75 FR 54627 - Best Management Practices for Unused Pharmaceuticals at Health Care Facilities

Science.gov (United States)

2010-09-08

... at very low concentrations. EPA has been studying unused pharmaceutical disposal practices at health... avoiding pharmaceutical waste; Practices for identifying and managing types of unused pharmaceuticals; and...: September 1, 2010. Ephraim S. King, Director, Office of Science and Technology. [FR Doc. 2010-22325 Filed 9...

Economic Potential of Biomass from Unused Agriculture Land for Energy Use

DEFF Research Database (Denmark)

Pfeifer, A.; Dominkovic, Dominik Franjo; Ćosić, B.

2015-01-01

In this paper the energy potential of biomass from growing short rotation coppice (SRC) on unused agricultural land in the Republic of Croatia was examined. At present, SRC is not completely recognized in Croatian legislative and considerations in energy strategy and action plans. The paper aspires...... to contribute to better understanding of the role SRC can take in national and local energy planning. The methodology is provided for regional analysis of biomass energy potential on unused agricultural land and for assessing the cost of the biomass at the power plant (PP) location considering transport...... plants and appropriate size of seasonal heat storage is discussed for each case study. Case studies have shown the potential for use of previously unused agricultural land to help achieve national targets for renewable energy sources as well as reducing carbon dioxide emissions, help diversify...

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Science.gov (United States)

Babbitt, Patricia C; Bagos, Pantelis G; Bairoch, Amos; Bateman, Alex; Chatonnet, Arnaud; Chen, Mark Jinan; Craik, David J; Finn, Robert D; Gloriam, David; Haft, Daniel H; Henrissat, Bernard; Holliday, Gemma L; Isberg, Vignir; Kaas, Quentin; Landsman, David; Lenfant, Nicolas; Manning, Gerard; Nagano, Nozomi; Srinivasan, Narayanaswamy; O'Donovan, Claire; Pruitt, Kim D; Sowdhamini, Ramanathan; Rawlings, Neil D; Saier, Milton H; Sharman, Joanna L; Spedding, Michael; Tsirigos, Konstantinos D; Vastermark, Ake; Vriend, Gerrit

2015-01-01

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Economic feasibility of CHP facilities fueled by biomass from unused agriculture land

DEFF Research Database (Denmark)

Pfeifer, Antun; Dominkovic, Dominik Franjo; Ćosić, Boris

2016-01-01

In this paper, the energy potential of biomass from growing short rotation coppice on unused agricultural land in the Republic of Croatia is used to investigate the feasibility of Combined Heat and Power (CHP) facilities fueled by such biomass. Large areas of agricultural land that remain unused...... work and is now used to investigate the conditions in which such energy facilities could be feasible. The overall potential of biomass from short rotation coppice cultivated on unused agricultural land in the scenarios with 30% of the area is up to 10PJ/year. The added value of fruit trees pruning...... biomass represents an incentive for the development of fruit production on such agricultural land. Sensitivity analysis was conducted for several parameters: cost of biomass, investment costs in CHP systems and combined change in biomass and technology cost....

Disposal practices of unused and expired pharmaceuticals among general public in Kabul

OpenAIRE

Bashaar, Mohammadk; Thawani, Vijay; Hassali, Mohamed Azmi; Saleem, Fahad

2017-01-01

Abstract Background Most of the medicine users remain unaware about the disposal of unused or expired medicines. The aim of this study was to know the disposal practices of unused and expired medicines among the general public in Kabul. Methods This was a descriptive, cross-sectional survey, conducted through face-to-face interviews using prevalidated structured questionnaire. Returned questionnaires were double-checked for accuracy. Statistical Package for Social Science (SPSS) version 23 wa...

The Universal Protein Resource (UniProt)

Data.gov (United States)

U.S. Department of Health & Human Services — The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase...

Pembuatan Kakas Pendeteksi Unused Method pada Kode Program PHP dengan Framework CodeIgniter Menggunakan Call Graph

Directory of Open Access Journals (Sweden)

Divi Galih Prasetyo Putri

2014-03-01

Full Text Available Proses evolusi dan perawatan dari sebuah sistem merupakan proses yang sangat penting dalam rekayasa perangkat lunak tidak terkecuali pada aplikasi web. Pada proses ini kebanyakan pengembang tidak lagi berpatokan pada rancangan sistem. Hal ini menyebabkan munculnya unused method. Bagian-bagian program ini tidak lagi terpakai namun masih berada dalam sistem. Keadaan ini meningkatkan kompleksitas dan mengurangi tingkat understandability sistem. Guna mendeteksi adanya unused method pada progam diperlukan teknik untuk melakukan code analysis. Teknik static analysis yang digunakan memanfaatkan call graph yang dibangun dari kode program untuk mengetahui adanya unused method. Call graph dibangun berdasarkan pemanggilan antar method. Aplikasi ini mendeteksi unused method pada kode program PHP yang dibangun menggunakan framework CodeIgniter. Kode program sebagai inputan diurai kedalam bentuk Abstract Syntax Tree (AST yang kemudian dimanfaatkan untuk melakukan analisis terhadap kode program. Proses analisis tersebut kemudian menghasilkan sebuah call graph. Dari call graph yang dihasilkan dapat dideteksi method-method mana saja yang tidak berhasil ditelusuri dan tergolong kedalam unused method. Kakas telah diuji coba pada 5 aplikasi PHP dengan hasil  rata-rata nilai presisi sistem sebesar 0.749 dan recall sebesar 1.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

NARCIS (Netherlands)

Babbitt, P.C.; Bagos, P.G.; Bairoch, A.; Bateman, A.; Chatonnet, A.; Chen, M.J.; Craik, D.J.; Finn, R.D.; Gloriam, D.; Haft, D.H.; Henrissat, B.; Holliday, G.L.; Isberg, V.; Kaas, Q.; Landsman, D.; Lenfant, N.; Manning, G.; Nagano, N.; Srinivasan, N.; O'Donovan, C.; Pruitt, K.D.; Sowdhamini, R.; Rawlings, N.D.; Saier, M.H., Jr.; Sharman, J.L.; Spedding, M.; Tsirigos, K.D.; Vastermark, A.; Vriend, G.

2015-01-01

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from

Outline and summary of research for a database of unused energy technologies; Miriyo energy ni kansuru data shu sakusei chosa

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-03-01

For effective promotion of the new energy utilization project of NEDO and preparation of the future new energy vision, the data on unused energy were systematically arranged. The definition of heat supply systems using unused energy was clarified, and the kind and property of unused energy were arranged. Some typical systems of heat supply facilities using unused energy were presented. The data were classified by energy source, temperature level and region, and the detailed database was prepared for the typical systems. The overseas database was prepared, in particular, for European and American systems. Domestic and overseas policies, laws and subsidy systems were arranged. The introduction effect of two heat supply facilities using unused energy was surveyed, and their operation costs were analyzed. Basic terminology related to unused energy was compiled and explained. Related organizations, in particular, manufacturers were surveyed and arranged. The main manufacturers of a heat recovery refrigerator and waste heat boiler as typical equipment, and the number of these equipment shipped were arranged. 51 figs., 116 tabs.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

DEFF Research Database (Denmark)

Babbitt, Patricia C.; Bagos, Pantelis G.; Bairoch, Amos

2015-01-01

During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from...... protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication...

Biodegradability of unused lubricating brake fluids in fresh and ...

African Journals Online (AJOL)

The biodegradability of four unused lubricating brake fluids (Total brake fluid, Allied brake fluid, Oando brake fluid and Ate brake fluid) was carried out in fresh and marine water obtained from Isiokpo stream and Bonny river of the Niger Delta, South South Nigeria. Biodegradability, of the brake fluids were obtained after a 56 ...

26 CFR 1.825-1 - Unused loss deduction; in general.

Science.gov (United States)

2010-04-01

... TAX (CONTINUED) INCOME TAXES Mutual Insurance Companies (other Than Life and Certain Marine Insurance Companies and Other Than Fire Or Flood Insurance Companies Which Operate on Basis of Perpetual Policies Or...) provides that the unused loss deduction of a mutual insurance company subject to the tax imposed by section...

26 CFR 1.825-2 - Unused loss carryovers and carrybacks.

Science.gov (United States)

2010-04-01

... TAX (CONTINUED) INCOME TAXES Mutual Insurance Companies (other Than Life and Certain Marine Insurance Companies and Other Than Fire Or Flood Insurance Companies Which Operate on Basis of Perpetual Policies Or... insurance company taxable under section 821(a) must first determine the part of any unused losses for any...

Have Changes to Unused Land in China Improved or Exacerbated Its Environmental Quality in the Past Three Decades?

Directory of Open Access Journals (Sweden)

Ling Yi

2016-02-01

Full Text Available Inappropriate land use has caused a series of environmental disasters such as floods and sand storms, and some of them involved unused land changes with highly localized distributions in arid and semi-arid regions with fragile ecosystems. As the third-rank category of first-level land use/cover in China, unused land (UL is now playing an increasingly important role in protection of the natural environment and sustainable utilization of land resources. In this article, we assessed the effects on regional eco-environments employing a quantitative EL (ecological effect index model, which can be used to evaluate and represent the contribution of UL changes to the eco-environmental quality. Results show that UL changes generally contributed to the deterioration of eco-environmental quality during the study period. Some major contributors to improving eco-environmental quality were transformation of sandy land and saline-alkali lands to grasslands, expansion of water bodies in UL areas, and reclamation of farmland in UL areas (except for marsh lands. In contrast, the main contributors to worsening eco-environmental quality were grassland degradation to UL (except marshes, reclamation of marsh areas, and shrinkage of water bodies to leave desert or saline-alkali land. Some suggestions are provided about UL management, utilization, and protection issues.

Economic feasibility of CHP facilities fueled by biomass from unused agriculture land: Case of Croatia

International Nuclear Information System (INIS)

Pfeifer, Antun; Dominković, Dominik Franjo; Ćosić, Boris; Duić, Neven

2016-01-01

Highlights: • Potential of unused agricultural land for biomass and fruit production is assessed. • Technical and energy potential of biomass from SRC and fruit pruning is calculated. • Economic feasibility of CHP plants utilizing biomass from SRC is presented for Croatia. • Sensitivity analysis and recommendations for shift toward feasibility are provided. - Abstract: In this paper, the energy potential of biomass from growing short rotation coppice on unused agricultural land in the Republic of Croatia is used to investigate the feasibility of Combined Heat and Power (CHP) facilities fueled by such biomass. Large areas of agricultural land that remain unused for food crops, represent significant potential for growing biomass that could be used for energy. This biomass could be used to supply power plants of up to 15 MW_e in accordance with heat demands of the chosen locations. The methodology for regional energy potential assessment was elaborated in previous work and is now used to investigate the conditions in which such energy facilities could be feasible. The overall potential of biomass from short rotation coppice cultivated on unused agricultural land in the scenarios with 30% of the area is up to 10 PJ/year. The added value of fruit trees pruning biomass represents an incentive for the development of fruit production on such agricultural land. Sensitivity analysis was conducted for several parameters: cost of biomass, investment costs in CHP systems and combined change in biomass and technology cost.

Implementation of unused production factors in agriculture by means of dynamic optimization models with random constraints

Directory of Open Access Journals (Sweden)

Jadwiga Zaród

2011-01-01

Full Text Available The farms of Western Pomerania province possess a large surplus of manpower. The dynamic optimization models with random constraints served the investigation of the possibilities of implementation of the unused man-hours. Those models regarded four successive years 2003-2006. The solution proceeded in two steps. The first step let us construct the assumption of the surplus or the deficiency of production factors. In the next step additional variables regarding the lease of arable grounds were introduced while the unused man-hours were implemented with various probability. The optimal solutions indicated the area of particular crops, the quantity of livestock and the farm income dependent on the use of the existing employment. This study aims at the presentation of the possibility of implementation of unused man-hours in farms dealing solely with the crop production and also the production of crop and livestock.

39 CFR 3010.25 - Limitation on unused rate adjustment authority rate adjustments.

Science.gov (United States)

2010-07-01

... only be applied together with inflation-based limitation rate adjustments or when inflation-based... used in lieu of an inflation-based limitation rate adjustment. ... 39 Postal Service 1 2010-07-01 2010-07-01 false Limitation on unused rate adjustment authority...

26 CFR 1.46-2 - Carryback and carryover of unused credit.

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 1 2010-04-01 2010-04-01 true Carryback and carryover of unused credit. 1.46-2 Section 1.46-2 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY INCOME TAX INCOME TAXES Rules for Computing Credit for Investment in Certain Depreciable Property § 1.46-2 Carryback and...

Quantity and economic value of unused oral anti-cancer and biological disease-modifying anti-rheumatic drugs among outpatient pharmacy patients who discontinue therapy.

Science.gov (United States)

Bekker, C L; Melis, E J; Egberts, A C G; Bouvy, M L; Gardarsdottir, H; van den Bemt, B J F

2018-03-24

Patients sometimes discontinue the use of expensive oral anti-cancer drug (OACD) or biological disease-modifying anti-rheumatic drug (bDMARD) therapies early, leading to medication waste if the patient has not used all dispensed medication. To determine the proportion of patients who have unused OACDs or bDMARDs after therapy discontinuation, and the quantity and economic value of these unused medications. Furthermore, patients' reasons for therapy discontinuation and their disposal method for unused medications were determined. In a retrospective follow-up study using a Dutch outpatient pharmacy database, patients (≥18 years) who did not refill an OACD or bDMARD prescription, dispensed between November 2015 and February 2016, within two weeks of the prescription end date were contacted by phone and asked about their unused medication and reasons thereof. The economic value was calculated using Dutch medication prices. Data were descriptively analyzed in STATA13. The database included 1173 patients, of whom 159 likely had discontinued therapy and were contacted. Of these, 88 patients were excluded (39 refilled, 47 missing, and 2 other). Of the 71 patients who had discontinued therapy, 39 (54.9%) had unused medications, comprising 22 OACD users (mean age 63.0 (SD ± 15.9) years, 50.0% female) and 17 bDMARD users (mean age 50.7 (SD ± 13.5) years, 47.1% female). A total of 59 packages were unused, with a total value of €60,341. Unused OACD packages and bDMARD packages had median values of €179 (IQR €24-2487) and €992 (IQR €681-1093), respectively. Patients primarily discontinued therapy due to adverse or insufficient effects. This study illustrates that more than half of patients discontinuing OACD or bDMARD therapies have unused medication. This emphasizes the need for waste-reducing interventions. Copyright © 2018 Elsevier Inc. All rights reserved.

Disposal practices of unused and expired pharmaceuticals among general public in Kabul

Directory of Open Access Journals (Sweden)

Mohammad Bashaar

2017-01-01

Full Text Available Abstract Background Most of the medicine users remain unaware about the disposal of unused or expired medicines. The aim of this study was to know the disposal practices of unused and expired medicines among the general public in Kabul. Methods This was a descriptive, cross-sectional survey, conducted through face-to-face interviews using prevalidated structured questionnaire. Returned questionnaires were double-checked for accuracy. Statistical Package for Social Science (SPSS version 23 was used for statistical analysis. Results Total of 301 valid questionnaires were returned with a response rate of 100% in which 73.4% men and 26.6% women participated. More than half of the respondents were university graduates. Interestingly, 83.4% of the interviewees purchased medicines on the prescription of which 47.2% were university graduates, while 14.6% purchased medicine over the counter. Among the respondents, 46.5/100 purchased antibiotics and the remaining purchased NSAIDs, anti-hypertensive and anti-diabetic medicines. Significantly, 97/100 checked the expiry date of medicine before buying. Majority (95.3% of the respondents’ stored medicines at home. 77.7% of the respondents discarded the expired medicines in household trash. Majority of respondents held government responsible for creation of awareness for proper medicine disposal. Almost entire sample (98% felt that improper disposal of unused and expired medicines can affect the environment and health. Conclusion Gaps exist in practices, therefore robust, safe and cost-effective pharmaceutical waste management program supported with media campaign is needed. Healthcare practitioners and community pharmacists should offer training to educate customers on standard medicine disposal practices.

Disposal practices of unused and expired pharmaceuticals among general public in Kabul.

Science.gov (United States)

Bashaar, Mohammad; Thawani, Vijay; Hassali, Mohamed Azmi; Saleem, Fahad

2017-01-07

Most of the medicine users remain unaware about the disposal of unused or expired medicines. The aim of this study was to know the disposal practices of unused and expired medicines among the general public in Kabul. This was a descriptive, cross-sectional survey, conducted through face-to-face interviews using prevalidated structured questionnaire. Returned questionnaires were double-checked for accuracy. Statistical Package for Social Science (SPSS) version 23 was used for statistical analysis. Total of 301 valid questionnaires were returned with a response rate of 100% in which 73.4% men and 26.6% women participated. More than half of the respondents were university graduates. Interestingly, 83.4% of the interviewees purchased medicines on the prescription of which 47.2% were university graduates, while 14.6% purchased medicine over the counter. Among the respondents, 46.5/100 purchased antibiotics and the remaining purchased NSAIDs, anti-hypertensive and anti-diabetic medicines. Significantly, 97/100 checked the expiry date of medicine before buying. Majority (95.3%) of the respondents' stored medicines at home. 77.7% of the respondents discarded the expired medicines in household trash. Majority of respondents held government responsible for creation of awareness for proper medicine disposal. Almost entire sample (98%) felt that improper disposal of unused and expired medicines can affect the environment and health. Gaps exist in practices, therefore robust, safe and cost-effective pharmaceutical waste management program supported with media campaign is needed. Healthcare practitioners and community pharmacists should offer training to educate customers on standard medicine disposal practices.

Present situation of unused uranium fuel in Tokyo Institute of Technology

International Nuclear Information System (INIS)

Obara, T.; Ogawa, M.

2008-01-01

Present situation of unused enriched uranium fuel in Tokyo Institute of Technology is described. The fuels were for sub-critical experiments. There is no special facility for transportation in the site. But there is no technical problem for it. One of the important issues to be done is a duty by national regulation against nuclear disaster. (author)

Adaptation in cloud resource configuration:a survey

OpenAIRE

Hummaida, Abdul R.; Paton, Norman W.; Sakellariou, Rizos

2016-01-01

With increased demand for computing resources at a lower cost by end-users, cloud infrastructure providers need to find ways to protect their revenue. To achieve this, infrastructure providers aim to increase revenue and lower operational costs. A promising approach to addressing these challenges is to modify the assignment of resources to workloads. This can be used, for example, to consolidate existing workloads; the new capability can be used to serve new requests or alternatively unused r...

Design of environment-friendly and next generation-type conversion system for unused carbon resources by developing highly functional materials; Kokino zairyo kaihatsu ni yoru kankyo chowagata jisedai miriyo tanso shigen tenkan system no kochiku

Energy Technology Data Exchange (ETDEWEB)

Wakabayashi, K; Morooka, S; Arai, Y [Kyushu University, Fukuoka (Japan). Faculty of Engineering; Sakanishi, K [Kyushu University, Fukuoka (Japan). Institute of Advanced Material Study

1997-02-01

Studies are conducted for the development of now-unused kinds of fossil carbon resources, such as low rank coal and heavy gravity crude oil, into higher-value liquid fuel. In the preliminary treatment process, the fossil carbon resources are dried by use of supercritical carbon dioxide, when it is found that the resources are disintegrated and water is desorbed. In a low rank coal liquefaction process using the NiMo/KB (Kefjen Black) catalyst, more than 60% is converted into oil, which rate is improved by use of the dual-temperature liquefaction process. This catalyst may be recovered by separation utilizing specific gravity difference. As a low temperature gasification catalyst, the alkaline carbonate-carried carbon catalyst is very quick at the initial stage of reaction. The perovskite-carried alkaline carbonate catalyst is high in carbon oxidizing/activating efficiency at low temperatures. The silica film deposited on an alumina-coated support tube is excellent in selectivity and speed as a hydrogen separating film, and a carbonized polyimide film as a carbon dioxide separating film. For the supercritical phase adsorption/separation of chemicals not to be distilled easily, the NaY-type zeolite functions effectively. Pd/ZrO2 serving as a carbon monoxide conversion catalyst enables the recovery of more MeOH when Pd grains are smaller in diameter.

Protein resources and aquafeed development in the Sultanate of Oman

Directory of Open Access Journals (Sweden)

Stephen Goddard

2015-01-01

Full Text Available The continued growth of intensive aquaculture is dependent on the development of sustainable protein sources to replace conventional fish meals in aquafeeds. Practical alternatives are plant-derived protein, protein from micro-organisms and protein from under-utilized marine resources. The challenges are to find alternative ingredients with high protein, suitable amino acid content, high palatability and absence of anti-nutritional factors. There is considerable biotechnology-based research in this area, including genetic modification of plant-based proteins, use of probiotics to enhance digestibility and the renewed application of fermentation technologies to produce single cell proteins. Research in Oman is focused on the utilization of marine protein resources. Fisheries by-catch and processing waste have been evaluated as liquid hydrolysates and as meals for inclusion in aquafeeds and new research is planned on the utilization of meso-pelagic fish (myctophids, which occur in abundance in the Arabian Sea and the Sea of Oman. Initial studies have been conducted on the biochemical composition of the lantern fish, Benthosema pterotum, which revealed favorable protein, amino acid and long-chain PUFA content. Potential limiting factors were high levels of saturated lipids and the heavy metals arsenic and cadmium. These results will be discussed within a general review of marine resources and aquafeed development in Oman.

The Universal Protein Resource (UniProt): an expanding universe of protein information.

Science.gov (United States)

Wu, Cathy H; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

2006-01-01

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

DETERMINATION OF THE POTENTIAL FOR ANAEROBIC DEGRADATION OF UNUSED PHARMACEUTICALS IN MUNICIPAL SOLID WASTE LANDFILLS

Science.gov (United States)

For many years the recommended method of disposal for unused household medications was the sewage system. However, research studies have emerged showing that many pharmaceuticals and endocrine disrupting compounds are not fully removed by wastewater treatment systems and enter t...

Households And Bio-Resources In Plateau State Nigeria

International Nuclear Information System (INIS)

Dasogot, A.D.

2002-01-01

The paper examines household dynamics as variables for bio-resource or biomass resource potentials and utilisation. Information was collected from 250 randomly selected households in five villages of the State, mainly using questionnaire administered on household heads, and a direct measurement/observation about what households have, do or say concerning the study problem. It was shown that insignificant quantity were utilised for various purposes like cooking and heating, but the bio-resources generated met both domestic and income needs of the households. It was concluded that beneficial use (compost, biogas or generation of electricity) should be found for the largely unused bio-resources and household dynamics should be integrated into bio-resource energy planning

Key challenges for the creation and maintenance of specialist protein resources

Science.gov (United States)

Holliday, Gemma L; Bairoch, Amos; Bagos, Pantelis G; Chatonnet, Arnaud; Craik, David J; Finn, Robert D; Henrissat, Bernard; Landsman, David; Manning, Gerard; Nagano, Nozomi; O’Donovan, Claire; Pruitt, Kim D; Rawlings, Neil D; Saier, Milton; Sowdhamini, Ramanathan; Spedding, Michael; Srinivasan, Narayanaswamy; Vriend, Gert; Babbitt, Patricia C; Bateman, Alex

2015-01-01

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long-term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value. Proteins 2015; 83:1005–1013. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:25820941

RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction

Science.gov (United States)

Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong

2014-01-01

Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA–RNA/RNA–protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA–RNA interactions and 1619 RNA–protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA–RNA/RNA–protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA–RNA/RNA–protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. PMID:24803509

The Protein Data Bank archive as an open data resource

Science.gov (United States)

Berman, Helen M.; Kleywegt, Gerard J.; Nakamura, Haruki; Markley, John L.

2014-10-01

The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.

26 CFR 1.642(h)-1 - Unused loss carryovers on termination of an estate or trust.

Science.gov (United States)

2010-04-01

... estate or trust. 1.642(h)-1 Section 1.642(h)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF....642(h)-1 Unused loss carryovers on termination of an estate or trust. (a) If, on the final termination...(h)(1) to the beneficiaries succeeding to the property of the estate or trust. See § 1.641(b)-3 for...

Using the CMS high level trigger as a cloud resource

International Nuclear Information System (INIS)

Colling, David; Huffman, Adam; Bauer, Daniela; McCrae, Alison; Cinquilli, Mattia; Gowdy, Stephen; Coarasa, Jose Antonio; Ozga, Wojciech; Chaze, Olivier; Lahiff, Andrew; Grandi, Claudio; Tiradani, Anthony; Sgaravatto, Massimo

2014-01-01

The CMS High Level Trigger is a compute farm of more than 10,000 cores. During data taking this resource is heavily used and is an integral part of the experiment's triggering system. However, outside of data taking periods this resource is largely unused. We describe why CMS wants to use the HLT as a cloud resource (outside of data taking periods) and how this has been achieved. In doing this we have turned a single-use cluster into an agile resource for CMS production computing. While we are able to use the HLT as a production cloud resource, there is still considerable further work that CMS needs to carry out before this resource can be used with the desired agility. This report, therefore, represents a snapshot of this activity at the time of CHEP 2013.

26 CFR 1.103(n)-4T - Elective carryforward of unused private activity bond limit (temporary).

Science.gov (United States)

2010-04-01

... bond limit (temporary). 1.103(n)-4T Section 1.103(n)-4T Internal Revenue INTERNAL REVENUE SERVICE... Excluded from Gross Income § 1.103(n)-4T Elective carryforward of unused private activity bond limit... carryforward for any one or more projects described in A-5 of this § 1.103(n)-4T (carryforward projects). Q-2...

PLMD: An updated data resource of protein lysine modifications.

Science.gov (United States)

Xu, Haodong; Zhou, Jiaqi; Lin, Shaofeng; Deng, Wankun; Zhang, Ying; Xue, Yu

2017-05-20

Post-translational modifications (PTMs) occurring at protein lysine residues, or protein lysine modifications (PLMs), play critical roles in regulating biological processes. Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types, here we greatly updated our previous studies, and presented a much more integrative resource of protein lysine modification database (PLMD). In PLMD, we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs, including ubiquitination, acetylation, sumoylation, methylation, succinylation, malonylation, glutarylation, glycation, formylation, hydroxylation, butyrylation, propionylation, crotonylation, pupylation, neddylation, 2-hydroxyisobutyrylation, phosphoglycerylation, carboxylation, lipoylation and biotinylation. Using the data set, a motif-based analysis was performed for each PLM type, and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the modifications. Moreover, various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other, and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine residues. Finally, various options were provided for accessing the data, while original references and other annotations were also present for each PLM substrate. Taken together, we anticipated the PLMD database can serve as a useful resource for further researches of PLMs. PLMD 3.0 was implemented in PHP + MySQL and freely available at http://plmd.biocuckoo.org. Copyright © 2017 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

The evolution of a Web resource: The Galactosemia Proteins Database 2.0.

Science.gov (United States)

d'Acierno, Antonio; Scafuri, Bernardina; Facchiano, Angelo; Marabotti, Anna

2018-01-01

Galactosemia Proteins Database 2.0 is a Web-accessible resource collecting information about the structural and functional effects of the known variations associated to the three different enzymes of the Leloir pathway encoded by the genes GALT, GALE, and GALK1 and involved in the different forms of the genetic disease globally called "galactosemia." It represents an evolution of two available online resources we previously developed, with new data deriving from new structures, new analysis tools, and new interfaces and filters in order to improve the quality and quantity of information available for different categories of users. We propose this new resource both as a landmark for the entire world community of galactosemia and as a model for the development of similar tools for other proteins object of variations and involved in human diseases. © 2017 Wiley Periodicals, Inc.

MPact: the MIPS protein interaction resource on yeast.

Science.gov (United States)

Güldener, Ulrich; Münsterkötter, Martin; Oesterheld, Matthias; Pagel, Philipp; Ruepp, Andreas; Mewes, Hans-Werner; Stümpflen, Volker

2006-01-01

In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein-protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been called a gold standard because of its quality and comprehensiveness [H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia, J. D. Han, N. Bertin, S. Chung, M. Vidal and M. Gerstein (2004) Genome Res., 14, 1107-1118]. MPact and the yeast protein localization catalog provide information related to the proximity of proteins in yeast. Beside the integration of high-throughput data, information about experimental evidence for PPIs in the literature was compiled by experts adding up to 4300 distinct PPIs connecting 1500 proteins in yeast. As the interaction data is a complementary part of CYGD, interactive mapping of data on other integrated data types such as the functional classification catalog [A. Ruepp, A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejs, I. Tetko, U. Güldener, G. Mannhaupt, M. Münsterkötter and H. W. Mewes (2004) Nucleic Acids Res., 32, 5539-5545] is possible. A survey of signaling proteins and comparison with pathway data from KEGG demonstrates that based on these manually annotated data only an extensive overview of the complexity of this functional network can be obtained in yeast. The implementation of a web-based PPI-analysis tool allows analysis and visualization of protein interaction networks and facilitates integration of our curated data with high-throughput datasets. The complete dataset as well as user-defined sub-networks can be retrieved easily in the standardized PSI-MI format. The resource can be accessed through http://mips.gsf.de/genre/proj/mpact.

The geographical distribution of fossil fuels unused when limiting global warming to 2 °C.

Science.gov (United States)

McGlade, Christophe; Ekins, Paul

2015-01-08

Policy makers have generally agreed that the average global temperature rise caused by greenhouse gas emissions should not exceed 2 °C above the average global temperature of pre-industrial times. It has been estimated that to have at least a 50 per cent chance of keeping warming below 2 °C throughout the twenty-first century, the cumulative carbon emissions between 2011 and 2050 need to be limited to around 1,100 gigatonnes of carbon dioxide (Gt CO2). However, the greenhouse gas emissions contained in present estimates of global fossil fuel reserves are around three times higher than this, and so the unabated use of all current fossil fuel reserves is incompatible with a warming limit of 2 °C. Here we use a single integrated assessment model that contains estimates of the quantities, locations and nature of the world's oil, gas and coal reserves and resources, and which is shown to be consistent with a wide variety of modelling approaches with different assumptions, to explore the implications of this emissions limit for fossil fuel production in different regions. Our results suggest that, globally, a third of oil reserves, half of gas reserves and over 80 per cent of current coal reserves should remain unused from 2010 to 2050 in order to meet the target of 2 °C. We show that development of resources in the Arctic and any increase in unconventional oil production are incommensurate with efforts to limit average global warming to 2 °C. Our results show that policy makers' instincts to exploit rapidly and completely their territorial fossil fuels are, in aggregate, inconsistent with their commitments to this temperature limit. Implementation of this policy commitment would also render unnecessary continued substantial expenditure on fossil fuel exploration, because any new discoveries could not lead to increased aggregate production.

Unused Medications Disposal Practice: The case of Patients Visiting University of Gondar Specialized Teaching Hospital, Gondar, Ethiopia

OpenAIRE

Tadele Atinafu; Abayneh Takele; Adeladlew Kassie; Adane Yehualaw; Getu Tesfaw; Tesfanesh Desseno; Tadesse Mekonnen; Mulugeta Fentie

2014-01-01

Background: The disposal of unwanted medications has been a concern in many countries, as pharmaceutical waste enters the ecosystem, ultimately having an effect on human health and environment. The main objective of this study was to assess unused medications disposal practice of patients Method: Institution based cross sectional study was used. Patients were systematically selected and interviewed using structured questionnaires. The Data was analyzed using SPSS version 20. Result: Out of...

Improving health care costing with resource consumption accounting.

Science.gov (United States)

Ozyapici, Hasan; Tanis, Veyis Naci

2016-07-11

Purpose - The purpose of this paper is to explore the differences between a traditional costing system (TCS) and resource consumption accounting (RCA) based on a case study carried out in a hospital. Design/methodology/approach - A descriptive case study was first carried out to identify the current costing system of the case hospital. An exploratory case study was then conducted to reveal how implementing RCA within the case hospital assigns costs differently to gallbladder surgeries than the current costing system (i.e. a TCS). Findings - The study showed that, in contrast to a TCS, RCA considers the unused capacity, which is the difference between the work that can be performed based on current resources and the work that is actually being performed. Therefore, it assigns lower total costs to open and laparoscopic gallbladder surgeries. The study also showed that by separating costs into fixed and variable RCA allows managers to benefit from a pricing strategy based on the difference between the service's selling price and variable costs incurred in providing that service. Research limitations/implications - The limitation of this study is that, because of time constraints, the implementation was performed in the general surgery department only. However, since RCA is an advanced system that has the same application procedures for any department inside in a hospital, managers need only time gaps to implement this system to all parts of the hospital. Practical implications - This study concluded that RCA is better than a TCS for use in health care settings that have high overhead costs because it accurately assigns overhead costs to services by considering unused capacities incurred by a hospital. Consequently, this study provides insight into both measuring and managing unused capacities within the health care sector. This study also concluded that RCA helps health care administrators increase their competitive advantage by allowing them to determine the lowest

Exploiting Dark Information Resources to Create New Value Added Services to Study Earth Science Phenomena

Science.gov (United States)

Ramachandran, Rahul; Maskey, Manil; Li, Xiang; Bugbee, Kaylin

2017-01-01

This paper presents two research applications exploiting unused metadata resources in novel ways to aid data discovery and exploration capabilities. The results based on the experiments are encouraging and each application has the potential to serve as a useful standalone component or service in a data system. There were also some interesting lessons learned while designing the two applications and these are presented next.

Re: Evaluation of the size and type of free particulates collected from unused asbestos-containing brake components as related to potential for respirability.

Science.gov (United States)

Paustenbach, Dennis J; Finley, Brent L; Sheehan, Patrick J; Brorby, Gregory P

2006-01-01

In Atkinson et al. 2004 rinsates of unused brake components were analyzed by transmission electron microscopy (TEM) for the presence of asbestos fibers. We do not believe that the findings of Atkinson et al. are informative and could have been predicted based on the study design and the fact that one would expect to find measurable TEM asbestos fibers on an unused brake component. We also find that the paper did not provide a full or even partial discussion of the published literature with respect to industrial hygiene or epidemiology data. The findings of Atkinson et al. do not, in our view, "further raise concerns" about historical asbestos exposures experienced by automotive mechanics because of the vast amount of published literature to the contrary. Am. J. Ind. Med. 49:60-61, 2006. (c) 2005 Wiley-Liss, Inc.

Wear And Tear Determination By Trace Multi-Element Analysis Of An Unused And Used Lubricant Oil Using Instrumental Neutron Activation Analysis

International Nuclear Information System (INIS)

Adeyemo, D.J.

2004-01-01

Instrumental neutron activation analysis technique using the Imperial College Centre consort M. K. II nuclear reactor was utilized for the determination of: As, Ba Ca CI, Co, Cr, Cu, Fe, K, Mn, Mo, Na Ni, Rb, Sb, Se, Ti, V, and Zn, in an imported and used car lubricant oil. The wear of the oil lubricated parts of the car engine was monitored by establishing a correlation between the results obtained in the analysis. The result obtained from the analysis of the unused and then used samples on a low performing oil leaking four stroke car engine showed an increase on all the elements determined except for Se and Rb. The precision for the multi-element analysis is less than 12% for most of the elements. The accuracy of the measurement is also validated by the result obtained from the analysis of NBS-SRM1635 (sub-bituminous) coal standard for the elements. The results obtained indicate that analysis of unused and used lubricant oil samples can aid in locating defects in engine parts and hence facilitated maintenance procedures

The DIMA web resource--exploring the protein domain network.

Science.gov (United States)

Pagel, Philipp; Oesterheld, Matthias; Stümpflen, Volker; Frishman, Dmitrij

2006-04-15

Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. http://mips.gsf.de/genre/proj/dima

Sytemic lupus erythematosus presenting with protein losing enteropathy in a resource limited centre: a case report

Directory of Open Access Journals (Sweden)

Ratnayake Eranda C

2012-01-01

Full Text Available Abstract Introduction Systemic lupus erythematosus is a disease which may initially present with varying symptoms, most commonly a photosensitive rash and arthritis. Protein losing enteropathy is a recognized but rare presenting manifestation. Diagnosing protein losing enteropathy in resource limited centres is challenging but possible through the exclusion of other possible causes of hypoalbunaemia. Case Presentation We report a case of protein losing gastroenteropathy secondary to intestinal lymphangiectasia as the initial manifestation of systemic lupus erythematosus in a 57 year old Sri Lankan (South Asian male patient. The diagnosis was made by the exclusion of other causes of hypoalbuminaemia as the gold standard investigations for protein losing enteropathy were not available at this centre. Conclusions Protein losing enteropathy is a diagnosis of exclusion in resource limited centres in the world. Systemic lupus erythematosus should be considered in the differential diagnosis of protein losing enteropathy. Intestinal lymphangiectasia should also be recognized as a possible pathophysiological mechanism.

Hydrogeothermal resources in spa areas of Serbia: Main properties and possible improvement of use

Directory of Open Access Journals (Sweden)

Dokmanović Petar B.

2012-01-01

Full Text Available Geological complexity of the territory of Serbia is a world curiosity: six main geo-tectonic regions and tens sub-regions are delineated in a small area of 88,000 km2. Geologic origin and regional structure of some areas has long been the subject of discussion. Notable magmatism and associated tectonic events in the Earth's crust provided for a fairly large hydrogeothermal resource potential, which is manifested in more than 250 warm (mainly mineral springs and more than 100 hydrothermal wells. Thermal springs and wells together discharge some 5 m3/s. This potential is used in part for balneal therapy (waters differ in temperature and chemical composition in the spa areas of Serbia. The amounts of thermal water unused therapeutically or the amounts of heat energy from unused geo-thermal water may be used in almost all spas for space heating/cooling and thus increase the efficiency of the thermal water energy utilization. This also will be cost-effective, reduce emission of noxious gases, and improve the environmental-health image of the resorts. The hydrogeothermal resources are described for 29 spas with 700 l/s total discharge capacity of water temperature between 25°C and 96ºC, or an overall heat energy of 78.40 MWt. Feasibility of additional energy utilization of thermal water in spas is generally considered.

The Potential and Utilization of Unused Energy Sources for Large-Scale Horticulture Facility Applications under Korean Climatic Conditions

Directory of Open Access Journals (Sweden)

In Tak Hyun

2014-07-01

Full Text Available As the use of fossil fuel has increased, not only in construction, but also in agriculture due to the drastic industrial development in recent times, the problems of heating costs and global warming are getting worse. Therefore, introduction of more reliable and environmentally-friendly alternative energy sources has become urgent and the same trend is found in large-scale horticulture facilities. In this study, among many alternative energy sources, we investigated the reserves and the potential of various different unused energy sources which have infinite potential, but are nowadays wasted due to limitations in their utilization. In addition, we utilized available unused energy as a heat source for a heat pump in a large-scale horticulture facility and analyzed its feasibility through EnergyPlus simulation modeling. Accordingly, the discharge flow rate from the Fan Coil Unit (FCU in the horticulture facility, the discharge air temperature, and the return temperature were analyzed. The performance and heat consumption of each heat source were compared with those of conventional boilers. The result showed that the power load of the heat pump was decreased and thus the heat efficiency was increased as the temperature of the heat source was increased. Among the analyzed heat sources, power plant waste heat which had the highest heat source temperature consumed the least electric energy and showed the highest efficiency.

Improving yield and composition of protein concentrates from green tea residue in an agri-food supply chain: Effect of pre-treatment

NARCIS (Netherlands)

Zhang, Chen; Krimpen, Van Marinus M.; Sanders, Johan P.M.; Bruins, Marieke E.

2016-01-01

Rather than improving crop-production yield, developing biorefinery technology for unused biomass from the agri-food supply chain may be the crucial factor to reach sustainable global food security. A successful example of food-driven biorefinery is the extraction of protein from green tea residues,

Rebonding of unused brackets with different orthodontic adhesives

Directory of Open Access Journals (Sweden)

Emigdio Enrique Orellana Jimenez

2012-04-01

Full Text Available OBJECTIVE: To compare in vitro shear bond strength (SBS of different orthodontic adhesives in bonding and repeatedly rebonding metal brackets, and to evaluate the bond failure site with the adhesive remnant index (ARI. METHODS: Specimens consisted of 90 extracted human first premolars, randomly divided into three groups (n=30. The adhesives Alpha Plast (AP, ConciseTM (CO and TransbondTM XT (TB were used in each group. Three SBS tests were performed, i.e., one at T0 (initial and the other two at T1 and T2 (first and second rebondings, respectively, observing a 24-hour interval. The tests were performed in a Shimadzu AG-I (10kN SBS testing machine, at a speed of 0.5 mm/min. RESULTS: SBS data were subjected to ANOVA, Tukey's test and Bonferroni test (p<0.05. For the ARI, the Kruskal Wallis test was performed, followed by the Dunn test. The results revealed that at T0 groups AP and CO showed SBS values that were near, but above TB values; and at T1 and T2, the highest SBS values were observed for the AP group, followed by the CO and TB groups. CONCLUSION: Statistically significant differences were found in SBS between groups AP, CO and TB during bonding and repeated rebondings of unused metal brackets, with group AP achieving the highest SBS value. Regarding ARI, adhesive AP exhibited bond failure at the enamel-adhesive interface, with a higher enamel fracture frequency.

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.

Science.gov (United States)

Kinjo, Akira R; Suzuki, Hirofumi; Yamashita, Reiko; Ikegawa, Yasuyo; Kudou, Takahiro; Igarashi, Reiko; Kengaku, Yumiko; Cho, Hasumi; Standley, Daron M; Nakagawa, Atsushi; Nakamura, Haruki

2012-01-01

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

PUBLIC-PRIVATE PARTNERSHIP IN SOCIOECONOMIC DEVELOPMENT OF THE MUSEUMS: UNUSED MODERNIZATION RESOURCE

Directory of Open Access Journals (Sweden)

N. V. Polyanskova

2015-01-01

Full Text Available Summary. Public-private partnership practically in all developed and developing countries of the world is recognized as the effective mechanism of social and economic tasks realization of society and state. The most popular use of the economic cooperation tools between business and government in areas such as the creation and modernization of infrastructure, transport infrastructure, road construction, municipal services (housing and communal services, the military-industrial complex, less social infrastructure. A large number of scientific, educational, recommendatory, reference and other books of domestic and foreign authors is developed for each of the called directions, various models of projects implementation of public-private partnership are developed and perfected. Unfortunately, to the sphere of culture it isn't paid due attention. State-private and municipal and private partnership in practice are quite successfully used for increase of efficiency of activity of establishments and objects of culture, but this positive experience isn't systematized and not fixed anywhere, the conceptual model of public-private partnership projects in culture is also not developed. Thus, a research objective is to design initiatives development and offers on modernization of the culture sphere on the basis of instruments of public-private partnership. The subject of the study is a set of administrative, economic and legal relations arising in the implementation of projects in the sphere of the Samara region culture on the basis of public-private partnerships. This article presents the results of a public-private partnerships study as uninvolved resource of the culture sphere modernization and the public-private partnership model developed by authors for projects in this sphere.

Optimizing the resource usage in Cloud based environments: the Synergy approach

Science.gov (United States)

Zangrando, L.; Llorens, V.; Sgaravatto, M.; Verlato, M.

2017-10-01

Managing resource allocation in a cloud based data centre serving multiple virtual organizations is a challenging issue. In fact, while batch systems are able to allocate resources to different user groups according to specific shares imposed by the data centre administrator, without a static partitioning of such resources, this is not so straightforward in the most common cloud frameworks, e.g. OpenStack. In the current OpenStack implementation, it is only possible to grant fixed quotas to the different user groups and these resources cannot be exceeded by one group even if there are unused resources allocated to other groups. Moreover in the existing OpenStack implementation, when there aren’t resources available, new requests are simply rejected: it is then up to the client to later re-issue the request. The recently started EU-funded INDIGO-DataCloud project is addressing this issue through “Synergy”, a new advanced scheduling service targeted for OpenStack. Synergy adopts a fair-share model for resource provisioning which guarantees that resources are distributed among users following the fair-share policies defined by the administrator, taken also into account the past usage of such resources. We present the architecture of Synergy, the status of its implementation, some preliminary results and the foreseen evolution of the service.

Role of blood bag temperature indicators in maintaining patent temperature of the returned unused blood bags in blood bank.

Science.gov (United States)

Nurasyikin, Y; Leong, C F; Fadhlullah, T M; Hafiz, W M; Nadiah, Z; Atieqah, A N; Ling, T J; Das, S

2011-01-01

The main objective of the present study was to evaluate the temperature chain of red blood cells (RBC) returned unused blood bags using blood temperature indicator and ascertain the factors like transportation time, type, size of coolant box and number of bags per box. A total of 250 blood bags with the indicator were observed for the temperature changes with other factors like transportation time, type and size of coolant box and number of bags per box. The recordings were performed at several checkpoints located between the blood bank and the wards. Out of the 250 bags, 74 (29.6%) showed colour changes in which 64 (86.3%) were returned unused (RU) blood bags. The transportation time for these 74 bags was 818.3 ± 941.643 min, significantly higher than bags without colour changes, (p=0.02). Interestingly, 71.4% of the colour changes occurred within the ward. The 7 litre coolant box with an average of 1-5 blood bags per box had a statistically significant higher percentage of colour change with 59.2% compared to the 5 litre coolant box (p=0.05). This study showed that the temperature chain of blood bags was often not well maintained. These results could be mainly due to the non-adherence to the standard operating procedure (SOP) of blood transfusion and the usage of non-standardized coolant boxes.

PredMP: A Web Resource for Computationally Predicted Membrane Proteins via Deep Learning

KAUST Repository

Wang, Sheng; Fei, Shiyang; Zongan, Wang; Li, Yu; Zhao, Feng; Gao, Xin

2018-01-01

structures in Protein Data Bank (PDB). To elucidate the MP structures computationally, we developed a novel web resource, denoted as PredMP (http://52.87.130.56:3001/#/proteinindex), that delivers one-dimensional (1D) annotation of the membrane topology

Resource rents: The effects of energy taxes and quantity instruments for climate protection

International Nuclear Information System (INIS)

Eisenack, Klaus; Edenhofer, Ottmar; Kalkuhl, Matthias

2012-01-01

Carbon dioxide emissions correspond to fossil resource use. When considering this supply side of climate protection, crucial questions come to fore. It seems likely that owners of fossil resources would object to emission reductions. Moreover, policy instruments such as taxes may not be effective at all: it seems individually rational to leave no fossil resources unused. In this context, it can be expected that economic sectors will react strategically to climate policy, aiming at a re-distribution of rents. To address these questions, we investigate the effectiveness, efficiency, and resource rents for energy taxes, resource taxes, and quantity rationing of emissions. The analysis is based on a game theoretic growth model with explicit factor markets and policy instruments. Market equilibrium depends on a government that acts as a Stackelberg leader with a climate protection goal. We find that resource taxes and quantity rationing achieve this objective efficiently, energy taxation is only second-best. The use of quantity rationing to achieve climate protection generates substantial rents for resource owners. - Highlights: ► Resource taxes and quantity rationing (carbon budgets) are efficient. ► Carbon budgets increase resource rents, while taxes decrease rents. ► Resource owners may support climate protection. ► Climate protection introduces a climate rent.

