Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Miller, Vadim; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Shumway, Martin; Sequeira, Edwin; Sherry, Steven T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L.; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2008-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:18045790

NABIC marker database: A molecular markers information network of agricultural crops.

PubMed

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Databases on biotechnology and biosafety of GMOs.

PubMed

Degrassi, Giuliano; Alexandrova, Nevena; Ripandelli, Decio

2003-01-01

Due to the involvement of scientific, industrial, commercial and public sectors of society, the complexity of the issues concerning the safety of genetically modified organisms (GMOs) for the environment, agriculture, and human and animal health calls for a wide coverage of information. Accordingly, development of the field of biotechnology, along with concerns related to the fate of released GMOs, has led to a rapid development of tools for disseminating such information. As a result, there is a growing number of databases aimed at collecting and storing information related to GMOs. Most of the sites deal with information on environmental releases, field trials, transgenes and related sequences, regulations and legislation, risk assessment documents, and literature. Databases are mainly established and managed by scientific, national or international authorities, and are addressed towards scientists, government officials, policy makers, consumers, farmers, environmental groups and civil society representatives. This complexity can lead to an overlapping of information. The purpose of the present review is to analyse the relevant databases currently available on the web, providing comments on their vastly different information and on the structure of the sites pertaining to different users. A preliminary overview on the development of these sites during the last decade, at both the national and international level, is also provided.

Database resources of the National Center for Biotechnology Information.

PubMed

2016-01-04

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Database resources of the National Center for Biotechnology Information.

PubMed

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Database resources of the National Center for Biotechnology Information

PubMed Central

Sayers, Eric W.; Barrett, Tanya; Benson, Dennis A.; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M.; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D.; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A.; Wagner, Lukas; Wang, Yanli; Wilbur, W. John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:22140104

Database resources of the National Center for Biotechnology Information

PubMed Central

2013-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264

Database resources of the National Center for Biotechnology Information.

PubMed

Wheeler, David L; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Ostell, James; Miller, Vadim; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Steven T; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene

2007-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene; Ye, Jian

2009-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Update on Genomic Databases and Resources at the National Center for Biotechnology Information.

PubMed

Tatusova, Tatiana

2016-01-01

The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI website, text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Comparative genome analysis tools lead to further understanding of evolution processes quickening the pace of discovery. Recent technological innovations have ignited an explosion in genome sequencing that has fundamentally changed our understanding of the biology of living organisms. This huge increase in DNA sequence data presents new challenges for the information management system and the visualization tools. New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data.

WWW Entrez: A Hypertext Retrieval Tool for Molecular Biology.

ERIC Educational Resources Information Center

Epstein, Jonathan A.; Kans, Jonathan A.; Schuler, Gregory D.

This article describes the World Wide Web (WWW) Entrez server which is based upon the National Center for Biotechnology Information's (NCBI) Entrez retrieval database and software. Entrez is a molecular sequence retrieval system that contains an integrated view of portions of Medline and all publicly available nucleotide and protein databases,…

Development of a DNA microarray to detect antimicrobial resistance genes identified in the national center for biotechnology information database

USDA-ARS?s Scientific Manuscript database

High density genotyping techniques are needed for investigating antimicrobial resistance especially in the case of multi-drug resistant (MDR) isolates. To achieve this all antimicrobial resistance genes in the NCBI Genbank database were identified by key word searches of sequence annotations and the...

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2011-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

PubMed Central

Bull, Alan T.; Ward, Alan C.; Goodfellow, Michael

2000-01-01

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology. PMID:10974127

Plant Genome Resources at the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Smith-White, Brian; Chetvernin, Vyacheslav; Resenchuk, Sergei; Dombrowski, Susan M.; Pechous, Steven W.; Tatusova, Tatiana; Ostell, James

2005-01-01

The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allow maps from all plant genomes covered by the Map Viewer to be searched in tandem to produce a display of aligned maps from several species. PlantBLAST searches against the sequences shown in the Map Viewer allow BLAST alignments to be viewed within a genomic context. In addition, precomputed sequence similarities, such as those for proteins offered by BLAST Link, enable fluid navigation from unannotated to annotated sequences, quickening the pace of discovery. NCBI Web pages for plants, such as Plant Genome Central, complete the system by providing centralized access to NCBI's genomic resources as well as links to organism-specific Web pages beyond NCBI. PMID:16010002

Database resources of the National Center for Biotechnology

PubMed Central

Wheeler, David L.; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Tatusova, Tatiana A.; Wagner, Lukas

2003-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:12519941

FCDD: A Database for Fruit Crops Diseases.

PubMed

Chauhan, Rupal; Jasrai, Yogesh; Pandya, Himanshu; Chaudhari, Suman; Samota, Chand Mal

2014-01-01

Fruit Crops Diseases Database (FCDD) requires a number of biotechnology and bioinformatics tools. The FCDD is a unique bioinformatics resource that compiles information about 162 details on fruit crops diseases, diseases type, its causal organism, images, symptoms and their control. The FCDD contains 171 phytochemicals from 25 fruits, their 2D images and their 20 possible sequences. This information has been manually extracted and manually verified from numerous sources, including other electronic databases, textbooks and scientific journals. FCDD is fully searchable and supports extensive text search. The main focus of the FCDD is on providing possible information of fruit crops diseases, which will help in discovery of potential drugs from one of the common bioresource-fruits. The database was developed using MySQL. The database interface is developed in PHP, HTML and JAVA. FCDD is freely available. http://www.fruitcropsdd.com/

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.

PubMed

Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Kyrpides, Nikos C

2008-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource that provides information on genome and metagenome projects worldwide. Complete and ongoing projects and their associated metadata can be accessed in GOLD through pre-computed lists and a search page. As of September 2007, GOLD contains information on more than 2900 sequencing projects, out of which 639 have been completed and their sequence data deposited in the public databases. GOLD continues to expand with the goal of providing metadata information related to the projects and the organisms/environments towards the Minimum Information about a Genome Sequence' (MIGS) guideline. GOLD is available at http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

PubMed Central

Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Kyrpides, Nikos C.

2008-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource that provides information on genome and metagenome projects worldwide. Complete and ongoing projects and their associated metadata can be accessed in GOLD through pre-computed lists and a search page. As of September 2007, GOLD contains information on more than 2900 sequencing projects, out of which 639 have been completed and their sequence data deposited in the public databases. GOLD continues to expand with the goal of providing metadata information related to the projects and the organisms/environments towards the Minimum Information about a Genome Sequence’ (MIGS) guideline. GOLD is available at http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/ PMID:17981842

Properties and biotechnological applications of ice-binding proteins in bacteria.

PubMed

Cid, Fernanda P; Rilling, Joaquín I; Graether, Steffen P; Bravo, Leon A; Mora, María de La Luz; Jorquera, Milko A

2016-06-01

Ice-binding proteins (IBPs), such as antifreeze proteins (AFPs) and ice-nucleating proteins (INPs), have been described in diverse cold-adapted organisms, and their potential applications in biotechnology have been recognized in various fields. Currently, both IBPs are being applied to biotechnological processes, primarily in medicine and the food industry. However, our knowledge regarding the diversity of bacterial IBPs is limited; few studies have purified and characterized AFPs and INPs from bacteria. Phenotypically verified IBPs have been described in members belonging to Gammaproteobacteria, Actinobacteria and Flavobacteriia classes, whereas putative IBPs have been found in Gammaproteobacteria, Alphaproteobacteria and Bacilli classes. Thus, the main goal of this minireview is to summarize the current information on bacterial IBPs and their application in biotechnology, emphasizing the potential application in less explored fields such as agriculture. Investigations have suggested the use of INP-producing bacteria antagonists and AFPs-producing bacteria (or their AFPs) as a very attractive strategy to prevent frost damages in crops. UniProt database analyses of reported IBPs (phenotypically verified) and putative IBPs also show the limited information available on bacterial IBPs and indicate that major studies are required. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data.

PubMed

Seol, Young-Joo; Lee, Tae-Ho; Park, Dong-Suk; Kim, Chang-Kug

2016-01-01

The National Agricultural Biotechnology Information Center developed an access portal to search, visualize, and share agricultural genomics data with a focus on South Korean information and resources. The portal features an agricultural biotechnology database containing a wide range of omics data from public and proprietary sources. We collected 28.4 TB of data from 162 agricultural organisms, with 10 types of omics data comprising next-generation sequencing sequence read archive, genome, gene, nucleotide, DNA chip, expressed sequence tag, interactome, protein structure, molecular marker, and single-nucleotide polymorphism datasets. Our genomic resources contain information on five animals, seven plants, and one fungus, which is accessed through a genome browser. We also developed a data submission and analysis system as a web service, with easy-to-use functions and cutting-edge algorithms, including those for handling next-generation sequencing data.

Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites.

PubMed

Hwang, Kyu-Sang; Kim, Hyun Uk; Charusanti, Pep; Palsson, Bernhard Ø; Lee, Sang Yup

2014-01-01

Streptomyces species continue to attract attention as a source of novel medicinal compounds. Despite a long history of studies on these microorganisms, they still have many biochemical mysteries to be elucidated. Investigations of novel secondary metabolites and their biosynthetic gene clusters have been more systematized with high-throughput techniques through inspections of correlations among components of the primary and secondary metabolisms at the genome scale. Moreover, up-to-date information on the genome of Streptomyces species with emphasis on their secondary metabolism has been collected in the form of databases and knowledgebases, providing predictive information and enabling one to explore experimentally unrecognized biological spaces of secondary metabolism. Herein, we review recent trends in the systems biology and biotechnology of Streptomyces species. © 2013.

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data

PubMed Central

Seol, Young-Joo; Lee, Tae-Ho; Park, Dong-Suk; Kim, Chang-Kug

2016-01-01

The National Agricultural Biotechnology Information Center developed an access portal to search, visualize, and share agricultural genomics data with a focus on South Korean information and resources. The portal features an agricultural biotechnology database containing a wide range of omics data from public and proprietary sources. We collected 28.4 TB of data from 162 agricultural organisms, with 10 types of omics data comprising next-generation sequencing sequence read archive, genome, gene, nucleotide, DNA chip, expressed sequence tag, interactome, protein structure, molecular marker, and single-nucleotide polymorphism datasets. Our genomic resources contain information on five animals, seven plants, and one fungus, which is accessed through a genome browser. We also developed a data submission and analysis system as a web service, with easy-to-use functions and cutting-edge algorithms, including those for handling next-generation sequencing data. PMID:26848255

SORTEZ: a relational translator for NCBI's ASN.1 database.

PubMed

Hart, K W; Searls, D B; Overton, G C

1994-07-01

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Virus Database and Online Inquiry System Based on Natural Vectors.

PubMed

Dong, Rui; Zheng, Hui; Tian, Kun; Yau, Shek-Chung; Mao, Weiguang; Yu, Wenping; Yin, Changchuan; Yu, Chenglong; He, Rong Lucy; Yang, Jie; Yau, Stephen St

2017-01-01

We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

PubMed Central

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna R.

2005-01-01

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

TECHNOLOGICAL INFORMATION REGARDING PREBIOTICS AND PROBIOTICS NUTRITION VERSUS THE PATENT REGISTERS: WHAT IS NEW?

PubMed Central

dos REIS, José Maciel Caldas; PINHEIRO, Maurício Fortuna; OTI, André Takashi; FEITOSA-JUNIOR, Denilson José Silva; PANTOJA, Mauro de Souza; BARROS, Rui Sérgio Monteiro

2016-01-01

ABSTRACT Introduction: Food is a key factor both in prevention and in promoting human health. Among the functional food are highlighted probiotics and prebiotics. Patent databases are the main source of technological information about innovation worldwide, providing extensive library for research sector. Objective: Perform mapping in the main patent databases about pre and probiotics, seeking relevant information regarding the use of biotechnology, nanotechnology and genetic engineering in the production of these foods. Method: Electronic consultation was conducted (online) in the main public databases of patents in Brazil (INPI), United States (USPTO) and the European Patent Bank (EPO). The research involved the period from January 2014 to July 2015, being used in the title fields and summary of patents, the following descriptors in INPI "prebiotic", "prebiotic" "probiotics", "probiotic" and the USPTO and EPO: "prebiotic", "prebiotics", "probiotic", "probiotics". Results: This search haven't found any deposit at the brazilian patents website (INPI) in this period; US Patent &Trademark Office had registered 60 titles in patents and the European Patent Office (EPO) showed 10 documents on the issue. Conclusion: Information technology offered by genetic engineering, biotechnology and nanotechnology deposited in the form of titles and abstracts of patents in relation to early nutritional intervention as functional foods, has increasingly required to decrease the risks and control the progression of health problems. But, the existing summaries, although attractive and promising in this sense, are still incipient to recommend them safely as a therapeutic tool. Therefore, they should be seen more as diet elements and healthy lifestyles. PMID:28076487

NCBI GEO: mining tens of millions of expression profiles--database and tools update.

