopy analyses. It is found that the resultant 3D FL-MoS2@TiO2 as a lithium-ion battery anode delivers an outstanding high-rate capability with an excellent cycling performance, relating to the unique structure of 3D FL-MoS2@TiO2. The 3D uniform coverage of few-layered (<4 layers) MoS2 onto the TiO2 can remarkably enhance the structure stability and effectively shortens the transfer paths of both lithium ions and electrons, while the strong synergistic effect between MoS2 and TiO2 can significantly facilitate the transport of ions and electrons across the interfaces, especially in the high-rate charge-discharge process. Moreover, the facile fabrication strategy can be easily extended to design other oxide/carbon-sulfide/oxide core-shell materials for extensive applications. Electronic supplementary information (ESI) available: Supplementary SEM, TEM, XPS and EIS analyses. See DOI: 10.1039/c5nr03334a

Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective.

PubMed

Findeisen, Peter; Neumaier, Michael

2009-01-01

Proteomics analysis has been heralded as a novel tool for identifying new and specific biomarkers that may improve diagnosis and monitoring of various disease states. Recent years have brought a number of proteomics profiling technologies. Although proteomics profiling has resulted in the detection of disease-associated differences and modification of proteins, current proteomics technologies display certain limitations that are hampering the introduction of these new technologies into clinical laboratory diagnostics and routine applications. In this review, we summarize current advances in mass spectrometry based biomarker discovery. The promises and challenges of this new technology are discussed with particular emphasis on diagnostic perspectives of mass-spectrometry based proteomics profiling for malignant diseases.

Controlled vocabularies and ontologies in proteomics: Overview, principles and practice☆

PubMed Central

Mayer, Gerhard; Jones, Andrew R.; Binz, Pierre-Alain; Deutsch, Eric W.; Orchard, Sandra; Montecchi-Palazzi, Luisa; Vizcaíno, Juan Antonio; Hermjakob, Henning; Oveillero, David; Julian, Randall; Stephan, Christian; Meyer, Helmut E.; Eisenacher, Martin

2014-01-01

This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the “mapping files” used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23429179

Evolution of complexity in the zebrafish synapse proteome

PubMed Central

Bayés, Àlex; Collins, Mark O.; Reig-Viader, Rita; Gou, Gemma; Goulding, David; Izquierdo, Abril; Choudhary, Jyoti S.; Emes, Richard D.; Grant, Seth G. N.

2017-01-01

The proteome of human brain synapses is highly complex and is mutated in over 130 diseases. This complexity arose from two whole-genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human diseases; however, its synapse proteome is uncharacterized, and whether the teleost-specific genome duplication (TSGD) influenced complexity is unknown. We report the characterization of the proteomes and ultrastructure of central synapses in zebrafish and analyse the importance of the TSGD. While the TSGD increases overall synapse proteome complexity, the postsynaptic density (PSD) proteome of zebrafish has lower complexity than mammals. A highly conserved set of ∼1,000 proteins is shared across vertebrates. PSD ultrastructural features are also conserved. Lineage-specific proteome differences indicate that vertebrate species evolved distinct synapse types and functions. The data sets are a resource for a wide range of studies and have important implications for the use of zebrafish in modelling human synaptic diseases. PMID:28252024

Proteomes and Phosphoproteomes of Anther and Pollen: Availability and Progress.

PubMed

Zhang, Zaibao; Hu, Menghui; Feng, Xiaobing; Gong, Andong; Cheng, Lin; Yuan, Hongyu

2017-10-01

In flowering plants, anther development plays crucial role in sexual reproduction. Within the anther, microspore mother cells meiosis produces microspores, which further develop into pollen grains that play decisive role in plant reproduction. Previous studies on anther biology mainly focused on single gene functions relying on genetic and molecular methods. Recently, anther development has been expanded from multiple OMICS approaches like transcriptomics, proteomics/phosphoproteomics, and metabolomics. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins which can characterize proteomes and their modulation during normal development, biotic and abiotic stresses in anther development. In this review, we summarize the achievements of proteomics and phosphoproteomics with anther and pollen organs from model plant and crop species (i.e. Arabidopsis, rice, tobacco). The increased proteomic information facilitated translation of information from the models to crops and thus aid in agricultural improvement. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Navigating the network: signaling cross-talk in hematopoietic cells

PubMed Central

Fraser, Iain D C; Germain, Ronald N

2009-01-01

Recent studies in hematopoietic cells have led to a growing appreciation of the diverse modes of molecular and functional cross-talk between canonical signaling pathways. However, these intersections represent only the tip of the iceberg. Emerging global analytical methods are providing an even richer and more complete picture of the many components that measurably interact in a network manner to produce cellular responses. Here we highlight the pieces in this Focus, emphasize the limitations of the present canonical pathway paradigm, and discuss the value of a systems biology approach using more global, quantitative experimental design and data analysis strategies. Lastly, we urge caution about overly facile interpretation of genome- and proteome-level studies. PMID:19295628

NCI's Proteome Characterization Centers Announced | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute (NCI), part of the National Institutes of Health, announces the launch of a Clinical Proteomic Tumor Analysis Consortium (CPTAC). CPTAC is a comprehensive, coordinated team effort to accelerate the understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows.

USING PROTEOMICS TO IMPROVE RISK ASSESSMENT OF HUMAN EXPOSURE TO ENVIRONMENTAL AGENTS

EPA Science Inventory

Using Proteomics to Improve Risk Assessment of Human Exposure to Environmental Agents.
Authors: Witold M. Winnik
Key Words (4): Proteomics, LC/MS, Western Blots, 1D and 2D gel electrophoresis, toxicity

The goal of this project is to use proteomics for the character...

CPTAC Releases Largest-Ever Breast Cancer Proteome Dataset from Previously Genome Characterized Tumors | Office of Cancer Clinical Proteomics Research

Cancer.gov

National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have released a dataset of proteins and  phosphopeptides identified through deep proteomic and phosphoproteomic analysis of breast tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.

PubMed

Hermjakob, Henning

2006-09-01

Proteomics is a key field of modern biomolecular research, with many small and large scale efforts producing a wealth of proteomics data. However, the vast majority of this data is never exploited to its full potential. Even in publicly funded projects, often the raw data generated in a specific context is analysed, conclusions are drawn and published, but little attention is paid to systematic documentation, archiving, and public access to the data supporting the scientific results. It is often difficult to validate the results stated in a particular publication, and even simple global questions like "In which cellular contexts has my protein of interest been observed?" can currently not be answered with realistic effort, due to a lack of standardised reporting and collection of proteomics data. The Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organisation (HUPO), defines community standards for data representation in proteomics to facilitate systematic data capture, comparison, exchange and verification. In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process.

Quantitative proteomics in cardiovascular research: global and targeted strategies

PubMed Central

Shen, Xiaomeng; Young, Rebeccah; Canty, John M.; Qu, Jun

2014-01-01

Extensive technical advances in the past decade have substantially expanded quantitative proteomics in cardiovascular research. This has great promise for elucidating the mechanisms of cardiovascular diseases (CVD) and the discovery of cardiac biomarkers used for diagnosis and treatment evaluation. Global and targeted proteomics are the two major avenues of quantitative proteomics. While global approaches enable unbiased discovery of altered proteins via relative quantification at the proteome level, targeted techniques provide higher sensitivity and accuracy, and are capable of multiplexed absolute quantification in numerous clinical/biological samples. While promising, technical challenges need to be overcome to enable full utilization of these techniques in cardiovascular medicine. Here we discuss recent advances in quantitative proteomics and summarize applications in cardiovascular research with an emphasis on biomarker discovery and elucidating molecular mechanisms of disease. We propose the integration of global and targeted strategies as a high-throughput pipeline for cardiovascular proteomics. Targeted approaches enable rapid, extensive validation of biomarker candidates discovered by global proteomics. These approaches provide a promising alternative to immunoassays and other low-throughput means currently used for limited validation. PMID:24920501

Proteomics in medical microbiology.