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

Science.gov (United States)

Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

2013-01-01

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

Using the Tools and Resources of the RCSB Protein Data Bank.

Science.gov (United States)

Costanzo, Luigi Di; Ghosh, Sutapa; Zardecki, Christine; Burley, Stephen K

2016-09-07

The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the U.S. data center for the PDB, distributing archival data and supporting both simple and complex queries that return results. These data can be freely downloaded, analyzed, and visualized using RCSB PDB tools and resources to gain a deeper understanding of fundamental biological processes, molecular evolution, human health and disease, and drug discovery. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Controlling collective dynamics in complex minority-game resource-allocation systems

Science.gov (United States)

Zhang, Ji-Qiang; Huang, Zi-Gang; Dong, Jia-Qi; Huang, Liang; Lai, Ying-Cheng

2013-05-01

Resource allocation takes place in various kinds of real-world complex systems, such as traffic systems, social services institutions or organizations, or even ecosystems. The fundamental principle underlying complex resource-allocation dynamics is Boolean interactions associated with minority games, as resources are generally limited and agents tend to choose the least used resource based on available information. A common but harmful dynamical behavior in resource-allocation systems is herding, where there are time intervals during which a large majority of the agents compete for a few resources, leaving many other resources unused. Accompanying the herd behavior is thus strong fluctuations with time in the number of resources being used. In this paper, we articulate and establish that an intuitive control strategy, namely pinning control, is effective at harnessing the herding dynamics. In particular, by fixing the choices of resources for a few agents while leaving the majority of the agents free, herding can be eliminated completely. Our investigation is systematic in that we consider random and targeted pinning and a variety of network topologies, and we carry out a comprehensive analysis in the framework of mean-field theory to understand the working of control. The basic philosophy is then that, when a few agents waive their freedom to choose resources by receiving sufficient incentives, the majority of the agents benefit in that they will make fair, efficient, and effective use of the available resources. Our work represents a basic and general framework to address the fundamental issue of fluctuations in complex dynamical systems with significant applications to social, economical, and political systems.

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.

Science.gov (United States)

Kinjo, Akira R; Bekker, Gert-Jan; Suzuki, Hirofumi; Tsuchiya, Yuko; Kawabata, Takeshi; Ikegawa, Yasuyo; Nakamura, Haruki

2017-01-04

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Survey report of FY 1997 on the feasibility of microbial biotechnology for reuse of environmental pollutants; 1997 nendo chosa hokokusho (kankyo osen busshitsu no shigenka no tame no biseibutsu bio technology no riyo kanosei chi kansuru chosa)

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-03-01

An investigation was conducted with the aim of elucidating the foundations for effective utilization of environmental pollutants or unused resources which are likely to be causal substances of environmental pollutants, as resources, using biotechnology. Composting of agricultural waste, production of microbial mycelium proteins and microbial fermentation materials were suggested as main examples of effective utilization of unused resources by microorganisms. Selection of active microorganisms in the livestock waste, clarification of the mechanism of action and the establishment of treatment conditions are essential to new developments in this field. In the field of marine products industry, it was pointed out that the recycling of waste using microorganisms and enzyme treatment is the most promising approach to the effective utilization of resources. In the field of food industry, applications as the culture media for mushrooms, for enzyme production and for the production of physiologically active materials as well as fuel were clarified. Was also pointed out the significance of studies on the microorganisms and enzymes in resources containing cellulose, hemicellulose and lignin, and the waste from these resources, lignocellulose. Were also proposed the composting of household waste, methane fermentation, and fermentative production of organic acid and hydrogen from waste. Possibility and significance of fermentative production of organic acid from sewage sludge were suggested. 314 refs., 46 figs., 33 tabs.

Study on the reaction mechanism of oxygen-added enzyme for effective use of unused seaweeds; Miriyo kaiso no shigenka ni shisuru sanso tenka koso no hanno kiko ni kansuru kenkyu

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-03-01

For effective use of unused seaweeds, efficient search of available microorganism systems and their conversion for effective use were studied. Since generally found Phaeophyceae includes a large amount of polyphenol such as phlorotannin, it is refused by plant-eating animals, inhibits protein from effective absorption, and is inadequate for livestock feed because of tasteless. Bacteria Rhodococcus sp. PG7-2 was isolated which can be effectively increased using phloroglucinol as substrate. Participation of oxygen- adding enzyme was suggested in the initial stage of decomposition which adds molecular oxygen to aromatic rings. In the experiment using combinations of extracted and isolated enzymes and various coenzymes, no significant decomposition was observed. Since phlorotannin of Phaeophyceae is the polymer which shows a matrix-like extent through difficult-to-decompose bond such as biphenyl bond and phenyl ether bond, its decomposition by one kind of bacterium is extremely difficult. Search of decomposition systems of polymer remains as the future issue. 15 refs., 30 figs., 5 tabs.

Microstructures and phase relationships of crystalline oxidation products formed on unused CANDU fuel exposed to aerated steam and aerated water near 200 degrees C

International Nuclear Information System (INIS)

Taylor, P.; Wood, D.D.; Owen, D.G.; Hutchings, W.G.; Duclos, A.M.

1991-11-01

This report reviews the findings from dry-, moist- and wet-air oxidation experiments on unused UO 2 fuel specimens at 200-225 degrees C, performed in support of the Dry Storage Program for used CANDU (CANada Deuterium Uranium) fuel. The presence of liquid water, or unsaturated steam, adds to the complexity of air oxidation of UO 2 . The following processes have been identified by using a combination of optical and scanning electron microscopy and X-ray diffraction to detect oxidation products, and are discussed in this report: oxidative dissolution of U(VI) and precipitation of hydrated UO 3 ; back-reduction of dissolved U(VI) and precipitation of U 3 O 8 on the UO 2 /U 3 O 7 surface; solid-state surface and grain-boundary oxidation of UO 2 to β-U 3 O 7 ; and, preferential dissolution of UO 2 grain boundaries, sometimes followed by the filling of the resulting gap with higher uranium oxide(s). Although moisture thus adds greatly to the variety of oxidation reactions that can occur on UO 2 surfaces, it does not appear to promote swelling and spalling of the fuel, in spite of the large increase in molar volume associated with formation of the hydrated phase. This conclusion is qualified, however, since variability in the reactivity of fuel specimens, particularly with respect to grain-boundary oxidation, makes it difficult to distinguish moisture effects. With unused fuel, grain-boundary alteration to U 3 O 7 is the primary process by which oxidation penetrates the fuel near 200 degrees C. Reactions involving water proceed on the specimen surface, and can also follow oxidized grain boundaries and (presumably) open porosity. Because of differences in the pore and grain-boundary structure of unused and used UO 2 fuel, as well as possible radiolytic processes in the latter, comparisons between these findings and the results of the ongoing CEX-1 (dry controlled-environment experiment) and CEX-2 (moist) used-fuel storage experiments at Whiteshell Laboratories must be

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.

Science.gov (United States)

Burley, Stephen K; Berman, Helen M; Christie, Cole; Duarte, Jose M; Feng, Zukang; Westbrook, John; Young, Jasmine; Zardecki, Christine

2018-01-01

The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Campus Grids: Bringing Additional Computational Resources to HEP Researchers

International Nuclear Information System (INIS)

Weitzel, Derek; Fraser, Dan; Bockelman, Brian; Swanson, David

2012-01-01

It is common at research institutions to maintain multiple clusters that represent different owners or generations of hardware, or that fulfill different needs and policies. Many of these clusters are consistently under utilized while researchers on campus could greatly benefit from these unused capabilities. By leveraging principles from the Open Science Grid it is now possible to utilize these resources by forming a lightweight campus grid. The campus grids framework enables jobs that are submitted to one cluster to overflow, when necessary, to other clusters within the campus using whatever authentication mechanisms are available on campus. This framework is currently being used on several campuses to run HEP and other science jobs. Further, the framework has in some cases been expanded beyond the campus boundary by bridging campus grids into a regional grid, and can even be used to integrate resources from a national cyberinfrastructure such as the Open Science Grid. This paper will highlight 18 months of operational experiences creating campus grids in the US, and the different campus configurations that have successfully utilized the campus grid infrastructure.

A resource for benchmarking the usefulness of protein structure models.

Science.gov (United States)

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

A resource for benchmarking the usefulness of protein structure models

Directory of Open Access Journals (Sweden)

Carbajo Daniel

2012-08-01

Full Text Available Abstract Background Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. Results This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. Conclusions The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. Implementation, availability and requirements Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php. Operating system(s: Platform independent. Programming language: Perl-BioPerl (program; mySQL, Perl DBI and DBD modules (database; php, JavaScript, Jmol scripting (web server. Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet and PSAIA. License: Free. Any

A resource for benchmarking the usefulness of protein structure models.

KAUST Repository

Carbajo, Daniel

2012-08-02

BACKGROUND: Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. RESULTS: This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. CONCLUSIONS: The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by

A resource for benchmarking the usefulness of protein structure models.

KAUST Repository

Carbajo, Daniel; Tramontano, Anna

2012-01-01

BACKGROUND: Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. RESULTS: This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. CONCLUSIONS: The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by

Sustainable use of biogenic fuels resources through industrial synergies

International Nuclear Information System (INIS)

Schuech, Andrea; Nelles, Michael; Nassour, Abdallah

2017-01-01

The term industrial symbiosis is used when traditionally separate companies and industries work together in a collective approach to physically exchange materials, energy, water and by-products with a mutual competitive advantage. Aim of the European project ''UBIS - Urban Baltic Industrial Symbiosis'' (INTERREG South-Baltic Programme) is to use biogenic resources as well as waste and residues sustainable in industrial symbiosis and to reduce emissions at the same time. Even if a lot has already been achieved in this area, there are still many unused material flows and there are possibilities to use them even more efficiently. In the project existing collaborations will be investigated as well as new ones identified and evaluated. This article introduces the UBIS project and provides an insight into the subject of industrial symbiosis as well examples described.

The RCSB Protein Data Bank: new resources for research and education.

Science.gov (United States)

Rose, Peter W; Bi, Chunxiao; Bluhm, Wolfgang F; Christie, Cole H; Dimitropoulos, Dimitris; Dutta, Shuchismita; Green, Rachel K; Goodsell, David S; Prlic, Andreas; Quesada, Martha; Quinn, Gregory B; Ramos, Alexander G; Westbrook, John D; Young, Jasmine; Zardecki, Christine; Berman, Helen M; Bourne, Philip E

2013-01-01

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher's PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.

ZifBASE: a database of zinc finger proteins and associated resources

Directory of Open Access Journals (Sweden)

Punetha Ankita

2009-09-01

Full Text Available Abstract Background Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develop chimeric proteins for targeted genome engineering and site-specific gene correction. There is a need to develop a computational resource of zinc finger proteins (ZFP to identify the potential binding sites and its location, which reduce the time of in vivo task, and overcome the difficulties in selecting the specific type of zinc finger protein and the target site in the DNA sequence. Description ZifBASE provides an extensive collection of various natural and engineered ZFP. It uses standard names and a genetic and structural classification scheme to present data retrieved from UniProtKB, GenBank, Protein Data Bank, ModBase, Protein Model Portal and the literature. It also incorporates specialized features of ZFP including finger sequences and positions, number of fingers, physiochemical properties, classes, framework, PubMed citations with links to experimental structures (PDB, if available and modeled structures of natural zinc finger proteins. ZifBASE provides information on zinc finger proteins (both natural and engineered ones, the number of finger units in each of the zinc finger proteins (with multiple fingers, the synergy between the adjacent fingers and their positions. Additionally, it gives the individual finger sequence and their target DNA site to which it binds for better and clear understanding on the interactions of adjacent fingers. The current version of ZifBASE contains 139 entries of which 89 are engineered ZFPs, containing 3-7F totaling to 296 fingers. There are 50 natural zinc finger protein entries ranging from 2-13F, totaling to 307 fingers. It has sequences and structures from literature, Protein Data Bank, ModBase and Protein Model Portal. The interface is cross linked to other public

Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses

Directory of Open Access Journals (Sweden)

Rayapadi G. Swetha

2016-01-01

Full Text Available Ebola Virus Disease (EVD is a life-threatening haemorrhagic fever in humans. Even though there are many reports on EVD, the protein precursor functions and virulent factors of ebolaviruses remain poorly understood. Comparative analyses of Ebolavirus genomes will help in the identification of these important features. This prompted us to develop the Ebolavirus Database (EDB and we have provided links to various tools that will aid researchers to locate important regions in both the genomes and proteomes of Ebolavirus. The genomic analyses of ebolaviruses will provide important clues for locating the essential and core functional genes. The aim of EDB is to act as an integrated resource for ebolaviruses and we strongly believe that the database will be a useful tool for clinicians, microbiologists, health care workers, and bioscience researchers.

A Human XPC Protein Interactome—A Resource

Directory of Open Access Journals (Sweden)

Abigail Lubin

2013-12-01

Full Text Available Global genome nucleotide excision repair (GG-NER is responsible for identifying and removing bulky adducts from non-transcribed DNA that result from damaging agents such as UV radiation and cisplatin. Xeroderma pigmentosum complementation group C (XPC is one of the essential damage recognition proteins of the GG-NER pathway and its dysfunction results in xeroderma pigmentosum (XP, a disorder involving photosensitivity and a predisposition to cancer. To better understand the identification of DNA damage by XPC in the context of chromatin and the role of XPC in the pathogenesis of XP, we characterized the interactome of XPC using a high throughput yeast two-hybrid screening. Our screening showed 49 novel interactors of XPC involved in DNA repair and replication, proteolysis and post-translational modifications, transcription regulation, signal transduction, and metabolism. Importantly, we validated the XPC-OTUD4 interaction by co-IP and provided evidence that OTUD4 knockdown in human cells indeed affects the levels of ubiquitinated XPC, supporting a hypothesis that the OTUD4 deubiquitinase is involved in XPC recycling by cleaving the ubiquitin moiety. This high-throughput characterization of the XPC interactome provides a resource for future exploration and suggests that XPC may have many uncharacterized cellular functions.

Resource allocation in grid computing

NARCIS (Netherlands)

Koole, Ger; Righter, Rhonda

2007-01-01

Grid computing, in which a network of computers is integrated to create a very fast virtual computer, is becoming ever more prevalent. Examples include the TeraGrid and Planet-lab.org, as well as applications on the existing Internet that take advantage of unused computing and storage capacity of

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

Science.gov (United States)

Sharpton, Thomas J; Jospin, Guillaume; Wu, Dongying; Langille, Morgan G I; Pollard, Katherine S; Eisen, Jonathan A

2012-10-13

New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as "Sifting Families," or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology-based analyses. We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/).

Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

Science.gov (United States)

Cormier, Catherine Y.; Mohr, Stephanie E.; Zuo, Dongmei; Hu, Yanhui; Rolfs, Andreas; Kramer, Jason; Taycher, Elena; Kelley, Fontina; Fiacco, Michael; Turnbull, Greggory; LaBaer, Joshua

2010-01-01

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery. PMID:19906724

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

Directory of Open Access Journals (Sweden)

Sharpton Thomas J

2012-10-01

Full Text Available Abstract Background New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. Results We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as “Sifting Families,” or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology–based analyses. Conclusions We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/.

Towards plant protein refinery: Review on protein extraction using alkalo and potential enzymatic assistance

NARCIS (Netherlands)

Sari, Y.W.; Mulder, W.J.; Sanders, J.P.M.; Bruins, M.E.

2015-01-01

The globally increasing protein demands require additional resources to those currently available. Furthermore, the optimal usage of protein fractions from both traditional and new protein resources, such as algae and leaves, is essential. Here, we present an overview on alkaline plant protein

PredMP: A Web Resource for Computationally Predicted Membrane Proteins via Deep Learning

KAUST Repository

Wang, Sheng

2018-02-06

Experimental determination of membrane protein (MP) structures is challenging as they are often too large for nuclear magnetic resonance (NMR) experiments and difficult to crystallize. Currently there are only about 510 non-redundant MPs with solved structures in Protein Data Bank (PDB). To elucidate the MP structures computationally, we developed a novel web resource, denoted as PredMP (http://52.87.130.56:3001/#/proteinindex), that delivers one-dimensional (1D) annotation of the membrane topology and secondary structure, two-dimensional (2D) prediction of the contact/distance map, together with three-dimensional (3D) modeling of the MP structure in the lipid bilayer, for each MP target from a given model organism. The precision of the computationally constructed MP structures is leveraged by state-of-the-art deep learning methods as well as cutting-edge modeling strategies. In particular, (i) we annotate 1D property via DeepCNF (Deep Convolutional Neural Fields) that not only models complex sequence-structure relationship but also interdependency between adjacent property labels; (ii) we predict 2D contact/distance map through Deep Transfer Learning which learns the patterns as well as the complex relationship between contacts/distances and protein features from non-membrane proteins; and (iii) we model 3D structure by feeding its predicted contacts and secondary structure to the Crystallography & NMR System (CNS) suite combined with a membrane burial potential that is residue-specific and depth-dependent. PredMP currently contains more than 2,200 multi-pass transmembrane proteins (length<700 residues) from Human. These transmembrane proteins are classified according to IUPHAR/BPS Guide, which provides a hierarchical organization of receptors, channels, transporters, enzymes and other drug targets according to their molecular relationships and physiological functions. Among these MPs, we estimated that our approach could predict correct folds for 1

A Minimalistic Resource Allocation Model to Explain Ubiquitous Increase in Protein Expression with Growth Rate.

Directory of Open Access Journals (Sweden)

Uri Barenholz

Full Text Available Most proteins show changes in level across growth conditions. Many of these changes seem to be coordinated with the specific growth rate rather than the growth environment or the protein function. Although cellular growth rates, gene expression levels and gene regulation have been at the center of biological research for decades, there are only a few models giving a base line prediction of the dependence of the proteome fraction occupied by a gene with the specific growth rate. We present a simple model that predicts a widely coordinated increase in the fraction of many proteins out of the proteome, proportionally with the growth rate. The model reveals how passive redistribution of resources, due to active regulation of only a few proteins, can have proteome wide effects that are quantitatively predictable. Our model provides a potential explanation for why and how such a coordinated response of a large fraction of the proteome to the specific growth rate arises under different environmental conditions. The simplicity of our model can also be useful by serving as a baseline null hypothesis in the search for active regulation. We exemplify the usage of the model by analyzing the relationship between growth rate and proteome composition for the model microorganism E.coli as reflected in recent proteomics data sets spanning various growth conditions. We find that the fraction out of the proteome of a large number of proteins, and from different cellular processes, increases proportionally with the growth rate. Notably, ribosomal proteins, which have been previously reported to increase in fraction with growth rate, are only a small part of this group of proteins. We suggest that, although the fractions of many proteins change with the growth rate, such changes may be partially driven by a global effect, not necessarily requiring specific cellular control mechanisms.

FY 1999 report on the results of the project on the industrial science technology R and D. Development of utilization technology of biological resources such as bioconsortium system (Development of the petroleum substituting fuel production technology using living organisms); 1999 nendo sangyo kagaku gijutsu kenkyu kaihatsu jigyo. Fukugou seibutsukei tou seibutsu shigen riyo gijutsu kaihatsu (Seibutsu riyo sekiyu daitai nenryo seizo gijutsu no kaihatsu) seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

For the purpose of establishing the high-grade utilization technology of unused seaweed/algae and production technology of useful substances using high-grade functions of bioconsortia, study was conducted, and the FY 1999 results were reported. In the analysis of the ocean environment adaptation mechanism, the R and D were made of a selection method of the marine microbial consortia using korormicin. In the study of the high-grade utilization technology of unused resources/substances such as marine-producing algae, several tens of the carrageenase producing microbial consortia were acquired from the surface of seaweed, and some carrageenase producing bacteria and non-producing bacteria were acquired by isolating as pure strains. In the study of the petroleum substituting useful resource production technology, developed was a monitoring system of the environmental stress using marine-product invertebrate/micro-algae symbiotic system. In the study of the high-grade utilization of large useful algae, elucidation of the related genes, fabrication of variants and analysis of genes were carried out for the bacterium BUP-7 which indicates activity of growth acceleration/shape formation of seaweed. (NEDO)

Analysis of Dust Samples Collected from an Unused Spent Nuclear Fuel Interim Storage Container at Hope Creek, Delaware.

Energy Technology Data Exchange (ETDEWEB)

Bryan, Charles R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Enos, David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2015-03-01

In July, 2014, the Electric Power Research Institute and industry partners sampled dust on the surface of an unused canister that had been stored in an overpack at the Hope Creek Nuclear Generating Station for approximately one year. The foreign material exclusion (FME) cover that had been on the top of the canister during storage, and a second recently - removed FME cover, were also sampled. This report summarizes the results of analyses of dust samples collected from the unused Hope Creek canister and the FME covers. Both wet and dry samples of the dust/salts were collected, using SaltSmart(TM) sensors and Scotch - Brite(TM) abrasive pads, respectively. The SaltSmart(TM) samples were leached and the leachate analyzed chemically to determine the composition and surface load per unit area of soluble salts present on the canister surface. The dry pad samples were analyzed by X-ray fluorescence and by scanning electron microscopy to determine dust texture and mineralogy; and by leaching and chemical analysis to deter mine soluble salt compositions. The analyses showed that the dominant particles on the canister surface were stainless steel particles, generated during manufacturing of the canister. Sparse environmentally - derived silicates and aluminosilicates were also present. Salt phases were sparse, and consisted of mostly of sulfates with rare nitrates and chlorides. On the FME covers, the dusts were mostly silicates/aluminosilicates; the soluble salts were consistent with those on the canister surface, and were dominantly sulfates. It should be noted that the FME covers were w ashed by rain prior to sampling, which had an unknown effect of the measured salt loads and compositions. Sulfate salts dominated the assemblages on the canister and FME surfaces, and in cluded Ca - SO₄ , but also Na - SO₄ , K - SO₄ , and Na - Al - SO₄ . It is likely that these salts were formed by particle - gas conversion reactions, either

Research report of fiscal 1997. Survey on creation of high-efficiency renewable resources, and bioconversion technology; 1997 nendo chosa hokokusho. Kokoritsu saisei kano shigen no sosei narabi ni bioconversion gijutsu ni kansuru chosa

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-03-01

Survey was made on material production technology using creation technology of high-efficiency renewable resources (photosynthesis reaction of plants). Industrially usable plant resources in overseas countries and Japan were arranged, and plant resources unused for food were also surveyed. The present state of genetic engineering necessary for metabolic engineering of higher plants such as fit and high-expression technology of genes, plant cell cultivation, and control technology of plant cell multiplication is described, and elementary technologies required for future gene-recombined plants are predicted. Survey was also made on the trend of creation technology of industrial plants for fat and oil, biodegradable polyester, amino acid, cellulose, fiber (cotton) and forest wood. A patent list on plant biotechnology was prepared, and study on bioconversion of plant resources was also surveyed. Overseas R & D trends on conversion and effective use technologies of renewable bio- resources are reported, and process design and its profitability were evaluated through a case study. 414 refs., 87 figs., 55 tabs.

FY 1998 report on the results of the development of the utilization technology of biological resources such as bioconsortia. Development of the petroleum substituting fuel production technology using biology; 1998 nendo fukugo seibutsukei nado seibutsu shigen riyo gijutsu kaihatsu seika hokokusho. Seibutsu riyo sekiyu daitai nenryo seizo gijutsu no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-03-01

For the purpose of establishing the analysis technology and industrial utilization technology required for the establishment of the utilization technology of consortia's high functions which are already used in the fermentation technology field over the limit of the conventional bio-technology using functions of single biological species, study was made. As a part of the study, the establishment was aimed at of the high-grade utilization technology of seaweed/algae using the degradation/conversion functions of the consortium base and the useful substance production technology by interaction of the consortium base of organism and flora/fauna. Studies for the establishment of the technology were made in the following two fields: technology to use unused resources such as lignocellulose and technology to produce petroleum substituting useful resources. As to the technology to use unused resources, the establishment was proceeded with of the technology to degrade/convert the seaweed-origin acidic polysaccharide into the useful substance using the consortium system. In FY 1998, in search of the excellent microorganism consortia which can degrade/solubilize carageenan, samples were picked up from the underwater of the Republic of Palau and incubated in the flat culture medium. Thirty-eight kinds of the degraded bacterium group were acquired. Using the degraded bacterium group, {kappa}-carrageenan was degraded and analyzed of the products. (NEDO)

FY 1998 report on the results of the development of the utilization technology of biological resources such as bioconsortia. Development of the petroleum substituting fuel production technology using biology; 1998 nendo fukugo seibutsukei nado seibutsu shigen riyo gijutsu kaihatsu seika hokokusho. Seibutsu riyo sekiyu daitai nenryo seizo gijutsu no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-03-01

For the purpose of establishing the analysis technology and industrial utilization technology required for the establishment of the utilization technology of consortia's high functions which are already used in the fermentation technology field over the limit of the conventional bio-technology using functions of single biological species, study was made. As a part of the study, the establishment was aimed at of the high-grade utilization technology of seaweed/algae using the degradation/conversion functions of the consortium base and the useful substance production technology by interaction of the consortium base of organism and flora/fauna. Studies for the establishment of the technology were made in the following two fields: technology to use unused resources such as lignocellulose and technology to produce petroleum substituting useful resources. As to the technology to use unused resources, the establishment was proceeded with of the technology to degrade/convert the seaweed-origin acidic polysaccharide into the useful substance using the consortium system. In FY 1998, in search of the excellent microorganism consortia which can degrade/solubilize carageenan, samples were picked up from the underwater of the Republic of Palau and incubated in the flat culture medium. Thirty-eight kinds of the degraded bacterium group were acquired. Using the degraded bacterium group, {kappa}-carrageenan was degraded and analyzed of the products. (NEDO)

Optimisation of a cheap and residential small-scale production of edible crickets with local by-products as an alternative protein-rich human food source in Ratanakiri Province, Cambodia.

Science.gov (United States)

Caparros Megido, Rudy; Alabi, Taofic; Nieus, Clément; Blecker, Christophe; Danthine, Sabine; Bogaert, Jan; Haubruge, Éric; Francis, Frédéric

2016-01-30

The health status of the indigenous people of Ratanakiri Province, Cambodia, is significantly lower compared with that of the rest of the nation. The domestication and mass production of insects may represent a sustainable, cost effective and high quality alternative source of protein to traditional livestock. This study aimed to optimise a cheap and residential cricket breeding system based on unused wild resources. The development of crickets, Teleogryllus testaceus (Walker), under seven diets composed of taro aerial parts, young cassava leaves, young cashew leaves and brown rice flour (with or without banana slices), versus a traditionally used broiler feed diet was studied. Cricket mortality was low in all diets, except the two cashew-based diets. Total biomass was significantly higher under the broiler feed, in addition to the two diets containing a combination of cassava leaf powder and brown rice. Yet, crickets fed with the taro diet had the highest percentage of protein. Concerning the breeding system cost, units using cassava leaves were the cheapest. Diets based on cassava leaves seem to be the most promising. Nevertheless, to produce crickets with a high body mass and a high protein level, a new experiments must be devised in which cassava leaf maturity will be adapted to fit with the cricket growth stage. Moreover, to reduce the cost of the breeding units, handmade local products should be used instead of purchased components. © 2015 Society of Chemical Industry.

The World's Present And Future Resources Of Protein Available For Human Nourishment, And The Possibilities For Utilizing These Resources; Les ressources mondiales actuelles et futures en proteines disponibles pour l'alimentation de l'homme - Leurs possibilites d'utilisation

Energy Technology Data Exchange (ETDEWEB)

Pion, R.; Fauconneau, G. [INRA, Centre National de Recherches Zootechniques, Jouy-en-Josas, Yvelines (France)

1968-07-01

Man must obtain from his food supply various essential and semi-essential amino acids, in combination with an adequate amount of non- differentiated nitrogen, necessary for satisfying his needs. These various essential amino acids are synthesized by land or aquatic plant organisms; the essential amino acids are for the most part taken up into the plant proteins, which are either consumed by man in their original state or transformed, with a rather low efficiency, into animal protein subsequently utilized by man. The protein resources available to man in those forms are now inadequate, and the increase in world population makes necessary both an increase in protein production and an improvement in the efficiency of protein utilization. A study of the various sources of nitrogenous food products and of their amino acid composition (the main factor in their quality) shows that there are a number of ways of increasing the resources available to man, both by the improvement of farming techniques and by the industrial-scale production of supplements. The principal methods of improving plant production are irrigation, use of fertilizers (especially nitrogenous ones) and genetic grain selection methods, with a view to obtaining better quality proteins from species now under cultivation and to utilizing plants of promising composition which are not yet being developed. The growing production and use of factory-produced supplements, particularly synthetic amino acids, should contribute to improved efficiency in the utilization of proteins of plant origin by monogastric species (man, pigs, poultry). Lastly, certain high-quality proteins (fish, milk) should be utilized directly by man on a larger scale. At the present stage of technology these proteins can be satisfactorily conserved. (author) [French] L'homme doit trouver dans son alimentation les differents acides amines indispensables et semi-indispensables, associes a une quantite suffisante d'azote indifferencie

Comparison of cost determination of both resource consumption accounting and time-driven activity-based costing systems in a healthcare setting.

Science.gov (United States)

Özyapıcı, Hasan; Tanış, Veyis Naci

2017-05-01

Objective The aim of the present study was to explore the differences between resource consumption accounting (RCA) and time-driven activity-based costing (TDABC) systems in determining the costs of services of a healthcare setting. Methods A case study was conducted to calculate the unit costs of open and laparoscopic gall bladder surgeries using TDABC and RCA. Results The RCA system assigns a higher cost both to open and laparoscopic gall bladder surgeries than TDABC. The total cost of unused capacity under the TDABC system is also double that in RCA. Conclusion Unlike TDABC, RCA calculates lower costs for unused capacities but higher costs for products or services in a healthcare setting in which fixed costs make up a high proportion of total costs. What is known about the topic? TDABC is a revision of the activity-based costing (ABC) system. RCA is also a new costing system that includes both the theoretical advantages of ABC and the practical advantages of German costing. However, little is known about the differences arising from application of TDABC and RCA. What does this paper add? There is no study comparing both TDABC and RCA in a single case study based on a real-world healthcare setting. Thus, the present study fills this gap in the literature and it is unique in the sense that it is the first case study comparing TDABC and RCA for open and laparoscopic gall bladder surgeries in a healthcare setting. What are the implications for practitioners? This study provides several interesting results for managers and cost accounting researchers. Thus, it will contribute to the spread of RCA studies in healthcare settings. It will also help the implementers of TDABC to revise data concerning the cost of unused capacity. In addition, by separating costs into fixed and variable, the paper will help managers to create a blended (combined) system that can improve both short- and long-term decisions.

Exploiting the ALICE HLT for PROOF by scheduling of Virtual Machines

International Nuclear Information System (INIS)

Meoni, Marco; Boettger, Stefan; Zelnicek, Pierre; Kebschull, Udo; Lindenstruth, Volker

2011-01-01

The HLT (High-Level Trigger) group of the ALICE experiment at the LHC has prepared a virtual Parallel ROOT Facility (PROOF) enabled cluster (HAF - HLT Analysis Facility) for fast physics analysis, detector calibration and reconstruction of data samples. The HLT-Cluster currently consists of 2860 CPU cores and 175TB of storage. Its purpose is the online filtering of the relevant part of data produced by the particle detector. However, data taking is not running continuously and exploiting unused cluster resources for other applications is highly desirable and improves the usage-cost ratio of the HLT cluster. As such, unused computing resources are dedicated to a PROOF-enabled virtual cluster available to the entire collaboration. This setup is especially aimed at the prototyping phase of analyses that need a high number of development iterations and a short response time, e.g. tuning of analysis cuts, calibration and alignment. HAF machines are enabled and disabled upon user request to start or complete analysis tasks. This is achieved by a virtual machine scheduling framework which dynamically assigns and migrates virtual machines running PROOF workers to unused physical resources. Using this approach we extend the HLT usage scheme to running both online and offline computing, thereby optimizing the resource usage.

Unused and expired medications disposal practices in the community: a cross-sectional survey in Cheras, Malaysia

Directory of Open Access Journals (Sweden)

Omotayo Fatokun*, Ai Wei Chang, Wan Nah Ng, Thashini Nair, Vanitha Balakrishnan

2011-09-01

Full Text Available Irresponsible disposal of unused and expired medicationsmay lead to both environmental and public health hazards andhas been subject of several studies [1-3]. The presence ofpharmaceuticals and their respective metabolites in theaquatic environment has become a source for rising concern inrecent years and several studies [2,3 ] have shown that theexistence of these substances in waste water and drinkingwater [4] and they may be potentially harmful to aquatic life.Besides, risk to human life remained a concern [2]. Therefore,the objective of this study was to assess medication disposalpractices and environmental risks awareness of improperdisposal of medications among individuals in the community.A 9-item structured questionnaire was developed based onexisting literature [1-3]. Following a pre-test on ten people in acommunity shopping mall, the final questionnaire wasadministered face-to-face to a convenience sample of 200participants at different areas in two large shopping malls andsurrounding restaurants in Cheras, Kuala Lumpur, Malaysia.Findings demonstrate that Majority of participants (51.5%were male. In terms of ethnic distribution, the majority ofparticipants surveyed were Chinese (66.5%, followed byMalays (17.0% and Indians (15.5%. Majority of participants(47.5% were aged between 20-29 years old.

French energy resources and needs. Incidence on the development of the national nuclear programme

International Nuclear Information System (INIS)

Martin, Roger.

1977-01-01

The energy flux diagram for France in 1970, underlines the disparity observed between the utilization factors in the final stage: 75% for the domestic and tertiary sector, 75% for industry and siderurgy, 65% for agriculture, and 25% for transports. The total utilization factor is 47.5% (124.4 MTEC used for 137.6 MTEC unused; the unit used being the Million of Tons Equivalent to Coal. Two dates are arbitrarily envisaged (1985 and 2000) in the evolution of the French energy technology and structure. The energy flux diagram predicted for 1985 should asked to atom nearly a quarter of the resources, with an enhanced part from hydraulics (+30%) and should involve geothermy, heat wastes and solar energy. An extrapolation predicts a spectacular-growth for 2000 due to the uranium share as a compensation to the decrease in that from oil, as for the transformation stage a neat increase in the electricity share is predicted together with 'tele-heat' and hydrogen production and, at the stage of utilization the mass penetration of 'tele-heat', especially of nuclear origin. The problem of the evolution of energy resources is also discussed [fr

Wood supply : what bioenergy resources are available as harvest residue and non-merchantable wood in New Brunswick?

International Nuclear Information System (INIS)

Forgrave, K.

2005-01-01

This paper examines resources available for bioenergy production in New Brunswick. An estimate of New Brunswick harvest levels, based on New Brunswick Forest Products Association web site figures was presented. Private wood lots harvest levels were also provided, with all estimates based on volume per year. Market conditions were discussed, with an emphasis on the dictates of price and availability for private wood lot owners. Market conditions and unused volume statistics were discussed. Various forest management options include the use of veneer, saw log, stud wood and pulp wood. Details of bioenergy percentages and potential were presented and general silviculture issues were discussed. It was concluded that many of the trade-offs of bioenergy involve placing more demands on forests, and that purchase prices will increasingly dictate volumes obtained from private wood lots. tabs, figs

The science of being a study participant: FEM-PrEP participants' explanations for overreporting adherence to the study pills and for the whereabouts of unused pills.

Science.gov (United States)

Corneli, Amy L; McKenna, Kevin; Perry, Brian; Ahmed, Khatija; Agot, Kawango; Malamatsho, Fulufhelo; Skhosana, Joseph; Odhiambo, Jacob; Van Damme, Lut

2015-04-15

FEM-PrEP was unable to determine whether once-daily, oral emtricitabine/tenofovir disoproxil fumarate reduces the risk of HIV acquisition among women because of low adherence. Self-reported adherence was high, and pill-count data suggested good adherence. Yet, drug concentrations revealed limited pill use. We conducted a follow-up study with former participants in Bondo, Kenya, and Pretoria, South Africa, to understand factors that had influenced overreporting of adherence and to learn the whereabouts of unused pills. Qualitative, semistructured interviews were conducted with 88 participants, and quantitative, audio computer-assisted self-interviews were conducted with 224 participants. We used thematic analysis and descriptive statistics to analyze the qualitative and quantitative data, respectively. In audio computer-assisted self-interviews, 31% (n = 70) said they had overreported adherence; the main reason was the belief that nonadherence would result in trial termination (69%, n = 48). A considerable percentage (35%, n = 78) acknowledged discarding unused pills. Few acknowledged giving their pills to someone else (4%, n = 10), and even fewer acknowledged giving them to someone with HIV (2%, n = 5). Many participants in the semistructured interviews said other participants had counted and removed pills from their bottles to appear adherent. Despite repeated messages that nonadherence would not upset staff, participants acknowledged several perceived negative consequences of reporting nonadherence, which made it difficult to report accurately. Uneasiness continued in the follow-up study, as many said they had not overreported during the trial. Efforts to improve self-reported measures should include identifying alternative methods for creating supportive environments that allow participants to feel comfortable reporting actual adherence.

Fiscal 1993 international research cooperation project. Feasibility study of finding out the seeds of international joint research (technology for environmental preservation using biotechnology, technology for effective use of unused hydrocarbon resource, technology for development of environmental harmony type catalyst); 1995 nendo kokusai kyoryoku jigyo. Kokusai kyodo kenkyu seeds hakkutsu no tame no FS chosa (biotechnology ni yoru kankyo taisaku gijutsu, miriyo tanka suiso shigen no yuko riyo gijutsu, kankyo chowagata shokubai kaihatsu gijutsu)

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-03-01

This project is aimed at internationally cooperating in the R and D of industrial technology and improving industrial technology of Japan. For it, the following three technologies were investigated: 1) environmental preservation technology using biotechnology, 2) technology for effective use of unused hydrocarbon resource, 3) technology for development of environmental harmony type catalyst. In 1), a survey was conducted of applicability of biological surfactant to prevention measures of pollution by heavy distillate. It showed that part of the biological surfactants is reaching a stage of its being industrially produced by gene recombination bacteria, but as a whole, biosynthetic genes have hardly been elucidated. In 2), a survey of high-grade treatment technology of petroleum coke was made. It pointed out that it is necessary to develop a technology which makes the most of features of petroleum coke and allows defects. In 3), scientists and engineers of Japan and Europe searched for themes on which they can jointly study in the fields of NOx removal catalyst, up-grading of fuel, and development of catalyst combustion of fuel. 287 refs., 136 figs., 128 tabs.

The Protein Model Portal--a comprehensive resource for protein structure and model information.

Science.gov (United States)

Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

2013-01-01

The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org.

The Protein Model Portal—a comprehensive resource for protein structure and model information

Science.gov (United States)

Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

2013-01-01

The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org PMID:23624946

Sustainable use of biogenic fuels resources through industrial synergies; Nachhaltige energetische Nutzung biogener Ressourcen durch industrielle Synergien

Energy Technology Data Exchange (ETDEWEB)

Schuech, Andrea [Rostock Univ. (Germany). Professur Abfall- und Stoffstromwirtschaft; Nelles, Michael [Rostock Univ. (Germany). Agrar- und Umweltwissenschaftliche Fakultaet; Nassour, Abdallah

2017-08-01

The term industrial symbiosis is used when traditionally separate companies and industries work together in a collective approach to physically exchange materials, energy, water and by-products with a mutual competitive advantage. Aim of the European project ''UBIS - Urban Baltic Industrial Symbiosis'' (INTERREG South-Baltic Programme) is to use biogenic resources as well as waste and residues sustainable in industrial symbiosis and to reduce emissions at the same time. Even if a lot has already been achieved in this area, there are still many unused material flows and there are possibilities to use them even more efficiently. In the project existing collaborations will be investigated as well as new ones identified and evaluated. This article introduces the UBIS project and provides an insight into the subject of industrial symbiosis as well examples described.

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

Science.gov (United States)

Bachman, John A; Gyori, Benjamin M; Sorger, Peter K

2018-06-28

For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers, a process known as named entity linking or "grounding." Correct grounding is essential for resolving relationships among mined information, curated interaction databases, and biological datasets. The accuracy of this process is largely dependent on the availability of machine-readable resources associating synonyms and abbreviations commonly found in biomedical literature with uniform identifiers. In a task involving automated reading of ∼215,000 articles using the REACH event extraction software we found that grounding was disproportionately inaccurate for multi-protein families (e.g., "AKT") and complexes with multiple subunits (e.g."NF- κB"). To address this problem we constructed FamPlex, a manually curated resource defining protein families and complexes as they are commonly encountered in biomedical text. In FamPlex the gene-level constituents of families and complexes are defined in a flexible format allowing for multi-level, hierarchical membership. To create FamPlex, text strings corresponding to entities were identified empirically from literature and linked manually to uniform identifiers; these identifiers were also mapped to equivalent entries in multiple related databases. FamPlex also includes curated prefix and suffix patterns that improve named entity recognition and event extraction. Evaluation of REACH extractions on a test corpus of ∼54,000 articles showed that FamPlex significantly increased grounding accuracy for families and complexes (from 15 to 71%). The hierarchical organization of entities in FamPlex also made it possible to integrate otherwise unconnected mechanistic information across families, subfamilies, and individual proteins. Applications of FamPlex to the TRIPS/DRUM reading system and the Biocreative VI Bioentity

Key skills by design: adapting a central Web resource to departmental contexts

Directory of Open Access Journals (Sweden)

Claire McAvinia

2002-12-01

Full Text Available Web-based delivery of support materials for students has proved to be a popular way of helping small teams to implement key skills policies within universities. The development of 'key' or 'transferable' skills is now encouraged throughout education, but resources (both in terms of staffing and budget tend to be limited. It is difficult for key skills teams to see learners face to face, and not feasible to print or distribute large amounts of paper-based material. Web-based delivery presents a means of overcoming these problems but it can result in generic study skills material simply being published online without due consideration of the needs of different groups of learners within different subject disciplines. Therefore, although a centralized Website for skills provision can overcome logistical problems, it may be perceived as irrelevant or unusable by the student population. This paper presents a model for Web-based delivery of support for key skills which incorporates two separate approaches to the design of these resources. The model was implemented as part of a wider key skills pilot project at University College London, over a period of one year. It includes a 'core' Website, containing information and resources for staff and students. These can also be accessed via customized, departmental key skills homepages. This paper presents the basis for the design choices made in preparing these materials, and the evaluation of some of the pilot departments using them. It then draws some wider conclusions about the effectiveness of this design for supporting skills development.

Olfactory Receptor Database: a sensory chemoreceptor resource

OpenAIRE

Skoufos, Emmanouil; Marenco, Luis; Nadkarni, Prakash M.; Miller, Perry L.; Shepherd, Gordon M.

2000-01-01

The Olfactory Receptor Database (ORDB) is a WWW-accessible database that has been expanded from an olfactory receptor resource to a chemoreceptor resource. It stores data on six classes of G-protein-coupled sensory chemoreceptors: (i) olfactory receptor-like proteins, (ii) vomeronasal receptors, (iii) insect olfactory receptors, (iv) worm chemoreceptors, (v) taste papilla receptors and (vi) fungal pheromone receptors. A complementary database of the ligands of these receptors (OdorDB) has bee...

SNP2Structure: A Public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures

Directory of Open Access Journals (Sweden)

Difei Wang

2015-01-01

Full Text Available One of the long-standing challenges in biology is to understand how non-synonymous single nucleotide polymorphisms (nsSNPs change protein structure and further affect their function. While it is impractical to solve all the mutated protein structures experimentally, it is quite feasible to model the mutated structures in silico. Toward this goal, we built a publicly available structure database resource (SNP2Structure, https://apps.icbi.georgetown.edu/snp2structure focusing on missense mutations, msSNP. Compared with web portals with similar aims, SNP2Structure has the following major advantages. First, our portal offers direct comparison of two related 3D structures. Second, the protein models include all interacting molecules in the original PDB structures, so users are able to determine regions of potential interaction changes when a protein mutation occurs. Third, the mutated structures are available to download locally for further structural and functional analysis. Fourth, we used Jsmol package to display the protein structure that has no system compatibility issue. SNP2Structure provides reliable, high quality mapping of nsSNPs to 3D protein structures enabling researchers to explore the likely functional impact of human disease-causing mutations.

Assessing the Resource Gap in a Changing Arctic

Science.gov (United States)

2013-04-01

the AFOSI caches, minimal storage options are required, ranging from prefabricated climate controlled structures to the use of refurbished pre-existing...buildings. Relative low cost, prefabricated structures, such as Shell’s canvas hanger to the refurbished possibilities of Barrow’s two unused...loss of life. Additionally, a SONS would also result in severe ecological contamination and economic loss for industry, the State of Alaska, and the

Information Resources in High-Energy Physics Surveying the Present Landscape and Charting the Future Course

CERN Document Server

Gentil-Beccot, Anne; Mele, Salvatore; Holtkamp, Annette; O'Connell, Heath B; Brooks, Travis C

2009-01-01

Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the field of information management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the field reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the field. The survey offers an insight into the most importan...

Protein complex prediction in large ontology attributed protein-protein interaction networks.

Science.gov (United States)

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-01-01

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

The Exploitation of Evolving Resources

CERN Document Server

McGlade, Jacqueline; Law, Richard

1993-01-01

The impact of man on the biosphere is profound. Quite apart from our capacity to destroy natural ecosystems and to drive species to extinction, we mould the evolution of the survivors by the selection pressures we apply to them. This has implications for the continued health of our natural biological resources and for the way in which we seek to optimise yield from those resources. Of these biological resources, fish stocks are particularly important to mankind as a source of protein. On a global basis, fish stocks provide the major source of protein for human consumption from natural ecosystems, amounting to some seventy million tonnes in 1970. Although fisheries management has been extensively developed over the last century, it has not hitherto considered the evolutionary consequences of fishing activity. While this omission may not have been serious in the past, the ever increasing intensity of exploitation and the deteriorating health of fish stocks has generated an urgent need for a better understanding...

Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.

Science.gov (United States)

Ahmed, Aqeel; Smith, Richard D; Clark, Jordan J; Dunbar, James B; Carlson, Heather A

2015-01-01

For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A model for detailed evaluation of fossil-energy saving by utilizing unused but possible energy-sources on a city scale

International Nuclear Information System (INIS)

Mori, Yasuhumi; Kikegawa, Yukihiro; Uchida, Hiroyuki

2007-01-01

There is growing interest in the utilization of unused, but possible, energy sources to reduce carbon-dioxide emissions and fossil-energy consumption, and especially to comply with the Kyoto Protocol which came into effect in 2005. Detailed considerations of plant location, land use and life cycle analysis, however, have not yet been fully estimated with a view to confirming the advantages of the new energy-source usage. A model for heat energy from river water and treated sewage water, and waste-heat energy from municipal solid-waste incineration plants was built and applied to the Tokyo urban area in Japan, considering the spatial and time-related distribution of demands and supplies, the shapes of buildings in the demand area, and life-cycle analysis. The model selected areas were those which should use these energies without prejudice, and sometimes the areas were far from the energy-source point. The reduction of carbon-dioxide emissions resulting from new energy-sources was about 8% of the reduction target for Tokyo in 1990. The model was able to precisely evaluate the new energy-usage, using data from both supply and demand sides. (author)

Water Resources Availability in Kabul, Afghanistan

Science.gov (United States)

Akbari, A. M.; Chornack, M. P.; Coplen, T. B.; Emerson, D. G.; Litke, D. W.; Mack, T. J.; Plummer, N.; Verdin, J. P.; Verstraeten, I. M.