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Rudnev, Dmitry; Evangelista, Carlos; Kim, Irene F; Soboleva, Alexandra; Tomashevsky, Maxim; Edgar, Ron

2007-01-01

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at http://www.ncbi.nlm.nih.gov/geo/

Building a genome database using an object-oriented approach.

PubMed

Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

2002-01-01

GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

PubMed

Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

2014-01-01

With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

In silico analysis of fragile histidine triad involved in regression of carcinoma.

PubMed

Rasheed, Muhammad Asif; Tariq, Fatima; Afzal, Sara; Mannanv, Shazia

2017-04-01

Hepatocellular carcinoma (HCCa) is a primary malignancy of the liver. Many different proteins are involved in HCCa including insulin growth factor (IGF) II , signal transducers and activators of transcription (STAT) 3, STAT4, mothers against decapentaplegic homolog 4 (SMAD 4), fragile histidine triad (FHIT) and selective internal radiation therapy (SIRT) etc. The present study is based on the bioinformatics analysis of FHIT protein in order to understand the proteomics aspect and improvement of the diagnosis of the disease based on the protein. Different information related to protein were gathered from different databases, including National Centre for Biotechnology Information (NCBI) Gene, Protein and Online Mendelian Inheritance in Man (OMIM) databases, Uniprot database, String database and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Moreover, the structure of the protein and evaluation of the quality of the structure were included from Easy modeler programme. Hence, this analysis not only helped to gather information related to the protein at one place, but also analysed the structure and quality of the protein to conclude that the protein has a role in carcinoma.

Cloning and submission to the Natural Center for Biotechnology Information (NCBI) database of two complete vitellogenin genes from the varroa mite, Varroa destructor

USDA-ARS?s Scientific Manuscript database

The varroa mite, Varroa destructor, is a honeybee ectoparasite considered the most important pest in apiaries throughout the US. Vitellogenins are the yolk proteins produced by the ovipositing female mite and deposited into the oocytes to provide nutrients to the developing embryo. Scientists at CMA...

From metaphor to practices: The introduction of "information engineers" into the first DNA sequence database.

PubMed

García-Sancho, Miguel

2011-01-01

This paper explores the introduction of professional systems engineers and information management practices into the first centralized DNA sequence database, developed at the European Molecular Biology Laboratory (EMBL) during the 1980s. In so doing, it complements the literature on the emergence of an information discourse after World War II and its subsequent influence in biological research. By the careers of the database creators and the computer algorithms they designed, analyzing, from the mid-1960s onwards information in biology gradually shifted from a pervasive metaphor to be embodied in practices and professionals such as those incorporated at the EMBL. I then investigate the reception of these database professionals by the EMBL biological staff, which evolved from initial disregard to necessary collaboration as the relationship between DNA, genes, and proteins turned out to be more complex than expected. The trajectories of the database professionals at the EMBL suggest that the initial subject matter of the historiography of genomics should be the long-standing practices that emerged after World War II and to a large extent originated outside biomedicine and academia. Only after addressing these practices, historians may turn to their further disciplinary assemblage in fields such as bioinformatics or biotechnology.

The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004.

PubMed

Wiechers, Ilse R; Perin, Noah C; Cook-Deegan, Robert

2013-01-01

Development of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through the 2000 to 2001 market bubble. A database was created based on an early survey of genomics firms, which was expanded using three web-based biotechnology services, scientific journals, and biotechnology trade and technical publications. Financial data for publicly traded firms was collected through the use of four databases specializing in firm financials. Patent searches were conducted using firm names in the US Patent and Trademark Office website search engine and the DNA Patent Database. A biotechnology subsector of genomics firms emerged in parallel to the publicly funded Human Genome Project. Trends among top firms show that hiring, capital improvement, and research and development expenditures continued to grow after a 2000 to 2001 bubble. The majority of firms are small businesses with great diversity in type of research and development, products, and services provided. Over half the public firms holding patents have the majority of their intellectual property portfolio in DNA-based patents. These data allow estimates of investment, research and development expenditures, and jobs that paralleled the rise of genomics as a sector within biotechnology between 1990 and 2004.

The NCBI BioCollections Database

PubMed Central

Sharma, Shobha; Ciufo, Stacy; Starchenko, Elena; Darji, Dakshesh; Chlumsky, Larry; Karsch-Mizrachi, Ilene

2018-01-01

Abstract The rapidly growing set of GenBank submissions includes sequences that are derived from vouchered specimens. These are associated with culture collections, museums, herbaria and other natural history collections, both living and preserved. Correct identification of the specimens studied, along with a method to associate the sample with its institution, is critical to the outcome of related studies and analyses. The National Center for Biotechnology Information BioCollections Database was established to allow the association of specimen vouchers and related sequence records to their home institutions. This process also allows cross-linking from the home institution for quick identification of all records originating from each collection. Database URL: https://www.ncbi.nlm.nih.gov/biocollections PMID:29688360

The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004

PubMed Central

2013-01-01

Background Development of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through the 2000 to 2001 market bubble. Methods A database was created based on an early survey of genomics firms, which was expanded using three web-based biotechnology services, scientific journals, and biotechnology trade and technical publications. Financial data for publicly traded firms was collected through the use of four databases specializing in firm financials. Patent searches were conducted using firm names in the US Patent and Trademark Office website search engine and the DNA Patent Database. Results A biotechnology subsector of genomics firms emerged in parallel to the publicly funded Human Genome Project. Trends among top firms show that hiring, capital improvement, and research and development expenditures continued to grow after a 2000 to 2001 bubble. The majority of firms are small businesses with great diversity in type of research and development, products, and services provided. Over half the public firms holding patents have the majority of their intellectual property portfolio in DNA-based patents. Conclusions These data allow estimates of investment, research and development expenditures, and jobs that paralleled the rise of genomics as a sector within biotechnology between 1990 and 2004. PMID:24050173

DNA Data Bank of Japan: 30th anniversary.

PubMed

Kodama, Yuichi; Mashima, Jun; Kosuge, Takehide; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Nakamura, Yasukazu; Takagi, Toshihisa

2018-01-04

The DNA Data Bank of Japan (DDBJ) Center (http://www.ddbj.nig.ac.jp) has been providing public data services for 30 years since 1987. We are collecting nucleotide sequence data and associated biological information from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with the US National Center for Biotechnology Information and the European Bioinformatics Institute. The DDBJ Center also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database Center to collect genotype and phenotype data of human individuals. Here, we outline our database activities for INSDC and JGA over the past year, and introduce submission, retrieval and analysis services running on our supercomputer system and their recent developments. Furthermore, we highlight our responses to the amended Japanese rules for the protection of personal information and the launch of the DDBJ Group Cloud service for sharing pre-publication data among research groups. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples

PubMed Central

Galli, Joakim; Oelrich, Johan; Taussig, Michael J.; Andreasson, Ulrika; Ortega-Paino, Eva; Landegren, Ulf

2015-01-01

We report the development of a new database of technology services and products for analysis of biobank samples in biomedical research. BARCdb, the Biobanking Analysis Resource Catalogue (http://www.barcdb.org), is a freely available web resource, listing expertise and molecular resource capabilities of research centres and biotechnology companies. The database is designed for researchers who require information on how to make best use of valuable biospecimens from biobanks and other sample collections, focusing on the choice of analytical techniques and the demands they make on the type of samples, pre-analytical sample preparation and amounts needed. BARCdb has been developed as part of the Swedish biobanking infrastructure (BBMRI.se), but now welcomes submissions from service providers throughout Europe. BARCdb can help match resource providers with potential users, stimulating transnational collaborations and ensuring compatibility of results from different labs. It can promote a more optimal use of European resources in general, both with respect to standard and more experimental technologies, as well as for valuable biobank samples. This article describes how information on service and reagent providers of relevant technologies is made available on BARCdb, and how this resource may contribute to strengthening biomedical research in academia and in the biotechnology and pharmaceutical industries. PMID:25336620

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2009-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank(R) staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.

PubMed

Liolios, Konstantinos; Chen, I-Min A; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor M; Kyrpides, Nikos C

2010-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

PubMed Central

Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor M.; Kyrpides, Nikos C.

2010-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/ PMID:19914934

Materials dispersion and biodynamics project research

NASA Technical Reports Server (NTRS)

Lewis, Marian L.

1992-01-01

The Materials Dispersion and Biodynamics Project (MDBP) focuses on dispersion and mixing of various biological materials and the dynamics of cell-to-cell communication and intracellular molecular trafficking in microgravity. Research activities encompass biomedical applications, basic cell biology, biotechnology (products from cells), protein crystal development, ecological life support systems (involving algae and bacteria), drug delivery (microencapsulation), biofilm deposition by living organisms, and hardware development to support living cells on Space Station Freedom (SSF). Project goals are to expand the existing microgravity science database through experiments on sounding rockets, the Shuttle, and COMET program orbiters and to evolve,through current database acquisition and feasibility testing, to more mature and larger-scale commercial operations on SSF. Maximized utilization of SSF for these science applications will mean that service companies will have a role in providing equipment for use by a number of different customers. An example of a potential forerunner of such a service for SSF is the Materials Dispersion Apparatus (MDA) 'mini lab' of Instrumentation Technology Associates, Inc. (ITA) in use on the Shuttle for the Commercial MDAITA Experiments (CMIX) Project. The MDA wells provide the capability for a number of investigators to perform mixing and bioprocessing experiments in space. In the area of human adaptation to microgravity, a significant database has been obtained over the past three decades. Some low-g effects are similar to Earth-based disorders (anemia, osteoporosis, neuromuscular diseases, and immune system disorders). As new information targets potential profit-making processes, services and products from microgravity, commercial space ventures are expected to expand accordingly. Cooperative CCDS research in the above mentioned areas is essential for maturing SSF biotechnology and to ensure U.S. leadership in space technology. Currently, the MDBP conducts collaborative research with investigators at the Rockefeller University, National Cancer Institute, and the Universities of California, Arizona, and Alabama in Birmingham. The growing database from these collaborations provides fundamental information applicable to development of cell products, manipulation of immune cell response, bone cell growth and mineralization, and other processes altered by low-gravity. Contacts with biotechnology and biopharmaceutical companies are being increased to reach uninformed potential SSF users, provide access through the CMDS to interested users for feasibility studies, and to continue active involvement of current participants. We encourage and actively seek participation of private sector companies, and university and government researchers interested in biopharmaceuticals, hardware development and fundamental research in microgravity.

Education resources of the National Center for Biotechnology Information.

PubMed

Cooper, Peter S; Lipshultz, Dawn; Matten, Wayne T; McGinnis, Scott D; Pechous, Steven; Romiti, Monica L; Tao, Tao; Valjavec-Gratian, Majda; Sayers, Eric W

2010-11-01

The National Center for Biotechnology Information (NCBI) hosts 39 literature and molecular biology databases containing almost half a billion records. As the complexity of these data and associated resources and tools continues to expand, so does the need for educational resources to help investigators, clinicians, information specialists and the general public make use of the wealth of public data available at the NCBI. This review describes the educational resources available at NCBI via the NCBI Education page (www.ncbi.nlm.nih.gov/Education/). These resources include materials designed for new users, such as About NCBI and the NCBI Guide, as well as documentation, Frequently Asked Questions (FAQs) and writings on the NCBI Bookshelf such as the NCBI Help Manual and the NCBI Handbook. NCBI also provides teaching materials such as tutorials, problem sets and educational tools such as the Amino Acid Explorer, PSSM Viewer and Ebot. NCBI also offers training programs including the Discovery Workshops, webinars and tutorials at conferences. To help users keep up-to-date, NCBI produces the online NCBI News and offers RSS feeds and mailing lists, along with a presence on Facebook, Twitter and YouTube.

Gene: a gene-centered information resource at NCBI.

PubMed

Brown, Garth R; Hem, Vichet; Katz, Kenneth S; Ovetsky, Michael; Wallin, Craig; Ermolaeva, Olga; Tolstoy, Igor; Tatusova, Tatiana; Pruitt, Kim D; Maglott, Donna R; Murphy, Terence D

2015-01-01

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Using GenBank.