PubMed

Cash, P

2000-04-01

The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

Meeting the State's Future Needs through a Competitive Higher Education Facility and Technology Infrastructure. Second Report on the Condition of Higher Education in Ohio

ERIC Educational Resources Information Center

Ohio Board of Regents, 2009

2009-01-01

The First Condition Report provided policymakers and the general public a snapshot of where Ohio stands in providing the higher education services Ohio needs to be competitive in today's world. This Second Report focuses on facilities and technology. Five questions form the core of The Condition Report. These are: (1) Are Ohio's higher education…

Mutagen Sensitivity, Apoptosis, and Polymorphism in DNA Repair as Measures of Prostate Cancer Risk

DTIC Science & Technology

2005-02-01

blood tubes are immediately refrigerated and delivered on ice within 6 hours to the GCRC core facility at Georgetown University for processing . Case...is CLIA certified. There is a centrally monitored storage facility with -80’C freezers. The established recruitment and optimized sample processing in...controls. We have established the recruitment procedures, sample collection, processing , repository, and data management. This is a substantial effort

The Stress Granule RNA-Binding Protein TIAR-1 Protects Female Germ Cells from Heat Shock in Caenorhabditis elegans.

PubMed

Huelgas-Morales, Gabriela; Silva-García, Carlos Giovanni; Salinas, Laura S; Greenstein, David; Navarro, Rosa E

2016-04-07

In response to stressful conditions, eukaryotic cells launch an arsenal of regulatory programs to protect the proteome. One major protective response involves the arrest of protein translation and the formation of stress granules, cytoplasmic ribonucleoprotein complexes containing the conserved RNA-binding proteins TIA-1 and TIAR. The stress granule response is thought to preserve mRNA for translation when conditions improve. For cells of the germline-the immortal cell lineage required for sexual reproduction-protection from stress is critically important for perpetuation of the species, yet how stress granule regulatory mechanisms are deployed in animal reproduction is incompletely understood. Here, we show that the stress granule protein TIAR-1 protects the Caenorhabditis elegans germline from the adverse effects of heat shock. Animals containing strong loss-of-function mutations in tiar-1 exhibit significantly reduced fertility compared to the wild type following heat shock. Analysis of a heat-shock protein promoter indicates that tiar-1 mutants display an impaired heat-shock response. We observed that TIAR-1 was associated with granules in the gonad core and oocytes during several stressful conditions. Both gonad core and oocyte granules are dynamic structures that depend on translation; protein synthesis inhibitors altered their formation. Nonetheless, tiar-1 was required for the formation of gonad core granules only. Interestingly, the gonad core granules did not seem to be needed for the germ cells to develop viable embryos after heat shock. This suggests that TIAR-1 is able to protect the germline from heat stress independently of these structures. Copyright © 2016 Huelgas-Morales et al.

The Stress Granule RNA-Binding Protein TIAR-1 Protects Female Germ Cells from Heat Shock in Caenorhabditis elegans

PubMed Central

Huelgas-Morales, Gabriela; Silva-García, Carlos Giovanni; Salinas, Laura S.; Greenstein, David; Navarro, Rosa E.

2016-01-01

In response to stressful conditions, eukaryotic cells launch an arsenal of regulatory programs to protect the proteome. One major protective response involves the arrest of protein translation and the formation of stress granules, cytoplasmic ribonucleoprotein complexes containing the conserved RNA-binding proteins TIA-1 and TIAR. The stress granule response is thought to preserve mRNA for translation when conditions improve. For cells of the germline—the immortal cell lineage required for sexual reproduction—protection from stress is critically important for perpetuation of the species, yet how stress granule regulatory mechanisms are deployed in animal reproduction is incompletely understood. Here, we show that the stress granule protein TIAR-1 protects the Caenorhabditis elegans germline from the adverse effects of heat shock. Animals containing strong loss-of-function mutations in tiar-1 exhibit significantly reduced fertility compared to the wild type following heat shock. Analysis of a heat-shock protein promoter indicates that tiar-1 mutants display an impaired heat-shock response. We observed that TIAR-1 was associated with granules in the gonad core and oocytes during several stressful conditions. Both gonad core and oocyte granules are dynamic structures that depend on translation; protein synthesis inhibitors altered their formation. Nonetheless, tiar-1 was required for the formation of gonad core granules only. Interestingly, the gonad core granules did not seem to be needed for the germ cells to develop viable embryos after heat shock. This suggests that TIAR-1 is able to protect the germline from heat stress independently of these structures. PMID:26865701

Explosion symmetry improvement of polyimide-coated tungsten wire in vacuum on negative discharge facility

NASA Astrophysics Data System (ADS)

Li, Mo; Wu, Jian; Lu, Yihan; Li, Xingwen; Li, Yang; Qiu, Mengtong

2018-01-01

Tungsten wire explosion is very asymmetric when fast current rate and insulated coatings are both applied on negative discharge facility using a 24-mm-diameter cathode geometry, which is commonly used on mega-ampere facilities. It is inferred, based on an analytical treatment of the guiding center drift and COMSOL simulations, that the large negative radial electric field causes early voltage breakdown and terminates energy deposition into the wire core on the anode side of the wire. After the anode side is short circuited, the radial electric field along the wire surface on the cathode side will change its polarity and thus leading to additional energy deposition into the wire core. This change causes ˜10 times larger energy deposition and ˜14 times faster explosion velocity in the cathode side than the anode side. In order to reduce this asymmetry, a hollow cylindrical cathode geometry was used to reverse the polarity of radial electric field and was optimized to use on multi-MA facilities. In this case, fully vaporized polyimide-coated tungsten wire with great symmetry improvement was achieved with energy deposition of ˜8.8 eV/atom. The atomic and electronic density distributions for the two different load geometries were obtained by the double-wavelength measurement.

The role of targeted chemical proteomics in pharmacology

PubMed Central

Sutton, Chris W

2012-01-01

Traditionally, proteomics is the high-throughput characterization of the global complement of proteins in a biological system using cutting-edge technologies (robotics and mass spectrometry) and bioinformatics tools (Internet-based search engines and databases). As the field of proteomics has matured, a diverse range of strategies have evolved to answer specific problems. Chemical proteomics is one such direction that provides the means to enrich and detect less abundant proteins (the ‘hidden’ proteome) from complex mixtures of wide dynamic range (the ‘deep’ proteome). In pharmacology, chemical proteomics has been utilized to determine the specificity of drugs and their analogues, for anticipated known targets, only to discover other proteins that bind and could account for side effects observed in preclinical and clinical trials. As a consequence, chemical proteomics provides a valuable accessory in refinement of second- and third-generation drug design for treatment of many diseases. However, determining definitive affinity capture of proteins by a drug immobilized on soft gel chromatography matrices has highlighted some of the challenges that remain to be addressed. Examples of the different strategies that have emerged using well-established drugs against pharmaceutically important enzymes, such as protein kinases, metalloproteases, PDEs, cytochrome P450s, etc., indicate the potential opportunity to employ chemical proteomics as an early-stage screening approach in the identification of new targets. PMID:22074351

Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative.

PubMed

Alberio, Tiziana; Pieroni, Luisa; Ronci, Maurizio; Banfi, Cristina; Bongarzone, Italia; Bottoni, Patrizia; Brioschi, Maura; Caterino, Marianna; Chinello, Clizia; Cormio, Antonella; Cozzolino, Flora; Cunsolo, Vincenzo; Fontana, Simona; Garavaglia, Barbara; Giusti, Laura; Greco, Viviana; Lucacchini, Antonio; Maffioli, Elisa; Magni, Fulvio; Monteleone, Francesca; Monti, Maria; Monti, Valentina; Musicco, Clara; Petrosillo, Giuseppe; Porcelli, Vito; Saletti, Rosaria; Scatena, Roberto; Soggiu, Alessio; Tedeschi, Gabriella; Zilocchi, Mara; Roncada, Paola; Urbani, Andrea; Fasano, Mauro

2017-12-01

The Mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed data sets were analyzed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and submitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted in nodes of this network but with a different ability in coisolating mitochondria-associated structures for each enrichment protocol/cell line pair.