2008-12-01

construction practices and little planning. By 2050, the available water resources in the Kabul Basin may be reduced as a result of Central Asian climate changes. Increasing air temperatures associated with climate change are likely to lead to a decreasing snowpack and an earlier growing season, resulting in less recharge from river leakage. As a result, more than 60 percent of existing supply wells may become dry or inoperative. The impacts of climate change would likely be greatest in the agricultural regions in the western areas of the basin. Water resources in the in northern areas of the basin may meet future water needs. However, in other areas of the basin, particularly the more urbanized southern areas adjacent to and including the city of Kabul, water resources may be stressed. Ground water in deep aquifers, more than 100 m below land surface, is presently unused. Conceptual ground-water-flow simulations indicate that ground water in deep aquifers may be thousands of years old. The deep aquifer may sustain limited increases in municipal water use, but may not support increased agricultural use which is much greater than municipal use. However, the hydraulic feasibility and quality of deep ground-water extractions are not well known and are being investigated.

UbiProt: a database of ubiquitylated proteins

Directory of Open Access Journals (Sweden)

Kondratieva Ekaterina V

2007-04-01

Full Text Available Abstract Background Post-translational protein modification with ubiquitin, or ubiquitylation, is one of the hottest topics in a modern biology due to a dramatic impact on diverse metabolic pathways and involvement in pathogenesis of severe human diseases. A great number of eukaryotic proteins was found to be ubiquitylated. However, data about particular ubiquitylated proteins are rather disembodied. Description To fill a general need for collecting and systematizing experimental data concerning ubiquitylation we have developed a new resource, UbiProt Database, a knowledgebase of ubiquitylated proteins. The database contains retrievable information about overall characteristics of a particular protein, ubiquitylation features, related ubiquitylation and de-ubiquitylation machinery and literature references reflecting experimental evidence of ubiquitylation. UbiProt is available at http://ubiprot.org.ru for free. Conclusion UbiProt Database is a public resource offering comprehensive information on ubiquitylated proteins. The resource can serve as a general reference source both for researchers in ubiquitin field and those who deal with particular ubiquitylated proteins which are of their interest. Further development of the UbiProt Database is expected to be of common interest for research groups involved in studies of the ubiquitin system.

Histopathological alterations of the gills, liver and kidneys in Anabas Testudineus (Bloch) fish living in an unused lignite mine, Li District, Lamphun Povince, Thailand

Energy Technology Data Exchange (ETDEWEB)

Saenphet, S.; Thaworn, W.; Saenphet, K. [Chiang Mai University, Chiang Mai (Thailand). Faculty of Science

2009-09-15

The acidity of mine water generally makes it toxic to most organisms. The gills, kidneys and livers of Anabas testudineus Bloch fish inhabiting the acidic water (pH 2-4) of an unused lignite mine in Li District, Lamphun Province, Thailand were examined and compared to those of farmed fish. Tissue abnormalities were found in all investigated organs. Deterioration and telangiectasia of gill filaments were found. Liver tissue revealed hemorrhages, blood congestion and necrotic cells with mononuclear cell infiltration. In addition, hypertrophy of the epithelial cells of the renal tubules with reduced lumens, aneurisms of the renal tubules, and contractions of the glomeruli in the Bowman's capsule were observed. These histopathological findings suggest the acidic water in this habitat causes severe damage to the internal organs of fish and consequently alter their physiological status. Since the water in this pond is utilized by local people, these findings highlight the need for adequate water treatment.

The reactive metabolite target protein database (TPDB)--a web-accessible resource.

Science.gov (United States)

Hanzlik, Robert P; Koen, Yakov M; Theertham, Bhargav; Dong, Yinghua; Fang, Jianwen

2007-03-16

The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common targets of multiple toxins. The literature of this field is widely scattered but expanding rapidly, suggesting the need for a comprehensive, searchable database of reactive metabolite target proteins. The Reactive Metabolite Target Protein Database (TPDB) is a comprehensive, curated, searchable, documented compilation of publicly available information on the protein targets of reactive metabolites of 18 well-studied chemicals and drugs of known toxicity. TPDB software enables i) string searches for author names and proteins names/synonyms, ii) more complex searches by selecting chemical compound, animal species, target tissue and protein names/synonyms from pull-down menus, and iii) commonality searches over multiple chemicals. Tabulated search results provide information, references and links to other databases. The TPDB is a unique on-line compilation of information on the covalent modification of cellular proteins by reactive metabolites of chemicals and drugs. Its comprehensiveness and searchability should facilitate the elucidation of mechanisms of reactive metabolite toxicity. The database is freely available at http://tpdb.medchem.ku.edu/tpdb.html.

Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants.

Science.gov (United States)

Gromiha, M Michael; Anoosha, P; Huang, Liang-Tsung

2016-01-01

Protein stability is the free energy difference between unfolded and folded states of a protein, which lies in the range of 5-25 kcal/mol. Experimentally, protein stability is measured with circular dichroism, differential scanning calorimetry, and fluorescence spectroscopy using thermal and denaturant denaturation methods. These experimental data have been accumulated in the form of a database, ProTherm, thermodynamic database for proteins and mutants. It also contains sequence and structure information of a protein, experimental methods and conditions, and literature information. Different features such as search, display, and sorting options and visualization tools have been incorporated in the database. ProTherm is a valuable resource for understanding/predicting the stability of proteins and it can be accessed at http://www.abren.net/protherm/ . ProTherm has been effectively used to examine the relationship among thermodynamics, structure, and function of proteins. We describe the recent progress on the development of methods for understanding/predicting protein stability, such as (1) general trends on mutational effects on stability, (2) relationship between the stability of protein mutants and amino acid properties, (3) applications of protein three-dimensional structures for predicting their stability upon point mutations, (4) prediction of protein stability upon single mutations from amino acid sequence, and (5) prediction methods for addressing double mutants. A list of online resources for predicting has also been provided.

Motor protein traffic regulation by supply–demand balance of resources

International Nuclear Information System (INIS)

Ciandrini, Luca; Dauloudet, Olivier; Parmeggiani, Andrea; Neri, Izaak; Walter, Jean Charles

2014-01-01

In cells and in in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or the flow chamber) and hence compete for recruiting the available motors, potentially depleting the reservoir and affecting cytoskeletal transport. In this work we provide a theoretical framework in which to study, analytically and numerically, how motor density profiles and crowding along cytoskeletal filaments depend on the competition of motors for their binding sites. We propose two models in which finite processive motor proteins actively advance along cytoskeletal filaments and are continuously exchanged with the motor pool. We first look at homogeneous reservoirs and then examine the effects of free motor diffusion in the surrounding medium. We consider as a reference situation recent in vitro experimental setups of kinesin-8 motors binding and moving along microtubule filaments in a flow chamber. We investigate how the crowding of linear motor proteins moving on a filament can be regulated by the balance between supply (concentration of motor proteins in the flow chamber) and demand (total number of polymerized tubulin heterodimers). We present analytical results for the density profiles of bound motors and the reservoir depletion, and propose novel phase diagrams that present the formation of jams of motor proteins on the filament as a function of two tuneable experimental parameters: the motor protein concentration and the concentration of tubulins polymerized into cytoskeletal filaments. Extensive numerical simulations corroborate the analytical results for parameters in the experimental range and also address the effects of diffusion of motor proteins in the reservoir. We then propose experiments for validating our models and discuss how the ‘supply–demand’ effects can regulate motor traffic also in in vivo

Introducing "biophysical redundancy": the global status and past evolution of unused water, land and productivity resources for food production

Science.gov (United States)

Fader, Marianela

2017-04-01

Countries have different resilience to sudden and long-term changes in food demand and supply. An important part of this resilience is the degree of biophysical redundancy, defined as the potential food production of 'spare land', available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. The presentation will show the results of a recently published paper1 on the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Results indicate that in 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as 'Low Income Economies (LIEs)' since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

Fiscal 1993 international research cooperation project. Feasibility study of finding out the seeds of international joint research (technology for environmental preservation using biotechnology, technology for effective use unused hydrocarbon resource, technology of solid electrolyte fuel cells for high-efficient electric vehicles); 1993 nendo kokusai kenkyu kyoryoku jigyo. Kokusai kyodo kenkyu seeds hakkutsu no tame no FS chosa (biotechnology ni yoru kankyo taisaku gijutsu, miriyo tanka suiso shigen no yuko riyo gijutsu, kokoritsu denki jidosha no kotai denkaishitsu nenryo denchi gijutsu)

Energy Technology Data Exchange (ETDEWEB)

NONE

1994-03-01

This project is aimed at internationally cooperating in the R and D of industrial technology and improving industrial technology of Japan. For it, the following three technologies were investigated: 1) environmental preservation technology using biotechnology, 2) technology for effective use of unused hydrocarbon resource, 3) solid electrolyte fuel cell (SOFC) technology for high-efficient electric vehicles. In 1), bio-remediation is a choice as the result of trially using technologies for remediation of the environment polluted by pollutant, but it is not a technically completed one, but one which will be improved by trial and error. By the application of gene engineering, the use of gene recombination enables wide spread of decomposition genes. In 2), technical subjects were studied such as superheavy distillate, oil shale, coalhead methane and methane hydrate. In 3), designed were cylinder type and planar type SOFC of 850degC operation and 10kW output. Accumulation and weight of a total SOFC system are 81 liters and 100 kg in cylinder type and 136 liters and 200 kg in planar type. The vehicle can be equipped with the SOFC. 171 refs., 72 figs., 54 tabs.

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource.

Science.gov (United States)

Druce, Megan; Hulo, Chantal; Masson, Patrick; Sommer, Paula; Xenarios, Ioannis; Le Mercier, Philippe; De Oliveira, Tulio

2016-01-01

The Human Immunodeficiency Virus (HIV) is one of the pathogens that cause the greatest global concern, with approximately 35 million people currently infected with HIV. Extensive HIV research has been performed, generating a large amount of HIV and host genomic data. However, no effective vaccine that protects the host from HIV infection is available and HIV is still spreading at an alarming rate, despite effective antiretroviral (ARV) treatment. In order to develop effective therapies, we need to expand our knowledge of the interaction between HIV and host proteins. In contrast to virus proteins, which often rapidly evolve drug resistance mutations, the host proteins are essentially invariant within all humans. Thus, if we can identify the host proteins needed for virus replication, such as those involved in transporting viral proteins to the cell surface, we have a chance of interrupting viral replication. There is no proteome resource that summarizes this interaction, making research on this subject a difficult enterprise. In order to fill this gap in knowledge, we curated a resource presents detailed annotation on the interaction between the HIV proteome and host proteins. Our resource was produced in collaboration with ViralZone and used manual curation techniques developed by UniProtKB/Swiss-Prot. Our new website also used previous annotations of the BioAfrica HIV-1 Proteome Resource, which has been accessed by approximately 10 000 unique users a year since its inception in 2005. The novel features include a dedicated new page for each HIV protein, a graphic display of its function and a section on its interaction with host proteins. Our new webpages also add information on the genomic location of each HIV protein and the position of ARV drug resistance mutations. Our improved BioAfrica HIV-1 Proteome Resource fills a gap in the current knowledge of biocuration.Database URL:http://www.bioafrica.net/proteomics/HIVproteome.html. © The Author(s) 2016. Published

The Ser/Thr Protein Kinase Protein-Protein Interaction Map of M. tuberculosis.

Science.gov (United States)

Wu, Fan-Lin; Liu, Yin; Jiang, He-Wei; Luan, Yi-Zhao; Zhang, Hai-Nan; He, Xiang; Xu, Zhao-Wei; Hou, Jing-Li; Ji, Li-Yun; Xie, Zhi; Czajkowsky, Daniel M; Yan, Wei; Deng, Jiao-Yu; Bi, Li-Jun; Zhang, Xian-En; Tao, Sheng-Ce

2017-08-01

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions. Bioinformatics analysis showed that the interacting proteins reflect diverse functions, including roles in two-component system, transcription, protein degradation, and cell wall integrity. Functional investigations confirmed that PknG regulates cell wall integrity through key components of peptidoglycan (PG) biosynthesis, e.g. MurC. The global STPK-KPIs network constructed here is expected to serve as a rich resource for understanding the key signaling pathways in Mtb, thus facilitating drug development and effective control of Mtb. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Invited review: Resource inputs and land, water and carbon footprints from the production of edible protein of animal origin

Directory of Open Access Journals (Sweden)

G. Flachowsky

2018-01-01

Full Text Available The objective of this review is to analyze crucial factors in the output from the production of proteins in food of animal origin, such as milk, meat and eggs. We then consider inputs such as land, water, fuel, minerals and feed, as well as characterize emissions. Finally, we estimate footprints for land (land footprint, LF, water (water footprint, WF and greenhouse gas emissions (i.e., carbon footprint, CF during the production process. The wide range of different land and water inputs per unit feed between various studies largely influences the results. Further influencing factors are species and categories of animals that produce edible protein, their yields and the feeding of animals. Coproducts with no or low humanly edible fractions and grassland as feed contribute to a lower need for arable land and lower LF, WF and CF. The most efficient land use or the lowest LF per kilogram of edible protein was estimated for higher milk and egg yields; the highest LF values were calculated for beef, followed by pork. The lowest WF and CF were calculated for edible protein of chicken meat and eggs. Edible protein from ruminants is mostly characterized by a higher CF because of the high greenhouse gas potential of methane produced in the rumen. A key prerequisite for further progress in this field is the harmonization of data collection and calculation methods. Alternatives to partial or complete replacement of protein of terrestrial animals, such as marine animals, insects, cell cultures, single-cell proteins or simulated animal products from plants, as well as changing eating patterns and reducing food losses are mentioned as further potential ways for more efficient feed production. For all those dealing with plant or animal breeding and cultivation and all those who are working along the whole food production chain, it is a major challenge to enhance the production of more food for more people with, at the same time, less, limited resources and

PPI-IRO: A two-stage method for protein-protein interaction extraction based on interaction relation ontology

KAUST Repository

Li, Chuanxi; Chen, Peng; Wang, Rujing; Wang, Xiujie; Su, Yaru; Li, Jinyan

2014-01-01

Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identifi cation of biological regulatory networks. This paper presents a novel method based on the idea

Protein-Protein Docking in Drug Design and Discovery.

Science.gov (United States)

Kaczor, Agnieszka A; Bartuzi, Damian; Stępniewski, Tomasz Maciej; Matosiuk, Dariusz; Selent, Jana

2018-01-01

Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

Thermodynamic database for proteins: features and applications.

Science.gov (United States)

Gromiha, M Michael; Sarai, Akinori

2010-01-01

We have developed a thermodynamic database for proteins and mutants, ProTherm, which is a collection of a large number of thermodynamic data on protein stability along with the sequence and structure information, experimental methods and conditions, and literature information. This is a valuable resource for understanding/predicting the stability of proteins, and it can be accessible at http://www.gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html . ProTherm has several features including various search, display, and sorting options and visualization tools. We have analyzed the data in ProTherm to examine the relationship among thermodynamics, structure, and function of proteins. We describe the progress on the development of methods for understanding/predicting protein stability, such as (i) relationship between the stability of protein mutants and amino acid properties, (ii) average assignment method, (iii) empirical energy functions, (iv) torsion, distance, and contact potentials, and (v) machine learning techniques. The list of online resources for predicting protein stability has also been provided.

Efficient cellular solid-state NMR of membrane proteins by targeted protein labeling

Energy Technology Data Exchange (ETDEWEB)

Baker, Lindsay A. [University of Oxford, Oxford Particle Imaging Centre, The Wellcome Trust Centre for Human Genetics, Division of Structural Biology, Nuffield Department of Medicine (United Kingdom); Daniëls, Mark; Cruijsen, Elwin A. W. van der; Folkers, Gert E.; Baldus, Marc, E-mail: m.baldus@uu.nl [Utrecht University, NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands)

2015-06-15

Solid-state NMR spectroscopy (ssNMR) has made significant progress towards the study of membrane proteins in their native cellular membranes. However, reduced spectroscopic sensitivity and high background signal levels can complicate these experiments. Here, we describe a method for ssNMR to specifically label a single protein by repressing endogenous protein expression with rifampicin. Our results demonstrate that treatment of E. coli with rifampicin during induction of recombinant membrane protein expression reduces background signals for different expression levels and improves sensitivity in cellular membrane samples. Further, the method reduces the amount of time and resources needed to produce membrane protein samples, enabling new strategies for studying challenging membrane proteins by ssNMR.

Efficient cellular solid-state NMR of membrane proteins by targeted protein labeling

International Nuclear Information System (INIS)

Baker, Lindsay A.; Daniëls, Mark; Cruijsen, Elwin A. W. van der; Folkers, Gert E.; Baldus, Marc

2015-01-01

Solid-state NMR spectroscopy (ssNMR) has made significant progress towards the study of membrane proteins in their native cellular membranes. However, reduced spectroscopic sensitivity and high background signal levels can complicate these experiments. Here, we describe a method for ssNMR to specifically label a single protein by repressing endogenous protein expression with rifampicin. Our results demonstrate that treatment of E. coli with rifampicin during induction of recombinant membrane protein expression reduces background signals for different expression levels and improves sensitivity in cellular membrane samples. Further, the method reduces the amount of time and resources needed to produce membrane protein samples, enabling new strategies for studying challenging membrane proteins by ssNMR

Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

Directory of Open Access Journals (Sweden)

Bradley Michael E

2006-02-01

Full Text Available Abstract Background When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1 multiple sequence alignments, 2 mapping of alignment sites to crystal structure sites, 3 phylogenetic trees, 4 inferred ancestral sequences at internal tree nodes, and 5 amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. Conclusion We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural

Energetic and Economic Assessment of Pipe Network Effects on Unused Energy Source System Performance in Large-Scale Horticulture Facilities

Directory of Open Access Journals (Sweden)

Jae Ho Lee

2015-04-01

Full Text Available As the use of fossil fuel has increased, not only in construction, but also in agriculture due to the drastic industrial development in recent times, the problems of heating costs and global warming are getting worse. Therefore, the introduction of more reliable and environmentally-friendly alternative energy sources has become urgent and the same trend is found in large-scale horticulture facilities. In this study, among many alternative energy sources, we investigated the reserves and the potential of various different unused energy sources which have infinite potential, but are nowadays wasted due to limitations in their utilization. This study investigated the effects of the distance between the greenhouse and the actual heat source by taking into account the heat transfer taking place inside the pipe network. This study considered CO2 emissions and economic aspects to determine the optimal heat source. Payback period analysis against initial investment cost shows that a heat pump based on a power plant’s waste heat has the shortest payback period of 7.69 years at a distance of 0 km. On the other hand, the payback period of a heat pump based on geothermal heat showed the shortest payback period of 10.17 year at the distance of 5 km, indicating that heat pumps utilizing geothermal heat were the most effective model if the heat transfer inside the pipe network between the greenhouse and the actual heat source is taken into account.

GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction

Directory of Open Access Journals (Sweden)

Zheng Huiru

2009-01-01

Full Text Available Abstract Background Information about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug targets and aid in the design of new therapeutic interventions. Efforts have been made to map interactions on a proteomic-wide scale using both experimental and computational techniques. Reference datasets that contain known interacting proteins (positive cases and non-interacting proteins (negative cases are essential to support computational prediction and validation of protein-protein interactions. Information on known interacting and non interacting proteins are usually stored within databases. Extraction of these data can be both complex and time consuming. Although, the automatic construction of reference datasets for classification is a useful resource for researchers no public resource currently exists to perform this task. Results GRIP (Gold Reference dataset constructor from Information on Protein complexes is a web-based system that provides researchers with the functionality to create reference datasets for protein-protein interaction prediction in Saccharomyces cerevisiae. Both positive and negative cases for a reference dataset can be extracted, organised and downloaded by the user. GRIP also provides an upload facility whereby users can submit proteins to determine protein complex membership. A search facility is provided where a user can search for protein complex information in Saccharomyces cerevisiae. Conclusion GRIP is developed to retrieve information on protein complex, cellular localisation, and physical and genetic interactions in Saccharomyces cerevisiae. Manual construction of reference datasets can be a time consuming process requiring programming knowledge. GRIP simplifies and speeds up this process by allowing users to automatically construct reference datasets. GRIP is free to access at http://rosalind.infj.ulst.ac.uk/GRIP/.

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

Science.gov (United States)

Profiti, Giuseppe; Martelli, Pier Luigi; Casadio, Rita

2017-07-03

BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Plant protein annotation in the UniProt Knowledgebase.

Science.gov (United States)

Schneider, Michel; Bairoch, Amos; Wu, Cathy H; Apweiler, Rolf

2005-05-01

The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium. UniProt presents three database layers: the UniProt Archive, the UniProt Knowledgebase (UniProtKB), and the UniProt Reference Clusters. The UniProtKB consists of two sections: UniProtKB/Swiss-Prot (fully manually curated entries) and UniProtKB/TrEMBL (automated annotation, classification and extensive cross-references). New releases are published fortnightly. A specific Plant Proteome Annotation Program (http://www.expasy.org/sprot/ppap/) was initiated to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Through UniProt, our aim is to provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information that will allow the plant community to fully explore and utilize the wealth of information available for both plant and non-plant model organisms.

The reactive metabolite target protein database (TPDB – a web-accessible resource

Directory of Open Access Journals (Sweden)

Dong Yinghua

2007-03-01

Full Text Available Abstract Background The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common targets of multiple toxins. The literature of this field is widely scattered but expanding rapidly, suggesting the need for a comprehensive, searchable database of reactive metabolite target proteins. Description The Reactive Metabolite Target Protein Database (TPDB is a comprehensive, curated, searchable, documented compilation of publicly available information on the protein targets of reactive metabolites of 18 well-studied chemicals and drugs of known toxicity. TPDB software enables i string searches for author names and proteins names/synonyms, ii more complex searches by selecting chemical compound, animal species, target tissue and protein names/synonyms from pull-down menus, and iii commonality searches over multiple chemicals. Tabulated search results provide information, references and links to other databases. Conclusion The TPDB is a unique on-line compilation of information on the covalent modification of cellular proteins by reactive metabolites of chemicals and drugs. Its comprehensiveness and searchability should facilitate the elucidation of mechanisms of reactive metabolite toxicity. The database is freely available at http://tpdb.medchem.ku.edu/tpdb.html

HitPredict version 4: comprehensive reliability scoring of physical protein?protein interactions from more than 100 species

OpenAIRE

L?pez, Yosvany; Nakai, Kenta; Patil, Ashwini

2015-01-01

HitPredict is a consolidated resource of experimentally identified, physical protein?protein interactions with confidence scores to indicate their reliability. The study of genes and their inter-relationships using methods such as network and pathway analysis requires high quality protein?protein interaction information. Extracting reliable interactions from most of the existing databases is challenging because they either contain only a subset of the available interactions, or a mixture of p...

Temporal and spatial characteristics of water resources in the Yeerqiang River Basin based on remote sensing

Science.gov (United States)

Y Ran, Q.; Y Bai, L.; Feng, J. Z.; Yang, Y. M.; Guo, M. Q.; Li, H. L.; Zhang, Q.; Zhang, P.; Cao, D.

2017-07-01

Surface water resources play an important role in the economic and social developments as well as the protection of natural ecological environment in the Yeerqiang River Basin. Based upon the six stages of land use data from 1990 to 2015, the temporal and spatial variation of surface water resources in the Yerqiang River Basin have been explored and analyzed. The results show that: (1) From 1990 to 2015, the area of natural landscape initially increased and then decreased, while the area of artificial landscape increased, which caused a slight increase in the land use degree in the study area. (2) The dynamic changes of water and glacier areas are somewhat consistent over the past 25 years, with a sharp decline between 2005-2010 and a small increase in the remaining years. The dynamic changes in areas of non-glacial water were moderate, with decrease in area of 9 km2 from 1990 to 2015. The beach area decreased, and the other water sub-classes initially increased and then decreased. (3) Over the past 25 years, the proportion of unchanged water area is 73.22%, the transfer-out proportion is 19.19%, and the transfer-in proportion is 7.59%. Generally, water types transferred to grassland and unused land. Additionally, significant transfers were observed for the conversions between glaciers and woodland, conversions between canal, lake, reservoir and beach, and conversions between beach and farmland.

A recyclable protein resource derived from cauliflower by-products: Potential biological activities of protein hydrolysates.

Science.gov (United States)

Xu, Yang; Li, Yuting; Bao, Tao; Zheng, Xiaodong; Chen, Wei; Wang, Jianxu

2017-04-15

Cauliflower by-products (CBP) are rich in leaf protein. Every year tons of CBP will lead to environmental pollution. Therefore, this study was conducted to extract leaf protein from CBP and investigate its biological activities. Our results showed that the optimal extraction parameters were: a liquid to solid ratio of 4mL/g, a pH of 11, an ultrasonic extraction lasting 15min, and at an applied power of 175W. Under these optimized conditions, 12.066g of soluble leaf protein (SLP) was obtained from 1000g of CBP and its extraction yield was 53.07%. The obtained SLP was further hydrolysed by Alcalase and the SLP hydrolysate (SLPH) showed a potent angiotensin I-converting enzyme (ACE) inhibitory activity with an IC 50 value of 138.545μg/mL in vitro. In addition, SLPH promoted the glucose consumption and enhanced the glycogen content in HepG2 cells. Overall, our results suggested that CBP may be recycled for designing future functional foods. Copyright © 2016 Elsevier Ltd. All rights reserved.

Information Resources in High-Energy Physics: Surveying the Present Landscape and Charting the Future Course

Energy Technology Data Exchange (ETDEWEB)

Gentil-Beccot, Anne; Mele, Salvatore; Holtkamp, Annette; O' Connell, Heath B.; Brooks, Travis C.

2008-04-22

Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the field of information management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the field reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the field. The survey offers an insight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally 'early adopters' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities.

Information Resources in High-Energy Physics: Surveying the Present Landscape and Charting the Future Course

International Nuclear Information System (INIS)

Gentil-Beccot, Anne; Mele, Salvatore; Holtkamp, Annette; O'Connell, Heath B.; Brooks, Travis C.

2008-01-01

Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the field of information management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the field reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the field. The survey offers an insight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally 'early adopters' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities

PATRIC, the bacterial bioinformatics database and analysis resource.

Science.gov (United States)

Wattam, Alice R; Abraham, David; Dalay, Oral; Disz, Terry L; Driscoll, Timothy; Gabbard, Joseph L; Gillespie, Joseph J; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K; Olson, Robert; Overbeek, Ross; Pusch, Gordon D; Shukla, Maulik; Schulman, Julie; Stevens, Rick L; Sullivan, Daniel E; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J C; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W

2014-01-01

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

Geothermal resource assessment of western San Luis Valley, Colorado

Energy Technology Data Exchange (ETDEWEB)

Zacharakis, Ted G.; Pearl, Richard Howard; Ringrose, Charles D.

1983-01-01

The Colorado Geological Survey initiated and carried out a fully integrated assessment program of the geothermal resource potential of the western San Luis Valley during 1979 and 1980. The San Luis Valley is a large intermontane basin located in southcentral Colorado. While thermal springs and wells are found throughout the Valley, the only thermal waters found along the western part of the Valley are found at Shaw Warm Springs which is a relatively unused spring located approximately 6 miles (9.66 km) north of Del Norte, Colorado. The waters at Shaws Warm Spring have a temperature of 86 F (30 C), a discharge of 40 gallons per minute and contain approximately 408 mg/l of total dissolved solids. The assessment program carried out din the western San Luis Valley consisted of: soil mercury geochemical surveys; geothermal gradient drilling; and dipole-dipole electrical resistivity traverses, Schlumberger soundings, Audio-magnetotelluric surveys, telluric surveys, and time-domain electro-magnetic soundings and seismic surveys. Shaw Warm Springs appears to be the only source of thermal waters along the western side of the Valley. From the various investigations conducted the springs appear to be fault controlled and is very limited in extent. Based on best evidence presently available estimates are presented on the size and extent of Shaw Warm Springs thermal system. It is estimated that this could have an areal extent of 0.63 sq. miles (1.62 sq. km) and contain 0.0148 Q's of heat energy.

Algae Resources

Energy Technology Data Exchange (ETDEWEB)

None

2016-06-01

Algae are highly efficient at producing biomass, and they can be found all over the planet. Many use sunlight and nutrients to create biomass, which contain key components—including lipids, proteins, and carbohydrates— that can be converted and upgraded to a variety of biofuels and products. A functional algal biofuels production system requires resources such as suitable land and climate, sustainable management of water resources, a supplemental carbon dioxide (CO2) supply, and other nutrients (e.g., nitrogen and phosphorus). Algae can be an attractive feedstock for many locations in the United States because their diversity allows for highpotential biomass yields in a variety of climates and environments. Depending on the strain, algae can grow by using fresh, saline, or brackish water from surface water sources, groundwater, or seawater. Additionally, they can grow in water from second-use sources such as treated industrial wastewater; municipal, agricultural, or aquaculture wastewater; or produced water generated from oil and gas drilling operations.

Plant Protein Annotation in the UniProt Knowledgebase1

Science.gov (United States)

Schneider, Michel; Bairoch, Amos; Wu, Cathy H.; Apweiler, Rolf

2005-01-01

The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium. UniProt presents three database layers: the UniProt Archive, the UniProt Knowledgebase (UniProtKB), and the UniProt Reference Clusters. The UniProtKB consists of two sections: UniProtKB/Swiss-Prot (fully manually curated entries) and UniProtKB/TrEMBL (automated annotation, classification and extensive cross-references). New releases are published fortnightly. A specific Plant Proteome Annotation Program (http://www.expasy.org/sprot/ppap/) was initiated to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Through UniProt, our aim is to provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information that will allow the plant community to fully explore and utilize the wealth of information available for both plant and nonplant model organisms. PMID:15888679

InSilico Proteomics System: Integration and Application of Protein and Protein-Protein Interaction Data using Microsoft .NET

Directory of Open Access Journals (Sweden)

Straßer Wolfgang

2006-12-01

Full Text Available In the last decades, biological databases became the major knowledge resource for researchers in the field of molecular biology. The distribution of information among these databases is one of the major problems. An overview about the subject area of data access and representation of protein and protein-protein interaction data within public biological databases is described. For a comprehensive and consistent way of searching and analysing integrated protein and protein-protein interaction data, the InSilico Proteomics (ISP project has been initiated. Its three main objectives are (1 to provide an integrated knowledge pool for data investigation and global network analysis functions for a better understanding of a cell’s interactome, (2 employment of public data for plausibility analysis and validation of in-house experimental data and (3 testing the applicability of Microsoft’s .NET architecture for bioinformatics applications. Data integrated into the ISP database can be queried through the Web portal PRIMOS (PRotein Interaction and MOlecule Search which is freely available at http://biomis.fh-hagenberg.at/isp/primos.

Treatment of Children with Protein – Losing Enteropathy After Fontan and Other Complex Congenital Heart Disease Procedures in Condition with Limited Human and Technical Resources

Science.gov (United States)

Bejiqi, Ramush; Retkoceri, Ragip; Zeka, Naim; Bejiqi, Hana; Vuqiterna, Armend; Maloku, Arlinda

2014-01-01

Background Protein-losing enteropathy (PLE) is a disorder characterized by abnormal and often profound enteric protein loss. It’s relatively uncommon complication of Fontan and other complex congenital heart disease (CCHD) procedures. Because of the complexity and rarity of this disease process, the pathogenesis and pathophysiology of protein-losing enteropathy remain poorly understood, and attempts at treatment seldom yield long-term success. Aim of presentation is to describe single centre experience in diagnosis, evaluation, management and treatment of children with protein-losing enteropathy after Fontan and other CCHD procedures in the current era and in centre with limited human and technical resources, follows with a comprehensive review of protein-losing enteropathy publications, and concludes with suggestions for prevention and treatment. Material and methodology Retrospectively we analyzed patients with CCHD and protein-losing enteropathy in our institution, starting from January 2000 to December 2012. The including criteria were age between two and 17 years, to have a complex congenital heart disease and available complete documentation of cardiac surgery under cardiopulmonary bypass. Results Of all patients we evaluated 18 cases with protein-losing enteropathy, aged 6 to 19 years (mean 14±9); there were three children who had undergone screening procedure for D-transposition, one Tetralogy of Fallot, and remaining 14 patients had undergone Fontan procedures; (anatomic diagnosis are: six with tricuspid atresia, seven with d-transposition, double outlet right ventricle and pulmonary atresia and two with hypoplastic left heart syndrome). The diagnosis of protein-losing enteropathy was made at median age of 5.6 years, ranging from 13 months to 15 years. Diagnosis was made using alpha 1-antitrypsin as a gold marker in stool. By physical examination in 14 patients edema was found, in three ascites, and six patients had pleural effusion. Laboratory findings

HC-IPSAG and GC-IPSAG algorithm proposals

DEFF Research Database (Denmark)

Bǎdoi, C.-I.; Croitoru, V.; Prasad, N.

2010-01-01

The cognitive radio (CR) technology was proposed as a solution for the lack of wireless resources in an environment with a rapidly growing number of users. The CR advances the dynamic utilization of the licensed users' unused spectrum channels by secondary users. The paper looks into large CR...

The Federated Satellite Systems paradigm: Concept and business case evaluation

Science.gov (United States)

Golkar, Alessandro; Lluch i Cruz, Ignasi

2015-06-01

This paper defines the paradigm of Federated Satellite Systems (FSS) as a novel distributed space systems architecture. FSS are networks of spacecraft trading previously inefficiently allocated and unused resources such as downlink bandwidth, storage, processing power, and instrument time. FSS holds the promise to enhance cost-effectiveness, performance and reliability of existing and future space missions, by networking different missions and effectively creating a pool of resources to exchange between participants in the federation. This paper introduces and describes the FSS paradigm, and develops an approach integrating mission analysis and economic assessments to evaluate the feasibility of the business case of FSS. The approach is demonstrated on a case study on opportunities enabled by FSS to enhance space exploration programs, with particular reference to the International Space Station. The application of the proposed methodology shows that the FSS concept is potentially able to create large commercial markets of in-space resources, by providing the technical platform to offer the opportunity for spacecraft to share or make use of unused resources within their orbital neighborhood. It is shown how the concept is beneficial to satellite operators, space agencies, and other stakeholders of the space industry to more flexibly interoperate space systems as a portfolio of assets, allowing unprecedented collaboration among heterogeneous types of missions.

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

Science.gov (United States)

Velankar, Sameer; Dana, José M.; Jacobsen, Julius; van Ginkel, Glen; Gane, Paul J.; Luo, Jie; Oldfield, Thomas J.; O’Donovan, Claire; Martin, Maria-Jesus; Kleywegt, Gerard J.

2013-01-01

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information. PMID:23203869

STRING 8--a global view on proteins and their functional interactions in 630 organisms

DEFF Research Database (Denmark)

Jensen, Lars Juhl; Kuhn, Michael; Stark, Manuel

2008-01-01

Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein-protein inter......Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein......-protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set...... of genomes and proteins. The most important new developments in STRING 8 over previous releases include a URL-based programming interface, which can be used to query STRING from other resources, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures...

Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions.

Science.gov (United States)

Guruharsha, K G; Obar, Robert A; Mintseris, Julian; Aishwarya, K; Krishnan, R T; Vijayraghavan, K; Artavanis-Tsakonas, Spyros

2012-01-01

Proteins perform essential cellular functions as part of protein complexes, often in conjunction with RNA, DNA, metabolites and other small molecules. The genome encodes thousands of proteins but not all of them are expressed in every cell type; and expressed proteins are not active at all times. Such diversity of protein expression and function accounts for the level of biological intricacy seen in nature. Defining protein-protein interactions in protein complexes, and establishing the when, what and where of potential interactions, is therefore crucial to understanding the cellular function of any protein-especially those that have not been well studied by traditional molecular genetic approaches. We generated a large-scale resource of affinity-tagged expression-ready clones and used co-affinity purification combined with tandem mass-spectrometry to identify protein partners of nearly 5,000 Drosophila melanogaster proteins. The resulting protein complex "map" provided a blueprint of metazoan protein complex organization. Here we describe how the map has provided valuable insights into protein function in addition to generating hundreds of testable hypotheses. We also discuss recent technological advancements that will be critical in addressing the next generation of questions arising from the map.

The Proteins API: accessing key integrated protein and genome information.

Science.gov (United States)

Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

2017-07-03

The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Algal Proteins: Extraction, Application, and Challenges Concerning Production

Directory of Open Access Journals (Sweden)

Stephen Bleakley

2017-04-01

Full Text Available Population growth combined with increasingly limited resources of arable land and fresh water has resulted in a need for alternative protein sources. Macroalgae (seaweed and microalgae are examples of under-exploited “crops”. Algae do not compete with traditional food crops for space and resources. This review details the characteristics of commonly consumed algae, as well as their potential for use as a protein source based on their protein quality, amino acid composition, and digestibility. Protein extraction methods applied to algae to date, including enzymatic hydrolysis, physical processes, and chemical extraction and novel methods such as ultrasound-assisted extraction, pulsed electric field, and microwave-assisted extraction are discussed. Moreover, existing protein enrichment methods used in the dairy industry and the potential of these methods to generate high value ingredients from algae, such as bioactive peptides and functional ingredients are discussed. Applications of algae in human nutrition, animal feed, and aquaculture are examined.

Algal Proteins: Extraction, Application, and Challenges Concerning Production

Science.gov (United States)

Bleakley, Stephen; Hayes, Maria

2017-01-01

Population growth combined with increasingly limited resources of arable land and fresh water has resulted in a need for alternative protein sources. Macroalgae (seaweed) and microalgae are examples of under-exploited “crops”. Algae do not compete with traditional food crops for space and resources. This review details the characteristics of commonly consumed algae, as well as their potential for use as a protein source based on their protein quality, amino acid composition, and digestibility. Protein extraction methods applied to algae to date, including enzymatic hydrolysis, physical processes, and chemical extraction and novel methods such as ultrasound-assisted extraction, pulsed electric field, and microwave-assisted extraction are discussed. Moreover, existing protein enrichment methods used in the dairy industry and the potential of these methods to generate high value ingredients from algae, such as bioactive peptides and functional ingredients are discussed. Applications of algae in human nutrition, animal feed, and aquaculture are examined. PMID:28445408

Unused natural variation can lift yield barriers in plant breeding.

Directory of Open Access Journals (Sweden)

Amit Gur

2004-10-01

Full Text Available Natural biodiversity is an underexploited sustainable resource that can enrich the genetic basis of cultivated plants with novel alleles that improve productivity and adaptation. We evaluated the progress in breeding for increased tomato (Solanum lycopersicum yield using genotypes carrying a pyramid of three independent yield-promoting genomic regions introduced from the drought-tolerant green-fruited wild species Solanum pennellii. Yield of hybrids parented by the pyramided genotypes was more than 50% higher than that of a control market leader variety under both wet and dry field conditions that received 10% of the irrigation water. This demonstration of the breaking of agricultural yield barriers provides the rationale for implementing similar strategies for other agricultural organisms that are important for global food security.

Protein-Protein Interactions Prediction Based on Iterative Clique Extension with Gene Ontology Filtering

Directory of Open Access Journals (Sweden)

Lei Yang

2014-01-01

Full Text Available Cliques (maximal complete subnets in protein-protein interaction (PPI network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in a network usually interfere with prediction. Therefore, we propose a method combining clique-based method of prediction and gene ontology (GO annotations to overcome the shortcoming and improve the accuracy of predictions. According to different GO correcting rules, we generate two predicted interaction sets which guarantee the quality and quantity of predicted protein interactions. The proposed method is applied to the PPI network from the Database of Interacting Proteins (DIP and most of the predicted interactions are verified by another biological database, BioGRID. The predicted protein interactions are appended to the original protein network, which leads to clique extension and shows the significance of biological meaning.

Information resources in high-energy physics. Surveying the present landscape and charting the future course

International Nuclear Information System (INIS)

Gentil-Beccot, A.; Mele, S.; Holtkamp, A.; O'Connell, H.B.; Brooks, T.C.

2008-04-01

Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the eld of infor- mation management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the eld reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the eld. The survey o ers an in- sight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally ''early adopters'' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities. (orig.)

Information resources in high-energy physics. Surveying the present landscape and charting the future course

Energy Technology Data Exchange (ETDEWEB)

Gentil-Beccot, A.; Mele, S. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Holtkamp, A. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); O' Connell, H.B. [Fermi National Accelerator Lab., Batavia, IL (United States); Brooks, T.C. [Stanford Linear Accelerator Center, Menlo Park, CA (United States)

2008-04-15

Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the eld of infor- mation management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the eld reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the eld. The survey o ers an in- sight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally 'early adopters' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities. (orig.)

Information resources in high-energy physics. Surveying the present landscape and charting the future course

Energy Technology Data Exchange (ETDEWEB)

Gentil-Beccot, A; Mele, S [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Holtkamp, A [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); O' Connell, H B [Fermi National Accelerator Lab., Batavia, IL (United States); Brooks, T C [Stanford Linear Accelerator Center, Menlo Park, CA (United States)

2008-04-15

Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the eld of infor- mation management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the eld reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the eld. The survey o ers an in- sight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally 'early adopters' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities. (orig.)

The PMDB Protein Model Database

Science.gov (United States)

Castrignanò, Tiziana; De Meo, Paolo D'Onorio; Cozzetto, Domenico; Talamo, Ivano Giuseppe; Tramontano, Anna

2006-01-01

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ∼240 proteins. The system is accessible at and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data. PMID:16381873

Comprehensive research concerning the development of effective utilizing techniques of biological resources (large scale research out of the framework). Seibutsu shigen no koritsuteki riyo gijutsu no kaihatsu ni kansuru sogo kenkyu (ogata betsuwaku kenkyu)

Energy Technology Data Exchange (ETDEWEB)

1991-10-25

This paper is a research report in which the cultivated production of forest resources, the development to useful substances and the systematization to take the root in a region were studied. The distribution maps of biological resources on respective woodland systems: that is, the nationwide distribution maps of the amount of resources in Japan as to the broadleaf trees in private forests and national forests, the available amount and kinds of tree were prepared. As for the establishment of cultivation technique of the super-short deforestation forest, that is, pursue of wooden growth to the maximum limit, the superior clone 26 system was selected from the willow group through the research of wooden cultivation and the clone which showed the maximum yield reached 24t/ha every year. As for the material preparation technique due to microbial enzymes, that is, the creation and breeding of fungi which have the high lignin decomposition power, a stock of fungi which has the high lignin decomposition power and the decomposition selectivity was created by the cell fusion and the UV (ultraviolet ray) radiation treatment. As for the use of effective components in wooden resources, many useful characteristics could be detected by applying the boiling, bursting and ozone treatment. As for the mushroom cultivation through the application of unused tree kinds, a new kind of mushroom for food service was selected to clarify the possibility of fruit body formation. The development of a new material from conifers is promising. 1 tab.

Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.

Directory of Open Access Journals (Sweden)

Shoukai Lin

2016-11-01

Full Text Available Single nucleotide polymorphisms (SNPs are widely used in functional genomics and genetics research work. The high-quality sequence of rice genome has provided a genome-wide SNP and proteome resource. However, the impact of SNPs on protein phosphorylation status in rice is not fully understood. In this paper, we firstly updated rice SNP resource based on the new rice genome Ver. 7.0, then systematically analyzed the potential impact of Non-synonymous SNPs (nsSNPs on the protein phosphorylation status. There were 3,897,312 SNPs in Ver. 7.0 rice genome, among which 9.9% was nsSNPs. Whilst, a total 2,508,261 phosphorylated sites were predicted in rice proteome. Interestingly, we observed that 150,197 (39.1% nsSNPs could influence protein phosphorylation status, among which 52.2% might induce changes of protein kinase (PK types for adjacent phosphorylation sites. We constructed a database, SNP_rice, to deposit the updated rice SNP resource and phosSNPs information. It was freely available to academic researchers at http://bioinformatics.fafu.edu.cn. As a case study, we detected five nsSNPs that potentially influenced heterotrimeric G proteins phosphorylation status in rice, indicating that genetic polymorphisms showed impact on the signal transduction by influencing the phosphorylation status of heterotrimeric G proteins. The results in this work could be a useful resource for future experimental identification and provide interesting information for better rice breeding.

Enzyme Enhanced Protein Recovery from Green Biomass Pulp

DEFF Research Database (Denmark)

Dotsenko, Gleb; Lange, Lene

2017-01-01

of local protein resources based on upgrade from e.g. green plant biomass. In present work we consider different strategies for protein recovery from white clover and ryegrass screw press pulps, using aqueous extraction, as well as carbohydrases and proteases enhanced extraction. Protein recovery...... in these studies was determined as a yield of solubilized protein with regard to the total protein in a screw press pulp. Aqueous extraction at pH 8.0 resulted in approx. 40 % protein recovery, while proteases application (Savinase 16.0L, Novozymes) enabled twice higher protein yield. Application of plant cell...... pulp proteolyzates, generated by Savinase 16.0L protease....

Gender and the Labour Market: Comparing Austria and Japan

OpenAIRE

Biffl, Gudrun

2006-01-01

Japan and Austria are among the OECD countries with an average labour force participation rate but an above average gender gap as far as employment opportunities and earnings are concerned. In Japan, women in the main working age have a fairly large margin of labour resources not employed in the market economy. In Austria in contrast, the proportion of unused labour resources of mature workers is high, and the gender gap is less pronounced than in Japan, which suggests that a different combin...

Improving strand quality of upland oaks for use in oriented strand board

Science.gov (United States)

David B. DeValliance; Jody D. Gray; Shawn T. Grushecky

2013-01-01

Past research estimates that more than 1 million tons of oak logging residues go unused in West Virginia each year. Much research has been done investigating potential products and markets for this underutilized resource. West Virginia is home to an oriented strand board (OSB) producer that consumes large volumes of small diameter, low quality round wood. However, the...

Petersburg Builds a Health Program. Bulletin, 1949, No. 9

Science.gov (United States)

Bathurst, Effie G.

1949-01-01

This bulletin is about an invasion that was welcomed. It tells how boys and girls of Petersburg, West Virginia, invaded their town to learn and to serve. Hotels, school lunchroom, alleys, creeks and swamps, unused park area, and other resources were utilized. The young invaders were welcomed by the adult citizens of the town because the principal…

Transcriptomics resources of human tissues and organs

DEFF Research Database (Denmark)

Uhlén, Mathias; Hallström, Björn M.; Lindskog, Cecilia

2016-01-01

a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome......Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide...