PubMed

Wheeler, David

2007-01-01

GenBank(R) is a comprehensive database of publicly available DNA sequences for more than 205,000 named organisms and for more than 60,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Molecular Biology Laboratory (EMBL) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure, and domain information and the biomedical journal literature through PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available through FTP. GenBank usage scenarios ranging from local analyses of the data available through FTP to online analyses supported by the NCBI Web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

DNA Data Bank of Japan

PubMed Central

Mashima, Jun; Kodama, Yuichi; Fujisawa, Takatomo; Katayama, Toshiaki; Okuda, Yoshihiro; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Nakamura, Yasukazu; Takagi, Toshihisa

2017-01-01

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data. PMID:27924010

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.

PubMed

Hamosh, Ada; Scott, Alan F; Amberger, Joanna S; Bocchini, Carol A; McKusick, Victor A

2005-01-01

Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (http://www.ncbi.nlm.nih.gov/omim/) is now distributed electronically by the National Center for Biotechnology Information, where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, HUGO nomenclature, MapViewer, GeneTests, patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics.

Analysing patent landscapes in plant biotechnology and new plant breeding techniques.

PubMed

Parisi, Claudia; Rodríguez-Cerezo, Emilio; Thangaraj, Harry

2013-02-01

This article aims to inform the reader of the importance of searching patent landscapes in plant biotechnology and the use of basic tools to perform a patent search. The recommendations for a patent search strategy are illustrated with the specific example of zinc finger nuclease technology for genetic engineering in plants. Within this scope, we provide a general introduction to searching using two online and free-access patent databases esp@cenet and PatentScope. The essential features of the two databases, and their functionality is described, together with short descriptions to enable the reader to understand patents, searching, their content, patent families, and their territorial scope. We mostly stress the value of patent searching for mining scientific, rather than legal information. Search methods through the use of keywords and patent codes are elucidated together with suggestions about how to search with or combine codes with keywords and we also comment on limitations of each method. We stress the importance of patent literature to complement more mainstream scientific literature, and the relative complexities and difficulties in searching patents compared to the latter. A parallel online resource where we describe detailed search exercises is available through reference for those intending further exploration. In essence this is aimed at a novice patent searcher who may want to examine accessory patent literature to complement knowledge gained from mainstream journal resources.

Human genetic databases and liberty.

PubMed

Adalsteinsson, Ragnar

2004-01-01

This paper examines an act of the Icelandic Parliament on health-sector databases. Both the legislation itself and the manner in which it was presented by the Government to the Parliament and the general public raise various questions about democratic parliamentary procedures, community consultation, autonomy, privacy, professional confidence, control of health data in hospitals and business relationships between medical doctors and biotechnology corporations. A major question to be asked is: In whose interest is it that such sensitive data are handed over to for-profit corporations? Furthermore, is it within the authority of the legislature to authorize politically appointed boards of health institutes to transfer such data without the direct informed consent of the patient and without the relevant physicians' having a say? Does experience teach us to entrust private companies with sensitive personal data? Should the Government be involved in the research policy-making of the biotechnology companies that have been given access to the genetic data of a population, or should the profit motive be the sole deciding influence? That is, should the interest of the shareholders of the companies prevail over the interest of underprivileged groups who are most in need of new methods or medicine to alleviate their situation due to incurable diseases? Or is the invisible hand of the market the only competent decision-maker? Finally, will the proliferation of databases containing sensitive personal data, such as human genetic data, limit our personal liberty?

The relationship of knowledge, attitudes and perceptions regarding biotechnology in college students

NASA Astrophysics Data System (ADS)

Sohan, Donna Elizabeth

Biotechnology is the latest in a series of technological innovations that have revolutionized such fields as agriculture and the health sciences. However, along with the benefits of biotechnology are concerns. For biotechnology's potential to be realized, it must be accepted on public and governmental levels. Although many studies focus on adult consumer attitudes, it will be the students of today who will be the consumers and leaders of tomorrow. Therefore, this study focused on the knowledge, attitudes, and perceptions of college students regarding biotechnology. More than 3,000 undergraduate students were surveyed from a variety of undergraduate courses at Texas A&M University in College Station, Texas during the 1997-1998 academic year. Information sought included students' knowledge regarding recent applications of biotechnology, demographic information, and their agreement or disagreement with statements regarding different aspects and applications of biotechnology. This study found that despite a low awareness or knowledge of biotechnology, students were accepting of specific applications or products of biotechnology. Those applications or products viewed as beneficial without involving animals had the highest acceptance levels. A majority of the students identified mass media as their major source of biotechnology while also indicating a high level of distrust of the media. Students also indicated that biotechnology information is needed and that such information is appropriate for high school students. Relationships between knowledge and attitudes were also investigated. A greater knowledge level correlated with a more favorable view of biotechnology. In addition, relationships between demographic variables such as gender and race were investigated. Individuals who identified themselves as scientists were found more accepting of biotechnology while females in general were found less accepting. Females majoring in education were found to be the least accepting of biotechnology. The findings in this study indicate that in order to prepare our future leaders for decisions they will have to make regarding biotechnology, accurate biotechnology information is needed at both the high school and college level.

Microbial culture collections as pillars for promoting fungal diversity, conservation and exploitation.

PubMed

Sette, Lara Durães; Pagnocca, Fernando Carlos; Rodrigues, André

2013-11-01

Fungi are a diverse group of organisms with an overall global number of 1.5M up to 3.3M species on Earth. Besides their ecological roles as decomposers, fungi are important in several aspects of applied research. Here, we review how culture collections may promote the knowledge on diversity, conservation and biotechnological exploitation of fungi. The impact of fungi diversity on biotechnological studies is discussed. We point out the major roles of microbial repositories, including fungal preservation, prospecting, identification, authentication and supply. A survey on the World Data Center for Microorganisms (WDCM) powered by the World Federation for Culture Collections and on the Genetic Heritage Management Council (CGEN) database revealed that 46 Brazilian culture collections registered in these databases are dedicate to preserving fungi. Most of these culture collections are located in the Southeast of Brazil. This scenario also demonstrates that Brazil has many collections focused on fungal strains, but the lack of up-to-date information in WDCM as well as of a solid national platform for culture collections registration do not allow accurate assessment of fungal preservation. Copyright © 2013 Elsevier Inc. All rights reserved.

Prefiltering Model for Homology Detection Algorithms on GPU.

PubMed

Retamosa, Germán; de Pedro, Luis; González, Ivan; Tamames, Javier

2016-01-01

Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA's graphics processing units (GPUs) and multicore processors. Depending on the sensitivity settings, this makes it possible to quickly reduce the sequence database by factors between 50% and 95%, while rejecting no significant sequences. Furthermore, this prefiltering application can be used together with multiple homology detection algorithms as a part of a next-generation sequencing system. Extensive performance and accuracy tests have been carried out in the Spanish National Centre for Biotechnology (NCB). The results show that GPU hardware can accelerate the execution times of former homology detection applications, such as National Centre for Biotechnology Information (NCBI), Basic Local Alignment Search Tool for Proteins (BLASTP), up to a factor of 4.

Patent Survey of Resveratrol, Taxol, Podophyllotoxin, Withanolides and Their Derivatives Used in Anticancer Therapy.

PubMed

Routh, Shreya; Nandagopal, Krishnadas

2017-01-01

Resveratrol, taxol, podophyllotoxin, withanolides and their derivatives find applications in anti-cancer therapy. They are plant-derived compounds whose chemical structures and synthesis limit their natural availability and restrict a large-scale industrial production. Hence, their production by various biotechnological approaches may hold promise for a continuous and reliable mode of supply. We review process and product patents in this regard. Accordingly, we provide a general outline to search the freely accessible WIPO, EPO, USPTO and Cambia databases with several keywords and patent codes. We have tabulated both granted and filed patents from the said databases. We retrieved ~40 patents from these databases. Novel biotechnological processes for production of these anticancer compounds include Agrobacterium rhizogenes-mediated hairy root culture, suspension culture, cell culture with elicitors, use of recombinant microorganisms, and bioreactors among others. The results are indicative of being both database-specific as well as queryspecific. A ten-year search window yielded 33 patents. The utility of the search strategy is discussed in the light of biotechnological developments in the field. Those who examine patent literature using similar search strategies may complement their knowledge obtained from perusal of mainstream journal resources. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The BRENDA enzyme information system-From a database to an expert system.

PubMed

Schomburg, I; Jeske, L; Ulbrich, M; Placzek, S; Chang, A; Schomburg, D

2017-11-10

Enzymes, representing the largest and by far most complex group of proteins, play an essential role in all processes of life, including metabolism, gene expression, cell division, the immune system, and others. Their function, also connected to most diseases or stress control makes them interesting targets for research and applications in biotechnology, medical treatments, or diagnosis. Their functional parameters and other properties are collected, integrated, and made available to the scientific community in the BRaunschweig ENzyme DAtabase (BRENDA). In the last 30 years BRENDA has developed into one of the most highly used biological databases worldwide. The data contents, the process of data acquisition, data integration and control, the ways to access the data, and visualizations provided by the website are described and discussed. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Biotechnology Education. Engaging the Learner: Embedding Information Literacy Skills into a Biotechnology Degree

ERIC Educational Resources Information Center

Ward, Helena; Hockey, Julie

2007-01-01

One of the challenges of the Biotechnology industry is keeping up to date with the rapid pace of change and that much of the information, which students learn in their undergraduate studies, will be out of date in a few years. It is therefore crucial that Biotechnology students have the skills to access the relevant information for their studies…

Biotechnology: An Era of Hopes and Fears

DTIC Science & Technology

2016-01-01

The human genome had yet to be sequenced, and cloning was still a the- ory. Now the world’s genetic databases contain 1.3 x 1012 bases of data...All life on earth is ultimately controlled by each organism’s unique ge- netic code carried in its DNA, and many human disease states can be at- LTC...hence information content, of the DNA.3 For example, noninfectious human disease states, such as cancer or sickle cell anemia, can be attributed to

Proteomic analysis of Rhodotorula mucilaginosa: dealing with the issues of a non-conventional yeast.

PubMed

Addis, Maria Filippa; Tanca, Alessandro; Landolfo, Sara; Abbondio, Marcello; Cutzu, Raffaela; Biosa, Grazia; Pagnozzi, Daniela; Uzzau, Sergio; Mannazzu, Ilaria

2016-08-01

Red yeasts ascribed to the species Rhodotorula mucilaginosa are gaining increasing attention, due to their numerous biotechnological applications, spanning carotenoid production, liquid bioremediation, heavy metal biotransformation and antifungal and plant growth-promoting actions, but also for their role as opportunistic pathogens. Nevertheless, their characterization at the 'omic' level is still scarce. Here, we applied different proteomic workflows to R. mucilaginosa with the aim of assessing their potential in generating information on proteins and functions of biotechnological interest, with a particular focus on the carotenogenic pathway. After optimization of protein extraction, we tested several gel-based (including 2D-DIGE) and gel-free sample preparation techniques, followed by tandem mass spectrometry analysis. Contextually, we evaluated different bioinformatic strategies for protein identification and interpretation of the biological significance of the dataset. When 2D-DIGE analysis was applied, not all spots returned a unambiguous identification and no carotenogenic enzymes were identified, even upon the application of different database search strategies. Then, the application of shotgun proteomic workflows with varying levels of sensitivity provided a picture of the information depth that can be reached with different analytical resources, and resulted in a plethora of information on R. mucilaginosa metabolism. However, also in these cases no proteins related to the carotenogenic pathway were identified, thus indicating that further improvements in sequence databases and functional annotations are strictly needed for increasing the outcome of proteomic analysis of this and other non-conventional yeasts. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Biotechnology: Commercialization and Economic Aspects, January 1993-June 1996. Quick Bibliography Series no. QB 96-10.

ERIC Educational Resources Information Center

Leonard, Scott A., Comp.; Dobert, Raymond, Comp.