Pre-fractionation strategies to resolve pea (Pisum sativum) sub-proteomes

PubMed Central

Meisrimler, Claudia-Nicole; Menckhoff, Ljiljana; Kukavica, Biljana M.; Lüthje, Sabine

2015-01-01

Legumes are important crop plants and pea (Pisum sativum L.) has been investigated as a model with respect to several physiological aspects. The sequencing of the pea genome has not been completed. Therefore, proteomic approaches are currently limited. Nevertheless, the increasing numbers of available EST-databases as well as the high homology of the pea and medicago genome (Medicago truncatula Gaertner) allow the successful identification of proteins. Due to the un-sequenced pea genome, pre-fractionation approaches have been used in pea proteomic surveys in the past. Aside from a number of selective proteome studies on crude extracts and the chloroplast, few studies have targeted other components such as the pea secretome, an important sub-proteome of interest due to its role in abiotic and biotic stress processes. The secretome itself can be further divided into different sub-proteomes (plasma membrane, apoplast, cell wall proteins). Cell fractionation in combination with different gel-electrophoresis, chromatography methods and protein identification by mass spectrometry are important partners to gain insight into pea sub-proteomes, post-translational modifications and protein functions. Overall, pea proteomics needs to link numerous existing physiological and biochemical data to gain further insight into adaptation processes, which play important roles in field applications. Future developments and directions in pea proteomics are discussed. PMID:26539198

Principles of proteome allocation are revealed using proteomic data and genome-scale models

PubMed Central

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.; Ebrahim, Ali; Saunders, Michael A.; Palsson, Bernhard O.

2016-01-01

Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the “generalist” (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions, prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thus represents a generalist ME model reflecting both growth rate maximization and “hedging” against uncertain environments and stresses, as indicated by significant enrichment of these sectors for the general stress response sigma factor σS. Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as demonstrated here. This flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models. PMID:27857205

A Proteomics View of the Molecular Mechanisms and Biomarkers of Glaucomatous Neurodegeneration

PubMed Central

Tezel, Gülgün

2013-01-01

Despite improving understanding of glaucoma, key molecular players of neurodegeneration that can be targeted for treatment of glaucoma, or molecular biomarkers that can be useful for clinical testing, remain unclear. Proteomics technology offers a powerful toolbox to accomplish these important goals of the glaucoma research and is increasingly being applied to identify molecular mechanisms and biomarkers of glaucoma. Recent studies of glaucoma using proteomics analysis techniques have resulted in the lists of differentially expressed proteins in human glaucoma and animal models. The global analysis of protein expression in glaucoma has been followed by cell-specific proteome analysis of retinal ganglion cells and astrocytes. The proteomics data have also guided targeted studies to identify post-translational modifications and protein-protein interactions during glaucomatous neurodegeneration. In addition, recent applications of proteomics have provided a number of potential biomarker candidates. Proteomics technology holds great promise to move glaucoma research forward toward new treatment strategies and biomarker discovery. By reviewing the major proteomics approaches and their applications in the field of glaucoma, this article highlights the power of proteomics in translational and clinical research related to glaucoma and also provides a framework for future research to functionally test the importance of specific molecular pathways and validate candidate biomarkers. PMID:23396249

Proteomics in Argentina - limitations and future perspectives: A special emphasis on meat proteomics.

PubMed

Fadda, Silvina; Almeida, André M

2015-11-01

Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case-study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics-based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Principles of proteome allocation are revealed using proteomic data and genome-scale models

DOE PAGES

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.; ...

2016-11-18

Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the “generalist” (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions, prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thusmore » represents a generalist ME model reflecting both growth rate maximization and “hedging” against uncertain environments and stresses, as indicated by significant enrichment of these sectors for the general stress response sigma factor σS. Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as demonstrated here. Furthermore, this flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models.« less

Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics.

PubMed

Lan, Jiayi; Núñez Galindo, Antonio; Doecke, James; Fowler, Christopher; Martins, Ralph N; Rainey-Smith, Stephanie R; Cominetti, Ornella; Dayon, Loïc

2018-04-06

Over the last two decades, EDTA-plasma has been used as the preferred sample matrix for human blood proteomic profiling. Serum has also been employed widely. Only a few studies have assessed the difference and relevance of the proteome profiles obtained from plasma samples, such as EDTA-plasma or lithium-heparin-plasma, and serum. A more complete evaluation of the use of EDTA-plasma, heparin-plasma, and serum would greatly expand the comprehensiveness of shotgun proteomics of blood samples. In this study, we evaluated the use of heparin-plasma with respect to EDTA-plasma and serum to profile blood proteomes using a scalable automated proteomic pipeline (ASAP 2 ). The use of plasma and serum for mass-spectrometry-based shotgun proteomics was first tested with commercial pooled samples. The proteome coverage consistency and the quantitative performance were compared. Furthermore, protein measurements in EDTA-plasma and heparin-plasma samples were comparatively studied using matched sample pairs from 20 individuals from the Australian Imaging, Biomarkers and Lifestyle (AIBL) Study. We identified 442 proteins in common between EDTA-plasma and heparin-plasma samples. Overall agreement of the relative protein quantification between the sample pairs demonstrated that shotgun proteomics using workflows such as the ASAP 2 is suitable in analyzing heparin-plasma and that such sample type may be considered in large-scale clinical research studies. Moreover, the partial proteome coverage overlaps (e.g., ∼70%) showed that measures from heparin-plasma could be complementary to those obtained from EDTA-plasma.

Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes

PubMed Central

Virant-Klun, Irma; Leicht, Stefan; Hughes, Christopher; Krijgsveld, Jeroen

2016-01-01

Oocytes undergo a range of complex processes via oogenesis, maturation, fertilization, and early embryonic development, eventually giving rise to a fully functioning organism. To understand proteome composition and diversity during maturation of human oocytes, here we have addressed crucial aspects of oocyte collection and proteome analysis, resulting in the first proteome and secretome maps of human oocytes. Starting from 100 oocytes collected via a novel serum-free hanging drop culture system, we identified 2,154 proteins, whose function indicate that oocytes are largely resting cells with a proteome that is tailored for homeostasis, cellular attachment, and interaction with its environment via secretory factors. In addition, we have identified 158 oocyte-enriched proteins (such as ECAT1, PIWIL3, NLRP7)1 not observed in high-coverage proteomics studies of other human cell lines or tissues. Exploiting SP3, a novel technology for proteomic sample preparation using magnetic beads, we scaled down proteome analysis to single cells. Despite the low protein content of only ∼100 ng per cell, we consistently identified ∼450 proteins from individual oocytes. When comparing individual oocytes at the germinal vesicle (GV) and metaphase II (MII) stage, we found that the Tudor and KH domain-containing protein (TDRKH) is preferentially expressed in immature oocytes, while Wee2, PCNA, and DNMT1 were enriched in mature cells, collectively indicating that maintenance of genome integrity is crucial during oocyte maturation. This study demonstrates that an innovative proteomics workflow facilitates analysis of single human oocytes to investigate human oocyte biology and preimplantation development. The approach presented here paves the way for quantitative proteomics in other quantity-limited tissues and cell types. Data associated with this study are available via ProteomeXchange with identifier PXD004142. PMID:27215607

Spatial-Resolution Cell Type Proteome Profiling of Cancer Tissue by Fully Integrated Proteomics Technology.