How and When Do Insects Rely on Endogenous Protein and Lipid Resources during Lethal Bouts of Starvation? A New Application for 13C-Breath testing.

Science.gov (United States)

McCue, Marshall D; Guzman, R Marena; Passement, Celeste A; Davidowitz, Goggy

2015-01-01

Most of our understanding about the physiology of fasting and starvation comes from studies of vertebrates; however, for ethical reasons, studies that monitor vertebrates through the lethal endpoint are scant. Insects are convenient models to characterize the comparative strategies used to cope with starvation because they have diverse life histories and have evolved under the omnipresent challenge of food limitation. Moreover, we can study the physiology of starvation through its natural endpoint. In this study we raised populations of five species of insects (adult grasshoppers, crickets, cockroaches, and larval beetles and moths) on diets labeled with either 13C-palmitic acid or 13C-leucine to isotopically enrich the lipids or the proteins in their bodies, respectively. The insects were allowed to become postabsorptive and then starved. We periodically measured the δ13C of the exhaled breath to characterize how each species adjusted their reliance on endogenous lipids and proteins as energy sources. We found that starving insects employ a wide range of strategies for regulating lipid and protein oxidation. All of the insects except for the beetle larvae were capable of sharply reducing reliance on protein oxidation; however, this protein sparing strategy was usually unsustainable during the entire starvation period. All insects increased their reliance on lipid oxidation, but while some species (grasshoppers, cockroaches, and beetle larvae) were still relying extensively on lipids at the time of death, other species (crickets and moth larvae) allowed rates of lipid oxidation to return to prestarvation levels. Although lipids and proteins are critical metabolic fuels for both vertebrates and insects, insects apparently exhibit a much wider range of strategies for rationing these limited resources during starvation.

How and When Do Insects Rely on Endogenous Protein and Lipid Resources during Lethal Bouts of Starvation? A New Application for 13C-Breath testing.

Directory of Open Access Journals (Sweden)

Marshall D McCue

Full Text Available Most of our understanding about the physiology of fasting and starvation comes from studies of vertebrates; however, for ethical reasons, studies that monitor vertebrates through the lethal endpoint are scant. Insects are convenient models to characterize the comparative strategies used to cope with starvation because they have diverse life histories and have evolved under the omnipresent challenge of food limitation. Moreover, we can study the physiology of starvation through its natural endpoint. In this study we raised populations of five species of insects (adult grasshoppers, crickets, cockroaches, and larval beetles and moths on diets labeled with either 13C-palmitic acid or 13C-leucine to isotopically enrich the lipids or the proteins in their bodies, respectively. The insects were allowed to become postabsorptive and then starved. We periodically measured the δ13C of the exhaled breath to characterize how each species adjusted their reliance on endogenous lipids and proteins as energy sources. We found that starving insects employ a wide range of strategies for regulating lipid and protein oxidation. All of the insects except for the beetle larvae were capable of sharply reducing reliance on protein oxidation; however, this protein sparing strategy was usually unsustainable during the entire starvation period. All insects increased their reliance on lipid oxidation, but while some species (grasshoppers, cockroaches, and beetle larvae were still relying extensively on lipids at the time of death, other species (crickets and moth larvae allowed rates of lipid oxidation to return to prestarvation levels. Although lipids and proteins are critical metabolic fuels for both vertebrates and insects, insects apparently exhibit a much wider range of strategies for rationing these limited resources during starvation.

A web-based resource for designing therapeutics against Ebola Virus

OpenAIRE

Sandeep Kumar Dhanda; Kumardeep Chaudhary; Sudheer Gupta; Samir Kumar Brahmachari; Gajendra P. S. Raghava

2016-01-01

In this study, we describe a web-based resource, developed for assisting the scientific community in designing an effective therapeutics against the Ebola virus. Firstly, we predicted and identified experimentally validated epitopes in each of the antigens/proteins of the five known ebolaviruses. Secondly, we generated all the possible overlapping 9mer peptides from the proteins of ebolaviruses. Thirdly, conserved peptides across all the five ebolaviruses (four human pathogenic species) with ...

Fiscal 1998 research report. Study on the feasibility of microorganism biotechnology for effective use of environmental pollutants. Pt. 2; 1998 nendochosa hokokusho. Kankyo osen busshitsu no shigenka no tame no biseibutsu bio technology riyo kanosei ni kansuru chosa. 2

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-03-01

Study was made on the feasibility of microorganism biotechnology for effective use of environmental pollutants and unused resources. Microorganisms and microorganism enzymes for decomposing lignocellulose were viewed, and uses of hydrolysis products were summarized. Production of microorganisms applicable to fodder, composting, and production of energy sources (methane, hydrogen, ethanol) were studied. Use of vegetable fiber residues such as beer lees as fungus cultivation medium and conversion to valuable substances were also studied. Microorganisms treatment (MT) of wastes in fats and oils industry was summarized. Effective use of MT of protein waste from marine products was studied. MT of manures with the greatest impact on environment as livestock waste was summarized. The necessity of separate collection of domestic wastes, and composting and methane fermentation of kitchen garbage were reported. The feasibility of MT of plastic wastes, and decomposition of halogenated methane with high toxicity were also studied. (NEDO)

Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

DEFF Research Database (Denmark)

Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

2016-01-01

An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal...... derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff...... between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used...

SHARPEN-Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network

KAUST Repository

Loksha, Ilya V.

2009-04-30

Algorithms for discrete optimization of proteins play a central role in recent advances in protein structure prediction and design. We wish to improve the resources available for computational biologists to rapidly prototype such algorithms and to easily scale these algorithms to many processors. To that end, we describe the implementation and use of two new open source resources, citing potential benefits over existing software. We discuss CHOMP, a new object-oriented library for macromolecular optimization, and SHARPEN, a framework for scaling CHOMP scripts to many computers. These tools allow users to develop new algorithms for a variety of applications including protein repacking, protein-protein docking, loop rebuilding, or homology model remediation. Particular care was taken to allow modular energy function design; protein conformations may currently be scored using either the OPLSaa molecular mechanical energy function or an all-atom semiempirical energy function employed by Rosetta. © 2009 Wiley Periodicals, Inc.

MIPS: curated databases and comprehensive secondary data resources in 2010.

Science.gov (United States)

Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

The Mini-Grid Framework: Application Programming Support for Ad hoc Volunteer Grids

DEFF Research Database (Denmark)

Venkataraman, Neela Narayanan

2013-01-01

To harvest idle, unused computational resources in networked environments, researchers have proposed different architectures for desktop grid infrastructure. However, most of the existing research work focus on centralized approach. In this thesis, we present the development and deployment of one......, and the performance of the framework in a real grid environment. The main contribution of this thesis are: i) modeling entities such as resources and applications using their context, ii) the context-based auction strategy for dynamic task distribution, iii) scheduling through application specific quality parameters...

Rheological and Functional Properties of Catfish Skin Protein Hydrolysates

Science.gov (United States)

Catfish skin is an abundant and underutilized resource that can be used as a unique protein source to make fish skin hydrolysates. The objectives of this study were to: isolating soluble and insoluble proteins from hydrolyzed catfish skin and study the chemical and functional properties of the prote...

Alexandra's Dreams: "The Mightiest of All Lovers" in Willa Cather's "O Pioneers!"

Science.gov (United States)

Mullins, Maire

2005-01-01

In her essay "Uses of the Erotic: The Erotic as Power," Audre Lorde writes, "There are many kinds of power, used and unused, acknowledged or otherwise. The erotic is a resource within each of us that lies in a deeply female and spiritual plane, firmly rooted in the power of our unexpressed or unrecognized feeling." Lorde notes that women often…

Supporting the emergence of female student entrepreneurs

DEFF Research Database (Denmark)

Geert Jensen, Birgitte; Kruse, Merethe

2011-01-01

intends to activate unused entrepreneurial potential at the AAA and increase the number of female design students who start their own business, during or after completion of study. The aim is that an independent career is made available for all, and not only for groups of particularly resourceful 'born......' entrepreneurs, where female students are underrepresented. This paper will show how enterprising elements...

FY 1998 annual report on the exploration and production of functional peptide from unutilized protein resources; 1998 nendo miriyo tanpakushitsugen kara no kinosei pepuchido no tansaku to seisan ni kansuru kenkyu hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-03-01

This project is aimed at promotion of effective utilization of unutilized resources by transforming histidine-containing peptide (anserine), enzymatically hydrolyzed muscle protein present in lean salmon swimming off the Sanriku District in the spawning season, into functional peptide. A reactor system, comprising an enzyme-immobilized column and rotary bioreactor, is investigated to efficiently produce peptide by enzymatically hydrolyzing the water-insoluble muscle protein. Anserine is isolated by ethanol extraction, ion-exchanging and partition chromatography. The TPTZ and ABTS methods are developed for speeding up measurement of the antioxidant activity. The salmon muscle protein is hydrolyzed by 3 types of enzymes, to measure the free radical erasing activity by the ABTS method. The enzymatically hydrolyzed protein is fractionated by gel permeation chromatography. The fractions having a molecular weight of 10,000 or less show strong antioxidant activity. The hydrolyzed protein shows improved activity by the iron rhodanide method when it has histidine at the center of tripeptide, and strong radical erasing function when it has thyrosine or tryptophan at the carboxyl terminal. (NEDO)

Analysis of gene and protein name synonyms in Entrez Gene and UniProtKB resources

KAUST Repository

Arkasosy, Basil

2013-01-01

be ambiguous, referring in some cases to more than one gene or one protein, or in others, to both genes and proteins at the same time. Public biological databases give a very useful insight about genes and proteins information, including their names

PDBTM: Protein Data Bank of transmembrane proteins after 8 years.

Science.gov (United States)

Kozma, Dániel; Simon, István; Tusnády, Gábor E

2013-01-01

The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ∼400 to 1700 entries but also new structural elements have been identified, in addition to the well-known α-helical bundle and β-barrel structures. Numerous 'exotic' transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community.

PATRIC, the bacterial bioinformatics database and analysis resource

Science.gov (United States)

Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Timothy; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J.C.; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W.

2014-01-01

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue. PMID:24225323

Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein.

Science.gov (United States)

Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

2016-11-08

An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.

Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

Science.gov (United States)

Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

2016-11-01

An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.

Grid production with the ATLAS Event Service

CERN Document Server

Benjamin, Douglas; The ATLAS collaboration

2018-01-01

ATLAS has developed and previously presented a new computing architecture, the Event Service, that allows real time delivery of fine grained workloads which process dispatched events (or event ranges) and immediately streams outputs. The principal aim was to profit from opportunistic resources such as commercial cloud, supercomputing, and volunteer computing, and otherwise unused cycles on clusters and grids. During the development and deployment phase, its utility also on the grid and conventional clusters for the exploitation of otherwise unused cycles became apparent. Here we describe our experience commissioning the Event Service on the grid in the ATLAS production system. We study the performance compared with standard simulation production. We describe the integration with the ATLAS data management system to ensure scalability and compatibility with object stores. Finally, we outline the remaining steps towards a fully commissioned system.

MIPS plant genome information resources.

Science.gov (United States)

Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

2007-01-01

The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

Potential of hydroelectric power in the Alps

International Nuclear Information System (INIS)

Schleiss, A.

2002-01-01

This article presents in detail the current hydro power production, consumption and export in the six main countries using this alpine energy resource: France, Germany, Austria, Italy, Slovenia and Switzerland. For the time being, one quarter of the Alps' hydro energy resource is still unused. The article discusses the opportunity offered by the current European electricity market deregulation to extend alpine hydro power use. For each country, the expected increase in production capacity, including technical, geographical and economic aspects, is analysed and reported in several figures and tables

Cheese whey: A potential resource to transform into bioprotein, functional/nutritional proteins and bioactive peptides.

Science.gov (United States)

Yadav, Jay Shankar Singh; Yan, Song; Pilli, Sridhar; Kumar, Lalit; Tyagi, R D; Surampalli, R Y

2015-11-01

The byproduct of cheese-producing industries, cheese whey, is considered as an environmental pollutant due to its high BOD and COD concentrations. The high organic load of whey arises from the presence of residual milk nutrients. As demand for milk-derived products is increasing, it leads to increased production of whey, which poses a serious management problem. To overcome this problem, various technological approaches have been employed to convert whey into value-added products. These technological advancements have enhanced whey utilization and about 50% of the total produced whey is now transformed into value-added products such as whey powder, whey protein, whey permeate, bioethanol, biopolymers, hydrogen, methane, electricity bioprotein (single cell protein) and probiotics. Among various value-added products, the transformation of whey into proteinaceous products is attractive and demanding. The main important factor which is attractive for transformation of whey into proteinaceous products is the generally recognized as safe (GRAS) regulatory status of whey. Whey and whey permeate are biotransformed into proteinaceous feed and food-grade bioprotein/single cell protein through fermentation. On the other hand, whey can be directly processed to obtain whey protein concentrate, whey protein isolate, and individual whey proteins. Further, whey proteins are also transformed into bioactive peptides via enzymatic or fermentation processes. The proteinaceous products have applications as functional, nutritional and therapeutic commodities. Whey characteristics, and its transformation processes for proteinaceous products such as bioproteins, functional/nutritional protein and bioactive peptides are covered in this review. Copyright © 2015 Elsevier Inc. All rights reserved.

Feeding Immunity: Physiological and Behavioral Responses to Infection and Resource Limitation

Directory of Open Access Journals (Sweden)

Sarah A. Budischak

2018-01-01

Full Text Available Resources are a core currency of species interactions and ecology in general (e.g., think of food webs or competition. Within parasite-infected hosts, resources are divided among the competing demands of host immunity and growth as well as parasite reproduction and growth. Effects of resources on immune responses are increasingly understood at the cellular level (e.g., metabolic predictors of effector function, but there has been limited consideration of how these effects scale up to affect individual energetic regimes (e.g., allocation trade-offs, susceptibility to infection, and feeding behavior (e.g., responses to local resource quality and quantity. We experimentally rewilded laboratory mice (strain C57BL/6 in semi-natural enclosures to investigate the effects of dietary protein and gastrointestinal nematode (Trichuris muris infection on individual-level immunity, activity, and behavior. The scale and realism of this field experiment, as well as the multiple physiological assays developed for laboratory mice, enabled us to detect costs, trade-offs, and potential compensatory mechanisms that mice employ to battle infection under different resource conditions. We found that mice on a low-protein diet spent more time feeding, which led to higher body fat stores (i.e., concentration of a satiety hormone, leptin and altered metabolite profiles, but which did not fully compensate for the effects of poor nutrition on albumin or immune defenses. Specifically, immune defenses measured as interleukin 13 (IL13 (a primary cytokine coordinating defense against T. muris and as T. muris-specific IgG1 titers were lower in mice on the low-protein diet. However, these reduced defenses did not result in higher worm counts in mice with poorer diets. The lab mice, living outside for the first time in thousands of generations, also consumed at least 26 wild plant species occurring in the enclosures, and DNA metabarcoding revealed that the consumption of different

CanisOme--The protein signatures of Canis lupus familiaris diseases.

Science.gov (United States)

Fernandes, Mónica; Rosa, Nuno; Esteves, Eduardo; Correia, Maria José; Arrais, Joel; Ribeiro, Paulo; Vala, Helena; Barros, Marlene

2016-03-16

Although the applications of Proteomics in Human Biomedicine have been explored for some time now, in animal and veterinary research, the potential of this resource has just started to be explored, especially when companion animal health is considered. In the last years, knowledge on the Canis lupus familiaris proteome has been accumulating in the literature and a resource compiling all this information and critically reviewing it was lacking. This article presents such a resource for the first time. CanisOme is a database of all proteins identified in Canis lupus familiaris tissues, either in health or in disease, annotated with information on the proteins present on the sample and on the donors. This database reunites information on 549 proteins, associated with 63 dog diseases and 33 dog breeds. Examples of how this information may be used to produce new hypothesis on disease mechanisms is presented both through the functional analysis of the proteins quantified in canine cutaneous mast cell tumors and through the study of the interactome of C. lupus familiaris and Leishmania infantum. Therefore, the usefulness of CanisOme for researchers looking for protein biomarkers in dogs and interested in a comprehensive analysis of disease mechanisms is demonstrated. This paper presents CanisOme, a database of proteomic studies with relevant protein annotation, allowing the enlightenment of disease mechanisms and the discovery of novel disease biomarkers for C. lupus familiaris. This knowledge is important not only for the improvement of animal health but also for the use of dogs as models for human health studies. Copyright © 2016 Elsevier B.V. All rights reserved.

ProteinTracker: an application for managing protein production and purification.

Science.gov (United States)

Ponko, Stefan C; Bienvenue, David

2012-05-10

Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks), or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS). Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes), cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org.

Key challenges for the creation and maintenance of specialist protein resources

NARCIS (Netherlands)

Holliday, G.L.; Bairoch, A.; Bagos, P.G.; Chatonnet, A.; Craik, D.J.; Finn, R.D.; Henrissat, B.; Landsman, D.; Manning, G.; Nagano, N.; O'Donovan, C.; Pruitt, K.D.; Rawlings, N.D.; Saier, M.; Sowdhamini, R.; Spedding, M.; Srinivasan, N.; Vriend, G.; Babbitt, P.C.; Bateman, A.

2015-01-01

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

Directory of Open Access Journals (Sweden)

Vakser Ilya A

2011-07-01

Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of

Network-driven design principles for neuromorphic systems

OpenAIRE

Partzsch, Johannes; Sch?ffny, Rene

2015-01-01

Synaptic connectivity is typically the most resource-demanding part of neuromorphic systems. Commonly, the architecture of these systems is chosen mainly on technical considerations. As a consequence, the potential for optimization arising from the inherent constraints of connectivity models is left unused. In this article, we develop an alternative, network-driven approach to neuromorphic architecture design. We describe methods to analyse performance of existing neuromorphic architectures i...

Cytogenetic Resources and Information.

Science.gov (United States)

De Braekeleer, Etienne; Huret, Jean-Loup; Mossafa, Hossain; Dessen, Philippe

2017-01-01

The main databases devoted stricto sensu to cancer cytogenetics are the "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ), the "Atlas of Genetics and Cytogenetics in Oncology and Haematology" ( http://atlasgeneticsoncology.org ), and COSMIC ( http://cancer.sanger.ac.uk/cosmic ).However, being a complex multistep process, cancer cytogenetics are broadened to "cytogenomics," with complementary resources on: general databases (nucleic acid and protein sequences databases; cartography browsers: GenBank, RefSeq, UCSC, Ensembl, UniProtKB, and Entrez Gene), cancer genomic portals associated with recent international integrated programs, such as TCGA or ICGC, other fusion genes databases, array CGH databases, copy number variation databases, and mutation databases. Other resources such as the International System for Human Cytogenomic Nomenclature (ISCN), the International Classification of Diseases for Oncology (ICD-O), and the Human Gene Nomenclature Database (HGNC) allow a common language.Data within the scientific/medical community should be freely available. However, most of the institutional stakeholders are now gradually disengaging, and well-known databases are forced to beg or to disappear (which may happen!).

The Protein Model Portal.

Science.gov (United States)

Arnold, Konstantin; Kiefer, Florian; Kopp, Jürgen; Battey, James N D; Podvinec, Michael; Westbrook, John D; Berman, Helen M; Bordoli, Lorenza; Schwede, Torsten

2009-03-01

Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploration of the protein structure space. One of the challenges in using model information effectively has been to access all models available for a specific protein in heterogeneous formats at different sites using various incompatible accession code systems. Often, structure models for hundreds of proteins can be derived from a given experimentally determined structure, using a variety of established methods. This has been done by all of the PSI centers, and by various independent modeling groups. The goal of the Protein Model Portal (PMP) is to provide a single portal which gives access to the various models that can be leveraged from PSI targets and other experimental protein structures. A single interface allows all existing pre-computed models across these various sites to be queried simultaneously, and provides links to interactive services for template selection, target-template alignment, model building, and quality assessment. The current release of the portal consists of 7.6 million model structures provided by different partner resources (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase, SWISS-MODEL Repository). The PMP is available at http://www.proteinmodelportal.org and from the PSI Structural Genomics Knowledgebase.

Cotton: A Massively Underutilized and Often Overlooked Protein and Biomass Resource

Science.gov (United States)

Every year the cotton crop on the planet produces about 11 million metric tons of protein. Unfortunately, the cotton plant has also evolved a chemical defense mechanism, a toxin (gossypol) that resides in tiny but visible pigment glands. Having a phenotypic marker for the toxin is unique and has all...

Resource Abundance and Resource Dependence in China

NARCIS (Netherlands)

Ji, K.; Magnus, J.R.; Wang, W.

2010-01-01

This paper reconsiders the ‘curse of resources’ hypothesis for the case of China, and distinguishes between resource abundance, resource rents, and resource dependence. Resource abundance and resource rents are shown to be approximately equivalent, and their association with resource dependence

The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

Science.gov (United States)

Rose, Peter W; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R; Christie, Cole H; Costanzo, Luigi Di; Duarte, Jose M; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y; Zardecki, Christine; Berman, Helen M; Burley, Stephen K

2017-01-04

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

ProteinTracker: an application for managing protein production and purification

Directory of Open Access Journals (Sweden)

Ponko Stefan C

2012-05-01

Full Text Available Abstract Background Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks, or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS. Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. Findings This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes, cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. Conclusions ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org.

ProteinTracker: an application for managing protein production and purification

Science.gov (United States)

2012-01-01

Background Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks), or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS). Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. Findings This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes), cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. Conclusions ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org. PMID:22574679

Application of InterPro for the functional classification of the proteins ...

Indian Academy of Sciences (India)

InterPro (http://www.ebi.ac.uk/interpro/) is an integrated documentation resource for protein families, domains and sites, developed initially as a means of rationalizing the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. It is a useful resource that aids the functional classification of ...

PDBe: Protein Data Bank in Europe.

Science.gov (United States)

Velankar, Sameer; Alhroub, Younes; Alili, Anaëlle; Best, Christoph; Boutselakis, Harry C; Caboche, Ségolène; Conroy, Matthew J; Dana, Jose M; van Ginkel, Glen; Golovin, Adel; Gore, Swanand P; Gutmanas, Aleksandras; Haslam, Pauline; Hirshberg, Miriam; John, Melford; Lagerstedt, Ingvar; Mir, Saqib; Newman, Laurence E; Oldfield, Tom J; Penkett, Chris J; Pineda-Castillo, Jorge; Rinaldi, Luana; Sahni, Gaurav; Sawka, Grégoire; Sen, Sanchayita; Slowley, Robert; Sousa da Silva, Alan Wilter; Suarez-Uruena, Antonio; Swaminathan, G Jawahar; Symmons, Martyn F; Vranken, Wim F; Wainwright, Michael; Kleywegt, Gerard J

2011-01-01

The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community. PDBe has developed a browser to access and analyze the structural archive using classification systems that are familiar to chemists and biologists. The PDBe web pages that describe individual PDB entries have been enhanced through the introduction of plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. Finally, the entire web site has been redesigned to make it substantially easier to use for expert and novice users alike. PDBe works closely with other teams at the European Bioinformatics Institute (EBI) and in the international scientific community to develop new resources with value-added information. The SIFTS initiative is an example of such a collaboration--it provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases. SIFTS is widely used by major bioinformatics resources.

MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.

Science.gov (United States)

Ohue, Masahito; Shimoda, Takehiro; Suzuki, Shuji; Matsuzaki, Yuri; Ishida, Takashi; Akiyama, Yutaka

2014-11-15

The application of protein-protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of >97% strong scaling. MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock. akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

A comprehensive curated resource for follicle stimulating hormone signaling

Directory of Open Access Journals (Sweden)

Sharma Jyoti

2011-10-01

Full Text Available Abstract Background Follicle stimulating hormone (FSH is an important hormone responsible for growth, maturation and function of the human reproductive system. FSH regulates the synthesis of steroid hormones such as estrogen and progesterone, proliferation and maturation of follicles in the ovary and spermatogenesis in the testes. FSH is a glycoprotein heterodimer that binds and acts through the FSH receptor, a G-protein coupled receptor. Although online pathway repositories provide information about G-protein coupled receptor mediated signal transduction, the signaling events initiated specifically by FSH are not cataloged in any public database in a detailed fashion. Findings We performed comprehensive curation of the published literature to identify the components of FSH signaling pathway and the molecular interactions that occur upon FSH receptor activation. Our effort yielded 64 reactions comprising 35 enzyme-substrate reactions, 11 molecular association events, 11 activation events and 7 protein translocation events that occur in response to FSH receptor activation. We also cataloged 265 genes, which were differentially expressed upon FSH stimulation in normal human reproductive tissues. Conclusions We anticipate that the information provided in this resource will provide better insights into the physiological role of FSH in reproductive biology, its signaling mediators and aid in further research in this area. The curated FSH pathway data is freely available through NetPath (http://www.netpath.org, a pathway resource developed previously by our group.

Analysis of gene and protein name synonyms in Entrez Gene and UniProtKB resources

KAUST Repository

Arkasosy, Basil

2013-05-11

Ambiguity in texts is a well-known problem: words can carry several meanings, and hence, can be read and interpreted differently. This is also true in the biological literature; names of biological concepts, such as genes and proteins, might be ambiguous, referring in some cases to more than one gene or one protein, or in others, to both genes and proteins at the same time. Public biological databases give a very useful insight about genes and proteins information, including their names. In this study, we made a thorough analysis of the nomenclatures of genes and proteins in two data sources and for six different species. We developed an automated process that parses, extracts, processes and stores information available in two major biological databases: Entrez Gene and UniProtKB. We analysed gene and protein synonyms, their types, frequencies, and the ambiguities within a species, in between data sources and cross-species. We found that at least 40% of the cross-species ambiguities are caused by names that are already ambiguous within the species. Our study shows that from the six species we analysed (Homo Sapiens, Mus Musculus, Arabidopsis Thaliana, Oryza Sativa, Bacillus Subtilis and Pseudomonas Fluorescens), rice (Oriza Sativa) has the best naming model in Entrez Gene database, with low ambiguities between data sources and cross-species.

Phylogenetic continuum indicates "galaxies" in the protein universe: preliminary results on the natural group structures of proteins.

Science.gov (United States)

Ladunga, I

1992-04-01

The markedly nonuniform, even systematic distribution of sequences in the protein "universe" has been analyzed by methods of protein taxonomy. Mapping of the natural hierarchical system of proteins has revealed some dense cores, i.e., well-defined clusterings of proteins that seem to be natural structural groupings, possibly seeds for a future protein taxonomy. The aim was not to force proteins into more or less man-made categories by discriminant analysis, but to find structurally similar groups, possibly of common evolutionary origin. Single-valued distance measures between pairs of superfamilies from the Protein Identification Resource were defined by two chi 2-like methods on tripeptide frequencies and the variable-length subsequence identity method derived from dot-matrix comparisons. Distance matrices were processed by several methods of cluster analysis to detect phylogenetic continuum between highly divergent proteins. Only well-defined clusters characterized by relatively unique structural, intracellular environmental, organismal, and functional attribute states were selected as major protein groups, including subsets of viral and Escherichia coli proteins, hormones, inhibitors, plant, ribosomal, serum and structural proteins, amino acid synthases, and clusters dominated by certain oxidoreductases and apolar and DNA-associated enzymes. The limited repertoire of functional patterns due to small genome size, the high rate of recombination, specific features of the bacterial membranes, or of the virus cycle canalize certain proteins of viruses and Gram-negative bacteria, respectively, to organismal groups.

Sperm proteins in teleostean and chondrostean (sturgeon) fishes.

Science.gov (United States)

Li, Ping; Hulak, Martin; Linhart, Otomar

2009-11-01

Sperm proteins in the seminal plasma and spermatozoa of teleostean and chondrostean have evolved adaptations due to the changes in the reproductive environment. Analysis of the composition and functions of these proteins provides new insights into sperm motility and fertilising abilities, thereby creating possibilities for improving artificial reproduction and germplasm resource conservation technologies (e.g. cryopreservation). Seminal plasma proteins are involved in the protection of spermatozoa during storage in the reproductive system, whereas all spermatozoa proteins contribute to the swimming and fertilising abilities of sperm. Compared to mammalian species, little data are available on fish sperm proteins and their functions. We review here the current state of the art in this field and focus on relevant subjects that require attention. Future research should concentrate on protein functions and their mode of action in fish species, especially on the role of spermatozoa surface proteins during fertilisation and on a description of sturgeon sperm proteins.

Trichomonas vaginalis surface proteins: a view from the genome

DEFF Research Database (Denmark)

Hirt, R. P.; Noel, C. J.; Sicheritz-Pontén, Thomas

2007-01-01

Surface proteins of mucosal microbial pathogens play multiple and essential roles in initiating and sustaining the colonization of the heavily defended mucosa. The protist Trichomonas vaginalis is one of the most common human sexually transmitted pathogens that colonize the urogenital mucosa....... However, little is known about its surface proteins. The recently completed draft genome sequence of T. vaginalis provides an invaluable resource to guide molecular and cellular characterization of surface proteins and to investigate their role in pathogenicity. Here, we review the existing data on T...

Land Use for Edible Protein of Animal Origin—A Review

Science.gov (United States)

Flachowsky, Gerhard; Meyer, Ulrich; Südekum, Karl-Heinz

2017-01-01

Simple Summary The growing world population has led to a higher demand for more and better quality food. In the future, there will be increasingly strong competition for arable land and other non-renewable resources. Proteins of animal origin are very valuable sources of essential nutrients, but their production consumes resources and causes emissions. The aim of this study was to calculate exemplarily the land use for production of edible animal protein from different animal species and categories in consideration of important influencing factors. Large differences were found with the highest amounts per kilogram of body weight produced by broiler chickens and the lowest yields in edible protein and the highest land need observed for beef cattle. Abstract The present period is characterized by a growing world population and a higher demand for more and better quality food, as well as other products for an improved standard of living. In the future, there will be increasingly strong competition for arable land and non-renewable resources such as fossil carbon-sources, water, and some minerals, as well as between food, feed, fuel, fiber, flowers, and fun (6 F’s). Proteins of animal origin like milk, meat, fish, eggs and, probably, insects are very valuable sources of essential amino acids, minerals and vitamins, but their production consumes some non-renewable resources including arable land and causes considerable emissions. Therefore, this study´s objective was to calculate some examples of the land use (arable land and grassland) for production of edible animal protein taking into consideration important animal species/categories, levels of plant and animal yields, the latter estimated with and without co-products from agriculture, and the food/biofuel industry in animal feeding. There are large differences between animal species/categories and their potential to produce edible protein depending on many influencing variables. The highest amounts per kilogram

Effects of gamma irradiation on physicochemical properties of heat-induced gel prepared with chicken salt-soluble proteins

International Nuclear Information System (INIS)

Choi, Yun-Sang; Kim, Hyun-Wook; Hwang, Ko-Eun; Song, Dong-Heon; Jeong, Tae-Jun; Seo, Kwang-Wook; Kim, Young-Boong; Kim, Cheon-Jei

2015-01-01

The technological effects of gamma irradiation (0, 3, 7, and 10 kGy) on chicken salt-soluble meat proteins in a model system were investigated. There were no significant differences in protein, fat, and ash content, and sarcoplasmic protein solubility among all samples. The samples with increasing gamma irradiation levels had higher pH, lightness, yellowness, and apparent viscosity, whereas moisture content, water holding capacity, redness, myofibrillar protein solubility, total protein solubility, hardness, springiness, cohesiveness, gumminess, and chewiness were the highest in the unirradiated control. The result from meat products using gamma irradiation was intended to provide a basic resource processing technology. - Highlights: • The effect of gamma irradiation on salt-soluble meat proteins was investigated. • Gelling properties of salt-soluble protein affected by gamma irradiation. • Gamma irradiation of meat products provides a basic resource processing technology

Amino Acid Composition, Molecular Weight Distribution and Gel Electrophoresis of Walnut (Juglans regia L. Proteins and Protein Fractionations

Directory of Open Access Journals (Sweden)

Xiaoying Mao

2014-01-01

Full Text Available As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE showed that the isoelectric point was mainly in the range of 4.8–6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa.

PCAS – a precomputed proteome annotation database resource

Directory of Open Access Journals (Sweden)

Luo Jingchu

2003-11-01

Full Text Available Abstract Background Many model proteomes or "complete" sets of proteins of given organisms are now publicly available. Much effort has been invested in computational annotation of those "draft" proteomes. Motif or domain based algorithms play a pivotal role in functional classification of proteins. Employing most available computational algorithms, mainly motif or domain recognition algorithms, we set up to develop an online proteome annotation system with integrated proteome annotation data to complement existing resources. Results We report here the development of PCAS (ProteinCentric Annotation System as an online resource of pre-computed proteome annotation data. We applied most available motif or domain databases and their analysis methods, including hmmpfam search of HMMs in Pfam, SMART and TIGRFAM, RPS-PSIBLAST search of PSSMs in CDD, pfscan of PROSITE patterns and profiles, as well as PSI-BLAST search of SUPERFAMILY PSSMs. In addition, signal peptide and TM are predicted using SignalP and TMHMM respectively. We mapped SUPERFAMILY and COGs to InterPro, so the motif or domain databases are integrated through InterPro. PCAS displays table summaries of pre-computed data and a graphical presentation of motifs or domains relative to the protein. As of now, PCAS contains human IPI, mouse IPI, and rat IPI, A. thaliana, C. elegans, D. melanogaster, S. cerevisiae, and S. pombe proteome. PCAS is available at http://pak.cbi.pku.edu.cn/proteome/gca.php Conclusion PCAS gives better annotation coverage for model proteomes by employing a wider collection of available algorithms. Besides presenting the most confident annotation data, PCAS also allows customized query so users can inspect statistically less significant boundary information as well. Therefore, besides providing general annotation information, PCAS could be used as a discovery platform. We plan to update PCAS twice a year. We will upgrade PCAS when new proteome annotation algorithms

Determination of the level of resource-use efficiency in Quality ...

African Journals Online (AJOL)

The study aimed at determining the level of resource use efficiency in Quality Protein Maize (QPM) production in Kaduna State. Multi stage sampling technique was used to sample 170 respondents from four L.G.As. where QPM is mostly produced. Data were collected through questionnaire administration during the 2009 ...

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

Science.gov (United States)

Burley, Stephen K; Berman, Helen M; Kleywegt, Gerard J; Markley, John L; Nakamura, Haruki; Velankar, Sameer

2017-01-01

The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

Wild inside: Urban wild boar select natural, not anthropogenic food resources.

Science.gov (United States)

Stillfried, Milena; Gras, Pierre; Busch, Matthias; Börner, Konstantin; Kramer-Schadt, Stephanie; Ortmann, Sylvia

2017-01-01

Most wildlife species are urban avoiders, but some became urban utilizers and dwellers successfully living in cities. Often, they are assumed to be attracted into urban areas by easily accessible and highly energetic anthropogenic food sources. We macroscopically analysed stomachs of 247 wild boar (Sus scrofa, hereafter WB) from urban areas of Berlin and from the surrounding rural areas. From the stomach contents we determined as predictors of food quality modulus of fineness (MOF,), percentage of acid insoluble ash (AIA) and macronutrients such as amount of energy and percentage of protein, fat, fibre and starch. We run linear mixed models to test: (1) differences in the proportion of landscape variables, (2) differences of nutrients consumed in urban vs. rural WB and (3) the impact of landscape variables on gathered nutrients. We found only few cases of anthropogenic food in the qualitative macroscopic analysis. We categorized the WB into five stomach content categories but found no significant difference in the frequency of those categories between urban and rural WB. The amount of energy was higher in stomachs of urban WB than in rural WB. The analysis of landscape variables revealed that the energy of urban WB increased with increasing percentage of sealing, while an increased human density resulted in poor food quality for urban and rural WB. Although the percentage of protein decreased in areas with a high percentage of coniferous forests, the food quality increased. High percentage of grassland decreased the percentage of consumed fat and starch and increased the percentage of fibre, while a high percentage of agricultural areas increased the percentage of consumed starch. Anthropogenic food such as garbage might serve as fallback food when access to natural resources is limited. We infer that urban WB forage abundant, natural resources in urban areas. Urban WB might use anthropogenic resources (e.g. garbage) if those are easier to exploit and more abundant

Engineering a novel multifunctional green fluorescent protein tag for a wide variety of protein research.

Directory of Open Access Journals (Sweden)

Takuya Kobayashi

Full Text Available BACKGROUND: Genetically encoded tag is a powerful tool for protein research. Various kinds of tags have been developed: fluorescent proteins for live-cell imaging, affinity tags for protein isolation, and epitope tags for immunological detections. One of the major problems concerning the protein tagging is that many constructs with different tags have to be made for different applications, which is time- and resource-consuming. METHODOLOGY/PRINCIPAL FINDINGS: Here we report a novel multifunctional green fluorescent protein (mfGFP tag which was engineered by inserting multiple peptide tags, i.e., octa-histidine (8xHis, streptavidin-binding peptide (SBP, and c-Myc tag, in tandem into a loop of GFP. When fused to various proteins, mfGFP monitored their localization in living cells. Streptavidin agarose column chromatography with the SBP tag successfully isolated the protein complexes in a native form with a high purity. Tandem affinity purification (TAP with 8xHis and SBP tags in mfGFP further purified the protein complexes. mfGFP was clearly detected by c-Myc-specific antibody both in immunofluorescence and immuno-electron microscopy (EM. These findings indicate that mfGFP works well as a multifunctional tag in mammalian cells. The tag insertion was also successful in other fluorescent protein, mCherry. CONCLUSIONS AND SIGNIFICANCE: The multifunctional fluorescent protein tag is a useful tool for a wide variety of protein research, and may have the advantage over other multiple tag systems in its higher expandability and compatibility with existing and future tag technologies.

Critical parameters in cost-effective alkaline extraction for high protein yield from leaves

NARCIS (Netherlands)

Zhang, C.; Sanders, J.P.M.; Bruins, M.E.

2014-01-01

Leaves are potential resources for feed or food, but their applications are limited due to a high proportion of insoluble protein and inefficient processing. To overcome these problems, parameters of alkaline extraction were evaluated using green tea residue (GTR). Protein extraction could be

A Caenorhabditis elegans Mass Spectrometric Resource for Neuropeptidomics

Science.gov (United States)

Van Bael, Sven; Zels, Sven; Boonen, Kurt; Beets, Isabel; Schoofs, Liliane; Temmerman, Liesbet

2018-01-01

Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies.

Online Resources

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics; Online Resources. Journal of Genetics. Online Resources. Volume 97. 2018 | Online resources. Volume 96. 2017 | Online resources. Volume 95. 2016 | Online resources. Volume 94. 2015 | Online resources. Volume 93. 2014 | Online resources. Volume 92. 2013 | Online resources ...

Production of Pharmaceutical Proteins in Solanaceae Food Crops

Directory of Open Access Journals (Sweden)

Giorgio De Guzman

2013-01-01

Full Text Available The benefits of increased safety and cost-effectiveness make vegetable crops appropriate systems for the production and delivery of pharmaceutical proteins. In particular, Solanaceae edible crops could be inexpensive biofactories for oral vaccines and other pharmaceutical proteins that can be ingested as minimally processed extracts or as partially purified products. The field of crop plant biotechnology is advancing rapidly due to novel developments in genetic and genomic tools being made available today for the scientific community. In this review, we briefly summarize data now available regarding genomic resources for the Solanaceae family. In addition, we describe novel strategies developed for the expression of foreign proteins in vegetable crops and the utilization of these techniques to manufacture pharmaceutical proteins.

Conceptual model of water resources in the Kabul Basin, Afghanistan

Science.gov (United States)

Mack, Thomas J.; Akbari, M. Amin; Ashoor, M. Hanif; Chornack, Michael P.; Coplen, Tyler B.; Emerson, Douglas G.; Hubbard, Bernard E.; Litke, David W.; Michel, Robert L.; Plummer, Niel; Rezai, M. Taher; Senay, Gabriel B.; Verdin, James P.; Verstraeten, Ingrid M.

2010-01-01

spring. In irrigated areas near uplands or major rivers, the annual recharge rate may be about 1.2 ? 10-3 meters per year; however, in areas at lower altitude with little irrigation, the recharge rate may average about 0.7 ? 10-3 meters per year. With increasing population, the water needs of the Kabul Basin are estimated to increase from 112,000 cubic meters per day to about 725,000 cubic meters per day by the year 2057. In some areas of the basin, particularly in the north along the western mountain front and near major rivers, water resources are generally adequate for current needs. In other areas of the basin, such as in the east and away from major rivers, the available water resources may not meet future needs. On the basis of the model simulations, increasing withdrawals are likely to result in declining water levels that may cause more than 50 percent of shallow (typically less than 50 meters deep) supply wells to become dry or inoperative. The water quality in the shallow (less than 100 meters thick), unconsolidated primary aquifer has deteriorated in urban areas because of poor sanitation. Concerns about water availability may be compounded by poor well-construction practices and lack of planning. Future water resources of the Kabul Basin will likely be reduced as a result of increasing air temperatures associated with global climate change. It is estimated that at least 60 percent of shallow groundwater-supply wells would be affected and may become dry or inoperative as a result of climate change. These effects of climate change would likely be greatest in the agricultural areas adjacent to the Paghman Mountains where a majority of springs, karezes, and wells would be affected. The water available in the shallow primary aquifer of the basin may meet future water needs in the northern areas of the Kabul Basin near the Panjsher River. Conceptual groundwater-flow simulations indicate that the basin likely has groundwater reserves in unused unconsolidate

Surface Proteins of Lactococcus lactis: Bacterial Resources for Muco-adhesion in the Gastrointestinal Tract

Directory of Open Access Journals (Sweden)

Muriel Mercier-Bonin

2017-11-01

Full Text Available Food and probiotic bacteria, in particular lactic acid bacteria, are ingested in large amounts by humans and are part of the transient microbiota which is increasingly considered to be able to impact the resident microbiota and thus possibly the host health. The lactic acid bacterium Lactococcus lactis is extensively used in starter cultures to produce dairy fermented food. Also because of a generally recognized as safe status, L. lactis has been considered as a possible vehicle to deliver in vivo therapeutic molecules with anti-inflammatory properties in the gastrointestinal tract. One of the key factors that may favor health effects of beneficial bacteria to the host is their capacity to colonize transiently the gut, notably through close interactions with mucus, which covers and protects the intestinal epithelium. Several L. lactis strains have been shown to exhibit mucus-binding properties and bacterial surface proteins have been identified as key determinants of such capacity. In this review, we describe the different types of surface proteins found in L. lactis, with a special focus on mucus-binding proteins and pili. We also review the different approaches used to investigate the adhesion of L. lactis to mucus, and particularly to mucins, one of its major components, and we present how these approaches allowed revealing the role of surface proteins in muco-adhesion.

Genomes2Drugs: identifies target proteins and lead drugs from proteome data.

LENUS (Irish Health Repository)

Toomey, David

2009-01-01

BACKGROUND: Genome sequencing and bioinformatics have provided the full hypothetical proteome of many pathogenic organisms. Advances in microarray and mass spectrometry have also yielded large output datasets of possible target proteins\\/genes. However, the challenge remains to identify new targets for drug discovery from this wealth of information. Further analysis includes bioinformatics and\\/or molecular biology tools to validate the findings. This is time consuming and expensive, and could fail to yield novel drugs if protein purification and crystallography is impossible. To pre-empt this, a researcher may want to rapidly filter the output datasets for proteins that show good homology to proteins that have already been structurally characterised or proteins that are already targets for known drugs. Critically, those researchers developing novel antibiotics need to select out the proteins that show close homology to any human proteins, as future inhibitors are likely to cross-react with the host protein, causing off-target toxicity effects later in clinical trials. METHODOLOGY\\/PRINCIPAL FINDINGS: To solve many of these issues, we have developed a free online resource called Genomes2Drugs which ranks sequences to identify proteins that are (i) homologous to previously crystallized proteins or (ii) targets of known drugs, but are (iii) not homologous to human proteins. When tested using the Plasmodium falciparum malarial genome the program correctly enriched the ranked list of proteins with known drug target proteins. CONCLUSIONS\\/SIGNIFICANCE: Genomes2Drugs rapidly identifies proteins that are likely to succeed in drug discovery pipelines. This free online resource helps in the identification of potential drug targets. Importantly, the program further highlights proteins that are likely to be inhibited by FDA-approved drugs. These drugs can then be rapidly moved into Phase IV clinical studies under \\'change-of-application\\' patents.

Genomes2Drugs: identifies target proteins and lead drugs from proteome data.

Directory of Open Access Journals (Sweden)

David Toomey

Full Text Available BACKGROUND: Genome sequencing and bioinformatics have provided the full hypothetical proteome of many pathogenic organisms. Advances in microarray and mass spectrometry have also yielded large output datasets of possible target proteins/genes. However, the challenge remains to identify new targets for drug discovery from this wealth of information. Further analysis includes bioinformatics and/or molecular biology tools to validate the findings. This is time consuming and expensive, and could fail to yield novel drugs if protein purification and crystallography is impossible. To pre-empt this, a researcher may want to rapidly filter the output datasets for proteins that show good homology to proteins that have already been structurally characterised or proteins that are already targets for known drugs. Critically, those researchers developing novel antibiotics need to select out the proteins that show close homology to any human proteins, as future inhibitors are likely to cross-react with the host protein, causing off-target toxicity effects later in clinical trials. METHODOLOGY/PRINCIPAL FINDINGS: To solve many of these issues, we have developed a free online resource called Genomes2Drugs which ranks sequences to identify proteins that are (i homologous to previously crystallized proteins or (ii targets of known drugs, but are (iii not homologous to human proteins. When tested using the Plasmodium falciparum malarial genome the program correctly enriched the ranked list of proteins with known drug target proteins. CONCLUSIONS/SIGNIFICANCE: Genomes2Drugs rapidly identifies proteins that are likely to succeed in drug discovery pipelines. This free online resource helps in the identification of potential drug targets. Importantly, the program further highlights proteins that are likely to be inhibited by FDA-approved drugs. These drugs can then be rapidly moved into Phase IV clinical studies under 'change-of-application' patents.

Filling and mining the reactive metabolite target protein database.

Science.gov (United States)

Hanzlik, Robert P; Fang, Jianwen; Koen, Yakov M

2009-04-15

The post-translational modification of proteins is a well-known endogenous mechanism for regulating protein function and activity. Cellular proteins are also susceptible to post-translational modification by xenobiotic agents that possess, or whose metabolites possess, significant electrophilic character. Such non-physiological modifications to endogenous proteins are sometimes benign, but in other cases they are strongly associated with, and are presumed to cause, lethal cytotoxic consequences via necrosis and/or apoptosis. The Reactive Metabolite Target Protein Database (TPDB) is a searchable, freely web-accessible (http://tpdb.medchem.ku.edu:8080/protein_database/) resource that attempts to provide a comprehensive, up-to-date listing of known reactive metabolite target proteins. In this report we characterize the TPDB by reviewing briefly how the information it contains came to be known. We also compare its information to that provided by other types of "-omics" studies relevant to toxicology, and we illustrate how bioinformatic analysis of target proteins may help to elucidate mechanisms of cytotoxic responses to reactive metabolites.