This bibliography on the commercialization and economic aspects of biotechnology was produced by the National Agricultural Library. It contains 151 citations in English from the AGRICOLA database. The search strategy is included, call numbers are given for each entry, and abstracts are provided for some citations. The bibliography concludes with…

An Integrated Korean Biodiversity and Genetic Information Retrieval System

PubMed Central

Lim, Jeongheui; Bhak, Jong; Oh, Hee-Mock; Kim, Chang-Bae; Park, Yong-Ha; Paek, Woon Kee

2008-01-01

Background On-line biodiversity information databases are growing quickly and being integrated into general bioinformatics systems due to the advances of fast gene sequencing technologies and the Internet. These can reduce the cost and effort of performing biodiversity surveys and genetic searches, which allows scientists to spend more time researching and less time collecting and maintaining data. This will cause an increased rate of knowledge build-up and improve conservations. The biodiversity databases in Korea have been scattered among several institutes and local natural history museums with incompatible data types. Therefore, a comprehensive database and a nation wide web portal for biodiversity information is necessary in order to integrate diverse information resources, including molecular and genomic databases. Results The Korean Natural History Research Information System (NARIS) was built and serviced as the central biodiversity information system to collect and integrate the biodiversity data of various institutes and natural history museums in Korea. This database aims to be an integrated resource that contains additional biological information, such as genome sequences and molecular level diversity. Currently, twelve institutes and museums in Korea are integrated by the DiGIR (Distributed Generic Information Retrieval) protocol, with Darwin Core2.0 format as its metadata standard for data exchange. Data quality control and statistical analysis functions have been implemented. In particular, integrating molecular and genetic information from the National Center for Biotechnology Information (NCBI) databases with NARIS was recently accomplished. NARIS can also be extended to accommodate other institutes abroad, and the whole system can be exported to establish local biodiversity management servers. Conclusion A Korean data portal, NARIS, has been developed to efficiently manage and utilize biodiversity data, which includes genetic resources. NARIS aims to be integral in maximizing bio-resource utilization for conservation, management, research, education, industrial applications, and integration with other bioinformation data resources. It can be found at . PMID:19091024

Education resources of the National Center for Biotechnology Information

PubMed Central

Lipshultz, Dawn; Matten, Wayne T.; McGinnis, Scott D.; Pechous, Steven; Romiti, Monica L.; Tao, Tao; Valjavec-Gratian, Majda; Sayers, Eric W.

2010-01-01

The National Center for Biotechnology Information (NCBI) hosts 39 literature and molecular biology databases containing almost half a billion records. As the complexity of these data and associated resources and tools continues to expand, so does the need for educational resources to help investigators, clinicians, information specialists and the general public make use of the wealth of public data available at the NCBI. This review describes the educational resources available at NCBI via the NCBI Education page (www.ncbi.nlm.nih.gov/Education/). These resources include materials designed for new users, such as About NCBI and the NCBI Guide, as well as documentation, Frequently Asked Questions (FAQs) and writings on the NCBI Bookshelf such as the NCBI Help Manual and the NCBI Handbook. NCBI also provides teaching materials such as tutorials, problem sets and educational tools such as the Amino Acid Explorer, PSSM Viewer and Ebot. NCBI also offers training programs including the Discovery Workshops, webinars and tutorials at conferences. To help users keep up-to-date, NCBI produces the online NCBI News and offers RSS feeds and mailing lists, along with a presence on Facebook, Twitter and YouTube. PMID:20570844

Engaging the learner: Embedding information literacy skills into a biotechnology degree.

PubMed

Ward, Helena; Hockey, Julie

2007-09-01

One of the challenges of the Biotechnology industry is keeping up to date with the rapid pace of change and that much of the information, which students learn in their undergraduate studies, will be out of date in a few years. It is therefore crucial that Biotechnology students have the skills to access the relevant information for their studies and critically evaluate the vast volume of information and its sources. By developing information literacy skills, which are part of lifelong learning, Biotechnology graduates are better prepared for their careers. Students also need to understand the issues related to the use of information such as social, political, ethical, and legal implications. This paper will outline the embedding of information literacy skills within the Biotechnology degree at the University of South Australia. Examples of specific activities and their link to assessment will be discussed. Copyright © 2007 International Union of Biochemistry and Molecular Biology, Inc.

Biotechnological Patents Applications of the Deuterium Oxide in Human Health.

PubMed

da S Mariano, Reysla M; Bila, Wendell C; Trindade, Maria Jaciara F; Lamounier, Joel A; Galdino, Alexsandro S

2017-01-01

Deuterium oxide is a molecule that has been used for decades in several studies related to human health. Currently, studies on D2O have mobilized a "Race for Patenting" worldwide. Several patents have been registered from biomedical and technological studies of D2O showing the potential of this stable isotope in industry and health care ecosystems. Most of the patents related to the applications of the deuterium oxide in human health have been summarized in this review. The following patents databases were consulted: European Patent Office (Espacenet), the United States Patent and Trademark Office (USPTO), the United States Latin America Patents (LATIPAT), Patent scope -Search International and National Patent Collections (WIPO), Google Patents and Free Patents Online. With this review, the information was collected on recent publications including 22 patents related to deuterium oxide and its applications in different areas. This review showed that deuterium oxide is a promising component in different areas, including biotechnology, chemistry and medicine. In addition, the knowledge of this compound was covered, reinforcing its importance in the field of biotechnology and human health. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

NCBI GEO: mining millions of expression profiles--database and tools.

PubMed

Barrett, Tanya; Suzek, Tugba O; Troup, Dennis B; Wilhite, Stephen E; Ngau, Wing-Chi; Ledoux, Pierre; Rudnev, Dmitry; Lash, Alex E; Fujibuchi, Wataru; Edgar, Ron

2005-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30,000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

PubMed searches: overview and strategies for clinicians.

PubMed

Lindsey, Wesley T; Olin, Bernie R

2013-04-01

PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.

Bayesian approach to transforming public gene expression repositories into disease diagnosis databases.

PubMed

Huang, Haiyan; Liu, Chun-Chi; Zhou, Xianghong Jasmine

2010-04-13

The rapid accumulation of gene expression data has offered unprecedented opportunities to study human diseases. The National Center for Biotechnology Information Gene Expression Omnibus is currently the largest database that systematically documents the genome-wide molecular basis of diseases. However, thus far, this resource has been far from fully utilized. This paper describes the first study to transform public gene expression repositories into an automated disease diagnosis database. Particularly, we have developed a systematic framework, including a two-stage Bayesian learning approach, to achieve the diagnosis of one or multiple diseases for a query expression profile along a hierarchical disease taxonomy. Our approach, including standardizing cross-platform gene expression data and heterogeneous disease annotations, allows analyzing both sources of information in a unified probabilistic system. A high level of overall diagnostic accuracy was shown by cross validation. It was also demonstrated that the power of our method can increase significantly with the continued growth of public gene expression repositories. Finally, we showed how our disease diagnosis system can be used to characterize complex phenotypes and to construct a disease-drug connectivity map.

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.

PubMed

Hamosh, Ada; Scott, Alan F; Amberger, Joanna; Bocchini, Carol; Valle, David; McKusick, Victor A

2002-01-01

Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support research and education in human genomics and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (www.ncbi.nlm.nih.gov/omim) is now distributed electronically by the National Center for Biotechnology Information (NCBI), where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, approved gene nomenclature, and the highly detailed mapviewer, as well as patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics.

[Patented technology status quo and development trend for Chinese herbal medicines].

PubMed

Li, Chang; Huang, Luqi

2009-06-01

Patent technology is regarded as technological trends under the market economy condition. The case showed the information form patent literature can be widely used in technology or economy. In this study, we analyzed the patent technology status quo and development trend for Chinese herbal medicines based on China patent database. The patent technology status quo is divided from the technology of biotechnology, quality control, cultivation and herb processing on Chinese herbal medicines. Furthermore, some recommendations of technology development and advices on patent protection for Chinese herbal medicines were suggested.

Connecting learners: The role of biotechnology programme in preparing students for the industry.

PubMed

Mohd Saruan, Nadiah; Sagran, Avinash; Fadzil, Kamal Solhaimi; Razali, Zuliana; Ow Phui San, Rebecca; Somasundram, Chandran

2015-01-01

The recent growth of biotechnology requires a wide range of expertise within the industry. Education is the primary platform for students to gain information and knowledge on biotechnology. In Malaysia where biotechnology is relatively new, education programs and courses must be tailored to meet the demands of the industry. A combination of theoretical knowledge as well as practical and industrial training is essential to ensure graduates are prepared for their career in the fields of biotechnology. Results from this study show that university students lack literacy on biotechnology information and access to facilities provided by the universities. This may be a significant contributing factor to the lack of knowledge and information amongst graduates. Furthermore comparative analysis on the biotechnology program in Malaysian universities with that of other countries show the need to restructure the program by offering more specialized courses as well as soft skills and business subjects. This is to meet the demands of the related professionals as well as the various branches that exist in the biotechnology industry. © 2015 The International Union of Biochemistry and Molecular Biology.

Bringing the human genome and the revolution in bioinformatics to the medical school classroom: a case report from Washington University School of Medicine.

PubMed

Magee, J; Gordon, J I; Whelan, A

2001-08-01

The human genome project is revolutionizing medical research and the practice of clinical medicine. To understand and participate in this revolution, physicians must be fluent in human genomics and bioinformatics. At Washington University School of Medicine (WUSM), the authors designed a module for teaching these skills to first-year students. The module uses clinical cases as a platform for accessing information stored in GenBank, Online Mendelian Inheritance in Man (OMIM), and PubMed databases at the National Center for Biotechnology Information (NCBI). This module, which is also designed to reinforce problem-solving skills, has been integrated into WUSM's first-year medical genetics course.

Biotechnology: from university to industry

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

Kenney, M.F.

1984-01-01

This study examines the birth of the biotechnology industry in the US. It is argued that biotechnology may have important implications for the future of American capitalism. The study is contextualized theoretically through the use of the idea of the capitalism experiences waves of innovations at certain historical periods. Finally, the idea of a new regime of accumulation based on information technologies is explored and biotechnology's potential position in the information society is explored. The first section of the study examines the role of the university in biotechnology. The various objectives of administrators and professors are explored as is themore » role of corporate gift giving in transforming the university into an institution more useful for capitalist accumulation. The second section examines the corporate role in biotechnology: both from the viewpoint of the small venture capital-financed biotechnology firms and the large multinational oil, chemical, and pharmaceutical companies that have made a number of important investments in biotechnology. The last chapter describes the unique effects that biotechnology will have upon the US agricultural sector.« less

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups

PubMed Central

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads

2017-01-01

Abstract Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. Database URL: http://www.midasfieldguide.org PMID:28365734

Online Mendelian Inheritance in Man (OMIM).

PubMed

Hamosh, A; Scott, A F; Amberger, J; Valle, D; McKusick, V A

2000-01-01

Online Mendelian Inheritance In Man (OMIM) is a public database of bibliographic information about human genes and genetic disorders. Begun by Dr. Victor McKusick as the authoritative reference Mendelian Inheritance in Man, it is now distributed electronically by the National Center for Biotechnology Information (NCBI). Material in OMIM is derived from the biomedical literature and is written by Dr. McKusick and his colleagues at Johns Hopkins University and elsewhere. Each OMIM entry has a full text summary of a genetic phenotype and/or gene and has copious links to other genetic resources such as DNA and protein sequence, PubMed references, mutation databases, approved gene nomenclature, and more. In addition, NCBI's neighboring feature allows users to identify related articles from PubMed selected on the basis of key words in the OMIM entry. Through its many features, OMIM is increasingly becoming a major gateway for clinicians, students, and basic researchers to the ever-growing literature and resources of human genetics. Copyright 2000 Wiley-Liss, Inc.

World Biotechnology Leaders to Gather for Conference

Science.gov Websites

Biotechnology Leaders to Gather for Conference For more information contact: e:mail: Public Affairs biotechnology leaders gather in Fort Collins, CO May 2-6 for the 21st Symposium on Biotechnology for Fuels and special session on funding opportunities for U.S. biotechnology projects. More than 175 presentations are

Biotechnology: Education and Training. Special Reference Briefs Series No. SRB 96-08.

ERIC Educational Resources Information Center

Dobert, Raymond

This document, prepared by The Biotechnology Information Center at the National Agricultural Library, contains sources of information that can provide a starting point for teachers, university faculty, extension agents, and other education leaders who have an interest in biotechnology education and training. Sections include a bibliography of the…

State FFA Officers' Confidence and Trustworthiness of Biotechnology Information Sources

ERIC Educational Resources Information Center

Wingenbach, Gary J.; Rutherford, Tracy A.

2007-01-01

Are state FFA officers' awareness levels of agricultural topics reported in mass media superior to those who do not serve in leadership roles? The purpose of this study was to determine elected state FFA officers' awareness of biotechnology, and their confidence and trust of biotechnology information sources. Descriptive survey methods were used…

75 FR 1749 - Syngenta Biotechnology, Inc.; Availability of Petition and Environmental Assessment for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-13

...] Syngenta Biotechnology, Inc.; Availability of Petition and Environmental Assessment for Determination of... Health Inspection Service has received a petition from Syngenta Biotechnology, Inc., seeking a....gov ). FOR FURTHER INFORMATION CONTACT: Dr. Subray Hegde, Biotechnology Regulatory Services, APHIS...

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses.

PubMed

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52-61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.

Biotechnology in Turkey: an overview.