PubMed

Xu, Ruilian; Tang, Jun; Deng, Quantong; He, Wan; Sun, Xiujie; Xia, Ligang; Cheng, Zhiqiang; He, Lisheng; You, Shuyuan; Hu, Jintao; Fu, Yuxiang; Zhu, Jian; Chen, Yixin; Gao, Weina; He, An; Guo, Zhengyu; Lin, Lin; Li, Hua; Hu, Chaofeng; Tian, Ruijun

2018-05-01

Increasing attention has been focused on cell type proteome profiling for understanding the heterogeneous multicellular microenvironment in tissue samples. However, current cell type proteome profiling methods need large amounts of starting materials which preclude their application to clinical tumor specimens with limited access. Here, by seamlessly combining laser capture microdissection and integrated proteomics sample preparation technology SISPROT, specific cell types in tumor samples could be precisely dissected with single cell resolution and processed for high-sensitivity proteome profiling. Sample loss and contamination due to the multiple transfer steps are significantly reduced by the full integration and noncontact design. H&E staining dyes which are necessary for cell type investigation could be selectively removed by the unique two-stage design of the spintip device. This easy-to-use proteome profiling technology achieved high sensitivity with the identification of more than 500 proteins from only 0.1 mm 2 and 10 μm thickness colon cancer tissue section. The first cell type proteome profiling of four cell types from one colon tumor and surrounding normal tissue, including cancer cells, enterocytes, lymphocytes, and smooth muscle cells, was obtained. 5271, 4691, 4876, and 2140 protein groups were identified, respectively, from tissue section of only 5 mm 2 and 10 μm thickness. Furthermore, spatially resolved proteome distribution profiles of enterocytes, lymphocytes, and smooth muscle cells on the same tissue slices and across four consecutive sections with micrometer distance were successfully achieved. This fully integrated proteomics technology, termed LCM-SISPROT, is therefore promising for spatial-resolution cell type proteome profiling of tumor microenvironment with a minute amount of clinical starting materials.

Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes.

PubMed

Virant-Klun, Irma; Leicht, Stefan; Hughes, Christopher; Krijgsveld, Jeroen

2016-08-01

Oocytes undergo a range of complex processes via oogenesis, maturation, fertilization, and early embryonic development, eventually giving rise to a fully functioning organism. To understand proteome composition and diversity during maturation of human oocytes, here we have addressed crucial aspects of oocyte collection and proteome analysis, resulting in the first proteome and secretome maps of human oocytes. Starting from 100 oocytes collected via a novel serum-free hanging drop culture system, we identified 2,154 proteins, whose function indicate that oocytes are largely resting cells with a proteome that is tailored for homeostasis, cellular attachment, and interaction with its environment via secretory factors. In addition, we have identified 158 oocyte-enriched proteins (such as ECAT1, PIWIL3, NLRP7)(1) not observed in high-coverage proteomics studies of other human cell lines or tissues. Exploiting SP3, a novel technology for proteomic sample preparation using magnetic beads, we scaled down proteome analysis to single cells. Despite the low protein content of only ∼100 ng per cell, we consistently identified ∼450 proteins from individual oocytes. When comparing individual oocytes at the germinal vesicle (GV) and metaphase II (MII) stage, we found that the Tudor and KH domain-containing protein (TDRKH) is preferentially expressed in immature oocytes, while Wee2, PCNA, and DNMT1 were enriched in mature cells, collectively indicating that maintenance of genome integrity is crucial during oocyte maturation. This study demonstrates that an innovative proteomics workflow facilitates analysis of single human oocytes to investigate human oocyte biology and preimplantation development. The approach presented here paves the way for quantitative proteomics in other quantity-limited tissues and cell types. Data associated with this study are available via ProteomeXchange with identifier PXD004142. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

First systematic plant proteomics workshop in Botany Department, University of Delhi: transferring proteomics knowledge to next-generation researchers and students.

PubMed

Deswal, Renu; Abat, Jasmeet Kaur; Sehrawat, Ankita; Gupta, Ravi; Kashyap, Prakriti; Sharma, Shruti; Sharma, Bhavana; Chaurasia, Satya Prakash; Chanu, Sougrakpam Yaiphabi; Masi, Antonio; Agrawal, Ganesh Kumar; Sarkar, Abhijit; Agrawal, Raj; Dunn, Michael J; Renaut, Jenny; Rakwal, Randeep

2014-07-01

International Plant Proteomics Organization (INPPO) outlined ten initiatives to promote plant proteomics in each and every country. With greater emphasis in developing countries, one of those was to "organize workshops at national and international levels to train manpower and exchange information". This third INPPO highlights covers the workshop organized for the very first time in a developing country, India, at the Department of Botany in University of Delhi on December 26-30, 2013 titled - "1(st) Plant Proteomics Workshop / Training Program" under the umbrella of INPPO India-Nepal chapter. Selected 20 participants received on-hand training mainly on gel-based proteomics approach along with manual booklet and parallel lectures on this and associated topics. In house, as well as invited experts drawn from other Universities and Institutes (national and international), delivered talks on different aspects of gel-based and gel-free proteomics. Importance of gel-free proteomics approach, translational proteomics, and INPPO roles were presented and interactively discussed by a group of three invited speakers Drs. Ganesh Kumar Agrawal (Nepal), Randeep Rakwal (Japan), and Antonio Masi (Italy). Given the output of this systematic workshop, it was proposed and thereafter decided to be organized every alternate year; the next workshop will be held in 2015. Furthermore, possibilities on providing advanced training to those students / researchers / teachers with basic knowledge in proteomics theory and experiments at national and international levels were discussed. INPPO is committed to generating next-generation trained manpower in proteomics, and it would only happen by the firm determination of scientists to come forward and do it. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular pathology of prostate cancer.

PubMed

Cazares, L H; Drake, R R; Esquela-Kirscher, A; Lance, R S; Semmes, O J; Troyer, D A

2010-01-01

This chapter includes discussion of the molecular pathology of tissue, blood, urine, and expressed prostatic secretions. Because we are unable to reliably image the disease in vivo, a 12 core method that oversamples the peripheral zone is widely used. This generates large numbers of cores that need to be carefully processed and sampled. In spite of the large number of tissue cores, the amount of tumor available for study is often quite limited. This is a particular challenge for research, as new biomarker assays will need to preserve tissue architecture intact for histopathology. Methods of processing and reporting pathology are discussed. With the exception of ductal variants, recognized subtypes of prostate cancer are largely confined to research applications, and most prostate cancers are acinar. Biomarker discovery in urine and expressed prostatic secretions would be useful since these are readily obtained and are proximate fluids. The well-known challenges of biomarker discovery in blood and urine are referenced and discussed. Mediators of carcinogenesis can serve as biomarkers as exemplified by mutations in PTEN and TMPRSS2:ERG fusion. The use of proteomics in biomarker discovery with an emphasis on imaging mass spectroscopy of tissues is discussed. Small RNAs are of great interest, however, their usefulness as biomarkers in clinical decision making remains the subject of ongoing research. The chapter concludes with an overview of blood biomarkers such as circulating nucleic acids and tumor cells and bound/free isoforms of prostate specific antigen (PSA).

Doxorubicin-loaded photosensitive magnetic liposomes for multi-modal cancer therapy.