Genenames.org: the HGNC and VGNC resources in 2017.

Science.gov (United States)

Yates, Bethan; Braschi, Bryony; Gray, Kristian A; Seal, Ruth L; Tweedie, Susan; Bruford, Elspeth A

2017-01-04

The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. Currently the HGNC database contains almost 40 000 approved gene symbols, over 19 000 of which represent protein-coding genes. In addition to naming genomic loci we manually curate genes into family sets based on shared characteristics such as homology, function or phenotype. We have recently updated our gene family resources and introduced new improved visualizations which can be seen alongside our gene symbol reports on our primary website http://www.genenames.org In 2016 we expanded our remit and formed the Vertebrate Gene Nomenclature Committee (VGNC) which is responsible for assigning names to vertebrate species lacking a dedicated nomenclature group. Using the chimpanzee genome as a pilot project we have approved symbols and names for over 14 500 protein-coding genes in chimpanzee, and have developed a new website http://vertebrate.genenames.org to distribute these data. Here, we review our online data and resources, focusing particularly on the improvements and new developments made during the last two years. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Proteopedia: A Collaborative, Virtual 3D Web-Resource for Protein and Biomolecule Structure and Function

Science.gov (United States)

Hodis, Eran; Prilusky, Jaime, Sussman, Joel L.

2010-01-01

Protein structures are hard to represent on paper. They are large, complex, and three-dimensional (3D)--four-dimensional if conformational changes count! Unlike most of their substrates, which can easily be drawn out in full chemical formula, drawing every atom in a protein would usually be a mess. Simplifications like showing only the surface of…

Behavior of VNC in high-latency environments and techniques for improvement

OpenAIRE

Tan-atichat, Taurin Pete

2008-01-01

Thin-client computing offers many advantages over traditional PC computing including lower costs, ubiquitous access to resources, higher security, and easier maintenance. Unfortunately thin clients rely upon the services of other networked computers to properly function. Because of this tight-knit relationship, high- latency environments can render thin clients practically unusable. With the VNC thin-client system, performance can be capped at 1 frame per round-trip time (RTT) due to its clie...

Grass leaves as potential hominin dietary resources.

Science.gov (United States)

Paine, Oliver C C; Koppa, Abigale; Henry, Amanda G; Leichliter, Jennifer N; Codron, Daryl; Codron, Jacqueline; Lambert, Joanna E; Sponheimer, Matt

2018-04-01

Discussions about early hominin diets have generally excluded grass leaves as a staple food resource, despite their ubiquity in most early hominin habitats. In particular, stable carbon isotope studies have shown a prevalent C 4 component in the diets of most taxa, and grass leaves are the single most abundant C 4 resource in African savannas. Grass leaves are typically portrayed as having little nutritional value (e.g., low in protein and high in fiber) for hominins lacking specialized digestive systems. It has also been argued that they present mechanical challenges (i.e., high toughness) for hominins with bunodont dentition. Here, we compare the nutritional and mechanical properties of grass leaves with the plants growing alongside them in African savanna habitats. We also compare grass leaves to the leaves consumed by other hominoids and demonstrate that many, though by no means all, compare favorably with the nutritional and mechanical properties of known primate foods. Our data reveal that grass leaves exhibit tremendous variation and suggest that future reconstructions of hominin dietary ecology take a more nuanced approach when considering grass leaves as a potential hominin dietary resource. Copyright © 2017. Published by Elsevier Ltd.

The impact of visual media to encourage low protein cooking in inherited metabolic disorders.

Science.gov (United States)

Evans, S; Daly, A; Hopkins, V; Davies, P; MacDonald, A

2009-10-01

The use of educational visual aids is one way to help children with inherited metabolic disorders (IMD) understand and develop a positive attitude towards their low protein diet. However, it is difficult to establish their effectiveness in the clinical setting. The present study aimed to evaluate the impact of a low protein recipe book and accompanying DVD for children with IMD. One hundred and five children (53% female; median age = 6-8 years) with IMD on low protein diets were each given a low protein recipe book and DVD. After 6 months, children and carers were posted a questionnaire asking whether they used these resources; identifying any change in frequency of low protein cooking; and the outcome when preparing recipes. One hundred and two questionnaires were returned, representing 105 patients. Seventy percent (n = 71) of questionnaires were from carers. Ninety-three percent (n = 66) of carers acknowledged receipt of the resource; one-third (n = 22) had not watched the DVD and 23% (n = 15) had not opened the recipe book; 55% (n = 36) had tried the recipes; and 71% (n = 47) said the recipe book and/or DVD motivated them to try new recipes. Children were more likely to have watched the DVD (75%; n = 21/28) and read the recipe book (86%; n = 24/28) than carers. Although a helpful educational tool, just over one-half of respondents had used the resource. Identifying visual media that, by itself, will motivate most families of children with IMD to prepare low protein recipes may be unrealistic. The combined approach of visual aids and 'hands-on' practical experience, such as low protein cooking workshops and individual counselling, may be more beneficial.

Protein Circular Dichroism Data Bank (PCDDB): data bank and website design.

Science.gov (United States)

Whitmore, Lee; Janes, Robert W; Wallace, B A

2006-06-01

The Protein Circular Dichroism Data Bank (PCDDB) is a new deposition data bank for validated circular dichroism spectra of biomacromolecules. Its aim is to be a resource for the structural biology and bioinformatics communities, providing open access and archiving facilities for circular dichroism and synchrotron radiation circular dichroism spectra. It is named in parallel with the Protein Data Bank (PDB), a long-existing valuable reference data bank for protein crystal and NMR structures. In this article, we discuss the design of the data bank structure and the deposition website located at http://pcddb.cryst.bbk.ac.uk. Our aim is to produce a flexible and comprehensive archive, which enables user-friendly spectral deposition and searching. In the case of a protein whose crystal structure and sequence are known, the PCDDB entry will be linked to the appropriate PDB and sequence data bank files, respectively. It is anticipated that the PCDDB will provide a readily accessible biophysical catalogue of information on folded proteins that may be of value in structural genomics programs, for quality control and archiving in industrial and academic labs, as a resource for programs developing spectroscopic structural analysis methods, and in bioinformatics studies. Copyright 2006 Wiley-Liss, Inc.

Effects of resource chemistry on the composition and function of stream hyporheic biofilms.

Science.gov (United States)

Hall, E.K.; Besemer, K.; Kohl, L.; Preiler, C.; Reidel, K.; Schneider, T.; Wanek, W.; Battin, T.J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems.

Effects of resource chemistry on the composition and function of hyporheic stream biofilms

Directory of Open Access Journals (Sweden)

Edward eHall

2012-02-01

Full Text Available Stream ecosystems process large quantities of dissolved organic matter as it moves from the headwaters to the sea. Interstitial sediments in the hyporheic zone are centers of high biogeochemical reactivity due to their high levels of microbial biomass and activity. However, the interaction between organic matter and microbial dynamics of these systems remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown interstitial biofilms. Specifically, we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of beta-proteobacter origin. We use this model system to link microbial form, (community composition and proteome, with function, (enzyme activity, in an attempt to develop a better understanding of the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems.

Study on the reaction mechanism of oxygen-added enzymes for the effective utilization of unused sea weeds; Miriyo kaiso no shigenka ni kansuru sanso tenka sanso no hanno kiko ni kansuru kenkyu

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-03-01

To effectively utilize unused sea weeds having ingestion obstructing activities for feed, the treatment by oxygen added enzyme has been investigated. Undaria pinnatifida was pasted and solidified with agar, to prepare the standard feed. Individuals of Holiotis discus hannai Ino were bred in the cistern. Extracts from ten kinds of sea weed distributed in the Sanriku Coast were added to the feed, which were compared with the standard feed to determine the ingestion obstructing activities. A testing method using cellulose painted aluminum sheet was also employed. All of the extracts from sea weeds having the ingestion obstructing activities exhibited the strong phenol reactions. The sensitivity of individuals of Holiotis discus hannai Ino depended greatly on the derived species and the chemical structures of phenolic substances. The {alpha}-hydroxymuconic acid semialdehyde (HMS), an enzyme decomposition product of catechol, provided no ingestion obstructing activity, and showed a little ingestion accelerating activity. This was considered to become ingestible through the biodegradation of phenolic substances. The HMS, a decomposition product of catechol 2,3-oxygen added enzyme derived from the petroleum decomposition bacteria, was prospective as a highly functional compound synthesizing material. 10 refs., 34 figs., 10 tabs.

Construction of ontology augmented networks for protein complex prediction.

Science.gov (United States)

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

2013-01-01

Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

Front Range Infrastructure Resources Project: water-resources activities

Science.gov (United States)

Robson, Stanley G.; Heiny, Janet S.

1998-01-01

Infrastructure, such as roads, buildings, airports, and dams, is built and maintained by use of large quantities of natural resources such as aggregate (sand and gravel), energy, and water. As urban area expand, local sources of these resource are becoming inaccessible (gravel cannot be mined from under a subdivision, for example), or the cost of recovery of the resource becomes prohibitive (oil and gas drilling in urban areas is costly), or the resources may become unfit for some use (pollution of ground water may preclude its use as a water supply). Governmental land-use decision and environmental mandates can further preclude development of natural resources. If infrastructure resources are to remain economically available. current resource information must be available for use in well-reasoned decisions bout future land use. Ground water is an infrastructure resource that is present in shallow aquifers and deeper bedrock aquifers that underlie much of the 2,450-square-mile demonstration area of the Colorado Front Range Infrastructure Resources Project. In 1996, mapping of the area's ground-water resources was undertaken as a U.S. Geological Survey project in cooperation with the Colorado Department of Natural Resources, Division of Water Resources, and the Colorado Water Conservation Board.

A Caenorhabditis elegans Mass Spectrometric Resource for Neuropeptidomics

Science.gov (United States)

Van Bael, Sven; Zels, Sven; Boonen, Kurt; Beets, Isabel; Schoofs, Liliane; Temmerman, Liesbet

2018-05-01

Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies. [Figure not available: see fulltext.

Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions.

Science.gov (United States)

Yamniuk, Aaron P; Newitt, John A; Doyle, Michael L; Arisaka, Fumio; Giannetti, Anthony M; Hensley, Preston; Myszka, David G; Schwarz, Fred P; Thomson, James A; Eisenstein, Edward

2015-12-01

A significant challenge in the molecular interaction field is to accurately determine the stoichiometry and stepwise binding affinity constants for macromolecules having >1 binding site. The mission of the Molecular Interactions Research Group (MIRG) of the Association of Biomolecular Resource Facilities (ABRF) is to show how biophysical technologies are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core technologies [such as biosensor, microcalorimetry, or analytic ultracentrifugation (AUC)]. In the present work, the MIRG has developed a robust model protein interaction pair consisting of a bivalent variant of the Bacillus amyloliquefaciens extracellular RNase barnase and a variant of its natural monovalent intracellular inhibitor protein barstar. It is demonstrated that this system can serve as a benchmarking tool for the quantitative analysis of 2-site protein-protein interactions. The protein interaction pair enables determination of precise binding constants for the barstar protein binding to 2 distinct sites on the bivalent barnase binding partner (termed binase), where the 2 binding sites were engineered to possess affinities that differed by 2 orders of magnitude. Multiple MIRG laboratories characterized the interaction using isothermal titration calorimetry (ITC), AUC, and surface plasmon resonance (SPR) methods to evaluate the feasibility of the system as a benchmarking model. Although general agreement was seen for the binding constants measured using solution-based ITC and AUC approaches, weaker affinity was seen for surface-based method SPR, with protein immobilization likely affecting affinity. An analysis of the results from multiple MIRG laboratories suggests that the bivalent barnase-barstar system is a suitable model for benchmarking new approaches for the quantitative characterization of complex biomolecular interactions.

Text Mining for Protein Docking.

Directory of Open Access Journals (Sweden)

Varsha D Badal

2015-12-01

Full Text Available The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking. Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu. The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound

CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation.

Science.gov (United States)

Thangakani, A Mary; Nagarajan, R; Kumar, Sandeep; Sakthivel, R; Velmurugan, D; Gromiha, M Michael

2016-01-01

Accurate distinction between peptide sequences that can form amyloid-fibrils or amorphous β-aggregates, identification of potential aggregation prone regions in proteins, and prediction of change in aggregation rate of a protein upon mutation(s) are critical to research on protein misfolding diseases, such as Alzheimer's and Parkinson's, as well as biotechnological production of protein based therapeutics. We have developed a Curated Protein Aggregation Database (CPAD), which has collected results from experimental studies performed by scientific community aimed at understanding protein/peptide aggregation. CPAD contains more than 2300 experimentally observed aggregation rates upon mutations in known amyloidogenic proteins. Each entry includes numerical values for the following parameters: change in rate of aggregation as measured by fluorescence intensity or turbidity, name and source of the protein, Uniprot and Protein Data Bank codes, single point as well as multiple mutations, and literature citation. The data in CPAD has been supplemented with five different types of additional information: (i) Amyloid fibril forming hexa-peptides, (ii) Amorphous β-aggregating hexa-peptides, (iii) Amyloid fibril forming peptides of different lengths, (iv) Amyloid fibril forming hexa-peptides whose crystal structures are available in the Protein Data Bank (PDB) and (v) Experimentally validated aggregation prone regions found in amyloidogenic proteins. Furthermore, CPAD is linked to other related databases and resources, such as Uniprot, Protein Data Bank, PUBMED, GAP, TANGO, WALTZ etc. We have set up a web interface with different search and display options so that users have the ability to get the data in multiple ways. CPAD is freely available at http://www.iitm.ac.in/bioinfo/CPAD/. The potential applications of CPAD have also been discussed.

Protein improvement in crop plants

International Nuclear Information System (INIS)

Rabson, R.

1974-01-01

There are compelling reasons for attempting to increase the quality and quantity of protein available in crop plants through plant breeding, despite the fact that some critics have argued that no worldwide protein shortage exists. What used to be thought of as a 'protein gap' has now come to be considered in terms of protein-calorie malnutrition. This is only right since protein and calorie nutrition are inextricable. t the moment there are still unanswered questions as to the precise protein requirements of humans as a function of age, health and ambient conditions. There are, in addition, some indications that the incidence of Kwashiorkor (protein deficiency disease) is increasing in different parts of the world. At a recent meeting of the Protein Advisory Group of the United Nations System, Dr. Jean Mayer, an eminent human nutritionist of Harvard University, U.S.A., indicated the reasons for concern for the current food situation generally, and the protein food supply in particular. These factors include: - Immoderate continuing human population increases, most pronounced in some poor developing countries. - The highly accelerated consumption of animal foods associated with increasing affluence in the richer countries of the world. The production of such foods as meat demands great expenditures of grain, which is an inefficient mode of obtaining the required calories and protein for human consumption. - The over-exploitation of many of the world's fishery resources resulting in reduced yields, perhaps irreversibly, of some fishes. - Recent price increases in petroleum and fertilizer products which have imposed a major obstacle to increasing crop production. - The apparent alteration of climates in places like Africa, Asia and other parts of the Northern hemisphere which may put significant restrictions on crop production. hey are cogent reasons to be seriously concerned about these matters. (author)

Protein improvement in crop plants

Energy Technology Data Exchange (ETDEWEB)

Rabson, R

1974-07-01

There are compelling reasons for attempting to increase the quality and quantity of protein available in crop plants through plant breeding, despite the fact that some critics have argued that no worldwide protein shortage exists. What used to be thought of as a 'protein gap' has now come to be considered in terms of protein-calorie malnutrition. This is only right since protein and calorie nutrition are inextricable. t the moment there are still unanswered questions as to the precise protein requirements of humans as a function of age, health and ambient conditions. There are, in addition, some indications that the incidence of Kwashiorkor (protein deficiency disease) is increasing in different parts of the world. At a recent meeting of the Protein Advisory Group of the United Nations System, Dr. Jean Mayer, an eminent human nutritionist of Harvard University, U.S.A., indicated the reasons for concern for the current food situation generally, and the protein food supply in particular. These factors include: - Immoderate continuing human population increases, most pronounced in some poor developing countries. - The highly accelerated consumption of animal foods associated with increasing affluence in the richer countries of the world. The production of such foods as meat demands great expenditures of grain, which is an inefficient mode of obtaining the required calories and protein for human consumption. - The over-exploitation of many of the world's fishery resources resulting in reduced yields, perhaps irreversibly, of some fishes. - Recent price increases in petroleum and fertilizer products which have imposed a major obstacle to increasing crop production. - The apparent alteration of climates in places like Africa, Asia and other parts of the Northern hemisphere which may put significant restrictions on crop production. hey are cogent reasons to be seriously concerned about these matters. (author)

Spectral affinity in protein networks.

Science.gov (United States)

Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu

2009-11-29

Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length. We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at predicting co-complex membership and finding functionally related proteins than other commonly used measures of closeness. Moreover, our experiments indicate that PageRank Affinity is very resilient to noise in the network. In addition, based on our method we build a tool that quickly finds nodes closest to a queried protein in any protein network, and easily scales to much larger biological networks. We define a meaningful way to assess the closeness of two proteins in a PPI network, and show that our closeness measure is more biologically significant than other commonly used methods. We also develop a tool, accessible at http://xialab.bu.edu/resources/pnns, that allows the user to quickly find nodes closest to a queried vertex in any protein

NovelFam3000 – Uncharacterized human protein domains conserved across model organisms

Science.gov (United States)

Kemmer, Danielle; Podowski, Raf M; Arenillas, David; Lim, Jonathan; Hodges, Emily; Roth, Peggy; Sonnhammer, Erik LL; Höög, Christer; Wasserman, Wyeth W

2006-01-01

Background Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. Description From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. Conclusion Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families. PMID:16533400

NovelFam3000 – Uncharacterized human protein domains conserved across model organisms

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Sonnhammer Erik LL

2006-03-01

Full Text Available Abstract Background Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. Description From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. Conclusion Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families.

Pervasive Adaptive Evolution in Primate Seminal Proteins.

Directory of Open Access Journals (Sweden)

2005-09-01

Full Text Available Seminal fluid proteins show striking effects on reproduction, involving manipulation of female behavior and physiology, mechanisms of sperm competition, and pathogen defense. Strong adaptive pressures are expected for such manifestations of sexual selection and host defense, but the extent of positive selection in seminal fluid proteins from divergent taxa is unknown. We identified adaptive evolution in primate seminal proteins using genomic resources in a tissue-specific study. We found extensive signatures of positive selection when comparing 161 human seminal fluid proteins and 2,858 prostate-expressed genes to those in chimpanzee. Seven of eight outstanding genes yielded statistically significant evidence of positive selection when analyzed in divergent primates. Functional clues were gained through divergent analysis, including several cases of species-specific loss of function in copulatory plug genes, and statistically significant spatial clustering of positively selected sites near the active site of kallikrein 2. This study reveals previously unidentified positive selection in seven primate seminal proteins, and when considered with findings in Drosophila, indicates that extensive positive selection is found in seminal fluid across divergent taxonomic groups.

Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function.

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Naoki Orii

Full Text Available Protein-protein interactions (PPIs are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist databases that are built exclusively to provide PPIs by curating them from published literature. The information provided in these web resources is protein-centric, and not PPI-centric. The PPIs are typically provided as lists of interactions of a given gene with links to interacting partners; they do not present a comprehensive view of the nature of both the proteins involved in the interactions. A web database that allows search and retrieval based on biomedical characteristics of PPIs is lacking, and is needed. We present Wiki-Pi (read Wiki-π, a web-based interface to a database of human PPIs, which allows users to retrieve interactions by their biomedical attributes such as their association to diseases, pathways, drugs and biological functions. Each retrieved PPI is shown with annotations of both of the participant proteins side-by-side, creating a basis to hypothesize the biological function facilitated by the interaction. Conceptually, it is a search engine for PPIs analogous to PubMed for scientific literature. Its usefulness in generating novel scientific hypotheses is demonstrated through the study of IGSF21, a little-known gene that was recently identified to be associated with diabetic retinopathy. Using Wiki-Pi, we infer that its association to diabetic retinopathy may be mediated through its interactions with the genes HSPB1, KRAS, TMSB4X and DGKD, and that it may be involved in cellular response to external stimuli, cytoskeletal organization and regulation of molecular activity. The website also provides a wiki-like capability allowing users

HIP2: An online database of human plasma proteins from healthy individuals

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Shen Changyu

2008-04-01

Full Text Available Abstract Background With the introduction of increasingly powerful mass spectrometry (MS techniques for clinical research, several recent large-scale MS proteomics studies have sought to characterize the entire human plasma proteome with a general objective for identifying thousands of proteins leaked from tissues in the circulating blood. Understanding the basic constituents, diversity, and variability of the human plasma proteome is essential to the development of sensitive molecular diagnosis and treatment monitoring solutions for future biomedical applications. Biomedical researchers today, however, do not have an integrated online resource in which they can search for plasma proteins collected from different mass spectrometry platforms, experimental protocols, and search software for healthy individuals. The lack of such a resource for comparisons has made it difficult to interpret proteomics profile changes in patients' plasma and to design protein biomarker discovery experiments. Description To aid future protein biomarker studies of disease and health from human plasma, we developed an online database, HIP2 (Healthy Human Individual's Integrated Plasma Proteome. The current version contains 12,787 protein entries linked to 86,831 peptide entries identified using different MS platforms. Conclusion This web-based database will be useful to biomedical researchers involved in biomarker discovery research. This database has been developed to be the comprehensive collection of healthy human plasma proteins, and has protein data captured in a relational database schema built to contain mappings of supporting peptide evidence from several high-quality and high-throughput mass-spectrometry (MS experimental data sets. Users can search for plasma protein/peptide annotations, peptide/protein alignments, and experimental/sample conditions with options for filter-based retrieval to achieve greater analytical power for discovery and validation.

Twister Protein: a ludic tool involving protein synthesis

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Aline Weyh

2015-07-01

Full Text Available Several studies show that students of various grade levels report the Genetics as an abstract theme and difficult to assimilate by the students, with multiple problems in the teaching-learning process and becoming necessary the development of auxiliary practices. Among the teaching tools, the game is the most currently opted playful activity by stimulating multiple intelligences, allowing greater student-teacher interaction. This work seeks the production of an innovative and dynamic educational game, Twister Protein, as a pedagogical resource for Genetics discipline. The development of the game was based on the use of easily accessible and low cost materials by teachers, allowing the knowledge of transcription, translation and protein folding. The activity was proposed and applied in the classroom with pilot undergraduate students. The fun associated with the knowledge of science not only allowed a better memorization of the content addressed, as aroused the curiosity, theme reflection, character building and collaborative spirits, as well as competitiveness through the interaction between class. This practice proved to be an effective tool in the escape from routine and fault repair of the theoretical process.

PPI-IRO: A two-stage method for protein-protein interaction extraction based on interaction relation ontology

KAUST Repository

Li, Chuanxi

2014-01-01

Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identifi cation of biological regulatory networks. This paper presents a novel method based on the idea of Interaction Relation Ontology (IRO), which specifi es and organises words of various proteins interaction relationships. Our method is a two-stage PPI extraction method. At fi rst, IRO is applied in a binary classifi er to determine whether sentences contain a relation or not. Then, IRO is taken to guide PPI extraction by building sentence dependency parse tree. Comprehensive and quantitative evaluations and detailed analyses are used to demonstrate the signifi cant performance of IRO on relation sentences classifi cation and PPI extraction. Our PPI extraction method yielded a recall of around 80% and 90% and an F1 of around 54% and 66% on corpora of AIMed and Bioinfer, respectively, which are superior to most existing extraction methods. Copyright © 2014 Inderscience Enterprises Ltd.

Unmet Needs and Unused Capacities: Time Banking as a Solution

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Neva Goodwin

2018-02-01

Full Text Available In market economies many human activities have little or no money value; these include, especially, the kinds of caring labor that are supplied, mostly by women, mostly in homes and communities. Nevertheless, there is, as ever, a great need for such activities. At the same time, wealthy societies are producing ever more people who suffer from feeling that they have little or nothing of value to offer to the world. Retired people, in their growing numbers, are the most obvious examples, but teenagers and other youth, who in other societies can contribute significantly to the well-being of a family or a community, are seldom seen as assets in modern economies. Market-dominated societies have had difficulty expressing the value of work that is not organized for profit. Such work is undertaken in the public purpose economy, consisting of governments and their agencies as well as non-profit organizations. Much of this kind of work is also undertaken in the core economy, where households and communities carry on their internal activities of resource management, production, distribution, and consumption. The core economy and the public purpose economy, together with the market economy, are a trio that are differentiated by their goals; by what kind of demand they respond to; by how they define and reward work; and by what kind of currency they use. TimeBanking is an innovation in currency that turns out to affect all of these areas by getting us out of the binary box that classifies all contributions in just two ways: work (defined in market terms, or volunteering (defined as uncompensated labor. Responding effectively to different values and goals than those recognized in the market, TimeBanking has been shown able to respond to a wide variety of unmet needs by creating relationships where everyone can get some of their needs met, and everyone is valued for what they can offer.  

EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases.

Science.gov (United States)

Wang, Yongbo; Liu, Zexian; Cheng, Han; Gao, Tianshun; Pan, Zhicheng; Yang, Qing; Guo, Anyuan; Xue, Yu

2014-01-01

We present here EKPD (http://ekpd.biocuckoo.org), a hierarchical database of eukaryotic protein kinases (PKs) and protein phosphatases (PPs), the key molecules responsible for the reversible phosphorylation of proteins that are involved in almost all aspects of biological processes. As extensive experimental and computational efforts have been carried out to identify PKs and PPs, an integrative resource with detailed classification and annotation information would be of great value for both experimentalists and computational biologists. In this work, we first collected 1855 PKs and 347 PPs from the scientific literature and various public databases. Based on previously established rationales, we classified all of the known PKs and PPs into a hierarchical structure with three levels, i.e. group, family and individual PK/PP. There are 10 groups with 149 families for the PKs and 10 groups with 33 families for the PPs. We constructed 139 and 27 Hidden Markov Model profiles for PK and PP families, respectively. Then we systematically characterized ∼50,000 PKs and >10,000 PPs in eukaryotes. In addition, >500 PKs and >400 PPs were computationally identified by ortholog search. Finally, the online service of the EKPD database was implemented in PHP + MySQL + JavaScript.

SwissPalm: Protein Palmitoylation database.

Science.gov (United States)

Blanc, Mathieu; David, Fabrice; Abrami, Laurence; Migliozzi, Daniel; Armand, Florence; Bürgi, Jérôme; van der Goot, Françoise Gisou

2015-01-01

Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm ( http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

[Process of land use transition and its impact on regional ecological quality in the Middle Reaches of Heihe River, China].

Science.gov (United States)

Wang, Fu Hong; Zhao, Rui Feng; Zhang, Li Hua; Li, Hong Wei

2017-12-01

Land use transition is one of the main drivers of regional ecosystem change in arid area, which directly affects human well-being. Based on the satellite images of 1987, 2001 and 2016, the change detection assessment model and ecological response model were used to analyze the process of land use transition and response of ecological quality during 1987-2016 in the ecologically fragile middle reaches of the Heihe River. The results showed that the land use change was significant during 1987-2016 and the total change increased significantly, as well as the continuous increase of the cultivated land and construction land. There was a strong tendency of transform from grassland to cultivated land, while the tendency of transforming unused land to other land classes was not strong under a random process of gain or loss. During 1987-2016, the ecological quality of the study area displayed a decreasing trend as a whole and the ecological land decreased by 2.8%. The land use transition with the greatest impact on the ecological environment degradation was the transition of the grassland to the cultivated land and unused land. Therefore, in order to promote the sustainable use of regional land resources and to improve the regional ecological quality, it is necessary to allocate the proportion of production land and ecological land according to the regional water resources.

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

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Shane Ó Conchúir

Full Text Available The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

Resource programs: Draft Environmental Impact Statement Resource Programs

International Nuclear Information System (INIS)

1992-03-01

Every two years, Bonneville Power Administration (BPA) prepares a Resource Program which identifies the resource actions BPA will take to meet its obligation to serve the forecasted power requirements of its customers. The Resource Program's Environmental Impact Statement (RPEIS) is a programmatic environmental document which will support decisions made in several future Resource Programs. Environmental documents tiered to the EIS may be prepared on a site-specific basis. The RPEIS includes a description of the environmental effects and mitigation for the various resource types available in order to evaluate the trade-offs among them. It also assesses the environmental impacts of adding thirteen alternative combinations of resources to the existing power system. This report contains the appendices to the RPEIS

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

Science.gov (United States)

López, Yosvany; Nakai, Kenta; Patil, Ashwini

2015-01-01

HitPredict is a consolidated resource of experimentally identified, physical protein-protein interactions with confidence scores to indicate their reliability. The study of genes and their inter-relationships using methods such as network and pathway analysis requires high quality protein-protein interaction information. Extracting reliable interactions from most of the existing databases is challenging because they either contain only a subset of the available interactions, or a mixture of physical, genetic and predicted interactions. Automated integration of interactions is further complicated by varying levels of accuracy of database content and lack of adherence to standard formats. To address these issues, the latest version of HitPredict provides a manually curated dataset of 398 696 physical associations between 70 808 proteins from 105 species. Manual confirmation was used to resolve all issues encountered during data integration. For improved reliability assessment, this version combines a new score derived from the experimental information of the interactions with the original score based on the features of the interacting proteins. The combined interaction score performs better than either of the individual scores in HitPredict as well as the reliability score of another similar database. HitPredict provides a web interface to search proteins and visualize their interactions, and the data can be downloaded for offline analysis. Data usability has been enhanced by mapping protein identifiers across multiple reference databases. Thus, the latest version of HitPredict provides a significantly larger, more reliable and usable dataset of protein-protein interactions from several species for the study of gene groups. Database URL: http://hintdb.hgc.jp/htp. © The Author(s) 2015. Published by Oxford University Press.

The OSG Open Facility: an on-ramp for opportunistic scientific computing

Science.gov (United States)

Jayatilaka, B.; Levshina, T.; Sehgal, C.; Gardner, R.; Rynge, M.; Würthwein, F.

2017-10-01

The Open Science Grid (OSG) is a large, robust computing grid that started primarily as a collection of sites associated with large HEP experiments such as ATLAS, CDF, CMS, and DZero, but has evolved in recent years to a much larger user and resource platform. In addition to meeting the US LHC community’s computational needs, the OSG continues to be one of the largest providers of distributed high-throughput computing (DHTC) to researchers from a wide variety of disciplines via the OSG Open Facility. The Open Facility consists of OSG resources that are available opportunistically to users other than resource owners and their collaborators. In the past two years, the Open Facility has doubled its annual throughput to over 200 million wall hours. More than half of these resources are used by over 100 individual researchers from over 60 institutions in fields such as biology, medicine, math, economics, and many others. Over 10% of these individual users utilized in excess of 1 million computational hours each in the past year. The largest source of these cycles is temporary unused capacity at institutions affiliated with US LHC computational sites. An increasing fraction, however, comes from university HPC clusters and large national infrastructure supercomputers offering unused capacity. Such expansions have allowed the OSG to provide ample computational resources to both individual researchers and small groups as well as sizable international science collaborations such as LIGO, AMS, IceCube, and sPHENIX. Opening up access to the Fermilab FabrIc for Frontier Experiments (FIFE) project has also allowed experiments such as mu2e and NOvA to make substantial use of Open Facility resources, the former with over 40 million wall hours in a year. We present how this expansion was accomplished as well as future plans for keeping the OSG Open Facility at the forefront of enabling scientific research by way of DHTC.

The OSG Open Facility: An On-Ramp for Opportunistic Scientific Computing

Energy Technology Data Exchange (ETDEWEB)

Jayatilaka, B. [Fermilab; Levshina, T. [Fermilab; Sehgal, C. [Fermilab; Gardner, R. [Chicago U.; Rynge, M. [USC - ISI, Marina del Rey; Würthwein, F. [UC, San Diego

2017-11-22

The Open Science Grid (OSG) is a large, robust computing grid that started primarily as a collection of sites associated with large HEP experiments such as ATLAS, CDF, CMS, and DZero, but has evolved in recent years to a much larger user and resource platform. In addition to meeting the US LHC community’s computational needs, the OSG continues to be one of the largest providers of distributed high-throughput computing (DHTC) to researchers from a wide variety of disciplines via the OSG Open Facility. The Open Facility consists of OSG resources that are available opportunistically to users other than resource owners and their collaborators. In the past two years, the Open Facility has doubled its annual throughput to over 200 million wall hours. More than half of these resources are used by over 100 individual researchers from over 60 institutions in fields such as biology, medicine, math, economics, and many others. Over 10% of these individual users utilized in excess of 1 million computational hours each in the past year. The largest source of these cycles is temporary unused capacity at institutions affiliated with US LHC computational sites. An increasing fraction, however, comes from university HPC clusters and large national infrastructure supercomputers offering unused capacity. Such expansions have allowed the OSG to provide ample computational resources to both individual researchers and small groups as well as sizable international science collaborations such as LIGO, AMS, IceCube, and sPHENIX. Opening up access to the Fermilab FabrIc for Frontier Experiments (FIFE) project has also allowed experiments such as mu2e and NOvA to make substantial use of Open Facility resources, the former with over 40 million wall hours in a year. We present how this expansion was accomplished as well as future plans for keeping the OSG Open Facility at the forefront of enabling scientific research by way of DHTC.

Developmental environment mediates male seminal protein investment in Drosophila melanogaster.

Science.gov (United States)

Wigby, Stuart; Perry, Jennifer C; Kim, Yon-Hee; Sirot, Laura K

2016-03-01

Males of many species fine-tune their ejaculates in response to sperm competition risk. Resource availability and the number of competitors during development can also strongly influence sperm production. However, despite the key role of seminal proteins in mediating reproductive processes, it is unclear whether seminal protein investment is dependent on the developmental environment.We manipulated the developmental environment of Drosophila melanogaster by rearing flies at low and high density. As expected, this resulted in large and small (i.e. high and low condition) adult phenotypes, respectively.As predicted, large males produced more of two key seminal proteins, sex peptide (SP) and ovulin, and were more successful at obtaining matings with both virgin and previously mated females. However, there was only a weak and non-significant trend for large males to transfer more absolute quantities of SP at mating, and thus, small males ejaculated proportionally more of their stored accessory gland SP resources.Males transferred more receptivity-inhibiting SP to large females. Despite this, large females remated more quickly than small females and thus responded to their developmental environment over and above the quantity of SP they received.The results are consistent with two non-mutually exclusive hypotheses. First, flies might respond to condition-dependent reproductive opportunities, with (i) small males investing heavily in ejaculates when mating opportunities arise and large males strategically partitioning SP resources and (ii) small females remating at reduced rates because they have higher mating costs or need to replenish sperm less often.Second, flies may be primed by their larval environment to deal with similar adult population densities, with (i) males perceiving high density as signalling increased competition, leading small males to invest proportionally more SP resources at mating and (ii) females perceiving high density as signalling abundant

genenames.org: the HGNC resources in 2011

Science.gov (United States)

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

Environmental Programs: Status of Work and Current Priorities for FY13

Energy Technology Data Exchange (ETDEWEB)

Jones, Patricia [Los Alamos National Laboratory

2012-08-17

Presentation outline is: Mission/overview, Regulatory framework, Current status of cleanup, Shift in priorities to address highest risk, Removal of above-ground waste, Continued focus on protecting water resources, and Priorities for fiscal year 2013. LANL's Environmental Mission is to: (1) Repack and ship legacy transuranic waste containers; (2) Investigate and remediate Cold War (legacy) hazardous and radioactive waste areas; (3) Demolish unused buildings; (4) Disposition solid waste from Laboratory operations; and (5) Lifecycle cost nearly $3 billion.

Protein Expression Landscape of Mouse Embryos during Pre-implantation Development

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Yawei Gao

2017-12-01

Full Text Available Pre-implantation embryo development is an intricate and precisely regulated process orchestrated by maternally inherited proteins and newly synthesized proteins following zygotic genome activation. Although genomic and transcriptomic studies have enriched our understanding of the genetic programs underlying this process, the protein expression landscape remains unexplored. Using quantitative mass spectrometry, we identified nearly 5,000 proteins from 8,000 mouse embryos of each stage (zygote, 2-cell, 4-cell, 8-cell, morula, and blastocyst. We found that protein expression in zygotes, morulas, and blastocysts is distinct from 2- to 8-cell embryos. Analysis of protein phosphorylation identified critical kinases and signal transduction pathways. We highlight key factors and their important roles in embryo development. Combined analysis of transcriptomic and proteomic data reveals coordinated control of RNA degradation, transcription, and translation and identifies previously undefined exon-junction-derived peptides. Our study provides an invaluable resource for further mechanistic studies and suggests core factors regulating pre-implantation embryo development.

The Pacific Ocean virome (POV: a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.

Directory of Open Access Journals (Sweden)

Bonnie L Hurwitz

Full Text Available Bacteria and their viruses (phage are fundamental drivers of many ecosystem processes including global biogeochemistry and horizontal gene transfer. While databases and resources for studying function in uncultured bacterial communities are relatively advanced, many fewer exist for their viral counterparts. The issue is largely technical in that the majority (often 90% of viral sequences are functionally 'unknown' making viruses a virtually untapped resource of functional and physiological information. Here, we provide a community resource that organizes this unknown sequence space into 27 K high confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacific Ocean that vary by season, depth, and proximity to land, and include some of the first deep pelagic ocean viral metagenomes. These protein clusters more than double currently available viral protein clusters, including those from environmental datasets. Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i from deep to surface waters, (ii from winter to summer, (iii and with distance from shore in surface waters only. These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.

The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.

Science.gov (United States)

Hurwitz, Bonnie L; Sullivan, Matthew B

2013-01-01

Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes including global biogeochemistry and horizontal gene transfer. While databases and resources for studying function in uncultured bacterial communities are relatively advanced, many fewer exist for their viral counterparts. The issue is largely technical in that the majority (often 90%) of viral sequences are functionally 'unknown' making viruses a virtually untapped resource of functional and physiological information. Here, we provide a community resource that organizes this unknown sequence space into 27 K high confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacific Ocean that vary by season, depth, and proximity to land, and include some of the first deep pelagic ocean viral metagenomes. These protein clusters more than double currently available viral protein clusters, including those from environmental datasets. Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only. These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.

Herpes - resources

Science.gov (United States)

Genital herpes - resources; Resources - genital herpes ... following organizations are good resources for information on genital herpes : March of Dimes -- www.marchofdimes.org/complications/sexually- ...

Spectral affinity in protein networks

Directory of Open Access Journals (Sweden)

Teng Shang-Hua

2009-11-01

Full Text Available Abstract Background Protein-protein interaction (PPI networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length. Results We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at predicting co-complex membership and finding functionally related proteins than other commonly used measures of closeness. Moreover, our experiments indicate that PageRank Affinity is very resilient to noise in the network. In addition, based on our method we build a tool that quickly finds nodes closest to a queried protein in any protein network, and easily scales to much larger biological networks. Conclusion We define a meaningful way to assess the closeness of two proteins in a PPI network, and show that our closeness measure is more biologically significant than other commonly used methods. We also develop a tool, accessible at http://xialab.bu.edu/resources/pnns, that allows the user to

Hospital Resource Utilisation by Patients with Community-Acquired Pneumonia

LENUS (Irish Health Repository)

McCarthy, S

2017-09-01

Little data is available on the resource utilisation of patients admitted with Community-Acquired Pneumonia (CAP) in Ireland. A retrospective review of 50 randomly-selected patients admitted to Beaumont Hospital with CAP was undertaken. The mean length of stay of patients with CAP was 12 days (+\\/- 16 days). All patients were emergency admissions, all had a chest x-ray, a C-reactive protein blood test, and occupied a public bed at some point during admission. Common antimicrobial therapies were intravenous (IV) amoxicillin\\/clavulanic acid and oral clarithromycin; 60% received physiotherapy. The estimated mean cost of CAP per patient was €14,802.17. Costs arising from admission to hospital with CAP are substantial, but efforts can be undertaken to ensure that resources are used efficiently to improve patient care such as discharge planning and fewer in-hospital ward transfers

HCVpro: Hepatitis C virus protein interaction database

KAUST Repository

Kwofie, Samuel K.

2011-12-01

It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.

Fiscal 1999 research cooperation project. Research cooperation on community-oriented practical photovoltaic power systems (Practical methane gas fermentation fuel cell power systems); 1999 nendo metan hakko gas nenryo denchi hatsuden system no jitsuyoka ni kansuru kenkyu kyoryoku

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

This report describes the research cooperation with developing countries on practical methane gas fermentation fuel cell power systems in 1999-2002. This research aims to construct the methane gas fermentation fuel cell power facility using livestock excreta which can supply power to the facility and peripheral areas. The facility controls various substance concentrations in waste water within environmental standards, and uses waste as compost. This project is very promising in use of environment-friendly energy, effective use of unused energy and power supply to unelectrified areas for China under serious conditions such as rapid increase in energy demand and various environment problems. There are such various issues to achieve this target as securing livestock (pig breeders) and excreta, and fermentation and recovery of suitable methane gas necessary for fuel cell power systems from excreta. This report is composed of 2 parts, (1) Current use of energy resources and use of unused energy in Guangdong province, and (2) Technical requirements for practical methane gas fermentation fuel cell power systems. (NEDO)

Geological evaluation on productibility of coal seam gas; Coal seam gas no chishitsugakuteki shigen hyoka ni tsuite

Energy Technology Data Exchange (ETDEWEB)

Fujii, K [University of Shizuoka, Shizuoka (Japan). Faculty of Education

1996-09-01

Coal seam gas is also called coal bed methane gas, indicating the gas existing in coal beds. The gas is distinguished from the oil field based gas, and also called non-conventional type gas. Its confirmed reserve is estimated to be 24 trillion m {sup 3}, with the trend of its development seen worldwide as utilization of unused resource. For the necessity of cultivating relevant technologies in Japan, this paper considers processes of production, movement, stockpiling, and accumulation of the gas. Its productibility is controlled by thickness of a coal bed, degree of coalification, gas content, permeability, groundwater flow, and deposition structure. Gas generation potential is evaluated by existing conditions of coal and degree of coalification, and methane production by biological origin and thermal origin. Economically viable methane gas is mainly of the latter origin. Evaluating gas reserve potential requires identification of the whole mechanism of adsorption, accumulation and movement of methane gas. The gas is expected of effect on environmental aspects in addition to availability as utilization of unused energy. 5 figs.

Future Oceans: Meeting the Challenges of Securing Aquatic Food Resources

OpenAIRE

Dieckmann, U.

2012-01-01

Seafood is the primary source of animal protein for more than one billion people. Many economies and communities, in particular those in developing nations and coastal regions, depend on fisheries. Whereas the dire effects of overfishing on open-access ocean fisheries are already recognized, impacts of catches on freshwater systems are still underestimated. IIASA’s fisheries research elucidates how to secure and expand aquatic food resources, emphasizing three topical challenges. First, impro...

Ontology driven framework for multimedia information retrieval in P2P network

CERN Document Server

Sokhn, Maria

During the last decade we have witnessed an exponential growth of digital documents and multimedia resources, including a vast amount of video resources. Videos are becoming one of the most popular media thanks to the rich audio, visual and textual content they may convey. The recent technological advances have made this large amount of multimedia resources available to users in a variety of areas, including the academic and scientific realms. However, without adequate techniques for effective content based multimedia retrieval, this large and valuable body of data is barely accessible and remains in effect unusable. This thesis explores semantic approaches to content based management browsing and visualization of the multimedia resources generated for and during scientific conferences. Indeed, a so-called semantic gap exists between the explicit knowledge representation required by users who search the multimedia resources and the implicit knowledge conveyed within a conference life cycle. The aim of this wo...

Reciprocal Relationships between Job Resources, Personal Resources, and Work Engagement

Science.gov (United States)

Xanthopoulou, Despoina; Bakker, Arnold B.; Demerouti, Evangelia; Schaufeli, Wilmar B.

2009-01-01

This study examined longitudinal relationships between job resources, personal resources, and work engagement. On the basis of Conservation of Resources theory, we hypothesized that job resources, personal resources, and work engagement are reciprocal over time. The study was conducted among 163 employees, who were followed-up over a period of 18…

Nutrition, modernity and the archaeological record: coastal resources and nutrition among Middle Stone Age hunter-gatherers on the Western Cape coast of South Africa.

Science.gov (United States)

Kyriacou, Katharine; Parkington, John E; Marais, Adrian D; Braun, David R

2014-12-01

In this paper, we assess the nutritional value of some marine and terrestrial food resources available to Middle Stone Age hunter-gatherers in the Western Cape of South Africa with respect to an important macronutrient (protein) and an essential micronutrient (iron) and introduce a framework for assessing the relative utility of marine and terrestrial resources. Whilst the ability to extract nutrients from the environment has always been a lynchpin in archaeologists' reconstructions of human evolution, a recent paradigm shift has recognized the role of marine resources in encephalization. Nutritional research indicates that marine ecosystems are the best source for long chain polyunsaturated fatty acids essential for proper brain development, and excavations at securely dated archaeological sites in South Africa provide firm evidence for the exploitation of marine resources by Middle Stone Age hunter-gatherers from at least Marine Isotope Stage 5 (130 ka), and possibly even earlier. Because marine molluscs are abundant, predictably located and easily harvested, they would have been readily available to all members of the community, in contrast to terrestrial resources. The improving archaeological record gives important clues to resource choice, but many more nutritional observations are needed to determine the extent to which marine resources could have met the nutrient requirements of prehistoric people. Our observations indicate that marine and terrestrial fauna are both excellent sources of protein, and that marine molluscs have higher iron concentrations than we expected for invertebrate fauna. We calculate the number of individual food items from a selection of marine and terrestrial species needed to provide the protein and iron requirements of a hypothetical group of hunter-gatherers, identify contrasts in peoples' requirements for and access to nutrients and resources, and discuss the implications for prehistoric subsistence strategies and human evolution

There is still unused capacity

Energy Technology Data Exchange (ETDEWEB)

Yurov, V D

1986-06-01

This report lists some areas where there is potential for higher coal output in Vorkutaugol' association mines. This association is highly mechanized (98% of coal mining and 90% of mine drivage work); in the 1970s coal losses were 600,000 t/a, whereas in 1985 they were only 90,000 t. The coal extraction coefficient for 1985 was 87% (second only to the Gukovugol' association in the USSR). Nevertheless stoppages owing to infringements of safety regulations cost over 1.5 million t of coal output during 1981-1985; the level of occupational injuries is high; about 14% of all mine roadways is in an unsatisfactory state; ventilation is inadequate in some mines (7500 m/sup 3//min deficit at the Vorgashorskaya mine); not enough attention is given to the use of more productive equipment, or to the use of equipment in more productive ways; coal preparation plants write off unnecessary losses of 100-150,000 t/a; and coal pillars could be extracted using modern technology (PK-3R machines). Financial incentives for mines and miners need revision to encourage more productive approaches.