PubMed

Ozdamar, Tunçer H

2009-07-01

The term biotechnology first appeared in the programs of the Scientific and Technological Research Council of Turkey (TUBITAK) in 1982. The State Planning Organization (SPO) in 1988 defined biotechnology and the scientific fields. Moreover, it put forward an institutional framework and suggested priority areas for research and development. Turkey has been researching and investing in biotechnology for almost four decades. This review covers the development of science and technology policy with its history, consensus and consequences, bio-industries in Turkey, and research activities in biotechnology at Turkish Universities. Details are provided by the research groups in response to a common request for information on their activities and major publications in the field. The information provided has been grouped under thematic topics within the broad theme of biotechnology, and summarized within these topics. Although many aspects of biotechnological research are being pursued in Turkey, it appears that the most common research activities of the field are in fermentation processes, environmental biotechnology, and biomedical engineering.

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

PubMed Central

2013-01-01

Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information.

PubMed

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Siążnik, Artur

2013-03-01

Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user's query, advanced data searching based on the specified user's query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.

An Information System for European culture collections: the way forward.

PubMed

Casaregola, Serge; Vasilenko, Alexander; Romano, Paolo; Robert, Vincent; Ozerskaya, Svetlana; Kopf, Anna; Glöckner, Frank O; Smith, David

2016-01-01

Culture collections contain indispensable information about the microorganisms preserved in their repositories, such as taxonomical descriptions, origins, physiological and biochemical characteristics, bibliographic references, etc. However, information currently accessible in databases rarely adheres to common standard protocols. The resultant heterogeneity between culture collections, in terms of both content and format, notably hampers microorganism-based research and development (R&D). The optimized exploitation of these resources thus requires standardized, and simplified, access to the associated information. To this end, and in the interest of supporting R&D in the fields of agriculture, health and biotechnology, a pan-European distributed research infrastructure, MIRRI, including over 40 public culture collections and research institutes from 19 European countries, was established. A prime objective of MIRRI is to unite and provide universal access to the fragmented, and untapped, resources, information and expertise available in European public collections of microorganisms; a key component of which is to develop a dynamic Information System. For the first time, both culture collection curators as well as their users have been consulted and their feedback, concerning the needs and requirements for collection databases and data accessibility, utilised. Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. Moreover, complex searches are rarely possible in online databases thus limiting the extent of search queries. Curators also consider that overall harmonization-including Standard Operating Procedures, data structure, and software tools-is necessary to facilitate their work and to make high-quality data easily accessible to their users. Clearly, the needs of culture collection curators coincide with those of users on the crucial point of database interoperability. In this regard, and in order to design an appropriate Information System, important aspects on which the culture collection community should focus include: the interoperability of data sets with the ontologies to be used; setting best practice in data management, and the definition of an appropriate data standard.

Translational genomics for plant breeding with the genome sequence explosion.

PubMed

Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Jeong, Haneul; Satyawan, Dani; Kim, Moon Young; Lee, Suk-Ha

2016-04-01

The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

78 FR 7387 - Advisory Committee on Biotechnology and 21st Century Agriculture; Renewal

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-01

... Biotechnology and 21st Century Agriculture; Renewal AGENCY: Agricultural Research Service, USDA. ACTION: Advisory Committee on Biotechnology and 21st Century Agriculture Renewal. SUMMARY: Notice is hereby given... agricultural biotechnology. The AC21 has been established to provide information and advice to the Secretary of...

Short and Long-Term Impacts of Biotechnology Education on Professionals Who Communicate Science to the Public

ERIC Educational Resources Information Center

Fritz, Susan M.; Ward, Sarah M.; Byrne, Pat F.; Namuth, Deana M.; Egger, Valerie A.

2004-01-01

Consumer acceptance or rejection of biotechnology is often shaped by information prepared by communicators with varying levels of scientific knowledge, awareness, and acceptance. This study compared the prior, post-workshop, and sustained (1 year) biotechnology awareness, acceptance, and attitudes of professionals who communicate biotechnology to…

Biotechnology: The U.S. Department of Agriculture's Biotechnology Research Efforts. Briefing Report. To the Chairman, Committee on Science and Technology, House of Representatives.

ERIC Educational Resources Information Center

General Accounting Office, Washington, DC.

Information pertaining to biotechnology research that was funded in whole or in part by the U.S. Department of Agriculture (USDA) is presented in this report. Findings obtained from state agricultural experimental stations and colleges of veterinary medicine are discussed in 11 appendices. These include: (1) information on USDA's biotechnology…

Opportunities for biotechnology and policy regarding mycotoxin issues in international trade.

PubMed

Kendra, David F; Dyer, Rex B

2007-10-20

Despite being introduced more than a decade ago, agricultural biotechnology still remains framed in controversy impacting both the global economy and international regulations. Controversies surrounding agricultural biotechnology produced crops and foods commonly focus on human and environmental safety, intellectual property rights, consumer choice, ethics, food security, poverty reduction and environmental conservation. Originally, some consumers were reluctant to accept the first generation agricultural biotechnology products because they appeared to primarily benefit agricultural producers; however, it is clear from continued evaluations that these technologies also improved both the safety and wholesomeness of food and helped improve the environment. Plants engineered to resist insect pests and tolerate less toxic pesticides resulted in improved yields thereby enabling farmers to produce more food per acre while reducing the need for herbicides, pesticides, and water and tilling. An indirect benefit of reduced pest damage in transgenic corn expressing genes to control insect pests is lower levels of mycotoxins, most notably those caused by the genus Fusarium. Mycotoxins are an important regulatory issue globally because of their toxic and carcinogenic potential to humans and animals. Complicating this issue is the fact that toxicological databases for mycotoxins are relatively incomplete compared to other food contaminants. Current debates about agricultural biotechnology and mycotoxins reveal significant differences in perception of associated risks and benefits. When faced with uncertainty, regulators tend to set limits as low as possible. Additionally, some regulators invoke the "Precautionary Principle" when limited information is available or disputes over interpretation exist for possible contaminants, including mycotoxins. A major concern regarding use of the "Precautionary Principle" is the appearance that regulators can justify setting any limit on the basis of inconclusive or unknown potential hazards of a contaminant which may significantly impact global trade because mycotoxin residues vary widely between countries. This paper describes the current economic and heath impact of these regulations and their impact on international trade.

Connecting Learners: The Role of Biotechnology Programme in Preparing Students for the Industry

ERIC Educational Resources Information Center

Mohd Saruan, Nadiah; Sagran, Avinash; Fadzil, Kamal Solhaimi; Razali, Zuliana; Ow Phui San, Rebecca; Somasundram, Chandran

2015-01-01

The recent growth of biotechnology requires a wide range of expertise within the industry. Education is the primary platform for students to gain information and knowledge on biotechnology. In Malaysia where biotechnology is relatively new, education programs and courses must be tailored to meet the demands of the industry. A combination of…

Knowledge and Attitudes towards Biotechnology of Elementary Education Preservice Teachers: The First Spanish Experience

ERIC Educational Resources Information Center

Casanoves, Marina; González, Ángel; Salvadó, Zoel; Haro, Juan; Novo, Maite

2015-01-01

Due to the important impact that biotechnology has on current Western societies, well-informed critical citizens are needed. People prepared to make conscious decisions about aspects of biotechnology that relate to their own lives. Teachers play a central role in all education systems. Thus, the biotechnological literacy of preservice teachers is…

Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy.

PubMed

Bekhuis, Tanja

2006-04-03

Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information. Developments in text mining and hypothesis discovery systems based on the early work of Swanson, a mathematician and information scientist, are coincident with the emergence of conceptual biology. Very little has been written to introduce biomedical digital librarians to these new trends. In this paper, background for data and text mining, as well as for knowledge discovery in databases (KDD) and in text (KDT) is presented, then a brief review of Swanson's ideas, followed by a discussion of recent approaches to hypothesis discovery and testing. 'Testing' in the context of text mining involves partially automated methods for finding evidence in the literature to support hypothetical relationships. Concluding remarks follow regarding (a) the limits of current strategies for evaluation of hypothesis discovery systems and (b) the role of literature-based discovery in concert with empirical research. Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians.

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses

PubMed Central

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55 000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52–61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov. PMID:22064861

Biotechnology Computing: Information Science for the Era of Molecular Medicine.

ERIC Educational Resources Information Center

Masys, Daniel R.

1989-01-01

The evolution from classical genetics to biotechnology, an area of research involving key macromolecules in living cells, is chronicled and the current state of biotechnology is described, noting related advances in computing and clinical medicine. (MSE)

DEOP: a database on osmoprotectants and associated pathways

PubMed Central

Bougouffa, Salim; Radovanovic, Aleksandar; Essack, Magbubah; Bajic, Vladimir B.

2014-01-01

Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, ‘Dragon Explorer of Osmoprotection associated Pathways’ (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at. Database URL: http://www.cbrc.kaust.edu.sa/deop/ PMID:25326239

Knowledge and Attitudes Towards Biotechnology of Elementary Education Preservice Teachers: The first Spanish experience

NASA Astrophysics Data System (ADS)

Casanoves, Marina; González, Ángel; Salvadó, Zoel; Haro, Juan; Novo, Maite

2015-11-01

Due to the important impact that biotechnology has on current Western societies, well-informed critical citizens are needed. People prepared to make conscious decisions about aspects of biotechnology that relate to their own lives. Teachers play a central role in all education systems. Thus, the biotechnological literacy of preservice teachers is an important consideration as they will become an influential collective as future teachers of the next generation of children. The attitudes toward science (and biotechnology) that teachers have affect their behavior and influence the way they implement their daily practice of science teaching in school. This study analyzes the attitudes and knowledge of Spanish preservice teachers toward biotechnology. We designed a new survey instrument that was completed by 407 university students who were taking official degree programs in preschool and primary education. Our results point out that although they are aware of biotechnology applications, topics concerning the structure of DNA, management of genetic information inside the cell, genetically modified organism technology and the use of microorganisms as biotechnological tools were not correctly answered. According to our attitude analysis, Spanish preservice teachers could be defined as opponents of genetically modified product acquisition, supporters of biotechnology for medical purposes and highly interested in increasing their knowledge about biotechnology and other scientific advances. Our results show a positive correlation between better knowledge and more positive attitudes toward biotechnology. A Spanish preservice teacher with positive attitudes toward biotechnology tends to be a student with a strong biology background who scored good marks in our knowledge test.

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.

PubMed

Nogales, Juan; Palsson, Bernhard Ø; Thiele, Ines

2008-09-16

Pseudomonas putida is the best studied pollutant degradative bacteria and is harnessed by industrial biotechnology to synthesize fine chemicals. Since the publication of P. putida KT2440's genome, some in silico analyses of its metabolic and biotechnology capacities have been published. However, global understanding of the capabilities of P. putida KT2440 requires the construction of a metabolic model that enables the integration of classical experimental data along with genomic and high-throughput data. The constraint-based reconstruction and analysis (COBRA) approach has been successfully used to build and analyze in silico genome-scale metabolic reconstructions. We present a genome-scale reconstruction of P. putida KT2440's metabolism, iJN746, which was constructed based on genomic, biochemical, and physiological information. This manually-curated reconstruction accounts for 746 genes, 950 reactions, and 911 metabolites. iJN746 captures biotechnologically relevant pathways, including polyhydroxyalkanoate synthesis and catabolic pathways of aromatic compounds (e.g., toluene, benzoate, phenylacetate, nicotinate), not described in other metabolic reconstructions or biochemical databases. The predictive potential of iJN746 was validated using experimental data including growth performance and gene deletion studies. Furthermore, in silico growth on toluene was found to be oxygen-limited, suggesting the existence of oxygen-efficient pathways not yet annotated in P. putida's genome. Moreover, we evaluated the production efficiency of polyhydroxyalkanoates from various carbon sources and found fatty acids as the most prominent candidates, as expected. Here we presented the first genome-scale reconstruction of P. putida, a biotechnologically interesting all-surrounder. Taken together, this work illustrates the utility of iJN746 as i) a knowledge-base, ii) a discovery tool, and iii) an engineering platform to explore P. putida's potential in bioremediation and bioplastic production.

Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*.

PubMed

Barrett, Tanya; Edgar, Ron

2006-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) has emerged as the leading fully public repository for gene expression data. This chapter describes how to use Web-based interfaces, applications, and graphics to effectively explore, visualize, and interpret the hundreds of microarray studies and millions of gene expression patterns stored in GEO. Data can be examined from both experiment-centric and gene-centric perspectives using user-friendly tools that do not require specialized expertise in microarray analysis or time-consuming download of massive data sets. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

NCBI Bookshelf: books and documents in life sciences and health care

PubMed Central

Hoeppner, Marilu A.