PubMed

Shah, Saqlain A; Aslam Khan, M U; Arshad, M; Awan, S U; Hashmi, M U; Ahmad, N

2016-12-01

Multifunctional magnetic nanosystems have attracted an enormous attention of researchers for their potential applications in cancer diagnostics and therapy. The localized nanotherapies triggered by the external stimuli, like magnetic fields and visible light, are significant in clinical applications. We report a liposomal system that aims to treat cancer by magnetic hyperthermia, photodynamic therapy and chemotherapy simultaneously. The liposomes enclose clinically used photosensitizer m-THPC (Foscan) and anti-cancer drug doxorubicin, in its hydrophobic lipid bilayers, and contains magnetite nanoparticles in hydrophilic core. Three different sizes of magnetic nanoparticles (10, 22 and 30nm) and liposomes (40, 70 and 110nm) were used in this study. Magnetite single domain nanoparticles forming the magnetic core were superparamagnetic but liposomes expressed slight coercivity and hysteresis due to the clustering of nanoparticles in the core. This enhanced the heating efficiency (specific power loss) of the liposomes under an AC field (375kHz, 170Oe). Cell viability and toxicity were studied on HeLa cells using MTT assay and proteomic analysis. Confocal and fluorescence microscopy were used to study the photosensitizer's profile and cells response to combined therapy. It revealed that combined therapy almost completely eliminated the cancer cells as opposed to the separate treatments. Magnetic hyperthermia and photodynamic therapies were almost equally effective whereas chemotherapy showed the least effect. Copyright © 2016. Published by Elsevier B.V.

Space Station Furnace Facility. Volume 2: Requirements definition and conceptual design study

NASA Technical Reports Server (NTRS)

1992-01-01

The Space Station Freedom Furnace (SSFF) Project is divided into two phases: phase 1, a definition study phase, and phase 2, a design and development phase. TBE was awarded a research study entitled, 'Space Station Furnace Facility Requirements Definition and Conceptual Design Study' on June 2, 1989. This report addresses the definition study phase only. Phase 2 is to be complete after completion of phase 1. The contract encompassed a requirements definition study and culminated in hardware/facility conceptual designs and hardware demonstration development models to test these conceptual designs. The study was divided into two parts. Part 1 (the basic part of the effort) encompassed preliminary requirements definition and assessment; conceptional design of the SSFF Core; fabrication of mockups; and preparation for the support of a conceptional design review (CoDR). Part 2 (the optional part of the effort) included detailed definition of the engineering and design requirements, as derived from the science requirements; refinement of the conceptual design of the SSFF Core; fabrication and testing of the 'breadboards' or development models; and preparation for and support of a requirements definition review.

Room-temperature synthesis of core-shell structured magnetic covalent organic frameworks for efficient enrichment of peptides and simultaneous exclusion of proteins.

PubMed

Lin, Guo; Gao, Chaohong; Zheng, Qiong; Lei, Zhixian; Geng, Huijuan; Lin, Zian; Yang, Huanghao; Cai, Zongwei

2017-03-28

Core-shell structured magnetic covalent organic frameworks (Fe 3 O 4 @COFs) were synthesized via a facile approach at room temperature. Combining the advantages of high porosity, magnetic responsiveness, chemical stability and selectivity, Fe 3 O 4 @COFs can serve as an ideal absorbent for the highly efficient enrichment of peptides and the simultaneous exclusion of proteins from complex biological samples.

A facile approach for cupric ion detection in aqueous media using polyethyleneimine/PMMA core-shell fluorescent nanoparticles

NASA Astrophysics Data System (ADS)

Chen, Jian; Zeng, Fang; Wu, Shuizhu; Su, Junhua; Zhao, Jianqing; Tong, Zhen

2009-09-01

A facile approach was developed to produce a dye-doped core-shell nanoparticle chemosensor for detecting Cu2+ in aqueous media. The core-shell nanoparticle sensor was prepared by a one-step emulsifier-free polymerization, followed by the doping of the fluorescent dye Nile red (9-diethylamino- 5H-benzo[alpha] phenoxazine-5-one, NR) into the particles. For the nanoparticles, the hydrophilic polyethyleneimine (PEI) chain segments serve as the shell and the hydrophobic polymethyl methacrylate (PMMA) constitutes the core of the nanoparticles. The non-toxic and biocompatible PEI chain segments on the nanoparticle surface exhibit a high affinity for Cu2+ ions in aqueous media, and the quenching of the NR fluorescence is observed upon binding of Cu2+ ions. This makes the core-shell nanoparticle system a water-dispersible chemosensor for Cu2+ ion detection. The quenching of fluorescence arises through intraparticle energy transfer (FRET) from the dye in the hydrophobic PMMA core to the Cu2+/PEI complexes on the nanoparticle surface. The energy transfer efficiency for PEI/PMMA particles with different diameters was determined, and it is found that the smaller nanoparticle sample exhibits higher quenching efficiency, and the limit for Cu2+ detection is 1 µM for a nanoparticle sample with a diameter of ~30 nm. The response of the fluorescent nanoparticle towards different metal ions was investigated and the nanoparticle chemosensor displays high selectivity and antidisturbance for the Cu2+ ion among the metal ions examined (Na+, K+, Mg2+, Ca2+, Zn2+, Hg2+, Mn2+, Fe2+, Ni2+, Co2+ and Pb2+). This emulsifier-free, biocompatible and sensitive fluorescent nanoparticle sensor may find applications in cupric ion detection in the biological and environmental areas.

A facile approach for cupric ion detection in aqueous media using polyethyleneimine/PMMA core-shell fluorescent nanoparticles.

PubMed

Chen, Jian; Zeng, Fang; Wu, Shuizhu; Su, Junhua; Zhao, Jianqing; Tong, Zhen

2009-09-09

A facile approach was developed to produce a dye-doped core-shell nanoparticle chemosensor for detecting Cu(2+) in aqueous media. The core-shell nanoparticle sensor was prepared by a one-step emulsifier-free polymerization, followed by the doping of the fluorescent dye Nile red (9-diethylamino- 5H-benzo[alpha] phenoxazine-5-one, NR) into the particles. For the nanoparticles, the hydrophilic polyethyleneimine (PEI) chain segments serve as the shell and the hydrophobic polymethyl methacrylate (PMMA) constitutes the core of the nanoparticles. The non-toxic and biocompatible PEI chain segments on the nanoparticle surface exhibit a high affinity for Cu(2+) ions in aqueous media, and the quenching of the NR fluorescence is observed upon binding of Cu(2+) ions. This makes the core-shell nanoparticle system a water-dispersible chemosensor for Cu(2+) ion detection. The quenching of fluorescence arises through intraparticle energy transfer (FRET) from the dye in the hydrophobic PMMA core to the Cu(2+)/PEI complexes on the nanoparticle surface. The energy transfer efficiency for PEI/PMMA particles with different diameters was determined, and it is found that the smaller nanoparticle sample exhibits higher quenching efficiency, and the limit for Cu(2+) detection is 1 microM for a nanoparticle sample with a diameter of approximately 30 nm. The response of the fluorescent nanoparticle towards different metal ions was investigated and the nanoparticle chemosensor displays high selectivity and antidisturbance for the Cu(2+) ion among the metal ions examined (Na(+), K(+), Mg(2+), Ca(2+), Zn(2+), Hg(2+), Mn(2+), Fe(2+), Ni(2+), Co(2+) and Pb(2+)). This emulsifier-free, biocompatible and sensitive fluorescent nanoparticle sensor may find applications in cupric ion detection in the biological and environmental areas.

New Funding Opportunity Announcements (FOAs): Reissuance of Clinical Proteomic Tumor Analysis Consortium (CPTAC) | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute is soliciting applications for the reissuance of its Clinical Proteomic Tumor Analysis Consortium (CPTAC) program.   CPTAC will support broad efforts focused on several cancer types to explore further the complexities of cancer proteomes and their connections to abnormalities in cancer genomes.

CPTC and KIST Join Efforts to Solve Complex Proteomic Issues | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute's (NCI) Clinical Proteomic Technologies for Cancer (CPTC) initiative at the National Institutes of Health has entered into a memorandum of understanding (MOU) with the Korea Institute of Science and Technology (KIST). This MOU promotes proteomic technology optimization and standards implementation in large-scale international programs.