Reclaiming unused IPv4 addresses

CERN Multimedia

IT Department

2016-01-01

As many people might know, the number of IPv4 addresses is limited and almost all have been allocated (see here and here for more information).   Although CERN has been allocated some 340,000 addresses, the way these are allocated across the site is not as efficient as we would like. As we face an increasing demand for IPv4 addresses with the growth in virtual machines, the IT Department’s Communication Systems Group will be reorganising address allocation during 2016 to make more efficient use of the IPv4 address ranges that have been allocated to CERN. We aim, wherever possible, to avoid giving out fixed IP addresses, and have all devices connected to the campus network obtain an address dynamically each time they connect. As a first stage, starting in February, IP addresses that have not been used for more than 9 months will be reclaimed. No information about the devices concerned will be deleted from LANDB, but a new IP address will have to be requested if they are ever reconnected to t...

Resource acquisition policy: Multiple account evaluation of electricity resource alternatives [and] resource acquisition strategy

International Nuclear Information System (INIS)

1994-06-01

British Columbia Hydro has been directed by the provincial government to develop evaluation procedures to rank electricity resource alternatives in terms of their social benefits and costs, and to acquire resources on the basis of need. The current state of development of social costing at BC Hydro is detailed along with its application to the multiple account evaluation of resources. In this evaluation, BC Hydro's corporate costs, customer cost, transfer payments to the province, direct costs incurred by provincial or regional governments or other Crown agences, direct environmental impact costs from air emissions and land/water use, community and social impact costs, and economic development impacts are taken into account. The BC Hydro resource acquisition strategy is also described as it was developed in response to provincial policy on electricity supply from independent power producers. This strategy includes a determination of need, a decision to acquire need-determined resources either by itself or from a private sector developer, and decisions to acquire resources in advance of need for reasons such as economic opportunity, long-term strategies, or load displacement. Background information is included on calculation of air emissions costs. An illustrative example is provided of the multiple account evaluation of several types of resource projects. 1 fig., 5 tabs

Australian uranium resources

International Nuclear Information System (INIS)

Battey, G.C.; Miezitis, Y.; McKay, A.D.

1987-01-01

Australia's uranium resources amount to 29% of the WOCA countries (world outside centrally-planned-economies areas) low-cost Reasonably Assured Resources and 28% of the WOCA countries low-cost Estimated Additional Resources. As at 1 January 1986, the Bureau of Mineral Resources estimated Australia's uranium resources as: (1) Cost range to US$80/kg U -Reasonably Assured Resources, 465 000 t U; Estimated Additional Resources, 256 000 t U; (2) Cost range US$80-130/kg U -Reasonably Assured Resources, 56 000 t U; Estimated Additional Resources, 127 000 t U. Most resources are contained in Proterozoic unconformity-related deposits in the Alligator Rivers uranium field in the Northern Territory (Jabiluka, Ranger, Koongarra, Nabarlek deposits) and the Proterozoic stratabound deposit at Olympic Dam on the Stuart Shelf in South Australia

Resource Recovery from Wastewater by Biological Technologies: Opportunities, Challenges, and Prospects

Science.gov (United States)

Puyol, Daniel; Batstone, Damien J.; Hülsen, Tim; Astals, Sergi; Peces, Miriam; Krömer, Jens O.

2017-01-01

Limits in resource availability are driving a change in current societal production systems, changing the focus from residues treatment, such as wastewater treatment, toward resource recovery. Biotechnological processes offer an economic and versatile way to concentrate and transform resources from waste/wastewater into valuable products, which is a prerequisite for the technological development of a cradle-to-cradle bio-based economy. This review identifies emerging technologies that enable resource recovery across the wastewater treatment cycle. As such, bioenergy in the form of biohydrogen (by photo and dark fermentation processes) and biogas (during anaerobic digestion processes) have been classic targets, whereby, direct transformation of lipidic biomass into biodiesel also gained attention. This concept is similar to previous biofuel concepts, but more sustainable, as third generation biofuels and other resources can be produced from waste biomass. The production of high value biopolymers (e.g., for bioplastics manufacturing) from organic acids, hydrogen, and methane is another option for carbon recovery. The recovery of carbon and nutrients can be achieved by organic fertilizer production, or single cell protein generation (depending on the source) which may be utilized as feed, feed additives, next generation fertilizers, or even as probiotics. Additionlly, chemical oxidation-reduction and bioelectrochemical systems can recover inorganics or synthesize organic products beyond the natural microbial metabolism. Anticipating the next generation of wastewater treatment plants driven by biological recovery technologies, this review is focused on the generation and re-synthesis of energetic resources and key resources to be recycled as raw materials in a cradle-to-cradle economy concept. PMID:28111567

The BioLexicon: a large-scale terminological resource for biomedical text mining

Directory of Open Access Journals (Sweden)

Thompson Paul

2011-10-01

Full Text Available Abstract Background Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events. Results This article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is

The BioLexicon: a large-scale terminological resource for biomedical text mining

Science.gov (United States)

2011-01-01

Background Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events) involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events. Results This article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized) together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is modelled using the Lexical

Research Resource: A Dual Proteomic Approach Identifies Regulated Islet Proteins During β-Cell Mass Expansion In Vivo

DEFF Research Database (Denmark)

Horn, Signe; Kirkegaard, Jeannette S.; Hoelper, Soraya

2016-01-01

to be up regulated as a response to pregnancy. These included several proteins, not previously associated with pregnancy-induced islet expansion, such as CLIC1, STMN1, MCM6, PPIB, NEDD4, and HLTF. Confirming the validity of our approach, we also identified proteins encoded by genes known to be associated...

Resource and energy recovery options for fermentation industry residuals

Energy Technology Data Exchange (ETDEWEB)

Chiesa, S C [Santa Clara Univ., CA (USA); Manning, Jr, J F [Alabama Univ., Birmingham, AL (USA)

1989-01-01

Over the last 40 years, the fermentation industry has provided facility planners, plant operators and environmental engineers with a wide range of residuals management challenges and resource/energy recovery opportunities. In response, the industry has helped pioneer the use of a number of innovative resource and energy recovery technologies. Production of animal feed supplements, composts, fertilizers, soil amendments, commercial baking additives and microbial protein materials have all been detailed in the literature. In many such cases, recovery of by-products significantly reduces the need for treatment and disposal facilities. Stable, reliable anaerobic biological treatment processes have also been developed to recover significant amounts of energy in the form of methane gas. Alternatively, dewatered or condensed organic fermentation industry residuals have been used as fuels for incineration-based energy recovery systems. The sale or use of recovered by-products and/or energy can be used to offset required processing costs and provide a technically and environmentally viable alternative to traditional treatment and disposal strategies. This review examines resource recovery options currently used or proposed for fermentation industry residuals and the conditions necessary for their successful application. (author).

Resources and Resourcefulness in Language Teaching and Learning

African Journals Online (AJOL)

Attempts will be made in this paper to examine what we mean by language, language teaching and learning, resources and resourcefulness in language teaching and learning and the benefit of teachers being resourceful in language teaching and learning to both the learners, the teachers, the society and the nation at ...

THPdb: Database of FDA-approved peptide and protein therapeutics.

Directory of Open Access Journals (Sweden)

Salman Sadullah Usmani

Full Text Available THPdb (http://crdd.osdd.net/raghava/thpdb/ is a manually curated repository of Food and Drug Administration (FDA approved therapeutic peptides and proteins. The information in THPdb has been compiled from 985 research publications, 70 patents and other resources like DrugBank. The current version of the database holds a total of 852 entries, providing comprehensive information on 239 US-FDA approved therapeutic peptides and proteins and their 380 drug variants. The information on each peptide and protein includes their sequences, chemical properties, composition, disease area, mode of activity, physical appearance, category or pharmacological class, pharmacodynamics, route of administration, toxicity, target of activity, etc. In addition, we have annotated the structure of most of the protein and peptides. A number of user-friendly tools have been integrated to facilitate easy browsing and data analysis. To assist scientific community, a web interface and mobile App have also been developed.

Single-particle tracking of quantum dot-conjugated prion proteins inside yeast cells

Energy Technology Data Exchange (ETDEWEB)

Tsuji, Toshikazu; Kawai-Noma, Shigeko [Department of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, B56, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501 (Japan); Pack, Chan-Gi [Cellular Informatics Laboratory, RIKEN Advanced Science Institute, Wako-shi, Saitama 351-0198 (Japan); Terajima, Hideki [Department of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, B56, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501 (Japan); Yajima, Junichiro; Nishizaka, Takayuki [Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588 (Japan); Kinjo, Masataka [Laboratory of Molecular Cell Dynamics, Graduate School of Life Sciences, Hokkaido University, Sapporo 001-0021 (Japan); Taguchi, Hideki, E-mail: taguchi@bio.titech.ac.jp [Department of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, B56, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501 (Japan)

2011-02-25

Research highlights: {yields} We develop a method to track a quantum dot-conjugated protein in yeast cells. {yields} We incorporate the conjugated quantum dot proteins into yeast spheroplasts. {yields} We track the motions by conventional or 3D tracking microscopy. -- Abstract: Yeast is a model eukaryote with a variety of biological resources. Here we developed a method to track a quantum dot (QD)-conjugated protein in the budding yeast Saccharomyces cerevisiae. We chemically conjugated QDs with the yeast prion Sup35, incorporated them into yeast spheroplasts, and tracked the motions by conventional two-dimensional or three-dimensional tracking microscopy. The method paves the way toward the individual tracking of proteins of interest inside living yeast cells.

Single-particle tracking of quantum dot-conjugated prion proteins inside yeast cells

International Nuclear Information System (INIS)

Tsuji, Toshikazu; Kawai-Noma, Shigeko; Pack, Chan-Gi; Terajima, Hideki; Yajima, Junichiro; Nishizaka, Takayuki; Kinjo, Masataka; Taguchi, Hideki

2011-01-01

Research highlights: → We develop a method to track a quantum dot-conjugated protein in yeast cells. → We incorporate the conjugated quantum dot proteins into yeast spheroplasts. → We track the motions by conventional or 3D tracking microscopy. -- Abstract: Yeast is a model eukaryote with a variety of biological resources. Here we developed a method to track a quantum dot (QD)-conjugated protein in the budding yeast Saccharomyces cerevisiae. We chemically conjugated QDs with the yeast prion Sup35, incorporated them into yeast spheroplasts, and tracked the motions by conventional two-dimensional or three-dimensional tracking microscopy. The method paves the way toward the individual tracking of proteins of interest inside living yeast cells.

Amelogenesis Imperfecta; Genes, Proteins, and Pathways

Directory of Open Access Journals (Sweden)

Claire E. L. Smith

2017-06-01

Full Text Available Amelogenesis imperfecta (AI is the name given to a heterogeneous group of conditions characterized by inherited developmental enamel defects. AI enamel is abnormally thin, soft, fragile, pitted and/or badly discolored, with poor function and aesthetics, causing patients problems such as early tooth loss, severe embarrassment, eating difficulties, and pain. It was first described separately from diseases of dentine nearly 80 years ago, but the underlying genetic and mechanistic basis of the condition is only now coming to light. Mutations in the gene AMELX, encoding an extracellular matrix protein secreted by ameloblasts during enamel formation, were first identified as a cause of AI in 1991. Since then, mutations in at least eighteen genes have been shown to cause AI presenting in isolation of other health problems, with many more implicated in syndromic AI. Some of the encoded proteins have well documented roles in amelogenesis, acting as enamel matrix proteins or the proteases that degrade them, cell adhesion molecules or regulators of calcium homeostasis. However, for others, function is less clear and further research is needed to understand the pathways and processes essential for the development of healthy enamel. Here, we review the genes and mutations underlying AI presenting in isolation of other health problems, the proteins they encode and knowledge of their roles in amelogenesis, combining evidence from human phenotypes, inheritance patterns, mouse models, and in vitro studies. An LOVD resource (http://dna2.leeds.ac.uk/LOVD/ containing all published gene mutations for AI presenting in isolation of other health problems is described. We use this resource to identify trends in the genes and mutations reported to cause AI in the 270 families for which molecular diagnoses have been reported by 23rd May 2017. Finally we discuss the potential value of the translation of AI genetics to clinical care with improved patient pathways and

Amelogenesis Imperfecta; Genes, Proteins, and Pathways.

Science.gov (United States)

Smith, Claire E L; Poulter, James A; Antanaviciute, Agne; Kirkham, Jennifer; Brookes, Steven J; Inglehearn, Chris F; Mighell, Alan J

2017-01-01

Amelogenesis imperfecta (AI) is the name given to a heterogeneous group of conditions characterized by inherited developmental enamel defects. AI enamel is abnormally thin, soft, fragile, pitted and/or badly discolored, with poor function and aesthetics, causing patients problems such as early tooth loss, severe embarrassment, eating difficulties, and pain. It was first described separately from diseases of dentine nearly 80 years ago, but the underlying genetic and mechanistic basis of the condition is only now coming to light. Mutations in the gene AMELX , encoding an extracellular matrix protein secreted by ameloblasts during enamel formation, were first identified as a cause of AI in 1991. Since then, mutations in at least eighteen genes have been shown to cause AI presenting in isolation of other health problems, with many more implicated in syndromic AI. Some of the encoded proteins have well documented roles in amelogenesis, acting as enamel matrix proteins or the proteases that degrade them, cell adhesion molecules or regulators of calcium homeostasis. However, for others, function is less clear and further research is needed to understand the pathways and processes essential for the development of healthy enamel. Here, we review the genes and mutations underlying AI presenting in isolation of other health problems, the proteins they encode and knowledge of their roles in amelogenesis, combining evidence from human phenotypes, inheritance patterns, mouse models, and in vitro studies. An LOVD resource (http://dna2.leeds.ac.uk/LOVD/) containing all published gene mutations for AI presenting in isolation of other health problems is described. We use this resource to identify trends in the genes and mutations reported to cause AI in the 270 families for which molecular diagnoses have been reported by 23rd May 2017. Finally we discuss the potential value of the translation of AI genetics to clinical care with improved patient pathways and speculate on the

The RCSB Protein Data Bank: redesigned web site and web services.

Science.gov (United States)

Rose, Peter W; Beran, Bojan; Bi, Chunxiao; Bluhm, Wolfgang F; Dimitropoulos, Dimitris; Goodsell, David S; Prlic, Andreas; Quesada, Martha; Quinn, Gregory B; Westbrook, John D; Young, Jasmine; Yukich, Benjamin; Zardecki, Christine; Berman, Helen M; Bourne, Philip E

2011-01-01

The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.

FragKB: structural and literature annotation resource of conserved peptide fragments and residues.

Directory of Open Access Journals (Sweden)

Ashish V Tendulkar

Full Text Available BACKGROUND: FragKB (Fragment Knowledgebase is a repository of clusters of structurally similar fragments from proteins. Fragments are annotated with information at the level of sequence, structure and function, integrating biological descriptions derived from multiple existing resources and text mining. METHODOLOGY: FragKB contains approximately 400,000 conserved fragments from 4,800 representative proteins from PDB. Literature annotations are extracted from more than 1,700 articles and are available for over 12,000 fragments. The underlying systematic annotation workflow of FragKB ensures efficient update and maintenance of this database. The information in FragKB can be accessed through a web interface that facilitates sequence and structural visualization of fragments together with known literature information on the consequences of specific residue mutations and functional annotations of proteins and fragment clusters. FragKB is accessible online at http://ubio.bioinfo.cnio.es/biotools/fragkb/. SIGNIFICANCE: The information presented in FragKB can be used for modeling protein structures, for designing novel proteins and for functional characterization of related fragments. The current release is focused on functional characterization of proteins through inspection of conservation of the fragments.

Chemical dependence - resources

Science.gov (United States)

Substance use - resources, Drug abuse - resources; Resources - chemical dependence ... are a good resource for information on drug dependence: National Council on Alcoholism and Drug Dependence -- ncadd. ...

A Review on the Fascinating World of Insect Resources: Reason for Thoughts

Directory of Open Access Journals (Sweden)

R. K. Lokeshwari

2010-01-01

Full Text Available Insect resources are vast and diverse due to their enormous diversity. The exploitation and utilization of insect resources is broadly classified into four different categories. The first category is the insects of industrial resources. This level includes the utilization of silk worm, honeybee, lac insect, dye insect, and aesthetic insect. The second category is the utilization of insects for edible and therapeutic purposes. Insects are high in protein and many are rich sources of vitamins and minerals. The third category is the use of insects in forensic investigation. By analyzing the stages of succession of insects at first, rough estimation of the postmortem intervals can be done. The fourth category is the insects of ecological importance. Many insect species act as potential predators and parasites of destructive pests of insect order Lepidoptera, Diptera, and Orthoptera. Insects are also used as bioindicator to assess the cumulative effects of environmental stressors such as pollutants. Despites these fascinating benefits, insect resources are often neglected in India due to lack of proper documentation, less expertise, and advance enterprises in these fields. Hence, the paper reviews the different fascinating facets of insect resources in order to explore and utilize it in a sustainable way with reference to Indian region.

FY 1996 report on the cooperative research on the development of environmentally friendly high efficiency mineral resource extraction/treatment technology. Basic design of pilot plant and a part of the detailed design; 1996 nendo kankyo chowagata kokoritsu kobutsu shigen chushutsu shori gijutsu no kaihatsu ni kansuru kenkyu kyoryoku. Pilot plant no kihon sekkei oyobi ichibu shosai sekkei

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-03-01

This project is a cooperative research on the development of environmental harmony type high efficiency mineral resource extraction/treatment technology. It aims to study/develop a system to recover valuable metals from unused resources in the Republic of Kazakhstan using the environmental harmony type technology which is easy to operate/maintain and is environmentally friendly with no mine pollution caused. In the project, which started in FY 1994, a pilot plant is finally constructed in Kazakhstan, a recovery system to be applied is demonstrated, and the comprehensive assessment of the system is made. Concretely, the recovery of Cu, Au, Ag, etc. is tried from the Nikolayevska low grade ore and Zhezkent tailings. This is a system into which the following techniques are integrated: treatment before dressing such as flotation, leaching of Cu, etc. by acid including bacteria, solvent leaching, electrowinning, cyanogen leaching activated carbon treatment and wastewater treatment of Au and Ag. As to the design/fabrication of pilot plant, conducted was the conceptual design in FY 1995, and the basic design, a part of the detailed design (crushing/grinding/leaching/dewatering facilities of the process of the acid (bacteria) leaching of Cu, etc.), and the fabrication in FY 1996. (NEDO).

The effects of human resource flexibility on human resources development

Directory of Open Access Journals (Sweden)

SeidMehdi Veise

2014-08-01

Full Text Available Human resources are the primary factor for development of competitiveness and innovation and reaching competitive advantage and they try to improve corporate capabilities through various characteristics such as value creation, scarcity and difficulty of imitation. This paper investigates the effect of human resource flexibility and its dimensions on human resource development and its dimensions. The survey was conducted using descriptive-correlation method that intended to describe how human resource flexibility was effective on human resource development. Questionnaire was tool of data collection. The statistical population included one hundred employees of the Electric Company in Ilam province, thus census method was used. Reliability of the questionnaire was measured via Cronbach's alpha equal to 0.96. The findings revealed that flexibility and its dimensions were effective on human resource development and dimensions of it. As a result, human resource flexibility should be considered for development of human resources and employees with the highest flexibility should be selected.

Exploring and linking biomedical resources through multidimensional semantic spaces.

Science.gov (United States)

Berlanga, Rafael; Jiménez-Ruiz, Ernesto; Nebot, Victoria

2012-01-25

The semantic integration of biomedical resources is still a challenging issue which is required for effective information processing and data analysis. The availability of comprehensive knowledge resources such as biomedical ontologies and integrated thesauri greatly facilitates this integration effort by means of semantic annotation, which allows disparate data formats and contents to be expressed under a common semantic space. In this paper, we propose a multidimensional representation for such a semantic space, where dimensions regard the different perspectives in biomedical research (e.g., population, disease, anatomy and protein/genes). This paper presents a novel method for building multidimensional semantic spaces from semantically annotated biomedical data collections. This method consists of two main processes: knowledge and data normalization. The former one arranges the concepts provided by a reference knowledge resource (e.g., biomedical ontologies and thesauri) into a set of hierarchical dimensions for analysis purposes. The latter one reduces the annotation set associated to each collection item into a set of points of the multidimensional space. Additionally, we have developed a visual tool, called 3D-Browser, which implements OLAP-like operators over the generated multidimensional space. The method and the tool have been tested and evaluated in the context of the Health-e-Child (HeC) project. Automatic semantic annotation was applied to tag three collections of abstracts taken from PubMed, one for each target disease of the project, the Uniprot database, and the HeC patient record database. We adopted the UMLS Meta-thesaurus 2010AA as the reference knowledge resource. Current knowledge resources and semantic-aware technology make possible the integration of biomedical resources. Such an integration is performed through semantic annotation of the intended biomedical data resources. This paper shows how these annotations can be exploited for

Water Resources

International Nuclear Information System (INIS)

Abira, M.A.

1997-01-01

Water is essential for life and ecological sustenance; its availability is essential component of national welfare and productivity.The country's socio-economic activities are largely dependent on the natural endowment of water resources. Kenya's water resources comprises of surface waters (rivers, lakes and wetlands) and ground water. Surface water forms 86% of total water resources while the rest is ground water Geological, topographical and climatic factors influence the natural availability and distribution of water with the rainfall distribution having the major influence. Water resources in Kenya are continuously under threat of depletion and quality degradation owing to rising population, industrialization, changing land use and settlement activities as well as natural changes. However, the anticipated climate change is likely to exacerbate the situation resulting in increased conflict over water use rights in particular, and, natural resource utilisation in general. The impacts of climate change on the water resources would lead to other impacts on environmental and socio-economic systems

The Identification of Land Utilization in Coastal Reclamation Areas in Tianjin Using High Resolution Remote Sensing Images

Science.gov (United States)

Meng, Y.; Cao, Y.; Tian, H.; Han, Z.

2018-04-01

In recent decades, land reclamation activities have been developed rapidly in Chinese coastal regions, especially in Bohai Bay. The land reclamation areas can effectively alleviate the contradiction between land resources shortage and human needs, but some idle lands that left unused after the government making approval the usage of sea areas are also supposed to pay attention to. Due to the particular features of land coverage identification in large regions, traditional monitoring approaches are unable to perfectly meet the needs of effectively and quickly land use classification. In this paper, Gaofen-1 remotely sensed satellite imagery data together with sea area usage ownership data were used to identify the land use classifications and find out the idle land resources. It can be seen from the result that most of the land use types and idle land resources can be identified precisely.

The Development of PIPA: An Integrated and Automated Pipeline for Genome-Wide Protein Function Annotation

National Research Council Canada - National Science Library

Yu, Chenggang; Zavaljevski, Nela; Desai, Valmik; Johnson, Seth; Stevens, Fred J; Reifman, Jaques

2008-01-01

.... With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method...

Expanding the biomass resource: sustainable oil production via fast pyrolysis of low input high diversity biomass and the potential integration of thermochemical and biological conversion routes.

Science.gov (United States)

Corton, J; Donnison, I S; Patel, M; Bühle, L; Hodgson, E; Wachendorf, M; Bridgwater, A; Allison, G; Fraser, M D

2016-09-01

Waste biomass is generated during the conservation management of semi-natural habitats, and represents an unused resource and potential bioenergy feedstock that does not compete with food production. Thermogravimetric analysis was used to characterise a representative range of biomass generated during conservation management in Wales. Of the biomass types assessed, those dominated by rush ( Juncus effuses ) and bracken ( Pteridium aquilinum ) exhibited the highest and lowest volatile compositions respectively and were selected for bench scale conversion via fast pyrolysis. Each biomass type was ensiled and a sub-sample of silage was washed and pressed. Demineralization of conservation biomass through washing and pressing was associated with higher oil yields following fast pyrolysis. The oil yields were within the published range established for the dedicated energy crops miscanthus and willow. In order to examine the potential a multiple output energy system was developed with gross power production estimates following valorisation of the press fluid, char and oil. If used in multi fuel industrial burners the char and oil alone would displace 3.9 × 10 5  tonnes per year of No. 2 light oil using Welsh biomass from conservation management. Bioenergy and product development using these feedstocks could simultaneously support biodiversity management and displace fossil fuels, thereby reducing GHG emissions. Gross power generation predictions show good potential.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

Energy Technology Data Exchange (ETDEWEB)

Beer, Tjaart A. P. de; Laskowski, Roman A. [European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom); Duban, Mark-Eugene [Northwestern University Feinberg School of Medicine, Chicago, Illinois (United States); Chan, A. W. Edith [University College London, London WC1E 6BT (United Kingdom); Anderson, Wayne F. [Northwestern University Feinberg School of Medicine, Chicago, Illinois (United States); Thornton, Janet M., E-mail: thornton@ebi.ac.uk [European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom)

2013-12-01

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

Peptides and proteins

Energy Technology Data Exchange (ETDEWEB)

Bachovchin, W.W.; Unkefer, C.J.

1994-12-01

Advances in magnetic resonance and vibrational spectroscopy make it possible to derive detailed structural information about biomolecular structures in solution. These techniques are critically dependent on the availability of labeled compounds. For example, NMR techniques used today to derive peptide and protein structures require uniformity {sup 13}C-and {sup 15}N-labeled samples that are derived biosynthetically from (U-6-{sup 13}C) glucose. These experiments are possible now because, during the 1970s, the National Stable Isotope Resource developed algal methods for producing (U-6-{sup 13}C) glucose. If NMR techniques are to be used to study larger proteins, we will need sophisticated labelling patterns in amino acids that employ a combination of {sup 2}H, {sup 13}C, and {sup 15}N labeling. The availability of these specifically labeled amino acids requires a renewed investment in new methods for chemical synthesis of labeled amino acids. The development of new magnetic resonance or vibrational techniques to elucidate biomolecular structure will be seriously impeded if we do not see rapid progress in labeling technology. Investment in labeling chemistry is as important as investment in the development of advanced spectroscopic tools.

Network resource management

NARCIS (Netherlands)

2009-01-01

The invention provides real time dynamic resource management to improve end-to-end QoS by mobile devices regularly updating a resource availability server (RAS) with resource update information. Examples of resource update information are device battery status, available memory, session bandwidth,

Roles for text mining in protein function prediction.

Science.gov (United States)

Verspoor, Karin M

2014-01-01

The Human Genome Project has provided science with a hugely valuable resource: the blueprints for life; the specification of all of the genes that make up a human. While the genes have all been identified and deciphered, it is proteins that are the workhorses of the human body: they are essential to virtually all cell functions and are the primary mechanism through which biological function is carried out. Hence in order to fully understand what happens at a molecular level in biological organisms, and eventually to enable development of treatments for diseases where some aspect of a biological system goes awry, we must understand the functions of proteins. However, experimental characterization of protein function cannot scale to the vast amount of DNA sequence data now available. Computational protein function prediction has therefore emerged as a problem at the forefront of modern biology (Radivojac et al., Nat Methods 10(13):221-227, 2013).Within the varied approaches to computational protein function prediction that have been explored, there are several that make use of biomedical literature mining. These methods take advantage of information in the published literature to associate specific proteins with specific protein functions. In this chapter, we introduce two main strategies for doing this: association of function terms, represented as Gene Ontology terms (Ashburner et al., Nat Genet 25(1):25-29, 2000), to proteins based on information in published articles, and a paradigm called LEAP-FS (Literature-Enhanced Automated Prediction of Functional Sites) in which literature mining is used to validate the predictions of an orthogonal computational protein function prediction method.

Land Use for Edible Protein of Animal Origin—A Review

Directory of Open Access Journals (Sweden)

Gerhard Flachowsky

2017-03-01

Full Text Available The present period is characterized by a growing world population and a higher demand for more and better quality food, as well as other products for an improved standard of living. In the future, there will be increasingly strong competition for arable land and non-renewable resources such as fossil carbon-sources, water, and some minerals, as well as between food, feed, fuel, fiber, flowers, and fun (6 F’s. Proteins of animal origin like milk, meat, fish, eggs and, probably, insects are very valuable sources of essential amino acids, minerals and vitamins, but their production consumes some non-renewable resources including arable land and causes considerable emissions. Therefore, this study´s objective was to calculate some examples of the land use (arable land and grassland for production of edible animal protein taking into consideration important animal species/categories, levels of plant and animal yields, the latter estimated with and without co-products from agriculture, and the food/biofuel industry in animal feeding. There are large differences between animal species/categories and their potential to produce edible protein depending on many influencing variables. The highest amounts per kilogram body weight are produced by growing broiler chicken followed by laying hens and dairy cows; the lowest yields in edible protein and the highest land need were observed for beef cattle. This review clearly indicates that the production of food of animal origin is a very complex process, and selective considerations, i.e., focusing on single factors, do not provide an assessment that reflects the complexity of the subject.

Laboratory information management system for membrane protein structure initiative--from gene to crystal.

Science.gov (United States)

Troshin, Petr V; Morris, Chris; Prince, Stephen M; Papiz, Miroslav Z

2008-12-01

Membrane Protein Structure Initiative (MPSI) exploits laboratory competencies to work collaboratively and distribute work among the different sites. This is possible as protein structure determination requires a series of steps, starting with target selection, through cloning, expression, purification, crystallization and finally structure determination. Distributed sites create a unique set of challenges for integrating and passing on information on the progress of targets. This role is played by the Protein Information Management System (PIMS), which is a laboratory information management system (LIMS), serving as a hub for MPSI, allowing collaborative structural proteomics to be carried out in a distributed fashion. It holds key information on the progress of cloning, expression, purification and crystallization of proteins. PIMS is employed to track the status of protein targets and to manage constructs, primers, experiments, protocols, sample locations and their detailed histories: thus playing a key role in MPSI data exchange. It also serves as the centre of a federation of interoperable information resources such as local laboratory information systems and international archival resources, like PDB or NCBI. During the challenging task of PIMS integration, within the MPSI, we discovered a number of prerequisites for successful PIMS integration. In this article we share our experiences and provide invaluable insights into the process of LIMS adaptation. This information should be of interest to partners who are thinking about using LIMS as a data centre for their collaborative efforts.

Ecotechnology - the magic word. Planning of technology according to ecological criteria

Energy Technology Data Exchange (ETDEWEB)

Herrmann, H [Gesellschaft fuer Systemtechnik, Essen (Germany, F.R.)

1978-08-01

By means of a system of ecological criteria it can be demonstrated, that alternative solutions for a certain technical task often create different levels of ecological stress. The solution to be favoured for ecological reasons shows partly higher but also partly lower costs than the presently introduced solution. Ecologically optimized technologies may lead to a resubstitution of consumption of resources and environmental stress by capital and labour and consequently to an utilisation of presently unused production capacities. The earlier an adaption is introduced, the lower will be the required expense.

Socioeconomic status, psychological resources, and inflammatory markers: Results from the MIDUS study.

Science.gov (United States)

Elliot, Ari J; Chapman, Benjamin P

2016-11-01

Our objective was to investigate interactions of psychological resources and socioeconomic status (SES)-as well as potential gender differences and the explanatory role of childhood and adult stress exposures, health behaviors, and negative and positive affect-in predicting markers of systemic inflammation. We utilized a sample of adults from the Midlife Development in the U.S. (MIDUS) study who provided biomarker data (N = 1,152). SES was operationalized as a composite of education, income, and occupational prestige, and the psychological resources construct was operationalized as a latent factor measured with optimism, perceived control, and self-esteem. Linear regression models examined these 2 factors and their interaction in predicting interleukin-6 (IL-6) and C-reactive protein (CRP) measured on average 2 years later, as well as 3-way interactions involving gender and the impact of covariate adjustment. Psychological resources interacted with SES in men (for IL-6: p low SES was moderately attenuated upon adjustment for negative affect. Socioeconomic status might modulate the linkage between psychological resources and systemic inflammation in men. At lower levels of SES, resources may be related to lower inflammation in part through lower negative affect. Associations with higher inflammation at higher SES add to growing evidence suggesting that adaptive psychological characteristics may be associated with markers of poorer physiological function under certain conditions. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools.

Science.gov (United States)

Schneider, Michel; Tognolli, Michael; Bairoch, Amos

2004-12-01

The Swiss-Prot protein knowledgebase provides manually annotated entries for all species, but concentrates on the annotation of entries from model organisms to ensure the presence of high quality annotation of representative members of all protein families. A specific Plant Protein Annotation Program (PPAP) was started to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Its main goal is the annotation of proteins from the model plant organism Arabidopsis thaliana. In addition to bibliographic references, experimental results, computed features and sometimes even contradictory conclusions, direct links to specialized databases connect amino acid sequences with the current knowledge in plant sciences. As protein families and groups of plant-specific proteins are regularly reviewed to keep up with current scientific findings, we hope that the wealth of information of Arabidopsis origin accumulated in our knowledgebase, and the numerous software tools provided on the Expert Protein Analysis System (ExPASy) web site might help to identify and reveal the function of proteins originating from other plants. Recently, a single, centralized, authoritative resource for protein sequences and functional information, UniProt, was created by joining the information contained in Swiss-Prot, Translation of the EMBL nucleotide sequence (TrEMBL), and the Protein Information Resource-Protein Sequence Database (PIR-PSD). A rising problem is that an increasing number of nucleotide sequences are not being submitted to the public databases, and thus the proteins inferred from such sequences will have difficulties finding their way to the Swiss-Prot or TrEMBL databases.

Finding local communities in protein networks.

Science.gov (United States)

Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu

2009-09-18

Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is available from BioGRID and other sources. The identification of communities in PPI networks is of great interest because they often reveal previously unknown functional ties between proteins. A large number of global clustering algorithms have been applied to protein networks, where the entire network is partitioned into clusters. Here we take a different approach by looking for local communities in PPI networks. We develop a tool, named Local Protein Community Finder, which quickly finds a community close to a queried protein in any network available from BioGRID or specified by the user. Our tool uses two new local clustering algorithms Nibble and PageRank-Nibble, which look for a good cluster among the most popular destinations of a short random walk from the queried vertex. The quality of a cluster is determined by proportion of outgoing edges, known as conductance, which is a relative measure particularly useful in undersampled networks. We show that the two local clustering algorithms find communities that not only form excellent clusters, but are also likely to be biologically relevant functional components. We compare the performance of Nibble and PageRank-Nibble to other popular and effective graph partitioning algorithms, and show that they find better clusters in the graph. Moreover, Nibble and PageRank-Nibble find communities that are more functionally coherent. The Local Protein Community Finder, accessible at http://xialab.bu.edu/resources/lpcf, allows the user to quickly find a high-quality community close to a queried protein in any network available from BioGRID or specified by the user. We show that the communities found by our tool form good clusters and are functionally coherent, making our application useful for biologists who wish to

Finding local communities in protein networks

Directory of Open Access Journals (Sweden)

Teng Shang-Hua

2009-09-01

Full Text Available Abstract Background Protein-protein interactions (PPIs play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is available from BioGRID and other sources. The identification of communities in PPI networks is of great interest because they often reveal previously unknown functional ties between proteins. A large number of global clustering algorithms have been applied to protein networks, where the entire network is partitioned into clusters. Here we take a different approach by looking for local communities in PPI networks. Results We develop a tool, named Local Protein Community Finder, which quickly finds a community close to a queried protein in any network available from BioGRID or specified by the user. Our tool uses two new local clustering algorithms Nibble and PageRank-Nibble, which look for a good cluster among the most popular destinations of a short random walk from the queried vertex. The quality of a cluster is determined by proportion of outgoing edges, known as conductance, which is a relative measure particularly useful in undersampled networks. We show that the two local clustering algorithms find communities that not only form excellent clusters, but are also likely to be biologically relevant functional components. We compare the performance of Nibble and PageRank-Nibble to other popular and effective graph partitioning algorithms, and show that they find better clusters in the graph. Moreover, Nibble and PageRank-Nibble find communities that are more functionally coherent. Conclusion The Local Protein Community Finder, accessible at http://xialab.bu.edu/resources/lpcf, allows the user to quickly find a high-quality community close to a queried protein in any network available from BioGRID or specified by the user. We show that the communities found by our tool form good clusters and are functionally coherent

SYSTEMATIC LITERATURE REVIEW ON RESOURCE ALLOCATION AND RESOURCE SCHEDULING IN CLOUD COMPUTING

OpenAIRE

B. Muni Lavanya; C. Shoba Bindu

2016-01-01

The objective the work is intended to highlight the key features and afford finest future directions in the research community of Resource Allocation, Resource Scheduling and Resource management from 2009 to 2016. Exemplifying how research on Resource Allocation, Resource Scheduling and Resource management has progressively increased in the past decade by inspecting articles, papers from scientific and standard publications. Survey materialized in three-fold process. Firstly, investigate on t...

MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

Science.gov (United States)

El Kennani, Sara; Adrait, Annie; Shaytan, Alexey K; Khochbin, Saadi; Bruley, Christophe; Panchenko, Anna R; Landsman, David; Pflieger, Delphine; Govin, Jérôme

2017-01-01

Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants. We propose two proteomics-oriented manually curated databases for mouse and human histone variants. We manually curated >1700 gene, transcript and protein entries to produce a non-redundant list of 83 mouse and 85 human histones. These entries were annotated in accordance with the current nomenclature and unified with the "HistoneDB2.0 with Variants" database. This resource is provided in a format that can be directly read by programs used for mass spectrometry data interpretation. In addition, it was used to interpret mass spectrometry data acquired on histones extracted from mouse testis. Several histone variants, which had so far only been inferred by homology or detected at the RNA level, were detected by mass spectrometry, confirming the existence of their protein form. Mouse and human histone entries were collected from different databases and subsequently curated to produce a non-redundant protein-centric resource, MS_HistoneDB. It is dedicated to the proteomic study of histones in mouse and human and will hopefully facilitate the identification and functional study of histone variants.

Predicting and validating protein interactions using network structure.

Directory of Open Access Journals (Sweden)

Pao-Yang Chen

2008-07-01

Full Text Available Protein interactions play a vital part in the function of a cell. As experimental techniques for detection and validation of protein interactions are time consuming, there is a need for computational methods for this task. Protein interactions appear to form a network with a relatively high degree of local clustering. In this paper we exploit this clustering by suggesting a score based on triplets of observed protein interactions. The score utilises both protein characteristics and network properties. Our score based on triplets is shown to complement existing techniques for predicting protein interactions, outperforming them on data sets which display a high degree of clustering. The predicted interactions score highly against test measures for accuracy. Compared to a similar score derived from pairwise interactions only, the triplet score displays higher sensitivity and specificity. By looking at specific examples, we show how an experimental set of interactions can be enriched and validated. As part of this work we also examine the effect of different prior databases upon the accuracy of prediction and find that the interactions from the same kingdom give better results than from across kingdoms, suggesting that there may be fundamental differences between the networks. These results all emphasize that network structure is important and helps in the accurate prediction of protein interactions. The protein interaction data set and the program used in our analysis, and a list of predictions and validations, are available at http://www.stats.ox.ac.uk/bioinfo/resources/PredictingInteractions.

Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

Science.gov (United States)

Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

2018-05-01

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.

Science.gov (United States)

de Oliveira, Saulo H P; Law, Eleanor C; Shi, Jiye; Deane, Charlotte M

2018-04-01

Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction. We observed that our sequential approach converges when fewer than 20 000 decoys have been produced, fewer than commonly expected. Using our software, SAINT2, we also compared the run time and quality of models produced in a sequential fashion against a standard, non-sequential approach. Sequential prediction produces an individual decoy 1.5-2.5 times faster than non-sequential prediction. When considering the quality of the best model, sequential prediction led to a better model being produced for 31 out of 41 soluble protein validation cases and for 18 out of 24 transmembrane protein cases. Correct models (TM-Score > 0.5) were produced for 29 of these cases by the sequential mode and for only 22 by the non-sequential mode. Our comparison reveals that a sequential search strategy can be used to drastically reduce computational time of de novo protein structure prediction and improve accuracy. Data are available for download from: http://opig.stats.ox.ac.uk/resources. SAINT2 is available for download from: https://github.com/sauloho/SAINT2. saulo.deoliveira@dtc.ox.ac.uk. Supplementary data are available at Bioinformatics online.

ASDB: a resource for probing protein functions with small molecules.

Science.gov (United States)

Liu, Zhihong; Ding, Peng; Yan, Xin; Zheng, Minghao; Zhou, Huihao; Xu, Yuehua; Du, Yunfei; Gu, Qiong; Xu, Jun

2016-06-01

: Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets. ASDB is freely available at http://www.rcdd.org.cn/asdb/with the major web browsers. junxu@biochemomes.com or xujun9@mail.sysu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Bumble bees regulate their intake of essential protein and lipid pollen macronutrients.

Science.gov (United States)

Vaudo, A D; Stabler, D; Patch, H M; Tooker, J F; Grozinger, C M; Wright, G A

2016-12-15

Bee population declines are linked to the reduction of nutritional resources due to land-use intensification, yet we know little about the specific nutritional needs of many bee species. Pollen provides bees with their primary source of protein and lipids, but nutritional quality varies widely among host-plant species. Therefore, bees might have adapted to assess resource quality and adjust their foraging behavior to balance nutrition from multiple food sources. We tested the ability of two bumble bee species, Bombus terrestris and Bombus impatiens, to regulate protein and lipid intake. We restricted B. terrestris adults to single synthetic diets varying in protein:lipid ratios (P:L). The bees over-ate protein on low-fat diets and over-ate lipid on high-fat diets to reach their targets of lipid and protein, respectively. The bees survived best on a 10:1 P:L diet; the risk of dying increased as a function of dietary lipid when bees ate diets with lipid contents greater than 5:1 P:L. Hypothesizing that the P:L intake target of adult worker bumble bees was between 25:1 and 5:1, we presented workers from both species with unbalanced but complementary paired diets to determine whether they self-select their diet to reach a specific intake target. Bees consumed similar amounts of proteins and lipids in each treatment and averaged a 14:1 P:L for B. terrestris and 12:1 P:L for B. impatiens These results demonstrate that adult worker bumble bees likely select foods that provide them with a specific ratio of P:L. These P:L intake targets could affect pollen foraging in the field and help explain patterns of host-plant species choice by bumble bees. © 2016. Published by The Company of Biologists Ltd.

An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction

Directory of Open Access Journals (Sweden)

Thahir Mohamed

2012-11-01

Full Text Available Abstract Background Machine learning approaches for classification learn the pattern of the feature space of different classes, or learn a boundary that separates the feature space into different classes. The features of the data instances are usually available, and it is only the class-labels of the instances that are unavailable. For example, to classify text documents into different topic categories, the words in the documents are features and they are readily available, whereas the topic is what is predicted. However, in some domains obtaining features may be resource-intensive because of which not all features may be available. An example is that of protein-protein interaction prediction, where not only are the labels ('interacting' or 'non-interacting' unavailable, but so are some of the features. It may be possible to obtain at least some of the missing features by carrying out a few experiments as permitted by the available resources. If only a few experiments can be carried out to acquire missing features, which proteins should be studied and which features of those proteins should be determined? From the perspective of machine learning for PPI prediction, it would be desirable that those features be acquired which when used in training the classifier, the accuracy of the classifier is improved the most. That is, the utility of the feature-acquisition is measured in terms of how much acquired features contribute to improving the accuracy of the classifier. Active feature acquisition (AFA is a strategy to preselect such instance-feature combinations (i.e. protein and experiment combinations for maximum utility. The goal of AFA is the creation of optimal training set that would result in the best classifier, and not in determining the best classification model itself. Results We present a heuristic method for active feature acquisition to calculate the utility of acquiring a missing feature. This heuristic takes into account the change in

How to spend it: Resource wealth and the distribution of resource rents

International Nuclear Information System (INIS)

Segal, Paul

2012-01-01

Natural resource revenues differ from other government revenues both in their time profile, and in their political and legal status: they are volatile and exhaustible, and belong to all citizens of the country in which they are located. This paper discusses the theory of natural resource revenues and examines expenditure practices in a range of resource-rich countries. It considers both the distributional impact and the efficiency of expenditure policies, focusing on the extent to which they succeed in providing all citizens with their share of the benefits due to natural resources. - Highlights: ► We examine the relationship between resource rents and government resource revenues. ► We discuss the intertemporal management of resource revenues in theory and in practice. ► We critically examine existing policies for distributing resource revenues to populations.

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

Science.gov (United States)

Ryan, Michael; Diekhans, Mark; Lien, Stephanie; Liu, Yun; Karchin, Rachel

2009-06-01

LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features. LS-SNP/PDB is available at (http://ls-snp.icm.jhu.edu/ls-snp-pdb) and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.

A model of optimal protein allocation during phototrophic growth

Czech Academy of Sciences Publication Activity Database

Faizi, M.; Zavřel, Tomáš; Loureiro, C.; Červený, Jan; Steuer, Ralf

2018-01-01

Roč. 166, apr (2018), s. 26-36 ISSN 0303-2647 R&D Projects: GA MŠk(CZ) LO1415; GA ČR(CZ) GA15-17367S; GA MŠk(CZ) LM2015055 Institutional support: RVO:86652079 Keywords : Cellular protein economy * Cyanobacteria * Microbial growth laws * Photosynthesis * Resource allocation * Systems biology Subject RIV: EI - Biotechnology ; Bionics OBOR OECD: Environmental biotechnology Impact factor: 1.652, year: 2016

Implementation of the resource recovery concept in the biotech industry

DEFF Research Database (Denmark)

Mitic, Aleksandar; Mansouri, Seyed Soheil; S.B.A. Udugama, Isuru

The concept of circular economy is attracting significant attention in modern biotech industry. Downstream processing plants are usually focused on the removal of impurities instead of their recovery in the form of value-added products for additional revenues. For example, carboxylic acids......, carbohydrates, proteins, lipids, inorganic ions and water itself are amongst various resources that are found in wastewater streams coming from bio-based production processes. Such compounds have a high value at the global market and could potentially be used as raw materials for the manufacturing feed and food...

Simplified Enrichment of Plasma Membrane Proteins from Arabidopsis thaliana Seedlings Using Differential Centrifugation and Brij-58 Treatment.

Science.gov (United States)

Collins, Carina A; Leslie, Michelle E; Peck, Scott C; Heese, Antje

2017-01-01

The plasma membrane (PM) forms a barrier between a plant cell and its environment. Proteins at this subcellular location play diverse and complex roles, including perception of extracellular signals to coordinate cellular changes. Analyses of PM proteins, however, are often limited by the relatively low abundance of these proteins in the total cellular protein pool. Techniques traditionally used for enrichment of PM proteins are time consuming, tedious, and require extensive optimization. Here, we provide a simple and reproducible enrichment procedure for PM proteins from Arabidopsis thaliana seedlings starting from total microsomal membranes isolated by differential centrifugation. To enrich for PM proteins, total microsomes are treated with the nonionic detergent Brij-58 to decrease the abundance of contaminating organellar proteins. This protocol combined with the genetic resources available in Arabidopsis provides a powerful tool that will enhance our understanding of proteins at the PM.