2013-01-01

Bookshelf (http://www.ncbi.nlm.nih.gov/books/) is a full-text electronic literature resource of books and documents in life sciences and health care at the National Center for Biotechnology Information (NCBI). Created in 1999 with a single book as an encyclopedic reference for resources such as PubMed and GenBank, it has grown to its current size of >1300 titles. Unlike other NCBI databases, such as GenBank and Gene, which have a strict data structure, books come in all forms; they are diverse in publication types, formats, sizes and authoring models. The Bookshelf data format is XML tagged in the NCBI Book DTD (Document Type Definition), modeled after the National Library of Medicine journal article DTDs. The book DTD has been used for systematically tagging the diverse data formats of books, a move that has set the foundation for the growth of this resource. Books at NCBI followed the route of journal articles in the PubMed Central project, using the PubMed Central architectural framework, workflows and processes. Through integration with other NCBI molecular databases, books at NCBI can be used to provide reference information for biological data and facilitate its discovery. This article describes Bookshelf at NCBI: its growth, data handling and retrieval and integration with molecular databases. PMID:23203889

NCBI Bookshelf: books and documents in life sciences and health care.

PubMed

Hoeppner, Marilu A

2013-01-01

Bookshelf (http://www.ncbi.nlm.nih.gov/books/) is a full-text electronic literature resource of books and documents in life sciences and health care at the National Center for Biotechnology Information (NCBI). Created in 1999 with a single book as an encyclopedic reference for resources such as PubMed and GenBank, it has grown to its current size of >1300 titles. Unlike other NCBI databases, such as GenBank and Gene, which have a strict data structure, books come in all forms; they are diverse in publication types, formats, sizes and authoring models. The Bookshelf data format is XML tagged in the NCBI Book DTD (Document Type Definition), modeled after the National Library of Medicine journal article DTDs. The book DTD has been used for systematically tagging the diverse data formats of books, a move that has set the foundation for the growth of this resource. Books at NCBI followed the route of journal articles in the PubMed Central project, using the PubMed Central architectural framework, workflows and processes. Through integration with other NCBI molecular databases, books at NCBI can be used to provide reference information for biological data and facilitate its discovery. This article describes Bookshelf at NCBI: its growth, data handling and retrieval and integration with molecular databases.

Epistemic Beliefs and Conceptual Understanding in Biotechnology: A Case Study

ERIC Educational Resources Information Center

Rebello, Carina M.; Siegel, Marcelle A.; Witzig, Stephen B.; Freyermuth, Sharyn K.; McClure, Bruce A.

2012-01-01

The purpose of this investigation was to explore students' epistemic beliefs and conceptual understanding of biotechnology. Epistemic beliefs can influence reasoning, how individuals evaluate information, and informed decision making abilities. These skills are important for an informed citizenry that will participate in debates regarding areas in…

Broad issues to consider for library involvement in bioinformatics*

PubMed Central

Geer, Renata C.

2006-01-01

Background: The information landscape in biological and medical research has grown far beyond literature to include a wide variety of databases generated by research fields such as molecular biology and genomics. The traditional role of libraries to collect, organize, and provide access to information can expand naturally to encompass these new data domains. Methods: This paper discusses the current and potential role of libraries in bioinformatics using empirical evidence and experience from eleven years of work in user services at the National Center for Biotechnology Information. Findings: Medical and science libraries over the last decade have begun to establish educational and support programs to address the challenges users face in the effective and efficient use of a plethora of molecular biology databases and retrieval and analysis tools. As more libraries begin to establish a role in this area, the issues they face include assessment of user needs and skills, identification of existing services, development of plans for new services, recruitment and training of specialized staff, and establishment of collaborations with bioinformatics centers at their institutions. Conclusions: Increasing library involvement in bioinformatics can help address information needs of a broad range of students, researchers, and clinicians and ultimately help realize the power of bioinformatics resources in making new biological discoveries. PMID:16888662

Current and Future Leaders' Perceptions of Agricultural Biotechnology

ERIC Educational Resources Information Center

Wingenbach, Gary J.; Miller, Rene P.

2009-01-01

Were elected state FFA officers' attitudes toward agricultural biotechnology significantly different from elected Texas legislators' attitudes about the same topic? The purpose of this study was to determine if differences existed in agricultural biotechnology perceptions or information source preferences when compared by leadership status:…

75 FR 31795 - Office of Biotechnology Activities; Recombinant DNA Research: Amended Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-04

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Office of Biotechnology Activities; Recombinant DNA Research: Amended Notice of Meeting ACTION: Notice of cancellation of... information. Dated: May 26, 2010. Jacqueline Corrigan-Curay, Acting Director, Office of Biotechnology...

A cross-sectional study of biotechnology awareness and teaching in European high schools.

PubMed

Vanderschuren, Hervé; Heinzmann, Dominik; Faso, Carmen; Stupak, Martin; Arga, Kazim Yalçin; Hoerzer, Helen; Laizet, Yech'an; Leduchowska, Paulina; Silva, Nádia; Simková, Klára

2010-12-31

Undoubtedly, biotechnology has a tremendous impact on our daily lives. As a result of this and in parallel to the advancement of knowledge in this field of applied research, consumer awareness of the potential benefits and risks of this technology has steadily increased, leading to a thorough investigation of the public perception of biotechnology in the past years. Indeed, it has become clear that it is in the general interest of science and especially of applied research to inform the public of its advances. A promising next step is to strengthen biotechnology communication in scholastic institutions. In this paper, we investigate the perception of biotechnology in a specific target group, namely high-school students in the 16-20-year-old age range. We conducted a questionnaire-based survey on a total of 1410 students in six European countries to investigate students' perception, concern, scientific knowledge, and awareness. Our data revealed some unexpected patterns of acceptance and concern about biotechnology. Knowledge analysis indicated that pupils lack specific knowledge about biotechnological applications and their interest in biotechnology appeared to be linked to knowledge. Analysis of specific questions about teaching practices at schools suggests that a better targeted choice in media as vehicles for information together with selected speakers could be instrumental in increasing students' interest in science and more specifically in biotechnology. Copyright © 2010 Elsevier B.V. All rights reserved.

Health-related biotechnology transfer to Africa: principal-agency relationship issues.

PubMed

Kirigia, J M; Muthuri, L K; Kirigia, D G

2007-01-01

The aim of this paper is to stimulate debate on the agency (principal-agent) in health-related biotechnology research. It attempts to answer the following questions: What is health-related biotechnology and biotechnology research? What is an agency? What factors are likely to undermine the principal's capacity to exercise informed consent? When might the principal-agency problem arise? How could the agency in biotechnology transfer be strengthened in Sub-Saharan Africa (SSA)? The transfer of health-related biotechnology to SSA ought to be preceded by research to ascertain the effectiveness of such technologies on population health. In that process, the national ethical review committee (REC), as an agent of every human research subject (principal), ought to ensure that international principles (e.g. beneficence, non-malfeasance, autonomy, justice, dignity, truthfulness and honesty) for human experimentation are observed by biotechnology researchers in order to satisfy moral, ethical and legal requirements. The key factors that undermine principals' sovereignty in exercising their right to informed consent to participate in biotechnology trials are discussed. The paper ends with a list of activities that can strengthen the agency, e.g. legislative requirement that all health-related biotechnology transfer should be preceded by rigorous evaluation; continuous update of the agents knowledge of the contents of the international ethical guidelines; and education of potential and actual principals on their human rights; among others.

Biotechnology awareness study, Part 1: Where scientists get their information.

PubMed Central

Grefsheim, S; Franklin, J; Cunningham, D

1991-01-01

A model study, funded by the National Library of Medicine (NLM) and conducted by the Southeastern/Atlantic Regional Medical Library (RML) and the University of Maryland Health Sciences Library, attempted to assess the information needs of researchers in the developing field of biotechnology and to determine the resources available to meet those needs in major academic health sciences centers. Nine medical schools in RML Region 2 were selected to participate in a biotechnology awareness study. A survey was conducted of the nine medical school libraries to assess their support of biotechnology research. To identify the information needs of scientists engaged in biotechnology-related research at the schools, a written survey was sent to the deans of the nine institutions and selected scientists they had identified. This was followed by individual, in-depth interviews with both the deans and scientists surveyed. In general, scientists obtained information from three major sources: their own experiments, personal communication with other scientists, and textual material (print or electronic). For textual information, most study participants relied on personal journal subscriptions. Tangential journals were scanned in the department's library. Only a few of these scientists came to the health sciences library on a regular basis. Further, the study found that personal computers have had a major impact on how biotechnologists get and use information. Implications of these findings for libraries and librarians are discussed. PMID:1998818

Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case

PubMed Central

Strope, Pooja K; Chaverri, Priscila; Gazis, Romina; Ciufo, Stacy; Domrachev, Michael; Schoch, Conrad L

2017-01-01

Abstract The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353 PMID:29220466

Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use.

PubMed

Games, Patrícia Dias; daSilva, Elói Quintas Gonçalves; Barbosa, Meire de Oliveira; Almeida-Souza, Hebréia Oliveira; Fontes, Patrícia Pereira; deMagalhães, Marcos Jorge; Pereira, Paulo Roberto Gomes; Prates, Maura Vianna; Franco, Gloria Regina; Faria-Campos, Alessandra; Campos, Sérgio Vale Aguiar; Baracat-Pereira, Maria Cristina

2016-12-15

Antimicrobial peptides from plants present mechanisms of action that are different from those of conventional defense agents. They are under-explored but have a potential as commercial antimicrobials. Bell pepper leaves ('Magali R') are discarded after harvesting the fruit and are sources of bioactive peptides. This work reports the isolation by peptidomics tools, and the identification and partially characterization by computational tools of an antimicrobial peptide from bell pepper leaves, and evidences the usefulness of records and the in silico analysis for the study of plant peptides aiming biotechnological uses. Aqueous extracts from leaves were enriched in peptide by salt fractionation and ultrafiltration. An antimicrobial peptide was isolated by tandem chromatographic procedures. Mass spectrometry, automated peptide sequencing and bioinformatics tools were used alternately for identification and partial characterization of the Hevein-like peptide, named HEV-CANN. The computational tools that assisted to the identification of the peptide included BlastP, PSI-Blast, ClustalOmega, PeptideCutter, and ProtParam; conventional protein databases (DB) as Mascot, Protein-DB, GenBank-DB, RefSeq, Swiss-Prot, and UniProtKB; specific for peptides DB as Amper, APD2, CAMP, LAMPs, and PhytAMP; other tools included in ExPASy for Proteomics; The Bioactive Peptide Databases, and The Pepper Genome Database. The HEV-CANN sequence presented 40 amino acid residues, 4258.8 Da, theoretical pI-value of 8.78, and four disulfide bonds. It was stable, and it has inhibited the growth of phytopathogenic bacteria and a fungus. HEV-CANN presented a chitin-binding domain in their sequence. There was a high identity and a positive alignment of HEV-CANN sequence in various databases, but there was not a complete identity, suggesting that HEV-CANN may be produced by ribosomal synthesis, which is in accordance with its constitutive nature. Computational tools for proteomics and databases are not adjusted for short sequences, which hampered HEV-CANN identification. The adjustment of statistical tests in large databases for proteins is an alternative to promote the significant identification of peptides. The development of specific DB for plant antimicrobial peptides, with information about peptide sequences, functional genomic data, structural motifs and domains of molecules, functional domains, and peptide-biomolecule interactions are valuable and necessary.

The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases

PubMed Central

Whetzel, Patricia L.; Grethe, Jeffrey S.; Banks, Davis E.; Martone, Maryann E.