NCI Blog Post: CPTAC, the Complementary Sibling of TCGA (An Interview with Dr. Henry Rodriguez about NCI’s Proteomics Program) | Office of Cancer Clinical Proteomics Research

Cancer.gov

What is proteomics? Proteomics is a highly automated and rapid method for measuring all the proteins in a biological sample. Proteins are the molecules that actually do most of the work inside a cell. When researchers develop cancer drugs, those drugs typically target proteins, so scientists and clinicians really have to understand what the proteins are doing. Proteomics researchers are now able to measure up to 10,000 proteins per tumor sample.

Proteomics in India: A Report on a Brainstorming Meeting at Hyderabad, India

PubMed Central

Chatterjee, Bhaswati; Makarov, Alexander; Clemmer, David E.; Steen, Hanno; Steen, Judith; Saffell-Clemmer, Wendy; Moghekar, Abhay R.; Mohan Rao, Chintalagiri; Bradshaw, Ralph A.; Thakur, Suman S.

2016-01-01

The Centre for Cellular and Molecular Biology, Hyderabad, India, was host for an international forum, or “brainstorming meeting,” on proteomics held in November 2014, which provided the opportunity to showcase proteomic science in India and to allow discussions between Indian scientists and students and several international visitors. This provided an amalgamation of speakers and participants whose interests lay mainly in developing and using mass-spectrometry-based proteomics to advance their research work. A week-long workshop with hands-on training in proteomic methodology followed the meeting. PMID:27114450

The state of proteome profiling in the fungal genus Aspergillus.

PubMed

Kim, Yonghyun; Nandakumar, M P; Marten, Mark R

2008-03-01

Aspergilli are an important genus of filamentous fungi that contribute to a multibillion dollar industry. Since many fungal genome sequencing were recently completed, it would be advantageous to profile their proteome to better understand the fungal cell factory. Here, we review proteomic data generated for the Aspergilli in recent years. Thus far, a combined total of 28 cell surface, 102 secreted and 139 intracellular proteins have been identified based on 10 different studies on Aspergillus proteomics. A summary proteome map highlighting identified proteins in major metabolic pathway is presented.

Human liver proteome project: plan, progress, and perspectives.

PubMed

He, Fuchu

2005-12-01

The Human Liver Proteome Project is the first initiative of the human proteome project for human organs/tissues and aims at writing a modern Prometheus myth. Its global scientific objectives are to reveal the "solar system" of the human liver proteome, expression profiles, modification profiles, a protein linkage (protein-protein interaction) map, and a proteome localization map, and to define an ORFeome, physiome, and pathome. Since it was first proposed in April 2002, the Human Liver Proteome Project has attracted more than 100 laboratories from all over the world. In the ensuing 3 years, we set up a management infrastructure, identified reference laboratories, confirmed standard operating procedures, initiated international research collaborations, and finally achieved the first set of expression profile data.

Environmental Microbial Community Proteomics: Status, Challenges and Perspectives.

PubMed

Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

2016-08-05

Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment.

Elucidating the fungal stress response by proteomics.

PubMed

Kroll, Kristin; Pähtz, Vera; Kniemeyer, Olaf

2014-01-31

Fungal species need to cope with stress, both in the natural environment and during interaction of human- or plant pathogenic fungi with their host. Many regulatory circuits governing the fungal stress response have already been discovered. However, there are still large gaps in the knowledge concerning the changes of the proteome during adaptation to environmental stress conditions. With the application of proteomic methods, particularly 2D-gel and gel-free, LC/MS-based methods, first insights into the composition and dynamic changes of the fungal stress proteome could be obtained. Here, we review the recent proteome data generated for filamentous fungi and yeasts. This article is part of a Special Issue entitled: Trends in Microbial Proteomics. Copyright © 2013 Elsevier B.V. All rights reserved.

Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets

PubMed Central

Barrera, Alejandro; Alastruey-Izquierdo, Ana; Martín, María J.; Cuesta, Isabel; Vizcaíno, Juan Antonio

2014-01-01

Over the past several years fungal infections have shown an increasing incidence in the susceptible population, and caused high mortality rates. In parallel, multi-resistant fungi are emerging in human infections. Therefore, the identification of new potential antifungal targets is a priority. The first task of this study was to analyse the protein domain and domain architecture content of the 137 fungal proteomes (corresponding to 111 species) available in UniProtKB (UniProt KnowledgeBase) by January 2013. The resulting list of core and exclusive domain and domain architectures is provided in this paper. It delineates the different levels of fungal taxonomic classification: phylum, subphylum, order, genus and species. The analysis highlighted Aspergillus as the most diverse genus in terms of exclusive domain content. In addition, we also investigated which domains could be considered promiscuous in the different organisms. As an application of this analysis, we explored three different ways to detect potential targets for antifungal drugs. First, we compared the domain and domain architecture content of the human and fungal proteomes, and identified those domains and domain architectures only present in fungi. Secondly, we looked for information regarding fungal pathways in public repositories, where proteins containing promiscuous domains could be involved. Three pathways were identified as a result: lovastatin biosynthesis, xylan degradation and biosynthesis of siroheme. Finally, we classified a subset of the studied fungi in five groups depending on their occurrence in clinical samples. We then looked for exclusive domains in the groups that were more relevant clinically and determined which of them had the potential to bind small molecules. Overall, this study provides a comprehensive analysis of the available fungal proteomes and shows three approaches that can be used as a first step in the detection of new antifungal targets. PMID:25033262

Daily chronomics of proteomic profile in aging and rotenone-induced Parkinson's disease model in male Wistar rat and its modulation by melatonin.

PubMed

Jagota, Anita; Mattam, Ushodaya

2017-08-01

Aging is associated with changes in several basic parameters of circadian timing system (CTS) in mammals leading to circadian dysfunction. We had reported earlier that upon aging and in rotenone induced Parkinson's disease (RIPD) rat model there were significant alterations in the core clock genes expression levels and daily pulses. To identify biomarkers of aging and PD chronomics of proteomic day-night profiles in suprachiasmatic nucleus (SCN), pineal and substantia nigra (SN) in 3 month (m), 12, 24 m and RIPD rat model were studied at two time points i.e. Zeitgeber Time (ZT)-6 (mid-day) and ZT-18 (mid-night). Proteome analysis was done by using two dimensional (2-D) electrophoresis and the spots showing robust day-night variations were identified by using MALDI TOF/TOF analysis. In 3 m rats the number of proteins showing day-night variations were relatively more than 12, 24 m and RIPD rat model in SCN and SN. But in pineal there was increase in number of protein spots showing day-night variations in 24 m. Mass spectroscopy of the protein spots showing robust day night variation in aging and RIPD rats were identified. As melatonin, a multitasking molecule, an endogenous synchronizer of rhythm, an antioxidant and an antiaging drug, declines with aging, the effects of melatonin administration on differential alterations in chronomics of 2-D protein profiles in aging and RIPD male Wistar rats were studied. We report here that the melatonin could be playing an important role in modulating the chronomics of 2-D protein profiles. Additionally, various proteins were identified for the first time in this study showing significant day night variation in SCN, pineal and SN may prove useful towards targeting novel treatments for circadian dysfunction, good health and longevity.

Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome

PubMed Central

Warren, Samantha; Wan, Xiu-Feng; Conant, Gavin; Korkin, Dmitry

2013-01-01

The H1N1 subtype of influenza A virus has caused two of the four documented pandemics and is responsible for seasonal epidemic outbreaks, presenting a continuous threat to public health. Co-circulating antigenically divergent influenza strains significantly complicates vaccine development and use. Here, by combining evolutionary, structural, functional, and population information about the H1N1 proteome, we seek to answer two questions: (1) do residues on the protein surfaces evolve faster than the protein core residues consistently across all proteins that constitute the influenza proteome? and (2) in spite of the rapid evolution of surface residues in influenza proteins, are there any protein regions on the protein surface that do not evolve? To answer these questions, we first built phylogenetically-aware models of the patterns of surface and interior substitutions. Employing these models, we found a single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins. The pattern is consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80’s, as well as the differences caused by the geographic origins of the virus. Next, we developed an automated computational pipeline to comprehensively detect regions of the protein surface residues that were 100% conserved over multiple years and in multiple host species. We identified conserved regions on the surface of 10 influenza proteins spread across all avian, swine, and human strains; with the exception of a small group of isolated strains that affected the conservation of three proteins. Surprisingly, these regions were also unaffected by genetic variation in the pandemic 2009 H1N1 viral population data obtained from deep sequencing experiments. Finally, the conserved regions were intrinsically related to the intra-viral macromolecular interaction interfaces. Our study may provide further insights towards the identification of novel protein targets for influenza antivirals. PMID:24282564

Proteome-wide inference of human endophilin 1-binding peptides.

PubMed

Wu, Gang; Zhang, Zeng-Li; Fu, Chun-Jiang; Lv, Feng-Lin; Tian, Fei-Fei

2012-10-01

Human endophilin 1 (hEndo1) is a multifunctional protein that was found to bind a wide spectrum of prolinerich endocytic proteins through its Src homology 3 (SH3) domain. In order to elucidate the unknown biological functions of hEndo1, it is essential to find out the cytoplasmic components that hEndo1 recognizes and binds. However, it is too time-consuming and expensive to synthesize all peptide candidates found in the human proteome and to perform hEndo1 SH3-peptide affinity assay to identify the hEndo1-binding partners. In the present work, we describe a structure/ sequence-hybrid approach to perform proteome-wide inference of human hEndo1-binding peptides using the information gained from both the primary sequence of affinity-known peptides and the interaction profile involved in hEndo1 SH3-peptide complex three-dimensional structures. Modeling results show that (i) different residue positions contribute distinctly to peptide affinity and specificity; P-1, P2 and P4 are most important, P1 and P3 are also effective, and P-3, P-2, P0, P5 and P6 are relatively insignificant, (ii) the consensus core PXXP motif is necessary but not sufficient for determining high affinity of peptides, and some other positions must be also essential in the hEndo1 SH3-peptide binding, and (iii) the alternating arrangement of polar and nonpolar amino acids along peptide sequence is critical for the high specificity of peptide recognition by hEndo1 SH3 domain. In addition, we also find that the residue type at a specific position of hEndo1-binding peptides is not stringently invariable; amino acids that possess similar polarity could replace each other without substantial influence on peptide affinity. In this way, hEndo1 presents a broad specificity in the peptide ligands that it binds.

Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.

PubMed

Barrera, Alejandro; Alastruey-Izquierdo, Ana; Martín, María J; Cuesta, Isabel; Vizcaíno, Juan Antonio

2014-07-01

Over the past several years fungal infections have shown an increasing incidence in the susceptible population, and caused high mortality rates. In parallel, multi-resistant fungi are emerging in human infections. Therefore, the identification of new potential antifungal targets is a priority. The first task of this study was to analyse the protein domain and domain architecture content of the 137 fungal proteomes (corresponding to 111 species) available in UniProtKB (UniProt KnowledgeBase) by January 2013. The resulting list of core and exclusive domain and domain architectures is provided in this paper. It delineates the different levels of fungal taxonomic classification: phylum, subphylum, order, genus and species. The analysis highlighted Aspergillus as the most diverse genus in terms of exclusive domain content. In addition, we also investigated which domains could be considered promiscuous in the different organisms. As an application of this analysis, we explored three different ways to detect potential targets for antifungal drugs. First, we compared the domain and domain architecture content of the human and fungal proteomes, and identified those domains and domain architectures only present in fungi. Secondly, we looked for information regarding fungal pathways in public repositories, where proteins containing promiscuous domains could be involved. Three pathways were identified as a result: lovastatin biosynthesis, xylan degradation and biosynthesis of siroheme. Finally, we classified a subset of the studied fungi in five groups depending on their occurrence in clinical samples. We then looked for exclusive domains in the groups that were more relevant clinically and determined which of them had the potential to bind small molecules. Overall, this study provides a comprehensive analysis of the available fungal proteomes and shows three approaches that can be used as a first step in the detection of new antifungal targets.

Plum Brook Reactor Facility Control Room during Facility Startup

NASA Image and Video Library

1961-02-21

Operators test the National Aeronautics and Space Administration’s (NASA) Plum Brook Reactor Facility systems in the months leading up to its actual operation. The “Reactor On” signs are illuminated but the reactor core was not yet ready for chain reactions. Just a couple weeks after this photograph, Plum Brook Station held a media open house to unveil the 60-megawatt test reactor near Sandusky, Ohio. More than 60 members of the print media and radio and television news services met at the site to talk with community leaders and representatives from NASA and Atomic Energy Commission. The Plum Brook reactor went critical for the first time on the evening of June 14, 1961. It was not until April 1963 that the reactor reached its full potential of 60 megawatts. The reactor control room, located on the second floor of the facility, was run by licensed operators. The operators manually operated the shim rods which adjusted the chain reaction in the reactor core. The regulating rods could partially or completely shut down the reactor. The control room also housed remote area monitoring panels and other monitoring equipment that allowed operators to monitor radiation sensors located throughout the facility and to scram the reactor instantly if necessary. The color of the indicator lights corresponded with the elevation of the detectors in the various buildings. The reactor could also shut itself down automatically if the monitors detected any sudden irregularities.

Synthesis and Plasmonic Understanding of Core/Satellite and Core Shell Nanostructures

NASA Astrophysics Data System (ADS)

Ruan, Qifeng

Localized surface plasmon resonance, which stems from the collective oscillations of conduction-band electrons, endows Au nanocrystals with unique optical properties. Au nanocrystals possess extremely large scattering/absorption cross-sections and enhanced local electromagnetic field, both of which are synthetically tunable. Moreover, when Au nanocrystals are closely placed or hybridized with semiconductors, the coupling and interaction between the individual components bring about more fascinating phenomena and promising applications, including plasmon-enhanced spectroscopies, solar energy harvesting, and cancer therapy. The continuous development in the field of plasmonics calls for further advancements in the preparation of high-quality plasmonic nanocrystals, the facile construction of hybrid plasmonic nanostructures with desired functionalities, as well as deeper understanding and efficient utilization of the interaction between plasmonic nanocrystals and semiconductor components. In this thesis, I developed a seed-mediated growth method for producing size-controlled Au nanospheres with high monodispersity and assembled Au nanospheres of different sizes into core/satellite nanostructures for enhancing Raman signals. For investigating the interactions between Au nanocrystals and semiconductors, I first prepared (Au core) (TiO2 shell) nanostructures, and then studied their synthetically controlled plasmonic properties and light-harvesting applications. Au nanocrystals with spherical shapes are desirable in plasmon-coupled systems owing to their high geometrical symmetry, which facilitates the analysis of electrodynamic responses in a classical electromagnetic framework and the investigation of quantum tunneling and nonlocal effects. I prepared remarkably uniform Au nanospheres with diameters ranging from 20 nm to 220 nm using a simple seed-mediated growth method associated with mild oxidation. Core/satellite nanostructures were assembled out of differently sized Au nanospheres with molecular linkers. The plasmon resonances of the core/satellite nanostructures undergo red shifts in comparison to those of the sole Au cores, which is consistent with Mie theory analysis. As predicted by finite-difference time-domain simulations, the assembled core/satellite nanostructures exhibit large enhancements for Raman scattering. The facile growth of Au nanospheres and assembly of core/satellite nanostructures blaze a new way to the design of nanoarchitectures with desired plasmonic properties and functions. Coating semiconductors onto Au nanocrystals to form core shell configurations can increase the interactions between the two materials, benefiting from their large active interfacial area. The shell can also protect the Au nanocrystal core from aggregation, reshaping, and chemical corrosion. In this thesis, (Au nanocrystal core) (titania shell) nanostructures with tunable shell thicknesses were prepared by a facile wetchemistry method. Au nanocrystals with strong and tunable plasmon resonances in the visible and near-infrared regions can enhance and broaden the light utilization of TiO2 through the scattering/absorption enhancement, sensitization, and hot-electron injection. The integration of Au nanocrystals therefore hold the prospect of breaking the light-harvesting limit of TiO2 arising from its wide band gap. The resultant (Au core) (TiO2 shell) nanostructures were examined to be capable of efficiently generating reactive oxygen species under near-infrared resonant excitation. On the other hand, the transverse plasmon modes of Au nanorods, which are often too weak to be observed on scattering spectra, are enhanced by the TiO2 shell through energy transfer. With the increment of the shell thickness, the intensity of the transverse plasmon mode increases significantly and even becomes comparable with the longitudinal plasmon mode. Interestingly, both the transverse and longitudinal modes of the (Au core) (TiO2 shell) nanostructures exhibit asymmetric Fano line shapes. The Fano resonances result from the coupling between the core and shell, as understood by the mechanical oscillator model. Besides varying the shell thickness, the plasmonic bands of the core shell nanostructures can also be tailored by employing Au nanorods with different aspect ratios. The synthetically tunable plasmonic properties and synergistic interactions between the gold core and the titania shell make the hybrid nanostructure a multifunctional nanomaterial and ideal system for studying the plasmonic hybrid nanostructures.