In Profile: Models of Ribosome Biogenesis Defects and Regulation of Protein Synthesis

NARCIS (Netherlands)

Essers, P.B.M.

2013-01-01

Ribosomes are the mediators of protein synthesis in the cell and therefore crucial to proper cell function. In addition, ribosomes are highly abundant, with ribosomal RNA making up 80% of the RNA in the cell. A large amount of resources go into maintaining this pool of ribosomes, so ribosome

World resources: engineering solutions

Energy Technology Data Exchange (ETDEWEB)

1976-01-01

The proceedings include 10 papers that contribute to population environment; fossil fuel resources and energy conservation; nuclear and solar power; production of ores and manufacture and use of metallic resources; resources of manufactured and natural nonmetallic materials; water as a reusable resource; and timber as a replaceable resource.

Semantic distributed resource discovery for multiple resource providers

NARCIS (Netherlands)

Pittaras, C.; Ghijsen, M.; Wibisono, A.; Grosso, P.; van der Ham, J.; de Laat, C.

2012-01-01

An emerging modus operandi among providers of cloud infrastructures is the one where they share and combine their heterogenous resources to offer end user services tailored to specific scientific and business needs. A challenge to overcome is the discovery of suitable resources among these multiple

PATtyFams: Protein families for the microbial genomes in the PATRIC database

Directory of Open Access Journals (Sweden)

James J Davis

2016-02-01

Full Text Available The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based function assignments available through RAST (Rapid Annotation using Subsystem Technology to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL. This new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.

Protein docking prediction using predicted protein-protein interface

Directory of Open Access Journals (Sweden)

Li Bin

2012-01-01

Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

Protein docking prediction using predicted protein-protein interface.

Science.gov (United States)

Li, Bin; Kihara, Daisuke

2012-01-10

Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

Competition over personal resources favors contribution to shared resources in human groups.

Directory of Open Access Journals (Sweden)

Jessica L Barker

Full Text Available Members of social groups face a trade-off between investing selfish effort for themselves and investing cooperative effort to produce a shared group resource. Many group resources are shared equitably: they may be intrinsically non-excludable public goods, such as vigilance against predators, or so large that there is little cost to sharing, such as cooperatively hunted big game. However, group members' personal resources, such as food hunted individually, may be monopolizable. In such cases, an individual may benefit by investing effort in taking others' personal resources, and in defending one's own resources against others. We use a game theoretic "tug-of-war" model to predict that when such competition over personal resources is possible, players will contribute more towards a group resource, and also obtain higher payoffs from doing so. We test and find support for these predictions in two laboratory economic games with humans, comparing people's investment decisions in games with and without the options to compete over personal resources or invest in a group resource. Our results help explain why people cooperatively contribute to group resources, suggest how a tragedy of the commons may be avoided, and highlight unifying features in the evolution of cooperation and competition in human and non-human societies.

Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

Directory of Open Access Journals (Sweden)

Peng Liu

2015-01-01

Full Text Available A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

U.S. Geological Survey Mineral Resources Program—Mineral resource science supporting informed decisionmaking

Science.gov (United States)

Wilkins, Aleeza M.; Doebrich, Jeff L.

2016-09-19

The USGS Mineral Resources Program (MRP) delivers unbiased science and information to increase understanding of mineral resource potential, production, and consumption, and how mineral resources interact with the environment. The MRP is the Federal Government’s sole source for this mineral resource science and information. Program goals are to (1) increase understanding of mineral resource formation, (2) provide mineral resource inventories and assessments, (3) broaden knowledge of the effects of mineral resources on the environment and society, and (4) provide analysis on the availability and reliability of mineral supplies.

Energy Resource Planning. Optimal utilization of energy resources

International Nuclear Information System (INIS)

Miclescu, T.; Domschke, W.; Bazacliu, G.; Dumbrava, V.

1996-01-01

For a thermal power plants system, the primary energy resources cost constitutes a significant percentage of the total system operational cost. Therefore a small percentage saving in primary energy resource allocation cost for a long term, often turns out to be a significant monetary value. In recent years, with a rapidly changing fuel supply situation, including the impact of energy policies changing, this area has become extremely sensitive. Natural gas availability has been restricted in many areas, coal production and transportation cost have risen while productivity has decreased, oil imports have increased and refinery capacity failed to meet demand. The paper presents a mathematical model and a practical procedure to solve the primary energy resource allocation. The objectives is to minimise the total energy cost over the planning period subject to constraints with regards to primary energy resource, transportation and energy consumption. Various aspects of the proposed approach are discussed, and its application to a power system is illustrated.(author) 2 figs., 1 tab., 3 refs

MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.

Science.gov (United States)

Catalano, Domenico; Licciulli, Flavio; Turi, Antonio; Grillo, Giorgio; Saccone, Cecilia; D'Elia, Domenica

2006-01-24

Mitochondria are sub-cellular organelles that have a central role in energy production and in other metabolic pathways of all eukaryotic respiring cells. In the last few years, with more and more genomes being sequenced, a huge amount of data has been generated providing an unprecedented opportunity to use the comparative analysis approach in studies of evolution and functional genomics with the aim of shedding light on molecular mechanisms regulating mitochondrial biogenesis and metabolism. In this context, the problem of the optimal extraction of representative datasets of genomic and proteomic data assumes a crucial importance. Specialised resources for nuclear-encoded mitochondria-related proteins already exist; however, no mitochondrial database is currently available with the same features of MitoRes, which is an update of the MitoNuc database extensively modified in its structure, data sources and graphical interface. It contains data on nuclear-encoded mitochondria-related products for any metazoan species for which this type of data is available and also provides comprehensive sequence datasets (gene, transcript and protein) as well as useful tools for their extraction and export. MitoRes http://www2.ba.itb.cnr.it/MitoRes/ consolidates information from publicly external sources and automatically annotates them into a relational database. Additionally, it also clusters proteins on the basis of their sequence similarity and interconnects them with genomic data. The search engine and sequence management tools allow the query/retrieval of the database content and the extraction and export of sequences (gene, transcript, protein) and related sub-sequences (intron, exon, UTR, CDS, signal peptide and gene flanking regions) ready to be used for in silico analysis. The tool we describe here has been developed to support lab scientists and bioinformaticians alike in the characterization of molecular features and evolution of mitochondrial targeting sequences. The

Gene Unprediction with Spurio: A tool to identify spurious protein sequences.

Science.gov (United States)

Höps, Wolfram; Jeffryes, Matt; Bateman, Alex

2018-01-01

We now have access to the sequences of tens of millions of proteins. These protein sequences are essential for modern molecular biology and computational biology. The vast majority of protein sequences are derived from gene prediction tools and have no experimental supporting evidence for their translation.  Despite the increasing accuracy of gene prediction tools there likely exists a large number of spurious protein predictions in the sequence databases.  We have developed the Spurio tool to help identify spurious protein predictions in prokaryotes.  Spurio searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. The tblastn matches are used to score the query sequence's likelihood of being a spurious protein prediction using a Gaussian process model. The most informative feature is the appearance of stop codons within the presumed translation of homologous DNA sequences. Benchmarking shows that the Spurio tool is able to distinguish spurious from true proteins. However, transposon proteins are prone to be predicted as spurious because of the frequency of degraded homologs found in the DNA sequence databases. Our initial experiments suggest that less than 1% of the proteins in the UniProtKB sequence database are likely to be spurious and that Spurio is able to identify over 60 times more spurious proteins than the AntiFam resource. The Spurio software and source code is available under an MIT license at the following URL: https://bitbucket.org/bateman-group/spurio.

Research for a database of alternative energy technologies; Miriyo energy ni kansuru data shu sakusei chosa

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-03-01

The paper collects and arranges data on the unused energy in terms of examples of the introduction in Japan and other countries, policies, laws and rules, subsidy systems, etc. In the overview of the system, described was typical heat supply systems utilizing unused energy. As to concrete examples of the introduction in Japan, the examples were arranged by unused energy source, by temperature level, and by region, and a detailed data book of the typical introduction examples was made. As to examples overseas, data were arranged on the introduction mainly in Europe and the U.S. With relation to policies, laws and rules, and subsidy systems in Japan and overseas, investigated were policies, laws and rules, and subsidy systems concerning unused energy mostly in Japan, Europe and the U.S. As to the production quantity, the actual amount of introduction, and the predicted amount of introduction, survey on the effect and arrangement of the data were conducted in terms of typical two heat supply facilities utilizing unused energy. The paper adds information pertaining to the cost, main related companies and groups, the distribution cost, etc.

Natural resources youth training program (NRYTP), resource rangers 2010

Energy Technology Data Exchange (ETDEWEB)

NONE

2010-09-15

In 2010, for a second year, the natural resources youth training program (NRYTP) was developed in northern Manitoba thanks to Manitoba Keewatinowi Okimakanak Inc. (MKO) and the collaboration of 42 sponsors. 16 aboriginal youth representing six northern communities took part in the five-week program located at the Egg Lake camp. The objective was to provide these resources rangers with knowledge and training in the most widespread resource sectors in northern Manitoba, including mining, forestry and hydropower. Trainers and experts provided by industry partners offered training sessions, hands-on work experience and other activities to help resource rangers to acquire a better understanding of the employability in this field in the northern region and the knowledge and skills the resource-based careers require. Life and professional skills training was given by the camp staff and local professionals. On-site elders and cultural events also allowed the integration of a northern Cree cultural component. Three staff members, a cook and elders assisted daily the resource rangers. Many improvements and refinements have been made since the success of the 2009 program, including the involvement of a larger number of communities, program contributors and program graduates. The program length has doubled and the number of jobs created has increased, important cultural aspects were introduced and the overall expenses were reduced.

Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses.

Science.gov (United States)

Chang, Hsiao-Han; Huber, Roland G; Bond, Peter J; Grad, Yonatan H; Camerini, David; Maurer-Stroh, Sebastian; Lipsitch, Marc

2017-07-01

To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya viruses as well as polymorphism between different Zika virus strains. We used published protein sequences for the Zika virus and obtained protein sequences for the other viruses from the National Center for Biotechnology Information (NCBI) protein database or the NCBI virus variation resource. We used BLASTP to find regions of identity between viruses. We quantified the identity between the Zika virus and each of the other viruses, as well as within-Zika virus polymorphism for all amino acid k -mers across the proteome, with k ranging from 6 to 100. We assessed accessibility of protein fragments by calculating the solvent accessible surface area for the envelope and nonstructural-1 (NS1) proteins. In total, we identified 294 Zika virus protein fragments with both low proportion of identity with other viruses and low levels of polymorphisms among Zika virus strains. The list includes protein fragments from all Zika virus proteins, except NS3. NS4A has the highest number (190 k -mers) of protein fragments on the list. We provide a candidate list of protein fragments that could be used when developing a sensitive and specific serological test to detect previous Zika virus infections.

Cultural resource management and the necessity of cultural and natural resource collaboration

Science.gov (United States)

Roderick Kevin Donald; Kara Kusche; Collin Gaines

2005-01-01

Cultural Resource Specialists function as interpreters of past and present human behavior through the analysis of cultural/natural resources vital to human ecological sustainability. When developing short and long-term preservation strategies for cultural resources, it is more current and innovative for Cultural Resource Specialists to think of past human populations...

Competition over personal resources favors contribution to shared resources in human groups

DEFF Research Database (Denmark)

Barker, Jessie; Barclay, Pat; Reeve, H. Kern

2013-01-01

laboratory economic games with humans, comparing people's investment decisions in games with and without the options to compete over personal resources or invest in a group resource. Our results help explain why people cooperatively contribute to group resources, suggest how a tragedy of the commons may......Members of social groups face a trade-off between investing selfish effort for themselves and investing cooperative effort to produce a shared group resource. Many group resources are shared equitably: they may be intrinsically non-excludable public goods, such as vigilance against predators, or so...... large that there is little cost to sharing, such as cooperatively hunted big game. However, group members' personal resources, such as food hunted individually, may be monopolizable. In such cases, an individual may benefit by investing effort in taking others' personal resources, and in defending one...

ProtaBank: A repository for protein design and engineering data.

Science.gov (United States)

Wang, Connie Y; Chang, Paul M; Ary, Marie L; Allen, Benjamin D; Chica, Roberto A; Mayo, Stephen L; Olafson, Barry D

2018-03-25

We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Neuronal process structure and growth proteins are targets of heavy PTM regulation during brain development

DEFF Research Database (Denmark)

Edwards, Alistair V G; Schwämmle, Veit; Larsen, Martin Røssel

2014-01-01

UNLABELLED: Brain development is a process requiring precise control of many different cell types. One method to achieve this is through specific and temporally regulated modification of proteins in order to alter structure and function. Post-translational modification (PTM) of proteins is known...... on protein-level events, this study also provides significant insight into detailed roles for individual modified proteins in the developing brain, helping to advance the understanding of the complex protein-driven processes that underlie development. Finally, the use of a novel bioinformatic analytical tool...... provides one of the most comprehensive sets of individual PTM site regulation data for mammalian brain tissue. This will provide a valuable resource for those wishing to perform comparisons or meta-analyses of large scale PTMomic data, as are becoming increasingly common. Furthermore, being focussed...

A protein engineered to bind uranyl selectively and with femtomolar affinity

Science.gov (United States)

Zhou, Lu; Bosscher, Mike; Zhang, Changsheng; Özçubukçu, Salih; Zhang, Liang; Zhang, Wen; Li, Charles J.; Liu, Jianzhao; Jensen, Mark P.; Lai, Luhua; He, Chuan

2014-03-01

Uranyl (UO22+), the predominant aerobic form of uranium, is present in the ocean at a concentration of ~3.2 parts per 109 (13.7 nM) however, the successful enrichment of uranyl from this vast resource has been limited by the high concentrations of metal ions of similar size and charge, which makes it difficult to design a binding motif that is selective for uranyl. Here we report the design and rational development of a uranyl-binding protein using a computational screening process in the initial search for potential uranyl-binding sites. The engineered protein is thermally stable and offers very high affinity and selectivity for uranyl with a Kd of 7.4 femtomolar (fM) and >10,000-fold selectivity over other metal ions. We also demonstrated that the uranyl-binding protein can repeatedly sequester 30-60% of the uranyl in synthetic sea water. The chemical strategy employed here may be applied to engineer other selective metal-binding proteins for biotechnology and remediation applications.

Functional equivalency inferred from "authoritative sources" in networks of homologous proteins.

Science.gov (United States)

Natarajan, Shreedhar; Jakobsson, Eric

2009-06-12

A one-on-one mapping of protein functionality across different species is a critical component of comparative analysis. This paper presents a heuristic algorithm for discovering the Most Likely Functional Counterparts (MoLFunCs) of a protein, based on simple concepts from network theory. A key feature of our algorithm is utilization of the user's knowledge to assign high confidence to selected functional identification. We show use of the algorithm to retrieve functional equivalents for 7 membrane proteins, from an exploration of almost 40 genomes form multiple online resources. We verify the functional equivalency of our dataset through a series of tests that include sequence, structure and function comparisons. Comparison is made to the OMA methodology, which also identifies one-on-one mapping between proteins from different species. Based on that comparison, we believe that incorporation of user's knowledge as a key aspect of the technique adds value to purely statistical formal methods.

Performance of the Life Insurance Industry Under Pressure : Efficiency, Competition, and Consolidation

NARCIS (Netherlands)

Bikker, Jacob A.

2016-01-01

This article investigates efficiency and competition in the Dutch life insurance market by estimating unused scale economies and measuring efficiency-market share dynamics during 1995-2010. Large unused scale economies exist for small- and medium-sized life insurers, indicating that further

The Natural Resources Conservation Service land resource hierarchy and ecological sites

Science.gov (United States)

Resource areas of the NRCS have long been important to soil geography. At both regional and landscape scales, resource areas are used to stratify programs and practices based on geographical areas where resource concerns, problems, or treatment needs are similar. However, the inability to quantifiab...

Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication*

Science.gov (United States)

Kito, Keiji; Ito, Haruka; Nohara, Takehiro; Ohnishi, Mihoko; Ishibashi, Yuko; Takeda, Daisuke

2016-01-01

Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under

Knowledge and Natural Resources

DEFF Research Database (Denmark)

Bertelsen, Rasmus Gjedssø; Justinussen, Jens Christian Svabo

2016-01-01

Arctic economies are generally natural resource based economies, whether they are indigenous economies largely dependent on living on the land or industrialized economies depending on marine resources, mineral resources or fossil or renewable energy resources. However, the central role of knowledge...

Natural Biomolecules and Protein Aggregation: Emerging Strategies against Amyloidogenesis

Directory of Open Access Journals (Sweden)

Antonella Sgarbossa

2012-12-01

Full Text Available Biomolecular self-assembly is a fundamental process in all organisms. As primary components of the life molecular machinery, proteins have a vast array of resources available to them for self-assembly in a functional structure. Protein self-assembly, however, can also occur in an aberrant way, giving rise to non-native aggregated structures responsible for severe, progressive human diseases that have a serious social impact. Different neurodegenerative disorders, like Huntington’s, Alzheimer’s, and spongiform encephalopathy diseases, have in common the presence of insoluble protein aggregates, generally termed “amyloid,” that share several physicochemical features: a fibrillar morphology, a predominantly beta-sheet secondary structure, birefringence upon staining with the dye Congo red, insolubility in common solvents and detergents, and protease resistance. Conformational constrains, hydrophobic and stacking interactions can play a key role in the fibrillogenesis process and protein–protein and peptide–peptide interactions—resulting in self-assembly phenomena of peptides yielding fibrils—that can be modulated and influenced by natural biomolecules. Small organic molecules, which possess both hydrophilic and hydrophobic moieties able to bind to peptide/protein molecules through hydrogen bonds and hydrophobic and aromatic interactions, are potential candidates against amyloidogenesis. In this review some significant case examples will be critically discussed.

RICD: A rice indica cDNA database resource for rice functional genomics

Directory of Open Access Journals (Sweden)

Zhang Qifa

2008-11-01

Full Text Available Abstract Background The Oryza sativa L. indica subspecies is the most widely cultivated rice. During the last few years, we have collected over 20,000 putative full-length cDNAs and over 40,000 ESTs isolated from various cDNA libraries of two indica varieties Guangluai 4 and Minghui 63. A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones. Results Rice Indica cDNA Database (RICD is an online MySQL-PHP driven database with a user-friendly web interface. It allows investigators to query the cDNA clones by keyword, genome position, nucleotide or protein sequence, and putative function. It also provides a series of information, including sequences, protein domain annotations, similarity search results, SNPs and InDels information, and hyperlinks to gene annotation in both The Rice Annotation Project Database (RAP-DB and The TIGR Rice Genome Annotation Resource, expression atlas in RiceGE and variation report in Gramene of each cDNA. Conclusion The online rice indica cDNA database provides cDNA resource with comprehensive information to researchers for functional analysis of indica subspecies and for comparative genomics. The RICD database is available through our website http://www.ncgr.ac.cn/ricd.

INNOVATIVE TECHNOLOGY FOR THE PRODUCTION OF FOOD ADDITIVES FROM PUMPKIN PROCESSING SECONDARY RESOURCES

OpenAIRE

Kupin G. A.; Kornen N. N.; Matvienko A. N.; Shahray T. A.; Pershakova T. V.

2016-01-01

The article presents data characterizing the composition of macro and micronutrients from secondary resources of pumpkin processing – pumpkin pomace. We have found that extracts of pumpkin are valuable raw materials for the production of food additives, as they contain proteins, dietary fiber, including pectin and protopectin, minerals, as well as such biologically active substances as vitamin C, β- carotene and P-active substances using nuclear magnetic relaxation, it is shown that pretreatm...

NATURAL RESOURCES ASSESSMENT

International Nuclear Information System (INIS)

D.F. Fenster

2000-01-01

The purpose of this report is to summarize the scientific work that was performed to evaluate and assess the occurrence and economic potential of natural resources within the geologic setting of the Yucca Mountain area. The extent of the regional areas of investigation for each commodity differs and those areas are described in more detail in the major subsections of this report. Natural resource assessments have focused on an area defined as the ''conceptual controlled area'' because of the requirements contained in the U.S. Nuclear Regulatory Commission Regulation, 10 CFR Part 60, to define long-term boundaries for potential radionuclide releases. New requirements (proposed 10 CFR Part 63 [Dyer 1999]) have obviated the need for defining such an area. However, for the purposes of this report, the area being discussed, in most cases, is the previously defined ''conceptual controlled area'', now renamed the ''natural resources site study area'' for this report (shown on Figure 1). Resource potential can be difficult to assess because it is dependent upon many factors, including economics (demand, supply, cost), the potential discovery of new uses for resources, or the potential discovery of synthetics to replace natural resource use. The evaluations summarized are based on present-day use and economic potential of the resources. The objective of this report is to summarize the existing reports and information for the Yucca Mountain area on: (1) Metallic mineral and mined energy resources (such as gold, silver, etc., including uranium); (2) Industrial rocks and minerals (such as sand, gravel, building stone, etc.); (3) Hydrocarbons (including oil, natural gas, tar sands, oil shales, and coal); and (4) Geothermal resources. Groundwater is present at the Yucca Mountain site at depths ranging from 500 to 750 m (about 1,600 to 2,500 ft) below the ground surface. Groundwater resources are not discussed in this report, but are planned to be included in the hydrology

Exploiting genomic data to identify proteins involved in abalone reproduction.

Science.gov (United States)

Mendoza-Porras, Omar; Botwright, Natasha A; McWilliam, Sean M; Cook, Mathew T; Harris, James O; Wijffels, Gene; Colgrave, Michelle L

2014-08-28

Aside from their critical role in reproduction, abalone gonads serve as an indicator of sexual maturity and energy balance, two key considerations for effective abalone culture. Temperate abalone farmers face issues with tank restocking with highly marketable abalone owing to inefficient spawning induction methods. The identification of key proteins in sexually mature abalone will serve as the foundation for a greater understanding of reproductive biology. Addressing this knowledge gap is the first step towards improving abalone aquaculture methods. Proteomic profiling of female and male gonads of greenlip abalone, Haliotis laevigata, was undertaken using liquid chromatography-mass spectrometry. Owing to the incomplete nature of abalone protein databases, in addition to searching against two publicly available databases, a custom database comprising genomic data was used. Overall, 162 and 110 proteins were identified in females and males respectively with 40 proteins common to both sexes. For proteins involved in sexual maturation, sperm and egg structure, motility, acrosomal reaction and fertilization, 23 were identified only in females, 18 only in males and 6 were common. Gene ontology analysis revealed clear differences between the female and male protein profiles reflecting a higher rate of protein synthesis in the ovary and higher metabolic activity in the testis. A comprehensive mass spectrometry-based analysis was performed to profile the abalone gonad proteome providing the foundation for future studies of reproduction in abalone. Key proteins involved in both reproduction and energy balance were identified. Genomic resources were utilised to build a database of molluscan proteins yielding >60% more protein identifications than in a standard workflow employing public protein databases. Copyright © 2014 Elsevier B.V. All rights reserved.

Renewable energy resources

DEFF Research Database (Denmark)

Ellabban, Omar S.; Abu-Rub, Haitham A.; Blaabjerg, Frede

2014-01-01

Electric energy security is essential, yet the high cost and limited sources of fossil fuels, in addition to the need to reduce greenhouse gasses emission, have made renewable resources attractive in world energy-based economies. The potential for renewable energy resources is enormous because...... they can, in principle, exponentially exceed the world's energy demand; therefore, these types of resources will have a significant share in the future global energy portfolio, much of which is now concentrating on advancing their pool of renewable energy resources. Accordingly, this paper presents how...... renewable energy resources are currently being used, scientific developments to improve their use, their future prospects, and their deployment. Additionally, the paper represents the impact of power electronics and smart grid technologies that can enable the proportionate share of renewable energy...

Unused energy sources inducing minimal pollution

Energy Technology Data Exchange (ETDEWEB)

Voss, A [Inst. fur Reaktorentwicklung, Kernforschungsanlage Julich GmbH, German Federal Republic

1974-01-01

The contribution of hydroelectricity to the growing worldwide energy demand is not expected to exceed 6%. As the largest amount of hydroelectric potential is located in developing nations, it will find its greatest development outside the currently industrialized sphere. The potential of 60 GW ascribed to tidal and geothermal energy is a negligible quantity. Solar energy represents an essentially inexhaustible source, but technological problems will preclude any major contribution from it during this century. The environmental problems caused by these 'new' energy sources are different from those engendered by fossil and nuclear power plants, but they are not negligible. It is irresponsible and misleading to describe them as pollution-free.

How to Dispose of Unused Medicines

Science.gov (United States)

... substances — have instructions for flushing to reduce the danger of overdose from unintentional or illegal use. One ... لعربية | Kreyòl Ayisyen | Français | Polski | Português | Italiano | Deutsch | 日本語 | ف ...

The Global Resource Nexus

NARCIS (Netherlands)

Ridder, M. de; Duijne, F. van; Jong, S. de; Jones, J.; Luit, E. van; Bekkers, F.F.; Auping, W.

2014-01-01

Supply and demand of resources are connected in a complex way. This interconnectivity has been framed as the global resource nexus and can conceivebly include all types of resources. This study focus on the nexus of five essential natural resources: land, food, energy, water and minerals. Together

Self managing experiment resources

International Nuclear Information System (INIS)

Stagni, F; Ubeda, M; Charpentier, P; Tsaregorodtsev, A; Romanovskiy, V; Roiser, S; Graciani, R

2014-01-01

Within this paper we present an autonomic Computing resources management system, used by LHCb for assessing the status of their Grid resources. Virtual Organizations Grids include heterogeneous resources. For example, LHC experiments very often use resources not provided by WLCG, and Cloud Computing resources will soon provide a non-negligible fraction of their computing power. The lack of standards and procedures across experiments and sites generated the appearance of multiple information systems, monitoring tools, ticket portals, etc... which nowadays coexist and represent a very precious source of information for running HEP experiments Computing systems as well as sites. These two facts lead to many particular solutions for a general problem: managing the experiment resources. In this paper we present how LHCb, via the DIRAC interware, addressed such issues. With a renewed Central Information Schema hosting all resources metadata and a Status System (Resource Status System) delivering real time information, the system controls the resources topology, independently of the resource types. The Resource Status System applies data mining techniques against all possible information sources available and assesses the status changes, that are then propagated to the topology description. Obviously, giving full control to such an automated system is not risk-free. Therefore, in order to minimise the probability of misbehavior, a battery of tests has been developed in order to certify the correctness of its assessments. We will demonstrate the performance and efficiency of such a system in terms of cost reduction and reliability.

Resource Structuring and Ambidexterity

DEFF Research Database (Denmark)

Ma, Yucheng; Li, Peter Ping

-shaped effect on organizational ambidexterity in new ventures. Further, because of the traditional culture and economic transition characteristics, new ventures actively leverage managerial ties as key social relations to obtain special resources or nurture business transactions. We propose that ties with other......Focusing on how resource structuring mechanisms and managerial ties influence organizational ambidexterity of new ventures in emerging economy, this study explores the effects of resource structuring mechanisms (i.e., resource acquiring and resource accumulating) on organizational ambidexterity....... It further examines the moderating effects of managerial ties, (i.e., ties with other firms and ties with the government) on the above relationships. Survey data from China¡¯s 202 new ventures demonstrates that the resource acquiring has an inverted U-shaped effect whereas the resource accumulating has a U...

Characteristics of foraging sites and protein status in wintering muskoxen: insights from isotopes of nitrogen

Science.gov (United States)

Gustine, David D.; Barboza, Perry S.; Lawler, James P.; Arthur, Stephen M.; Shults, Brad S.; Persons, Kate; Adams, Layne G.

2011-01-01

Identifying links between nutritional condition of individuals and population trajectories greatly enhances our understanding of the ecology, conservation, and management of wildlife. For northern ungulates, the potential impacts of a changing climate to populations are predicted to be nutritionally mediated through an increase in the severity and variance in winter conditions. Foraging conditions and the availability of body protein as a store for reproduction in late winter may constrain productivity in northern ungulates, yet the link between characteristics of wintering habitats and protein status has not been established for a wild ungulate. We used a non‐invasive proxy of protein status derived from isotopes of N in excreta to evaluate the influence of winter habitats on the protein status of muskoxen in three populations in Alaska (2005–2008). Multiple regression and an information‐theoretic approach were used to compare models that evaluated the influence of population, year, and characteristics of foraging sites (components of diet and physiography) on protein status for groups of muskoxen. The observed variance in protein status among groups of muskoxen across populations and years was partially explained (45%) by local foraging conditions that affected forage availability. Protein status improved for groups of muskoxen as the amount of graminoids in the diet increased (−0.430 ± 0.31, β± 95% CI) and elevation of foraging sites decreased (0.824 ± 0.67). Resources available for reproduction in muskoxen are highly dependent upon demographic, environmental, and physiographic constraints that affect forage availability in winter. Due to their very sedentary nature in winter, muskoxen are highly susceptible to localized foraging conditions; therefore, the spatial variance in resource availability may exert a strong effect on productivity. Consequently, there is a clear need to account for climate–topography effects in winter at multiple scales

Resources for our Future. Key issues and best practices in resource efficiency

Energy Technology Data Exchange (ETDEWEB)

Weterings, R.; Bastein, T.; Tukker, A. [TNO, Delft (Netherlands); Rademaker, M.; De Ridder, M. [The Hague Centre for Strategic studies HCSS, Den Haag (Netherlands)

2013-08-15

This book provides an analysis of the issues surrounding international resources and inspiring accounts of industrial best practices. The book consists of two distinct parts. The first part of the book brings together the results of years of research into the geopolitical, economic and ecological dimensions of material scarcity and resource efficiency. Chapter 2 discusses the main challenges and constraints related to the use of energy resources, water and land, industrial and metallic minerals, construction minerals and biotic resources, including water use and ecosystem degradation. The chapter also addresses important linkages between these various resources. Chapter 3 describes the international trends that are shaping the geopolitics of natural resources and looks at the implications for Europe and the Netherlands. Chapter 4 presents a wide range of strategies by which governments, producers and consumers may contribute to the more sustainable use of natural resources. The second part of the book describes 21 inspiring best practices in resource efficiency in a variety of industrial sectors. Based on a series of interviews with industrial pioneers, these chapters relate their first-hand experiences in improving resource efficiency. These business cases demonstrate that innovation and entrepreneurship can result in substantial improvements in resource efficiency. Chapter 5 focuses on best practices in the built environment, where substantial amounts of energy and minerals are used. Chapter 6 presents four ambitious strategies to promote sustainable food production and consumption. Chapter 7 describes recent developments in the chemical process industry, which produces most of the ingredients, compounds and semi-products for the vast range of products used by society. Chapter 8 provides four examples of the state-of-the-art in resource efficiency in the metal and high-tech industries. This chapter presents four business cases highlighting the benefits of the

When resources get sparse

DEFF Research Database (Denmark)

Graungaard, Anette Hauskov; Andersen, John Sahl; Skov, Liselotte

2011-01-01

resources through positive cognitive reappraisals of their circumstances, the consequences of those circumstances and their coping possibilities. Nine main coping strategies were identified constituting transformative pathways in resource-creation. A theory of resource-creation is proposed as an addition...... coped with parenting a disabled child and how they maintained their energy and personal resources. We explored parents' experiences, coping and resources over a two-year period after their child was diagnosed with a severely disabling condition using a qualitative, longitudinal approach. Findings were...... to the current understanding of coping and the role of positive emotions. Coping and resources were found to be closely interrelated and portals of intervention are discussed....

Sharing network resources

CERN Document Server

Parekh, Abhay

2014-01-01

Resource Allocation lies at the heart of network control. In the early days of the Internet the scarcest resource was bandwidth, but as the network has evolved to become an essential utility in the lives of billions, the nature of the resource allocation problem has changed. This book attempts to describe the facets of resource allocation that are most relevant to modern networks. It is targeted at graduate students and researchers who have an introductory background in networking and who desire to internalize core concepts before designing new protocols and applications. We start from the fun

World energy resources

Science.gov (United States)

Clerici, A.; Alimonti, G.

2015-08-01

As energy is the main "fuel" for social and economic development and since energy-related activities have significant environmental impacts, it is important for decision-makers to have access to reliable and accurate data in an user-friendly format. The World Energy Council (WEC) has for decades been a pioneer in the field of energy resources and every three years publishes its flagship report Survey of Energy Resources. A commented analysis in the light of latest data summarized in such a report, World Energy Resources (WER) 2013, is presented together with the evolution of the world energy resources over the last twenty years.

The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.

Science.gov (United States)

Tenenbaum, Jessica D; Whetzel, Patricia L; Anderson, Kent; Borromeo, Charles D; Dinov, Ivo D; Gabriel, Davera; Kirschner, Beth; Mirel, Barbara; Morris, Tim; Noy, Natasha; Nyulas, Csongor; Rubenson, David; Saxman, Paul R; Singh, Harpreet; Whelan, Nancy; Wright, Zach; Athey, Brian D; Becich, Michael J; Ginsburg, Geoffrey S; Musen, Mark A; Smith, Kevin A; Tarantal, Alice F; Rubin, Daniel L; Lyster, Peter

2011-02-01

The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. In addition, an increasing number of shared electronic resources have been developed. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be aware of the myriad resources available, or to effectively perform resource discovery when the need arises. In this paper, we describe the development and use of the Biomedical Resource Ontology (BRO) to enable semantic annotation and discovery of biomedical resources. We also describe the Resource Discovery System (RDS) which is a federated, inter-institutional pilot project that uses the BRO to facilitate resource discovery on the Internet. Through the RDS framework and its associated Biositemaps infrastructure, the BRO facilitates semantic search and discovery of biomedical resources, breaking down barriers and streamlining scientific research that will improve human health. Copyright © 2010 Elsevier Inc. All rights reserved.

Vegetable and cereal protein exploitation for fish feed

CSIR Research Space (South Africa)

Erasmus, C

2009-01-01

Full Text Available cultivated fish (Naylor et al., 2000). Therefore, considerable amounts of resources are currently being used worldwide to evaluate the nutritional quality and possible health implications of alternative plant-based feed- stuffs with the potential... and storage. All of this needs to be implemented without excessive costs, as the feed costs usually make up around 40–75% of the total running cost of rearing fish (Young and Muir, 2000). As the challenges for utilising legume and cereal protein sources...

State Electricity Regulatory Policy and Distributed Resources: Distributed Resources and Electric System Reliability

Energy Technology Data Exchange (ETDEWEB)

Cowart, R.; Harrington, C.; Moskovitz, D.; Shirley, W.; Weston, F.; Sedano, R.

2002-10-01

Designing and implementing credit-based pilot programs for distributed resources distribution is a low-cost, low-risk opportunity to find out how these resources can help defer or avoid costly electric power system (utility grid) distribution upgrades. This report describes implementation options for deaveraged distribution credits and distributed resource development zones. Developing workable programs implementing these policies can dramatically increase the deployment of distributed resources in ways that benefit distributed resource vendors, users, and distribution utilities. This report is one in the State Electricity Regulatory Policy and Distributed Resources series developed under contract to NREL (see Annual Technical Status Report of the Regulatory Assistance Project: September 2000-September 2001, NREL/SR-560-32733). Other titles in this series are: (1) Accommodating Distributed Resources in Wholesale Markets, NREL/SR-560-32497; (2) Distributed Resources and Electric System Re liability, NREL/SR-560-32498; (3) Distribution System Cost Methodologies for Distributed Generation, NREL/SR-560-32500; (4) Distribution System Cost Methodologies for Distributed Generation Appendices, NREL/SR-560-32501.

Duality between resource reservation and proportional share resource allocation

Science.gov (United States)

Stoica, Ion; Abdel-Wahab, Hussein; Jeffay, Kevin

1997-01-01

We describe anew framework for resource allocation that unifies the well-known proportional share and resource reservation policies. Each client is characterized by two parameters: a weight that represents the rate at which the client 'pays' for the resource, and a share that represents the fraction of the resource that the client should receive. A fixed rate corresponds to a proportional share allocation, while a fixed share corresponds to a reservation. Furthermore, rates and shares are duals of each other. Once one parameters is fixed the other becomes fixed as well. If a client asks for a fixed share then the level of competition for the resource determines the rate at which it has to pay, while if the rate is fixed, level of competition determines the service time the clients should receive. To implement this framework we use a new proportional share algorithm, called earliest eligible virtual deadline first, that achieves optical accuracy in the rates at which process execute. This makes it possible to provide support for highly predictable, real-time services. As a proof of concept we have implemented a prototype of a CPU scheduler under the FreeBSD operating system. The experimental results show that our scheduler achieves the goal of providing integrated support for batch and real-time applications.

Plasticity in learning causes immediate and trans-generational changes in allocation of resources.

Science.gov (United States)

Snell-Rood, Emilie C; Davidowitz, Goggy; Papaj, Daniel R

2013-08-01

Plasticity in the development and expression of behavior may allow organisms to cope with novel and rapidly changing environments. However, plasticity itself may depend on the developmental experiences of an individual. For instance, individuals reared in complex, enriched environments develop enhanced cognitive abilities as a result of increased synaptic connections and neurogenesis. This suggests that costs associated with behavioral plasticity-in particular, increased investment in "self" at the expense of reproduction-may also be flexible. Using butterflies as a system, this work tests whether allocation of resources changes as a result of experiences in "difficult" environments that require more investment in learning. We contrast allocation of resources among butterflies with experience in environments that vary in the need for learning. Butterflies with experience searching for novel (i.e., red) hosts, or searching in complex non-host environments, allocate more resources (protein and carbohydrate reserves) to their own flight muscle. In addition, butterflies with experience in these more difficult environments allocate more resources per individual offspring (i.e., egg size and/or lipid reserves). This results in a mother's experience having significant effects on the growth of her offspring (i.e., dry mass and wing length). A separate study showed this re-allocation of resources comes at the expense of lifetime fecundity. These results suggest that investment in learning, and associated changes in life history, can be adjusted depending on an individual's current need, and their offspring's future needs, for learning.

Large-scale identification of odorant-binding proteins and chemosensory proteins from expressed sequence tags in insects

Science.gov (United States)

2009-01-01

Background Insect odorant binding proteins (OBPs) and chemosensory proteins (CSPs) play an important role in chemical communication of insects. Gene discovery of these proteins is a time-consuming task. In recent years, expressed sequence tags (ESTs) of many insect species have accumulated, thus providing a useful resource for gene discovery. Results We have developed a computational pipeline to identify OBP and CSP genes from insect ESTs. In total, 752,841 insect ESTs were examined from 54 species covering eight Orders of Insecta. From these ESTs, 142 OBPs and 177 CSPs were identified, of which 117 OBPs and 129 CSPs are new. The complete open reading frames (ORFs) of 88 OBPs and 123 CSPs were obtained by electronic elongation. We randomly chose 26 OBPs from eight species of insects, and 21 CSPs from four species for RT-PCR validation. Twenty two OBPs and 16 CSPs were confirmed by RT-PCR, proving the efficiency and reliability of the algorithm. Together with all family members obtained from the NCBI (OBPs) or the UniProtKB (CSPs), 850 OBPs and 237 CSPs were analyzed for their structural characteristics and evolutionary relationship. Conclusions A large number of new OBPs and CSPs were found, providing the basis for deeper understanding of these proteins. In addition, the conserved motif and evolutionary analysis provide some new insights into the evolution of insect OBPs and CSPs. Motif pattern fine-tune the functions of OBPs and CSPs, leading to the minor difference in binding sex pheromone or plant volatiles in different insect Orders. PMID:20034407

Timber resource statistics for the central coast resource area of California.

Science.gov (United States)

Karen L. Waddell; Patricia M. Bassett

1996-01-01

This report is a summary of timber resource statistics for the Central Coast Resource Area of California, which includes Alameda, Contra Costa, Marin, Monterey, San Benito, San Francisco, San Luis Obispo, San Mateo, Santa Barbara, Santa Clara, Santa Cruz, Solano, and Ventura Counties. Data were collected as part of a statewide multi-resource inventory. The inventory...

Uranium resources

International Nuclear Information System (INIS)

Gangloff, A.

1978-01-01

It is first indicated how to evaluate the mining resources as a function of the cost of production and the degree of certainty in the knowledge of the deposit. A table is given of the world resources (at the beginning 1977) and resources and reserves are compared. There is a concordance between requirements and possible production until 1990. The case of France is examined: known reserves, present and future prospection, present production (In 1978 2200 T of U metal will be produced from 3 French processing plants), production coming from Cogema. A total production of 2000 T in 1980 and 10.000 in 1985 is expected [fr

Pesticide behaviour in pumice and rockwool growth media; adsorption and transformation of metalaxyl, oxamyl and carbendazim

NARCIS (Netherlands)

Matser, A.M.; Leistra, M.

1997-01-01

Interactions of pesticides with substrates were studied. The adsorption of metalaxyl, oxamyl and carbendazim on unused pumice and rock-wool is much weaker than that on soils. The transformation rate of the pesticides in nutrient solution in contact with unused substrates is low. Metalaxyl is

NATURAL RESOURCES ASSESSMENT

Energy Technology Data Exchange (ETDEWEB)

D.F. Fenster

2000-12-11

The purpose of this report is to summarize the scientific work that was performed to evaluate and assess the occurrence and economic potential of natural resources within the geologic setting of the Yucca Mountain area. The extent of the regional areas of investigation for each commodity differs and those areas are described in more detail in the major subsections of this report. Natural resource assessments have focused on an area defined as the ''conceptual controlled area'' because of the requirements contained in the U.S. Nuclear Regulatory Commission Regulation, 10 CFR Part 60, to define long-term boundaries for potential radionuclide releases. New requirements (proposed 10 CFR Part 63 [Dyer 1999]) have obviated the need for defining such an area. However, for the purposes of this report, the area being discussed, in most cases, is the previously defined ''conceptual controlled area'', now renamed the ''natural resources site study area'' for this report (shown on Figure 1). Resource potential can be difficult to assess because it is dependent upon many factors, including economics (demand, supply, cost), the potential discovery of new uses for resources, or the potential discovery of synthetics to replace natural resource use. The evaluations summarized are based on present-day use and economic potential of the resources. The objective of this report is to summarize the existing reports and information for the Yucca Mountain area on: (1) Metallic mineral and mined energy resources (such as gold, silver, etc., including uranium); (2) Industrial rocks and minerals (such as sand, gravel, building stone, etc.); (3) Hydrocarbons (including oil, natural gas, tar sands, oil shales, and coal); and (4) Geothermal resources. Groundwater is present at the Yucca Mountain site at depths ranging from 500 to 750 m (about 1,600 to 2,500 ft) below the ground surface. Groundwater resources are not discussed in this

Uranium resource assessments

International Nuclear Information System (INIS)

1981-01-01

The objective of this investigation is to examine what is generally known about uranium resources, what is subject to conjecture, how well do the explorers themselves understand the occurrence of uranium, and who are the various participants in the exploration process. From this we hope to reach a better understanding of the quality of uranium resource estimates as well as the nature of the exploration process. The underlying questions will remain unanswered. But given an inability to estimate precisely our uranium resources, how much do we really need to know. To answer this latter question, the various Department of Energy needs for uranium resource estimates are examined. This allows consideration of whether or not given the absence of more complete long-term supply data and the associated problems of uranium deliverability for the electric utility industry, we are now threatened with nuclear power plants eventually standing idle due to an unanticipated lack of fuel for their reactors. Obviously this is of some consequence to the government and energy consuming public. The report is organized into four parts. Section I evaluates the uranium resource data base and the various methodologies of resource assessment. Part II describes the manner in which a private company goes about exploring for uranium and the nature of its internal need for resource information. Part III examines the structure of the industry for the purpose of determining the character of the industry with respect to resource development. Part IV arrives at conclusions about the emerging pattern of industrial behavior with respect to uranium supply and the implications this has for coping with national energy issues

Oligomeric protein structure networks: insights into protein-protein interactions

Directory of Open Access Journals (Sweden)

Brinda KV

2005-12-01

Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

Virtual Machine Scheduling in Dedicated Computing Clusters

CERN Document Server

Boettger, Stefan; Zicari, V Roberto

2014-01-08

Time-critical applications process a continuous stream of input data and have to meet specific timing constraints. A common approach to ensure that such an application satisfies its constraints is over-provisioning: The application is deployed in a dedicated cluster environment with enough processing power to achieve the target performance for every specified data input rate. This approach comes with a drawback: At times of decreased data input rates, the cluster resources are not fully utilized. A typical use case is the HLT-Chain application that processes physics data at runtime of the ALICE experiment at CERN. From a perspective of cost and efficiency it is desirable to exploit temporarily unused cluster resources. Existing approaches aim for that goal by running additional applications. These approaches, however, a) lack in flexibility to dynamically grant the time-critical application the resources it needs, b) are insufficient for isolating the time-critical application from harmful side-effects i...

[Application of job demands-resources model in research on relationships between job satisfaction, job resources, individual resources and job demands].

Science.gov (United States)

Potocka, Adrianna; Waszkowska, Małgorzata

2013-01-01

The aim of this study was to explore the relationships between job demands, job resourses, personal resourses and job satisfaction and to assess the usefulness of the Job Demands-Resources (JD-R) model in the explanation of these phenomena. The research was based on a sample of 500 social workers. The "Psychosocial Factors" and "Job satisfaction" questionnaires were used to test the hypothesis. The results showed that job satisfaction increased with increasing job accessibility and personal resources (r = 0.44; r = 0.31; p job resources and job demands [F(1.474) = 4.004; F(1.474) = 4.166; p job satisfaction. Moreover, interactions between job demands and job resources [F(3,474) = 2.748; p job demands and personal resources [F(3.474) = 3.021; p job satisfaction. The post hoc tests showed that 1) in low job demands, but high job resources employees declared higher job satisfaction, than those who perceived them as medium (p = 0.0001) or low (p = 0.0157); 2) when the level of job demands was perceived as medium, employees with high personal resources declared significantly higher job satisfaction than those with low personal resources (p = 0.0001). The JD-R model can be used to investigate job satisfaction. Taking into account fundamental factors of this model, in organizational management there are possibilities of shaping job satisfaction among employees.

World energy resources

Directory of Open Access Journals (Sweden)

Clerici A.

2015-01-01

Full Text Available As energy is the main “fuel” for social and economic development and since energy-related activities have significant environmental impacts, it is important for decision-makers to have access to reliable and accurate data in an user-friendly format. The World Energy Council (WEC has for decades been a pioneer in the field of energy resources and every three years publishes its flagship report Survey of Energy Resources. A commented analysis in the light of latest data summarized in such a report, World Energy Resources (WER 2013, is presented together with the evolution of the world energy resources over the last twenty years.