2015-01-01

The NIDDK Information Network (dkNET; http://dknet.org) was launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources that advance the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). By research resources, we mean the multitude of data, software tools, materials, services, projects and organizations available to researchers in the public domain. Most of these are accessed via web-accessible databases or web portals, each developed, designed and maintained by numerous different projects, organizations and individuals. While many of the large government funded databases, maintained by agencies such as European Bioinformatics Institute and the National Center for Biotechnology Information, are well known to researchers, many more that have been developed by and for the biomedical research community are unknown or underutilized. At least part of the problem is the nature of dynamic databases, which are considered part of the “hidden” web, that is, content that is not easily accessed by search engines. dkNET was created specifically to address the challenge of connecting researchers to research resources via these types of community databases and web portals. dkNET functions as a “search engine for data”, searching across millions of database records contained in hundreds of biomedical databases developed and maintained by independent projects around the world. A primary focus of dkNET are centers and projects specifically created to provide high quality data and resources to NIDDK researchers. Through the novel data ingest process used in dkNET, additional data sources can easily be incorporated, allowing it to scale with the growth of digital data and the needs of the dkNET community. Here, we provide an overview of the dkNET portal and its functions. We show how dkNET can be used to address a variety of use cases that involve searching for research resources. PMID:26393351

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

PubMed

O'Leary, Nuala A; Wright, Mathew W; Brister, J Rodney; Ciufo, Stacy; Haddad, Diana; McVeigh, Rich; Rajput, Bhanu; Robbertse, Barbara; Smith-White, Brian; Ako-Adjei, Danso; Astashyn, Alexander; Badretdin, Azat; Bao, Yiming; Blinkova, Olga; Brover, Vyacheslav; Chetvernin, Vyacheslav; Choi, Jinna; Cox, Eric; Ermolaeva, Olga; Farrell, Catherine M; Goldfarb, Tamara; Gupta, Tripti; Haft, Daniel; Hatcher, Eneida; Hlavina, Wratko; Joardar, Vinita S; Kodali, Vamsi K; Li, Wenjun; Maglott, Donna; Masterson, Patrick; McGarvey, Kelly M; Murphy, Michael R; O'Neill, Kathleen; Pujar, Shashikant; Rangwala, Sanjida H; Rausch, Daniel; Riddick, Lillian D; Schoch, Conrad; Shkeda, Andrei; Storz, Susan S; Sun, Hanzhen; Thibaud-Nissen, Francoise; Tolstoy, Igor; Tully, Raymond E; Vatsan, Anjana R; Wallin, Craig; Webb, David; Wu, Wendy; Landrum, Melissa J; Kimchi, Avi; Tatusova, Tatiana; DiCuccio, Michael; Kitts, Paul; Murphy, Terence D; Pruitt, Kim D

2016-01-04

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups.

PubMed

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads; Nielsen, Per Halkjær

2017-01-01

Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. http://www.midasfieldguide.org. © The Author(s) 2017. Published by Oxford University Press.

Biotechnology Education and the Internet. ERIC Digest.

ERIC Educational Resources Information Center

Lee, Thomas

The world of modern biotechnology is based on recent developments in molecular biology, especially those in genetic engineering. Since this is a relatively new and rapidly advancing field of study, there are few traditional sources of information and activities. This digest highlights biotechnology resources including those that can be found on…

75 FR 7274 - Agency Information Collection Activities; Proposed Collection; Comment Request; Guidance on...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-18

... (Biotechnology Final Consultation),'' which developers may use to prepare the final consultation in a standard... those varieties that are developed through biotechnology, to consult with FDA during the plant... who use biotechnology in the manufacture or development of foods and food ingredients to work...

VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening.

PubMed

Schäffer, Alejandro A; Nawrocki, Eric P; Choi, Yoon; Kitts, Paul A; Karsch-Mizrachi, Ilene; McVeigh, Richard

2018-03-01

Nucleic acid sequences in public databases should not contain vector contamination, but many sequences in GenBank do (or did) contain vectors. The National Center for Biotechnology Information uses the program VecScreen to screen submitted sequences for contamination. Additional tools are needed to distinguish true-positive (contamination) from false-positive (not contamination) VecScreen matches. A principal reason for false-positive VecScreen matches is that the sequence and the matching vector subsequence originate from closely related or identical organisms (for example, both originate in Escherichia coli). We collected information on the taxonomy of sources of vector segments in the UniVec database used by VecScreen. We used that information in two overlapping software pipelines for retrospective analysis of contamination in GenBank and for prospective analysis of contamination in new sequence submissions. Using the retrospective pipeline, we identified and corrected over 8000 contaminated sequences in the nonredundant nucleotide database. The prospective analysis pipeline has been in production use since April 2017 to evaluate some new GenBank submissions. Data on the sources of UniVec entries were included in release 10.0 (ftp://ftp.ncbi.nih.gov/pub/UniVec/). The main software is freely available at https://github.com/aaschaffer/vecscreen_plus_taxonomy. aschaffe@helix.nih.gov. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

Impact of Biotechnology on Libraries and Educational Resources.

ERIC Educational Resources Information Center

Adams, Mignon; And Others

1990-01-01

As biotechnology continues to influence significantly the environment of pharmacy educators, it brings pharmacy librarians opportunity for changes in many sectors, notably the profession of librarianship, the nature of information resources, and delivery of information services. More human, financial, and material resources will be needed to…

Mining Microarray Data at NCBI’s Gene Expression Omnibus (GEO)*

PubMed Central

Barrett, Tanya; Edgar, Ron

2006-01-01

Summary The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) has emerged as the leading fully public repository for gene expression data. This chapter describes how to use Web-based interfaces, applications, and graphics to effectively explore, visualize, and interpret the hundreds of microarray studies and millions of gene expression patterns stored in GEO. Data can be examined from both experiment-centric and gene-centric perspectives using user-friendly tools that do not require specialized expertise in microarray analysis or time-consuming download of massive data sets. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo. PMID:16888359

Genes Downregulated in Endometriosis Are Located Near the Known Imprinting Genes

PubMed Central

Higashiura, Yumi; Koike, Natsuki; Akasaka, Juria; Uekuri, Chiharu; Iwai, Kana; Niiro, Emiko; Morioka, Sachiko; Yamada, Yuki

2014-01-01

There is now accumulating evidence that endometriosis is a disease associated with an epigenetic disorder. Genomic imprinting is an epigenetic phenomenon known to regulate DNA methylation of either maternal or paternal alleles. We hypothesize that hypermethylated endometriosis-associated genes may be enriched at imprinted gene loci. We sought to determine whether downregulated genes associated with endometriosis susceptibility are associated with chromosomal location of the known paternally and maternally expressed imprinting genes. Gene information has been gathered from National Center for Biotechnology Information database geneimprint.com. Several researchers have identified specific loci with strong DNA methylation in eutopic endometrium and ectopic lesion with endometriosis. Of the 29 hypermethylated genes in endometriosis, 19 genes were located near 45 known imprinted foci. There may be an association of the genomic location between genes specifically downregulated in endometriosis and epigenetically imprinted genes. PMID:24615936

76 FR 68126 - Office of the Under Secretary, Research, Education, and Economics; Notice of the Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-03

... Secretary, Research, Education, and Economics; Notice of the Advisory Committee on Biotechnology and 21st... Department of Agriculture announces two meetings of the Advisory Committee on Biotechnology and 21st Century... Agriculture on topics related to the use of biotechnology in agriculture. Background information regarding the...

A Case for Teaching Biotechnology

ERIC Educational Resources Information Center

Lazaros, Edward; Embree, Caleb

2016-01-01

Biotechnology is an innovative field that is consistently growing in popularity. It is important that students are taught about this technology at an early age, so they are motivated to join the field, or at least motivated to become informed citizens and consumers (Gonzalez, et al, 2013). An increase in biotechnology knowledge can result in an…

Biotechnology in agriculture, 1986-May 1992. Citation from agricola concerning diseases and other environmental considerations. Bibliographies and literature of agriculture (Final)

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

Bebee, C.N.

1992-08-01

The citations in this bibliography, Biotechnology in Agriculture, 1986 - May 1992, are selected from the AGRICOLA database and cover diseases, insects, nematodes, weeds, chemicals, and other environmental considerations. This is the 46th volume in a series of commodity-oriented listings of citations from AGRICOLA. Entries in the bibliography are subdivided into a series of section headings used in the contents of the Bibliography of Agriculture. Each item appears under every section heading assigned to the cited document. A personal author index accompanies this publication.

Effect of Religious Belief on Informal Reasoning about Biotechnology Issues

ERIC Educational Resources Information Center

Pope, Timothy; Dawson, Vaille; Koul, Rekha

2017-01-01

The advances of modern biotechnology provide teachers with a number of opportunities to explore socioscientific issues, and in doing so to enhance students' reasoning skills. Although some attempt has been made to understand cultural differences in students' informal reasoning across international and regional boundaries, there is limited research…

De novo sequencing and analysis of the transcriptome of Panax ginseng in the leaf-expansion period.

PubMed

Liu, Shichao; Wang, Siming; Liu, Meichen; Yang, Fei; Zhang, Hui; Liu, Shiyang; Wang, Qun; Zhao, Yu

2016-08-01

Panax ginseng, a traditional Chinese medicine, is used worldwide for its variety of health benefits and its treatment efficacy. However, it is difficult to cultivate due to its vulnerability to environmental stresses. The present study provided the first report, to the best of our knowledge, of transcriptome analysis of ginseng at the leaf‑expansion stage. Using the Illumina sequencing platform, >40,000,000 high‑quality paired‑end reads were obtained and assembled into 100,533 unique sequences. When the sequences were searched against the publicly available National Center for Biotechnology Information protein database using The Basic Local Alignment Search Tool, 61,599 sequences exhibited similarity to known proteins. Functional annotation and classification, including use of the Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases, revealed that the activated genes in ginseng were predominantly ribonuclease‑like storage genes, environmental stress genes, pathogenesis-related genes and other antioxidant genes. A number of candidate genes in environmental stress‑associated pathways were also identified. These novel data provide useful information on the growth and development stages of ginseng, and serve as an important public information platform for further understanding of the molecular mechanisms and functional genomics of ginseng.

IMGT, the international ImMunoGeneTics information system®

PubMed Central

Lefranc, Marie-Paule; Giudicelli, Véronique; Kaas, Quentin; Duprat, Elodie; Jabado-Michaloud, Joumana; Scaviner, Dominique; Ginestoux, Chantal; Clément, Oliver; Chaume, Denys; Lefranc, Gérard

2005-01-01

The international ImMunoGeneTics information system® (IMGT) (http://imgt.cines.fr), created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier II and CNRS) at Montpellier, France, is a high-quality integrated knowledge resource specializing in the immunoglobulins (IGs), T cell receptors (TRs), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune systems (RPI) that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT includes several sequence databases (IMGT/LIGM-DB, IMGT/PRIMER-DB, IMGT/PROTEIN-DB and IMGT/MHC-DB), one genome database (IMGT/GENE-DB) and one three-dimensional (3D) structure database (IMGT/3Dstructure-DB), Web resources comprising 8000 HTML pages (IMGT Marie-Paule page), and interactive tools. IMGT data are expertly annotated according to the rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY concepts. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in normal physiological and pathological situations. IMGT is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow up of residual diseases) and therapeutical approaches (graft, immunotherapy and vaccinology). IMGT is freely available at http://imgt.cines.fr. PMID:15608269

Knowledge of, and Attitudes towards Health-Related Biotechnology Applications amongst Australian Year 10 High School Students

ERIC Educational Resources Information Center

van Lieshout, Emile; Dawson, Vaille

2016-01-01

Modern biotechnology has a large and rapidly increasing impact on society. New advances in genetics, stem cells and other areas hold great potential for human health but also presenting socioscientific issues that commonly divide public opinion. While knowledge is necessary to develop informed opinions about biotechnology, they may also be…

An Exploration of Attitudes towards Modern Biotechnology: A Study among Dutch Secondary School Students

ERIC Educational Resources Information Center

Klop, Tanja; Severiens, Sabine

2007-01-01

Modern biotechnology will have a large impact on society and requires informed decision-making and critical attitudes toward biotechnology among the public. This study aims to explore these attitudes in secondary education. For this purpose, a questionnaire was constructed according to the general tripartite theory of attitudes. A total of 574…

An Exploration of High School (12-17 Year Old) Students' Understandings of, and Attitudes towards Biotechnology Processes

ERIC Educational Resources Information Center

Dawson, Vaille

2007-01-01

The products of modern biotechnology processes such as genetic engineering, DNA testing and cloning will increasingly impact on society. It is essential that young people have a well-developed scientific understanding of biotechnology and associated processes so that they are able to contribute to public debate and make informed personal…

78 FR 17220 - Request for Information (RFI) Regarding the Planned Biotechnology Development Module (BDM) As...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-20

... DEPARTMENT OF HOMELAND SECURITY [Docket No. DHS-2013-0018] Request for Information (RFI) Regarding the Planned Biotechnology Development Module (BDM) As Part of the National Bio and Agro-Defense... Development Module (BDM) a planned component of the National Bio and Agro-Defense Facility (NBAF) and...

Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology.

PubMed

Ju, Feng; Zhang, Tong

2015-11-03

Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.

VIRUS NOMENCLATURE BELOW THE SPECIES LEVEL: A STANDARDIZED NOMENCLATURE FOR LABORATORY ANIMAL-ADAPTED STRAINS AND VARIANTS OF VIRUSES ASSIGNED TO THE FAMILY FILOVIRIDAE

PubMed Central

Kuhn, Jens H.; Bao, Yiming; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brister, J. Rodney; Bukreyev, Alexander A.; Caì, Yíngyún; Chandran, Kartik; Davey, Robert A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Gonzalez, Jean-Paul; Formenty, Pierre; Freiberg, Alexander N.; Hensley, Lisa E.; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Karl M.; Klenk, Hans-Dieter; Kobinger, Gary; Lackemeyer, Matthew G.; Leroy, Eric M.; Lever, Mark S.; Lofts, Loreen L.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

2013-01-01

The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming ( ///-) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed. PMID:23358612

NCBI Epigenomics: what's new for 2013.