Space Station Furnace Facility Preliminary Project Implementation Plan (PIP). Volume 2, Appendix 2

NASA Technical Reports Server (NTRS)

Perkey, John K.

1992-01-01

The Space Station Furnace Facility (SSFF) is an advanced facility for materials research in the microgravity environment of the Space Station Freedom and will consist of Core equipment and various sets of Furnace Module (FM) equipment in a three-rack configuration. This Project Implementation Plan (PIP) document was developed to satisfy the requirements of Data Requirement Number 4 for the SSFF study (Phase B). This PIP shall address the planning of the activities required to perform the detailed design and development of the SSFF for the Phase C/D portion of this contract.

Mapping arginine methylation in the human body and cardiac disease.

PubMed

Onwuli, Donatus O; Rigau-Roca, Laura; Cawthorne, Chris; Beltran-Alvarez, Pedro

2017-01-01

Arginine methylation (ArgMe) is one of the most ubiquitous PTMs, and hundreds of proteins undergo ArgMe in, for example, brain. However, the scope of ArgMe in many tissues, including the heart, is currently underexplored. Here, we aimed to (i) identify proteins undergoing ArgMe in human organs, and (ii) expose the relevance of ArgMe in cardiac disease. The publicly available proteomic data is used to search for ArgMe in 13 human tissues. To induce H9c2 cardiac-like cell hypertrophy glucose is used. The results show that ArgMe is mainly tissue-specific; nevertheless, the authors suggest an embryonic origin of core ArgMe events. In the heart, 103 mostly novel ArgMe sites in 58 nonhistone proteins are found. The authors provide compelling evidence that cardiac protein ArgMe is relevant to cardiomyocyte ontology, and important for proper cardiac function. This is highlighted by the fact that genetic mutations affecting methylated arginine positions are often associated with cardiac disease, including hypertrophic cardiomyopathy. The pilot experimental data suggesting significant changes in ArgMe profiles of H9c2 cells upon induction of cell hypertrophy using glucose is provided. The work calls for in-depth investigation of ArgMe in normal and diseased tissues using methods including clinical proteomics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrative FourD omics approach profiles the target network of the carbon storage regulatory system.

PubMed

Sowa, Steven W; Gelderman, Grant; Leistra, Abigail N; Buvanendiran, Aishwarya; Lipp, Sarah; Pitaktong, Areen; Vakulskas, Christopher A; Romeo, Tony; Baldea, Michael; Contreras, Lydia M

2017-02-28

Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genetic Background is a Key Determinant of Glomerular Extracellular Matrix Composition and Organization

PubMed Central

Randles, Michael J.; Woolf, Adrian S.; Huang, Jennifer L.; Byron, Adam; Humphries, Jonathan D.; Price, Karen L.; Kolatsi-Joannou, Maria; Collinson, Sophie; Denny, Thomas; Knight, David; Mironov, Aleksandr; Starborg, Toby; Korstanje, Ron; Humphries, Martin J.; Long, David A.

2015-01-01

Glomerular disease often features altered histologic patterns of extracellular matrix (ECM). Despite this, the potential complexities of the glomerular ECM in both health and disease are poorly understood. To explore whether genetic background and sex determine glomerular ECM composition, we investigated two mouse strains, FVB and B6, using RNA microarrays of isolated glomeruli combined with proteomic glomerular ECM analyses. These studies, undertaken in healthy young adult animals, revealed unique strain- and sex-dependent glomerular ECM signatures, which correlated with variations in levels of albuminuria and known predisposition to progressive nephropathy. Among the variation, we observed changes in netrin 4, fibroblast growth factor 2, tenascin C, collagen 1, meprin 1-α, and meprin 1-β. Differences in protein abundance were validated by quantitative immunohistochemistry and Western blot analysis, and the collective differences were not explained by mutations in known ECM or glomerular disease genes. Within the distinct signatures, we discovered a core set of structural ECM proteins that form multiple protein–protein interactions and are conserved from mouse to man. Furthermore, we found striking ultrastructural changes in glomerular basement membranes in FVB mice. Pathway analysis of merged transcriptomic and proteomic datasets identified potential ECM regulatory pathways involving inhibition of matrix metalloproteases, liver X receptor/retinoid X receptor, nuclear factor erythroid 2-related factor 2, notch, and cyclin-dependent kinase 5. These pathways may therefore alter ECM and confer susceptibility to disease. PMID:25896609

Plasma membrane proteome analysis identifies a role of barley membrane steroid binding protein in root architecture response to salinity.

PubMed

Witzel, Katja; Matros, Andrea; Møller, Anders L B; Ramireddy, Eswarayya; Finnie, Christine; Peukert, Manuela; Rutten, Twan; Herzog, Andreas; Kunze, Gotthard; Melzer, Michael; Kaspar-Schoenefeld, Stephanie; Schmülling, Thomas; Svensson, Birte; Mock, Hans-Peter

2018-06-01

Although the physiological consequences of plant growth under saline conditions have been well described, understanding the core mechanisms conferring plant salt adaptation has only started. We target the root plasma membrane proteomes of two barley varieties, cvs. Steptoe and Morex, with contrasting salinity tolerance. In total, 588 plasma membrane proteins were identified by mass spectrometry, of which 182 were either cultivar or salinity stress responsive. Three candidate proteins with increased abundance in the tolerant cv. Morex were involved either in sterol binding (a GTPase-activating protein for the adenosine diphosphate ribosylation factor [ZIGA2], and a membrane steroid binding protein [MSBP]) or in phospholipid synthesis (phosphoethanolamine methyltransferase [PEAMT]). Overexpression of barley MSBP conferred salinity tolerance to yeast cells, whereas the knock-out of the heterologous AtMSBP1 increased salt sensitivity in Arabidopsis. Atmsbp1 plants showed a reduced number of lateral roots under salinity, and root-tip-specific expression of barley MSBP in Atmsbp1 complemented this phenotype. In barley, an increased abundance of MSBP correlates with reduced root length and lateral root formation as well as increased levels of auxin under salinity being stronger in the tolerant cv. Morex. Hence, we concluded the involvement of MSBP in phytohormone-directed adaptation of root architecture in response to salinity. © 2018 John Wiley & Sons Ltd.