High performance workflow implementation for protein surface characterization using grid technology

Directory of Open Access Journals (Sweden)

Clematis Andrea

2005-12-01

Full Text Available Abstract Background This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the exposed residues of the protein surface. The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites. Methods Workflows are very common in Bioinformatics because they allow to process large quantities of data by delegating the management of resources to the information streaming. Grid technology optimizes the computational load during the different workflow steps, dividing the more expensive tasks into a set of small jobs. Results Grid technology allows efficient database management, a crucial problem for obtaining good results in Bioinformatics applications. The proposed workflow is implemented to integrate huge amounts of data and the results themselves must be stored into a relational database, which results as the added value to the global knowledge. Conclusion A web interface has been developed to make this technology accessible to grid users. Once the workflow has started, by means of the simplified interface, it is possible to follow all the different steps throughout the data processing. Eventually, when the workflow has been terminated, the different features of the protein, like the amino acids exposed on the protein surface, can be compared with the data present in the output database.

The proteome response to amyloid protein expression in vivo.

Directory of Open Access Journals (Sweden)

Ricardo A Gomes

Full Text Available Protein misfolding disorders such as Alzheimer, Parkinson and transthyretin amyloidosis are characterized by the formation of protein amyloid deposits. Although the nature and location of the aggregated proteins varies between different diseases, they all share similar molecular pathways of protein unfolding, aggregation and amyloid deposition. Most effects of these proteins are likely to occur at the proteome level, a virtually unexplored reality. To investigate the effects of an amyloid protein expression on the cellular proteome, we created a yeast expression system using human transthyretin (TTR as a model amyloidogenic protein. We used Saccharomyces cerevisiae, a living test tube, to express native TTR (non-amyloidogenic and the amyloidogenic TTR variant L55P, the later forming aggregates when expressed in yeast. Differential proteome changes were quantitatively analyzed by 2D-differential in gel electrophoresis (2D-DIGE. We show that the expression of the amyloidogenic TTR-L55P causes a metabolic shift towards energy production, increased superoxide dismutase expression as well as of several molecular chaperones involved in protein refolding. Among these chaperones, members of the HSP70 family and the peptidyl-prolyl-cis-trans isomerase (PPIase were identified. The latter is highly relevant considering that it was previously found to be a TTR interacting partner in the plasma of ATTR patients but not in healthy or asymptomatic subjects. The small ubiquitin-like modifier (SUMO expression is also increased. Our findings suggest that refolding and degradation pathways are activated, causing an increased demand of energetic resources, thus the metabolic shift. Additionally, oxidative stress appears to be a consequence of the amyloidogenic process, posing an enhanced threat to cell survival.

Defense Human Resources Activity > PERSEREC

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Biological activities and applications of dioscorins, the major tuber storage proteins of yam.

Science.gov (United States)

Lu, Yeh-Lin; Chia, Cho-Yun; Liu, Yen-Wenn; Hou, Wen-Chi

2012-01-01

Yam tubers, a common tuber crop and an important traditional Chinese medicine in Taiwan, have many bioactive substances, including phenolic compounds, mucilage polysaccharides, steroidal saponins and proteins. Among the total soluble proteins, 80% of them are dioscorins. In the past two decades, many studies showed that dioscorins exhibited biological activities both in vitro and in vivo, including the enzymatic, antioxidant, antihypertensive, immunomodulatory, lectin activities and the protecting role on airway epithelial cells against allergens in vitro. Some of these activities are survived after chemical, heating process or enzymatic digestion. Despite of lacking the intact structural information and the detail action mechanisms in the cells, yam dioscorins are potential resources for developing as functional foods and interesting targets for food protein researchers.

Biological Activities and Applications of Dioscorins, the Major Tuber Storage Proteins of Yam

Directory of Open Access Journals (Sweden)

Yeh-Lin Lu

2012-01-01

Full Text Available Yam tubers, a common tuber crop and an important traditional Chinese medicine in Taiwan, have many bioactive substances, including phenolic compounds, mucilage polysaccharides, steroidal saponins and proteins. Among the total soluble proteins, 80% of them are dioscorins. In the past two decades, many studies showed that dioscorins exhibited biological activities both in vitro and in vivo, including the enzymatic, antioxidant, antihypertensive, immunomodulatory, lectin activities and the protecting role on airway epithelial cells against allergens in vitro. Some of these activities are survived after chemical, heating process or enzymatic digestion. Despite of lacking the intact structural information and the detail action mechanisms in the cells, yam dioscorins are potential resources for developing as functional foods and interesting targets for food protein researchers.

PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome.

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Kroeze, Wesley K; Sassano, Maria F; Huang, Xi-Ping; Lansu, Katherine; McCorvy, John D; Giguère, Patrick M; Sciaky, Noah; Roth, Bryan L

2015-05-01

G protein-coupled receptors (GPCRs) are essential mediators of cellular signaling and are important targets of drug action. Of the approximately 350 nonolfactory human GPCRs, more than 100 are still considered to be 'orphans' because their endogenous ligands remain unknown. Here, we describe a unique open-source resource that allows interrogation of the druggable human GPCRome via a G protein-independent β-arrestin-recruitment assay. We validate this unique platform at more than 120 nonorphan human GPCR targets, demonstrate its utility for discovering new ligands for orphan human GPCRs and describe a method (parallel receptorome expression and screening via transcriptional output, with transcriptional activation following arrestin translocation (PRESTO-Tango)) for the simultaneous and parallel interrogation of the entire human nonolfactory GPCRome.

Protein nanoparticles for therapeutic protein delivery.

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Herrera Estrada, L P; Champion, J A

2015-06-01

Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

Using constitutive activity to define appropriate high-throughput screening assays for orphan g protein-coupled receptors.

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Ngo, Tony; Coleman, James L J; Smith, Nicola J

2015-01-01

Orphan G protein-coupled receptors represent an underexploited resource for drug discovery but pose a considerable challenge for assay development because their cognate G protein signaling pathways are often unknown. In this methodological chapter, we describe the use of constitutive activity, that is, the inherent ability of receptors to couple to their cognate G proteins in the absence of ligand, to inform the development of high-throughput screening assays for a particular orphan receptor. We specifically focus on a two-step process, whereby constitutive G protein coupling is first determined using yeast Gpa1/human G protein chimeras linked to growth and β-galactosidase generation. Coupling selectivity is then confirmed in mammalian cells expressing endogenous G proteins and driving accumulation of transcription factor-fused luciferase reporters specific to each of the classes of G protein. Based on these findings, high-throughput screening campaigns can be performed on the already miniaturized mammalian reporter system.

Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors*

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Deshmukh, Atul S.; Murgia, Marta; Nagaraj, Nagarjuna; Treebak, Jonas T.; Cox, Jürgen; Mann, Matthias

2015-01-01

Skeletal muscle constitutes 40% of individual body mass and plays vital roles in locomotion and whole-body metabolism. Proteomics of skeletal muscle is challenging because of highly abundant contractile proteins that interfere with detection of regulatory proteins. Using a state-of-the art MS workflow and a strategy to map identifications from the C2C12 cell line model to tissues, we identified a total of 10,218 proteins, including skeletal muscle specific transcription factors like myod1 and myogenin and circadian clock proteins. We obtain absolute abundances for proteins expressed in a muscle cell line and skeletal muscle, which should serve as a valuable resource. Quantitation of protein isoforms of glucose uptake signaling pathways and in glucose and lipid metabolic pathways provides a detailed metabolic map of the cell line compared with tissue. This revealed unexpectedly complex regulation of AMP-activated protein kinase and insulin signaling in muscle tissue at the level of enzyme isoforms. PMID:25616865

Disposal of household pharmaceuticals in insular communities: social attitude, behaviour evaluation and prevention activities.

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Zorpas, Antonis A; Dimitriou, Maria; Voukkali, Irene

2017-06-25

The increase in medicine and drug consumption have resulted in identifying these emerging pollutants in all aquatic compartments, ranging from surface water and groundwater resources to the marine environment. Pharmaceuticals are an indispensable part of life today. A large number of pharmaceuticals are used in a daily basis in the treatment, prevention, cure or diagnosis of diseases or to otherwise enhance people's physical or mental well-being. This paper focuses on the evaluation of the attitude of citizens in Cyprus regarding the disposal of pharmaceuticals as well as to identify the main reasons why pharmaceutical wastes are produced. The result indicted that in Cyprus, there is lack of data regarding the amount of pharmaceutical wastes that are discarded into household waste and sinks. The survey audit showed that 86.6% of men's and 83.3% of women's used pharmacy with or without doctor's recipe. Social behaviour is considered to be the most significant reason that pharmaceutical are produced. The results indicated that, citizens mainly keep unused medicines and drugs at home in case they are needed again as well as patients use to cut-off or to reduce their treatment in case that on the first 3-6 days they feel better. The survey indicated that the main disposal method of unused or expired medicines and drugs is in household waste followed from the sink and the toilet. Furthermore, the main disposal solution of unused or expired medicines and drugs remain the household bin as well as the sewage system (sink or toilet), while a percentage more than 55% of the participants indicated that they will follow a specific waste management program if existing in place. Moreover, in order to reduce the production of pharmaceutical wastes, specific prevention activities must be considered.

Household medical waste disposal policy in Israel.

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Barnett-Itzhaki, Zohar; Berman, Tamar; Grotto, Itamar; Schwartzberg, Eyal

2016-01-01

Large amounts of expired and unused medications accumulate in households. This potentially exposes the public to hazards due to uncontrolled use of medications. Most of the expired or unused medications that accumulate in households (household medical waste) is thrown to the garbage or flushed down to the sewage, potentially contaminating waste-water, water resources and even drinking water. There is evidence that pharmaceutical active ingredients reach the environment, including food, however the risk to public health from low level exposure to pharmaceuticals in the environment is currently unknown. In Israel, there is no legislation regarding household medical waste collection and disposal. Furthermore, only less than 14 % of Israelis return unused medications to Health Maintenance Organization (HMO) pharmacies. In this study, we investigated world-wide approaches and programs for household medical waste collection and disposal. In many countries around the world there are programs for household medical waste collection. In many countries there is legislation to address the issue of household medical waste, and this waste is collected in hospitals, clinics, law enforcement agencies and pharmacies. Furthermore, in many countries, medication producers and pharmacies pay for the collection and destruction of household medical waste, following the "polluter pays" principle. Several approaches and methods should be considered in Israel: (a) legislation and regulation to enable a variety of institutes to collect household medical waste (b) implementing the "polluter pays" principle and enforcing medical products manufactures to pay for the collection and destruction of household medical waste. (c) Raising awareness of patients, pharmacists, and other medical health providers regarding the health and environmental risks in accumulation of drugs and throwing them to the garbage, sink or toilet. (d) Adding specific instructions regarding disposal of the drug, in the

Improving protein function prediction methods with integrated literature data

Directory of Open Access Journals (Sweden)

Gabow Aaron P

2008-04-01

, but co-occurrence data still proves beneficial. Conclusion Co-occurrence data is a valuable supplemental source for graph-theoretic function prediction algorithms. A rapidly growing literature corpus ensures that co-occurrence data is a readily-available resource for nearly every studied organism, particularly those with small protein interaction databases. Though arguably biased toward known genes, co-occurrence data provides critical additional links to well-studied regions in the interaction network that graph-theoretic function prediction algorithms can exploit.

Optimal FCFS allocation rules for periodic-review assemble-to-order systems

NARCIS (Netherlands)

Huang, K.; Kok, de A.G.

2015-01-01

In Assemble-To-Order (ATO) systems, situations may arise in which customer demand must be backlogged due to a shortage of some components, leaving available stock of other components unused. Such unused component stock is called remnant stock. Remnant stock is a consequence of both component

Evidence-based human resource management: a study of nurse leaders' resource allocation.

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Fagerström, Lisbeth

2009-05-01

The aims were to illustrate how the RAFAELA system can be used to facilitate evidence-based human resource management. The theoretical framework of the RAFAELA system is based on a holistic view of humankind and a view of leadership founded on human resource management. Nine wards from three central hospitals in Finland participated in the study. The data, stemming from 2006-2007, were taken from the critical indicators (ward-related and nursing intensity information) for national benchmarking used in the RAFAELA system. The data were analysed descriptively. The daily nursing resources per classified patient ratio is a more specific method of measurement than the nurse-to-patient ratio. For four wards, the nursing intensity per nurse surpassed the optimal level 34% to 62.2% of days. Resource allocation was clearly improved in that a better balance between patients' care needs and available nursing resources was maintained. The RAFAELA system provides a rational, systematic and objective foundation for evidence-based human resource management. Data from a systematic use of the RAFAELA system offer objective facts and motives for evidence-based decision making in human resource management, and will therefore enhance the nurse leaders' evidence and scientific based way of working.

Enterprise Resource Planning Software in the Human Resource Classroom

Science.gov (United States)

Bedell, Michael D.; Floyd, Barry D.; Nicols, Kay McGlashan; Ellis, Rebecca

2007-01-01

The relatively recent development of comprehensive human resource information systems (HRIS) software has led to a large demand for technologically literate human resource (HR) professionals. For the college student who is about to begin the search for that first postcollege job, the need to develop technology literacy is even more necessary. To…

Protein-protein interactions: an application of Tus-Ter mediated protein microarray system.

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Sitaraman, Kalavathy; Chatterjee, Deb K

2011-01-01

In this chapter, we present a novel, cost-effective microarray strategy that utilizes expression-ready plasmid DNAs to generate protein arrays on-demand and its use to validate protein-protein interactions. These expression plasmids were constructed in such a way so as to serve a dual purpose of synthesizing the protein of interest as well as capturing the synthesized protein. The microarray system is based on the high affinity binding of Escherichia coli "Tus" protein to "Ter," a 20 bp DNA sequence involved in the regulation of DNA replication. The protein expression is carried out in a cell-free protein synthesis system, with rabbit reticulocyte lysates, and the target proteins are detected either by labeled incorporated tag specific or by gene-specific antibodies. This microarray system has been successfully used for the detection of protein-protein interaction because both the target protein and the query protein can be transcribed and translated simultaneously in the microarray slides. The utility of this system for detecting protein-protein interaction is demonstrated by a few well-known examples: Jun/Fos, FRB/FKBP12, p53/MDM2, and CDK4/p16. In all these cases, the presence of protein complexes resulted in the localization of fluorophores at the specific sites of the immobilized target plasmids. Interestingly, during our interactions studies we also detected a previously unknown interaction between CDK2 and p16. Thus, this Tus-Ter based system of protein microarray can be used for the validation of known protein interactions as well as for identifying new protein-protein interactions. In addition, it can be used to examine and identify targets of nucleic acid-protein, ligand-receptor, enzyme-substrate, and drug-protein interactions.

Natural resource dependence, human capital accumulation, and economic growth: A combined explanation for the resource curse and the resource blessing

International Nuclear Information System (INIS)

Shao, Shuai; Yang, Lili

2014-01-01

In existing studies, no consensus has been reached on the relationship between natural resource dependence and human capital accumulation. To narrow the divergence, this paper carries out a normative research to explain the co-existence of the phenomena of the resource curse and the resource blessing based on an organic combination of conceptual and mathematical models. It first establishes a conceptual model to analyse the potential effects of the government's policy preference and natural resource development activities on human capital accumulation and economic growth. Furthermore, it develops an endogenous growth model to normatively illuminate the effects in the conceptual model and to explore the condition for the occurrence of the resource curse. The conceptual model analysis indicates that the rate of return on education investment and government behaviours play the crucial role in promoting the formation of the economic virtuous circle at the micro-level and macro-level, respectively, while resource development activities exert dual impacts on the circle. The main mechanisms in the conceptual model can be validated in the mathematical model. The rise in the subjective discount rate, the elasticity of intertemporal substitution, and resource goods price are adverse to the economic virtuous circle, while high-quality education and the institutional environment giving priority to manufacturing can become the necessary condition and sufficient condition for forming the circle, respectively. The allocation efficiency of production factors plays a decisive role in whether the blessing occurs, whereas sufficient human capital is an essential guarantee for evading the curse. - Highlights: • We conduct normative research combining a conceptual model and a mathematical model. • We discuss the potential impact of resource dependence on human capital and growth. • We explain the co-existence of the resource blessing and resource curse phenomena. �

Truly Absorbed Microbial Protein Synthesis, Rumen Bypass Protein, Endogenous Protein, and Total Metabolizable Protein from Starchy and Protein-Rich Raw Materials

NARCIS (Netherlands)

Parand, Ehsan; Vakili, Alireza; Mesgaran, Mohsen Danesh; Duinkerken, Van Gert; Yu, Peiqiang

2015-01-01

This study was carried out to measure truly absorbed microbial protein synthesis, rumen bypass protein, and endogenous protein loss, as well as total metabolizable protein, from starchy and protein-rich raw feed materials with model comparisons. Predictions by the DVE2010 system as a more

Cultural Resource Predictive Modeling

Science.gov (United States)

2017-10-01

CR cultural resource CRM cultural resource management CRPM Cultural Resource Predictive Modeling DoD Department of Defense ESTCP Environmental...resource management ( CRM ) legal obligations under NEPA and the NHPA, military installations need to demonstrate that CRM decisions are based on objective...maxim “one size does not fit all,” and demonstrate that DoD installations have many different CRM needs that can and should be met through a variety

Resource quality or competition: why increase resource acceptance in the presence of conspecifics?

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Davis, Jeremy M; Nufio, César R; Papaj, Daniel R

2011-07-01

Some animal species increase resource acceptance rates in the presence of conspecifics. Such responses may be adaptive if the presence of conspecifics is a reliable indicator of resource quality. Similarly, these responses could represent an adaptive reduction in choosiness under high levels of scramble competition. Although high resource quality and high levels of scramble competition should both favor increased resource acceptance, the contexts in which the increase occurs should differ. In this paper, we tested the effect of social environment on egg-laying and aggressive behavior in the walnut fly, Rhagoletis juglandis, in multiple contexts to determine whether increased resource acceptance in the presence of conspecifics was better viewed as a response to increased host quality or increased competition. We found that grouped females oviposit more readily than isolated females when provided small (low-quality) artificial hosts but not when provided large (high-quality) artificial hosts, indicating that conspecific presence reduces choosiness. Increased resource acceptance was observed even when exposure to conspecifics was temporally or spatially separate from exposure to the resource. Finally, we found that individuals showed reduced aggression after being housed in groups, as expected under high levels of scramble competition. These results indicate that the pattern of resource acceptance in the presence of conspecifics may be better viewed as a response to increased scramble competition rather than as a response to public information about resource quality.

Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana

KAUST Repository

Bigeard, Jean

2014-07-10

The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.

Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana

KAUST Repository

Bigeard, Jean; Rayapuram, Naganand; Bonhomme, Ludovic; Hirt, Heribert; Pflieger, Delphine

2014-01-01

The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.

Proteomic identification of secreted proteins of Propionibacterium acnes

Directory of Open Access Journals (Sweden)

Holland Carsten

2010-08-01

Full Text Available Abstract Background The anaerobic Gram-positive bacterium Propionibacterium acnes is a human skin commensal that resides preferentially within sebaceous follicles; however, it also exhibits many traits of an opportunistic pathogen, playing roles in a variety of inflammatory diseases such as acne vulgaris. To date, the underlying disease-causing mechanisms remain ill-defined and knowledge of P. acnes virulence factors remains scarce. Here, we identified proteins secreted during anaerobic cultivation of a range of skin and clinical P. acnes isolates, spanning the four known phylogenetic groups. Results Culture supernatant proteins of P. acnes were separated by two-dimensional electrophoresis (2-DE and all Coomassie-stained spots were subsequently identified by MALDI mass spectrometry (MALDI-MS. A set of 20 proteins was secreted in the mid-exponential growth phase by the majority of strains tested. Functional annotation revealed that many of these common proteins possess degrading activities, including glycoside hydrolases with similarities to endoglycoceramidase, β-N-acetylglucosaminidase and muramidase; esterases such as lysophospholipase and triacylglycerol lipase; and several proteases. Other secreted factors included Christie-Atkins-Munch-Petersen (CAMP factors, glyceraldehyde 3-phosphate dehydrogenase (GAPDH, and several hypothetical proteins, a few of which are unique to P. acnes. Strain-specific differences were apparent, mostly in the secretion of putative adhesins, whose genes exhibit variable phase variation-like sequence signatures. Conclusions Our proteomic investigations have revealed that the P. acnes secretome harbors several proteins likely to play a role in host-tissue degradation and inflammation. Despite a large overlap between the secretomes of all four P. acnes phylotypes, distinct differences between predicted host-tissue interacting proteins were identified, providing potential insight into the differential virulence

Library resources on the Internet

Science.gov (United States)

Buchanan, Nancy L.

1995-07-01

Library resources are prevalent on the Internet. Library catalogs, electronic books, electronic periodicals, periodical indexes, reference sources, and U.S. Government documents are available by telnet, Gopher, World Wide Web, and FTP. Comparatively few copyrighted library resources are available freely on the Internet. Internet implementations of library resources can add useful features, such as full-text searching. There are discussion lists, Gophers, and World Wide Web pages to help users keep up with new resources and changes to existing ones. The future will bring more library resources, more types of library resources, and more integrated implementations of such resources to the Internet.

Hijacked then lost in translation: the plight of the recombinant host cell in membrane protein structural biology projects.

Science.gov (United States)

Bill, Roslyn M; von der Haar, Tobias

2015-06-01

Membrane protein structural biology is critically dependent upon the supply of high-quality protein. Over the last few years, the value of crystallising biochemically characterised, recombinant targets that incorporate stabilising mutations has been established. Nonetheless, obtaining sufficient yields of many recombinant membrane proteins is still a major challenge. Solutions are now emerging based on an improved understanding of recombinant host cells; as a 'cell factory' each cell is tasked with managing limited resources to simultaneously balance its own growth demands with those imposed by an expression plasmid. This review examines emerging insights into the role of translation and protein folding in defining high-yielding recombinant membrane protein production in a range of host cells. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana

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Yuan Tong

2010-01-01

Full Text Available Abstract Background Transmembrane receptor kinases play critical roles in both animal and plant signaling pathways regulating growth, development, differentiation, cell death, and pathogenic defense responses. In Arabidopsis thaliana, there are at least 223 Leucine-rich repeat receptor-like kinases (LRR-RLKs, representing one of the largest protein families. Although functional roles for a handful of LRR-RLKs have been revealed, the functions of the majority of members in this protein family have not been elucidated. Results As a resource for the in-depth analysis of this important protein family, the complementary DNA sequences (cDNAs of 194 LRR-RLKs were cloned into the GatewayR donor vector pDONR/ZeoR and analyzed by DNA sequencing. Among them, 157 clones showed sequences identical to the predictions in the Arabidopsis sequence resource, TAIR8. The other 37 cDNAs showed gene structures distinct from the predictions of TAIR8, which was mainly caused by alternative splicing of pre-mRNA. Most of the genes have been further cloned into GatewayR destination vectors with GFP or FLAG epitope tags and have been transformed into Arabidopsis for in planta functional analysis. All clones from this study have been submitted to the Arabidopsis Biological Resource Center (ABRC at Ohio State University for full accessibility by the Arabidopsis research community. Conclusions Most of the Arabidopsis LRR-RLK genes have been isolated and the sequence analysis showed a number of alternatively spliced variants. The generated resources, including cDNA entry clones, expression constructs and transgenic plants, will facilitate further functional analysis of the members of this important gene family.

Studies on plant materials as energy resources 2. Jojoba-new raw material for industry. Energy-gen to shiteno baiomas no tansaku to hyoka ni kansuru kenkyu dai 2 ho. Miriyo YURYO shokubutsu hohoba saibai no genjyo to kaihatsu jyo no kadai

Energy Technology Data Exchange (ETDEWEB)

Suganuma, Hirotoshi.

1989-02-01

The studies have the objective of searching and evaluating biomass as energy resources and in this report, the current situation and the issues concerning development of cultivation of jojoba which has been an unused oily plant growing in arid and semi-arid areas in the southwestern USA. Its summary is as follows: (1) Jojoba is cultivated experimentally over about 20,000ha in the tropical and semitropical arid and semiarid regions at the almost same latitudes of the areas where it grows wild, (2) With regard to the areas qualified for development in the Chaco region of the western Paraguay, the La Rioja Province in the northwestern Argentina and the Eastern Province in the eastern Kenya, ample production can be expected judging from their natural environmental conditions and the growing characteristics of jojoba. (3) Jojoba is a dioecious plant and it takes 4-5 years from seeding to flowering. During this period, its sex difference cannot be identified, but a conclusion was obtained that the sex difference might possibly be identified by the isozyme method at its stage of young seedlings. (4) When cultivation techniques are firmly established and its price goes down to about 2 dollars/kg, jojoba becomes promising as substitute for sperm whale oil. 20 refs., 8 figs., 18 tabs.

Can individual and social patterns of resource use buffer animal populations against resource decline?

Directory of Open Access Journals (Sweden)

Sam C Banks

Full Text Available Species in many ecosystems are facing declines of key resources. If we are to understand and predict the effects of resource loss on natural populations, we need to understand whether and how the way animals use resources changes under resource decline. We investigated how the abundance of arboreal marsupials varies in response to a critical resource, hollow-bearing trees. Principally, we asked what mechanisms mediate the relationship between resources and abundance? Do animals use a greater or smaller proportion of the remaining resource, and is there a change in cooperative resource use (den sharing, as the availability of hollow trees declines? Analyses of data from 160 sites surveyed from 1997 to 2007 showed that hollow tree availability was positively associated with abundance of the mountain brushtail possum, the agile antechinus and the greater glider. The abundance of Leadbeater's possum was primarily influenced by forest age. Notably, the relationship between abundance and hollow tree availability was significantly less than 1:1 for all species. This was due primarily to a significant increase by all species in the proportional use of hollow-bearing trees where the abundance of this resource was low. The resource-sharing response was weaker and inconsistent among species. Two species, the mountain brushtail possum and the agile antechinus, showed significant but contrasting relationships between the number of animals per occupied tree and hollow tree abundance. The discrepancies between the species can be explained partly by differences in several aspects of the species' biology, including body size, types of hollows used and social behaviour as it relates to hollow use. Our results show that individual and social aspects of resource use are not always static in response to resource availability and support the need to account for dynamic resource use patterns in predictive models of animal distribution and abundance.

GAMDB: a web resource to connect microRNAs with autophagy in gerontology.

Science.gov (United States)

Zhang, Lan; Xie, Tao; Tian, Mao; Li, Jingjing; Song, Sicheng; Ouyang, Liang; Liu, Bo; Cai, Haoyang

2016-04-01

MicroRNAs (miRNAs) are endogenous ~23 nucleotides (nt) RNAs, regulating gene expression by pairing to the mRNAs of protein-coding genes to direct their post-transcriptional repression. Both in normal and aberrant activities, miRNAs contribute to a recurring paradigm of cellular behaviors in pathological settings, especially in gerontology. Autophagy, a multi-step lysosomal degradation process with function to degrade long-lived proteins and damaged organelles, has significant impact on gerontology. Thus, elucidating how miRNAs participate in autophagy may enlarge the scope of miRNA in autophagy and facilitate researches in gerontology. Herein, based upon the published studies, predicted targets and gerontology-related diseases, we constructed a web resource named Gerontology-Autophagic-MicroRNA Database (GAMDB) (http://gamdb.liu-lab.com/index.php), which contained 836 autophagy-related miRNAs, 197 targeted genes/proteins and 56 aging-related diseases such as Parkinson' disease, Alzheimer's disease and Huntington's disease. We made use of large amounts of data to elucidate the intricate relationships between microRNA-regulated autophagic mechanisms and gerontology. This database will facilitate better understanding of autophagy regulation network in gerontology and thus promoting gerontology-related therapy in the future. © 2016 John Wiley & Sons Ltd.

The Protein Data Bank in Europe (PDBe): bringing structure to biology

International Nuclear Information System (INIS)

Velankar, Sameer; Kleywegt, Gerard J.

2011-01-01

Some future challenges for the PDB and its guardians are discussed and current and future activities in structural bioinformatics at the Protein Data Bank in Europe (PDBe) are described. The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described

The Protein Data Bank in Europe (PDBe): bringing structure to biology

Energy Technology Data Exchange (ETDEWEB)

Velankar, Sameer; Kleywegt, Gerard J., E-mail: gerard@ebi.ac.uk [Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom)

2011-04-01

Some future challenges for the PDB and its guardians are discussed and current and future activities in structural bioinformatics at the Protein Data Bank in Europe (PDBe) are described. The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.

The cellulose resource matrix

NARCIS (Netherlands)

Keijsers, E.R.P.; Yilmaz, G.; Dam, van J.E.G.

2013-01-01

The emerging biobased economy is causing shifts from mineral fossil oil based resources towards renewable resources. Because of market mechanisms, current and new industries utilising renewable commodities, will attempt to secure their supply of resources. Cellulose is among these commodities, where

Resource management: Hotel Zira human resource management department analysis

Directory of Open Access Journals (Sweden)

Petrović Jelena

2015-01-01

Full Text Available The world is changing at a fast pace in a number of different areas, economically, politically technologically and socially. All these facts have strong impact on how managers organize their work. Traditionally they focus on delivering efficiency through large bureaucracies which are hierarchical in nature, very much around process and stability. What this mitigates against perhaps it is innovation and flexibility. A demand is no longer predictable and service has to be equally flexible for demand that exists nowadays. The emergence of post bureaucratic organizations is about being leaner, flatter and being much more network-based. Within that network employees are being empowered to take responsibility for producing innovations themselves. In order to speed up the process it is critical to systematize the process of managing people in the back office. Human Resource Management strategies are being transformed by internal social networks and social human resource technologies to better collaborative, transition into social enterprises, and change the positioning of human resource departments from back office to front office activities. All of these subjects are applied and the case study of hotel Zira human resource department is explained and showed in detail with the specific questionnaire. One of the main challenges that human resource management is also facing is the talent management and the number one responsibility of leadership is how to manage talent, how to attract it, utilize and eventually retain it.

A web-based resource for designing therapeutics against Ebola Virus

Science.gov (United States)

Dhanda, Sandeep Kumar; Chaudhary, Kumardeep; Gupta, Sudheer; Brahmachari, Samir Kumar; Raghava, Gajendra P. S.

2016-04-01

In this study, we describe a web-based resource, developed for assisting the scientific community in designing an effective therapeutics against the Ebola virus. Firstly, we predicted and identified experimentally validated epitopes in each of the antigens/proteins of the five known ebolaviruses. Secondly, we generated all the possible overlapping 9mer peptides from the proteins of ebolaviruses. Thirdly, conserved peptides across all the five ebolaviruses (four human pathogenic species) with no identical sequence in the human proteome, based on 1000 Genomes project, were identified. Finally, we identified peptide or epitope-based vaccine candidates that could activate both the B- and T-cell arms of the immune system. In addition, we also identified efficacious siRNAs against the mRNA transcriptome (absent in human transcriptome) of all the five ebolaviruses. It was observed that three species can potentially be targeted by a single siRNA (19mer) and 75 siRNAs can potentially target at least two species. A web server, EbolaVCR, has been developed that incorporates all the above information and useful computational tools (http://crdd.osdd.net/oscadd/ebola/).

Integrated load distribution and production planning in series-parallel multi-state systems with failure rate depending on load

International Nuclear Information System (INIS)

Nourelfath, Mustapha; Yalaoui, Farouk

2012-01-01

A production system containing a set of machines (also called components) arranged according to a series-parallel configuration is addressed. A set of products must be produced in lots on this production system during a specified finite planning horizon. This paper presents a method for integrating load distribution decisions, and tactical production planning considering the costs of capacity change and the costs of unused capacity. The objective is to minimize the sum of capacity change costs, unused capacity costs, setup costs, holding costs, backorder costs, and production costs. The main constraints consist in satisfying the demand for all products over the entire horizon, and in not exceeding available repair resource. The production series-parallel system is modeled as a multi-state system with binary-state components. The proposed model takes into account the dependence of machines' failure rates on their load. Universal generating function technique can be used in the optimization algorithm for evaluating the expected system production rate in each period. We show how the formulated problem can be solved by comparing the results of several multi-product lot-sizing problems with capacity associated costs. The importance of integrating load distribution decisions and production planning is illustrated through numerical examples.

Management of development of renewable energy sources

Directory of Open Access Journals (Sweden)

Inić Branimir P.

2014-01-01

Full Text Available The aim of the paper: 'Management of development of renewable energy sources is to point out the possible solutions for neutralizing the threat of energy shortages. The paper outlines major short and long term energy problems facing humanity. The increase of world human population is, inevitably, accompanied by higher energy consumption. Reserves decrease of nonrenewable energy sources like oil, gas, and coal is a major threat to maintaining current living conditions, and thus requires solutions in order to neutralize the threat. This is why the management of development of renewable energy sources is an imperative for Serbia. The paper emphasizes the use of solar energy, because the annual average of solar radiation in Serbia is about 40% higher than the European average, however, the actual use of the sun's energy to generate electricity in Serbia is far behind the countries of the European Union. Solar energy is clean, renewable, and the fact that 4.2 kilowatt-hours are received daily per square meter averaged over the entire surface of the planet, makes it an almost unused energy source, Compared to EU countries, the price of non-renewable derived energy is, on average, higher in Serbia. Taking this into consideration, the use of solar energy, as an unused resource, imposes itself as indispensable.

Energy potential through agricultural biomass using geographical information system - A case study of Punjab

International Nuclear Information System (INIS)

Singh, Jagtar; Panesar, B.S.; Sharma, S.K.

2008-01-01

Agricultural biomass has immense potential for power production in an Indian state like Punjab. A judicious use of biomass energy could potentially play an important role in mitigating environmental impacts of non-renewable energy sources particularly global warming and acid rain. But the availability of agricultural biomass is spatially scattered. The spatial distribution of this resource and the associate costs of collection and transportation are major bottlenecks for the success of biomass energy conversion facilities. Biomass, being scattered and loose, has huge collection and transportation costs, which can be reduced by properly planning and locating the biomass collection centers for biomass-based power plants. Before planning the collection centers, it is necessary to evaluate the biomass, energy and collection cost of biomass in the field. In this paper, an attempt has been made to evaluate the spatial potential of biomass with geographical information system (GIS) and a mathematical model for collection of biomass in the field has been developed. The total amount of unused agricultural biomass is about 13.73 Mt year -1 . The total power generation capacity from unused biomass is approximately 900 MW. The collection cost in the field up to the carrier unit is US$3.90 t -1 . (author)

Space and Planetary Resources

Science.gov (United States)

Abbud-Madrid, Angel

2018-02-01

The space and multitude of celestial bodies surrounding Earth hold a vast wealth of resources for a variety of space and terrestrial applications. The unlimited solar energy, vacuum, and low gravity in space, as well as the minerals, metals, water, atmospheric gases, and volatile elements on the Moon, asteroids, comets, and the inner and outer planets of the Solar System and their moons, constitute potential valuable resources for robotic and human space missions and for future use in our own planet. In the short term, these resources could be transformed into useful materials at the site where they are found to extend mission duration and to reduce the costly dependence from materials sent from Earth. Making propellants and human consumables from local resources can significantly reduce mission mass and cost, enabling longer stays and fueling transportation systems for use within and beyond the planetary surface. Use of finely grained soils and rocks can serve for habitat construction, radiation protection, solar cell fabrication, and food growth. The same material could also be used to develop repair and replacement capabilities using advanced manufacturing technologies. Following similar mining practices utilized for centuries on Earth, identifying, extracting, and utilizing extraterrestrial resources will enable further space exploration, while increasing commercial activities beyond our planet. In the long term, planetary resources and solar energy could also be brought to Earth if obtaining these resources locally prove to be no longer economically or environmentally acceptable. Throughout human history, resources have been the driving force for the exploration and settling of our planet. Similarly, extraterrestrial resources will make space the next destination in the quest for further exploration and expansion of our species. However, just like on Earth, not all challenges are scientific and technological. As private companies start working toward

Comparison of the adhesive performances of soy meal, water washed meal fractions, and protein isolates

Science.gov (United States)

Adhesive bonding of wood plays an increasing role in the forest products industry and is a key factor for efficiently utilizing timber and other lignocellulosic resources. In this work, we obtained five soy meal products through commercial sources or in-house preparations. The protein content was 49...

Symposium 20 - PABMB: Teaching biochemistry in a connected world: KEEPING 3D RESOURCES IN THE WEB TO LEARN ON PROTEIN STRUCTURE

Directory of Open Access Journals (Sweden)

Raul Herrera

2015-08-01

Full Text Available Symposium 20 - PABMB: Teaching biochemistry in a connected world Chair: Miguel Castanho, Universidade de Lisboa, PortugalAbstract:The new paradigm of higher education requires new teaching strategies to meet the learning objectives of biochemistry courses. Teaching biochemistry in the current state of science and society requires a special motivation for learning, especially for students of degrees other than Biochemistry. The traditional way of teaching, based on the teacher-student relationship, mostly unidirectional, does not fulfil the needs imposed in this era. Considering the current situation universities students require new abilities in their training and the use of computers can constitute a place for discovery and research, enabling the experience of new and diverse situations. The design of teaching material for undergraduate students who take biochemistry courses as complementary subject on their careers should be seen as an opportunity to complement theoretical aspects on the current courses. Three different approaches could be used: (I a description of the basic concepts, like in a book but using dynamics figures. (II Modelling proteins highlighting key motifs at the three-dimensional structure and residues where inhibitors can be attached. And (III elaborating active quizzes where students can be driven on their learning. Building knowledge based on practical experience can improve student competences on basic science and the learning process can be complemented in the use of dynamics models. On the other hand, exploring protein structures from the web could give students a better comprehension of residues interaction and non-covalent forces involved in protein-protein or protein-ligand interaction. The use of dynamic models improves the comprehension of protein structure and their special link to amino acids residues or ligands. This work was supported by Anillo ACT1110 project. Key Words: protein structure, 3D source, learning

Hydrography - Water Resources

Data.gov (United States)

NSGIC Education | GIS Inventory — A Water Resource is a DEP primary facility type related to the Water Use Planning Program. The sub-facility types related to Water Resources that are included are:...

Transcriptomic and functional resources for the small hive beetle Aethina tumida, a worldwide parasite of honey bees

Directory of Open Access Journals (Sweden)

Matthew R. Tarver

2016-09-01

Full Text Available The small hive beetle (SHB, Aethina tumida, is a major pest of managed honey bee (Apis mellifera colonies in the United States and Australia, and an emergent threat in Europe. While strong honey bee colonies generally keep SHB populations in check, weak or stressed colonies can succumb to infestations. This parasite has spread from a sub-Saharan Africa to three continents, leading to immense management and regulatory costs. We performed a transcriptomic analysis involving deep sequencing of multiple life stages and both sexes of this species. The assembled transcriptome appears to be nearly complete, as judged by conserved insect orthologs and the ability to find plausible homologs for 11,952 proteins described from the genome of the red flour beetle. Expressed genes include each of the major metabolic, developmental and sensory groups, along with genes for proteins involved with immune defenses and insecticide resistance. We also present a total of 23,085 high-quality SNP's for the assembled contigs. We highlight potential differences between this beetle and its honey bee hosts, and suggest mechanisms of future research into the biology and control of this species. SNP resources will allow functional genetic analyses and analyses of dispersal for this invasive pest. All resources are posted as Supplemental Tables at https://data.nal.usda.gov/dataset/data-transcriptomic-and-functional-resources-small-hive-beetle-aethina-tumida-worldwide, and at NCBI under Bioproject PRJNA256171.

Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces.

Directory of Open Access Journals (Sweden)

Ruzianisra Mohamed

Full Text Available Protein-protein interactions (PPIs play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP complexes, and 161 protein-ligand (PL complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.

Resources for Sale: Corruption, Democracy and the Natural Resource Curse

NARCIS (Netherlands)

Damania, R.; Bulte, E.H.

2008-01-01

A puzzling piece of empirical evidence suggests that resource-abundant countries tend to grow slower than their resource-poor counterparts. We attempt to explain this phenomenon by developing a lobbying game in which rent seeking firms interact with corrupt governments. The presence or absence of

Timber resource statistics for the North Coast resource area of California 1994.

Science.gov (United States)

Karen L. Waddell; Patricia M. Bassett

1996-01-01

This report is a summary of timber resource statistics for the North Coast Resource Area of California, which includes Del Norte, Humboldt, Mendocino, and Sonoma Counties. Data were collected by the Pacific Northwest Research Station as part of a State-wide multi-resource inventory. The inventory sampled private and public lands except reserved areas and National...

2005 resource options report

International Nuclear Information System (INIS)

Morris, T.

2005-01-01

This resource options report (ROR) fulfils regulatory requirements in British Columbia's two-year resource planning process. It identifies a wide range of resources and technologies that could be used to meet BC Hydro's future electricity demand. As such, it facilitates a transparent public review of resource options which include both supply-side and demand-side options. The resource options that will be used in the 2005 integrated electricity plan (IEP) were characterized. This ROR also documents where there is a general agreement or disagreement on the resource type characterization, based on the First Nations and Stakeholder engagement. BC Hydro used current information to provide realistic ranges on volume and cost to characterize environmental and social attributes. The BC Hydro system was modelled to assess the benefit and cost of various resource options. The information resulting from this ROR and IEP will help in making decisions on how to structure competitive acquisition calls and to determine the level of transmission services needed to advance certain BC Hydro projects. The IEP forecasts the nature and quantity of domestic resources required over the next 20 years. A strategic direction on how those needs will be met has been created to guide the management of BC Hydro's energy resources. Supply-side options include near-commercial technologies such as energy storage, ocean waves, tidal, fuel cells and integrated coal gasification combined cycle technology. Supply-side options also include natural gas, coal, biomass, geothermal, wind, and hydro. 120 refs., 39 tabs., 21 figs., 6 appendices

Protein levels and colony development of Africanized and European honey bees fed natural and artificial diets

OpenAIRE

Morais, Michelle Manfrini [UNIFESP; Turcatto, Aline Patricia; Pereira, Rogerio Aparecido; Francoy, Tiago Mauricio; Guidugli-Lazzarini, Karina Rosa; Goncalves, Lionel Segui; Almeida, Joyce Mayra Volpini de; Ellis, J. D.; De Jong, David

2013-01-01

Pollen substitute diets are a valuable resource for maintaining strong and health honey bee colonies. Specific diets may be useful in one region or country and inadequate or economically unviable in others. We compared two artificial protein diets that had been formulated from locally-available ingredients in Brazil with bee bread and a non-protein sucrose diet. Groups of 100 newly-emerged, adult workers of Africanized honey bees in Brazil and European honey bees in the USA were confined in s...

Improvements in the Protein Identifier Cross-Reference service.

Science.gov (United States)

Wein, Samuel P; Côté, Richard G; Dumousseau, Marine; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan A

2012-07-01

The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a 'best-guess' mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/.

The rebound effect of resource efficiency; Het reboundeffect bij resource efficiency

Energy Technology Data Exchange (ETDEWEB)

Oosterhuis, F.; Bouma, J. [Instituut voor Milieuvraagstukken IVM, Vrije Universiteit, Amsterdam (Netherlands); Hanemaaijer, A. [Planbureau voor de Leefomgeving PBL, Den Haag (Netherlands)

2013-12-15

As a result of efficient use of natural resources production and use of goods and services can be made cheaper, which increases demand. However, that might partially offset savings in energy and other natural resources. This so-called 'rebound effect' can not be ignored. It is therefore worthwhile to keep that in formulating 'resource efficiency' policy [Dutch] Door efficienter om te gaan met natuurlijke hulpbronnen kunnen de productie en het gebruik van goederen en diensten goedkoper worden, waardoor de vraag ernaar toeneemt. Dat kan de besparingen op energie en andere natuurlijke hulpbronnen deels weer teniet doen. Dit 'rebound-effect' is niet verwaarloosbaar. Het is zinvol om hier bij beleid gericht op 'resource efficiency' rekening mee te houden.

Preliminary research on quantitative methods of water resources carrying capacity based on water resources balance sheet

Science.gov (United States)

Wang, Yanqiu; Huang, Xiaorong; Gao, Linyun; Guo, Biying; Ma, Kai

2018-06-01

Water resources are not only basic natural resources, but also strategic economic resources and ecological control factors. Water resources carrying capacity constrains the sustainable development of regional economy and society. Studies of water resources carrying capacity can provide helpful information about how the socioeconomic system is both supported and restrained by the water resources system. Based on the research of different scholars, major problems in the study of water resources carrying capacity were summarized as follows: the definition of water resources carrying capacity is not yet unified; the methods of carrying capacity quantification based on the definition of inconsistency are poor in operability; the current quantitative research methods of water resources carrying capacity did not fully reflect the principles of sustainable development; it is difficult to quantify the relationship among the water resources, economic society and ecological environment. Therefore, it is necessary to develop a better quantitative evaluation method to determine the regional water resources carrying capacity. This paper proposes a new approach to quantifying water resources carrying capacity (that is, through the compilation of the water resources balance sheet) to get a grasp of the regional water resources depletion and water environmental degradation (as well as regional water resources stock assets and liabilities), figure out the squeeze of socioeconomic activities on the environment, and discuss the quantitative calculation methods and technical route of water resources carrying capacity which are able to embody the substance of sustainable development.

Mining protein interactomes to improve their reliability and support the advancement of network medicine

KAUST Repository

Alanis Lobato, Gregorio

2015-09-23

High-throughput detection of protein interactions has had a major impact in our understanding of the intricate molecular machinery underlying the living cell, and has permitted the construction of very large protein interactomes. The protein networks that are currently available are incomplete and a significant percentage of their interactions are false positives. Fortunately, the structural properties observed in good quality social or technological networks are also present in biological systems. This has encouraged the development of tools, to improve the reliability of protein networks and predict new interactions based merely on the topological characteristics of their components. Since diseases are rarely caused by the malfunction of a single protein, having a more complete and reliable interactome is crucial in order to identify groups of inter-related proteins involved in disease etiology. These system components can then be targeted with minimal collateral damage. In this article, an important number of network mining tools is reviewed, together with resources from which reliable protein interactomes can be constructed. In addition to the review, a few representative examples of how molecular and clinical data can be integrated to deepen our understanding of pathogenesis are discussed.

Mining protein interactomes to improve their reliability and support the advancement of network medicine

Directory of Open Access Journals (Sweden)

Gregorio eAlanis-Lobato

2015-09-01

Full Text Available High-throughput detection of protein interactions has had a major impact in our understanding of the intricate molecular machinery underlying the living cell, and has permitted the construction of very large protein interactomes. The protein networks that are currently available are incomplete and a significant percentage of their interactions are false positives. Fortunately, the structural properties observed in good quality social or technological networks are also present in biological systems. This has encouraged the development of tools, to improve the reliability of protein networks and predict new interactions based merely on the topological characteristics of their components. Since diseases are rarely caused by the malfunction of a single protein, having a more complete and reliable interactome is crucial in order to identify groups of inter-related proteins involved in disease aetiology. These system components can then be targeted with minimal collateral damage. In this article, an important number of network mining tools is reviewed, together with resources from which reliable protein interactomes can be constructed. In addition to the review, a few representative examples of how molecular and clinical data can be integrated to deepen our understanding of pathogenesis are discussed.

Ohio Water Resources Council

Science.gov (United States)