PubMed

Fingerman, Ian M; Zhang, Xuan; Ratzat, Walter; Husain, Nora; Cohen, Robert F; Schuler, Gregory D

2013-01-01

The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements.

NCBI Epigenomics: What’s new for 2013

PubMed Central

Fingerman, Ian M.; Zhang, Xuan; Ratzat, Walter; Husain, Nora; Cohen, Robert F.; Schuler, Gregory D.

2013-01-01

The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements. PMID:23193265

NCBI GEO: archive for functional genomics data sets--10 years on.

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Muertter, Rolf N; Holko, Michelle; Ayanbule, Oluwabukunmi; Yefanov, Andrey; Soboleva, Alexandra

2011-01-01

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Androgen-responsive gene database: integrated knowledge on androgen-responsive genes.

PubMed

Jiang, Mei; Ma, Yunsheng; Chen, Congcong; Fu, Xuping; Yang, Shu; Li, Xia; Yu, Guohua; Mao, Yumin; Xie, Yi; Li, Yao

2009-11-01

Androgen signaling plays an important role in many biological processes. Androgen Responsive Gene Database (ARGDB) is devoted to providing integrated knowledge on androgen-controlled genes. Gene records were collected on the basis of PubMed literature collections. More than 6000 abstracts and 950 original publications were manually screened, leading to 1785 human genes, 993 mouse genes, and 583 rat genes finally included in the database. All the collected genes were experimentally proved to be regulated by androgen at the expression level or to contain androgen-responsive regions. For each gene important details of the androgen regulation experiments were collected from references, such as expression change, androgen-responsive sequence, response time, tissue/cell type, experimental method, ligand identity, and androgen amount, which will facilitate further evaluation by researchers. Furthermore, the database was integrated with multiple annotation resources, including National Center for Biotechnology Information, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway, to reveal the biological characteristics and significance of androgen-regulated genes. The ARGDB web site is mainly composed of the Browse, Search, Element Scan, and Submission modules. It is user friendly and freely accessible at http://argdb.fudan.edu.cn. Preliminary analysis of the collected data was performed. Many disease pathways, such as prostate carcinogenesis, were found to be enriched in androgen-regulated genes. The discovered androgen-response motifs were similar to those in previous reports. The analysis results are displayed in the web site. In conclusion, ARGDB provides a unified gateway to storage, retrieval, and update of information on androgen-regulated genes.

Evaluation of Brazilian biotechnology patent activity from 1975 to 2010.

PubMed

Dias, F; Delfim, F; Drummond, I; Carmo, A O; Barroca, T M; Horta, C C; Kalapothakis, E

2012-08-01

The analysis of patent activity is one methodology used for technological monitoring. In this paper, the activity of biotechnology-related patents in Brazil were analyzed through 30 International Patent Classification (IPC) codes published by the Organization for Economic Cooperation and Development (OECD). We developed a program to analyse the dynamics of the major patent applicants, countries and IPC codes extracted from the Brazilian Patent Office (INPI) database. We also identified Brazilian patent applicants who tried to expand protection abroad via the Patent Cooperation Treaty (PCT). We had access to all patents published online at the INPI from 1975 to July 2010, including 9,791 biotechnology patent applications in Brazil, and 163 PCTs published online at World Intellectual Property Organization (WIPO) from 1997 to December 2010. To our knowledge, there are no other online reports of biotechnology patents previous to the years analyzed here. Most of the biotechnology patents filed in the INPI (10.9%) concerned measuring or testing processes involving nucleic acids. The second and third places belonged to patents involving agro-technologies (recombinant DNA technology for plant cells and new flowering plants, i.e. angiosperms, or processes for obtaining them, and reproduction of flowering plants by tissue culture techniques). The majority of patents (87.2%) were filed by nonresidents, with USA being responsible for 51.7% of all biotechnology patents deposited in Brazil. Analyzing the resident applicants per region, we found a hub in the southeast region of Brazil. Among the resident applicants for biotechnology patents filed in the INPI, 43.5% were from São Paulo, 18.3% were from Rio de Janeiro, and 9.7% were from Minas Gerais. Pfizer, Novartis, and Sanofi were the largest applicants in Brazil, with 339, 288, and 245 biotechnology patents filed, respectively. For residents, the largest applicant was the governmental institution FIOCRUZ (Oswaldo Cruz Foundation), which filed 69 biotechnology patents within the period analyzed. The first biotechnology patent applications via PCT were submitted by Brazilians in 1997, with 3 from UFMG (university), 2 from individuals, and 1 from EMBRAPA (research institute).

Frontiers in biomedical engineering and biotechnology.

PubMed

Liu, Feng; Goodarzi, Ali; Wang, Haifeng; Stasiak, Joanna; Sun, Jianbo; Zhou, Yu

2014-01-01

The 2nd International Conference on Biomedical Engineering and Biotechnology (iCBEB 2013), held in Wuhan on 11–13 October 2013, is an annual conference that aims at providing an opportunity for international and national researchers and practitioners to present the most recent advances and future challenges in the fields of Biomedical Information, Biomedical Engineering and Biotechnology. The papers published by this issue are selected from this conference, which witnesses the frontier in the field of Biomedical Engineering and Biotechnology, which particularly has helped improving the level of clinical diagnosis in medical work.

In Silico Screening of the Human Gut Metaproteome Identifies Th17-Promoting Peptides Encrypted in Proteins of Commensal Bacteria

PubMed Central

Hidalgo-Cantabrana, Claudio; Moro-García, Marco A.; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Lourenço, Anália; Alonso-Arias, Rebeca; Sánchez, Borja

2017-01-01

Scientific studies focused on the role of the human microbiome over human health have generated billions of gigabits of genetic information during the last decade. Nowadays integration of all this information in public databases and development of pipelines allowing us to biotechnologically exploit this information are urgently needed. Prediction of the potential bioactivity of the products encoded by the human gut microbiome, or metaproteome, is the first step for identifying proteins responsible for the molecular interaction between microorganisms and the immune system. We have recently published the Mechanism of Action of the Human Microbiome (MAHMI) database (http://www.mahmi.org), conceived as a resource compiling peptide sequences with a potential immunomodulatory activity. Fifteen out of the 300 hundred million peptides contained in the MAHMI database were synthesized. These peptides were identified as being encrypted in proteins produced by gut microbiota members, they do not contain cleavage points for the major intestinal endoproteases and displayed high probability to have immunomodulatory bioactivity. The bacterial peptides FR-16 and LR-17 encrypted in proteins from Bifidobacterium longum DJ010A and Bifidobacterium fragilis YCH46 respectively, showed the higher immune modulation capability over human peripheral blood mononuclear cells. Both peptides modulated the immune response toward increases in the Th17 and decreases in the Th1 cell response, together with an induction of IL-22 production. These results strongly suggest the combined use of bioinformatics and in vitro tools as a first stage in the screening of bioactive peptides encrypted in the human gut metaproteome. PMID:28943872

Agricultural Science Teachers' Barriers, Roles, and Information Source Preferences for Teaching Biotechnology Topics

ERIC Educational Resources Information Center

Mowen, Diana L.; Wingenbach, Gary J.; Roberts, T. Grady; Harlin, Julie F.

2007-01-01

The purpose of this study was to determine barriers, roles, and information source preferences for teaching agricultural biotechnology topics. Agricultural science teachers were described primarily as 37 year-old males who had taught for 12 years, had bachelor's degrees, and had lived or worked on a farm or ranch. Equipment was perceived as the…

Public perceptions of biotechnology.

PubMed

McHughen, Alan

2007-09-01

The very term 'Biotechnology' elicits a range of emotions, from wonder and awe to downright fear and hostility. This is especially true among non-scientists, particularly in respect of agricultural and food biotechnology. These emotions indicate just how poorly understood agricultural biotechnology is and the need for accurate, dispassionate information in the public sphere to allow a rational public debate on the actual, as opposed to the perceived, risks and benefits of agricultural biotechnology. This review considers first the current state of public knowledge on agricultural biotechnology, and then explores some of the popular misperceptions and logical inconsistencies in both Europe and North America. I then consider the problem of widespread scientific illiteracy, and the role of the popular media in instilling and perpetuating misperceptions. The impact of inappropriate efforts to provide 'balance' in a news story, and of belief systems and faith also impinges on public scientific illiteracy. Getting away from the abstract, we explore a more concrete example of the contrasting approach to agricultural biotechnology adoption between Europe and North America, in considering divergent approaches to enabling coexistence in farming practices. I then question who benefits from agricultural biotechnology. Is it only the big companies, or is it society at large--and the environment--also deriving some benefit? Finally, a crucial aspect in such a technologically complex issue, ordinary and intelligent non-scientifically trained consumers cannot be expected to learn the intricacies of the technology to enable a personal choice to support or reject biotechnology products. The only reasonable and pragmatic alternative is to place trust in someone to provide honest advice. But who, working in the public interest, is best suited to provide informed and accessible, but objective, advice to wary consumers?

37 CFR 41.110 - Filing claim information.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., each party must file a clean copy of its involved claims and, if a biotechnology material sequence is a... in a drawing or biotechnology material sequence, file an annotated copy of the claim indicating in...

37 CFR 41.110 - Filing claim information.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., each party must file a clean copy of its involved claims and, if a biotechnology material sequence is a... in a drawing or biotechnology material sequence, file an annotated copy of the claim indicating in...

Life sciences today and tomorrow: emerging biotechnologies.

PubMed

Williamson, E Diane

2017-08-01

The purpose of this review is to survey current, emerging and predicted future biotechnologies which are impacting, or are likely to impact in the future on the life sciences, with a projection for the coming 20 years. This review is intended to discuss current and future technical strategies, and to explore areas of potential growth during the foreseeable future. Information technology approaches have been employed to gather and collate data. Twelve broad categories of biotechnology have been identified which are currently impacting the life sciences and will continue to do so. In some cases, technology areas are being pushed forward by the requirement to deal with contemporary questions such as the need to address the emergence of anti-microbial resistance. In other cases, the biotechnology application is made feasible by advances in allied fields in biophysics (e.g. biosensing) and biochemistry (e.g. bio-imaging). In all cases, the biotechnologies are underpinned by the rapidly advancing fields of information systems, electronic communications and the World Wide Web together with developments in computing power and the capacity to handle extensive biological data. A rationale and narrative is given for the identification of each technology as a growth area. These technologies have been categorized by major applications, and are discussed further. This review highlights: Biotechnology has far-reaching applications which impinge on every aspect of human existence. The applications of biotechnology are currently wide ranging and will become even more diverse in the future. Access to supercomputing facilities and the ability to manipulate large, complex biological datasets, will significantly enhance knowledge and biotechnological development.

Teaching biotechnology in NSW schools

NASA Astrophysics Data System (ADS)

Steele, Frances A.

Agriculture, industry and medicine are being altered by new biological technologies. Today's students are the citizens who will make decisions about associated ethical issues. They need to have the knowledge that will enable them to make informed choices. Hence biotechnology has an important place in science education. The aims of the research were to: 1. describe the state of biotechnology teaching in NSW; 2. determine whether teachers in NSW do not teach biotechnology because they do not have the necessary knowledge and experience; 3. identify other reasons why NSW teachers choose not to teach biotechnology; 4. describe problems encountered in teaching biotechnology in NSW; 5. suggest ways in which the problems encountered in the teaching of biotechnology can be overcome. Quantitative and qualitative methods were used in a complementary way to investigate these aims. In a sample of teachers surveyed, many reported that they chose not to teach biotechnology because they did not have adequate knowledge and experience. Other obstacles were identified. These were: 1. the difficulty of the subject matter; 2. the lack of practical work; 3. lack of a program for biotechnology in junior science. The results of this trial suggested that a biotechnology unit should be developed in collaboration with the teacher and that time needs to be made available for school based program development.

Thirty years of European biotechnology programmes: from biomolecular engineering to the bioeconomy.

PubMed

Aguilar, Alfredo; Magnien, Etienne; Thomas, Daniel

2013-06-25

This article traces back thirty years of biotechnology research sponsored by the European Union (EU). It outlines the crucial role played by De Nettancourt, Goffeau and Van Hoeck to promote and prepare the first European programme on biotechnology (1982-1986) run by the European Commission. Following this first biotechnology programme, others followed until the current one, part of the seventh Framework Programme for Research, Technological Development and Demonstration (2007-2013) (FP7). Particular attention is given to the statutory role of the European institutions in the design and orientation of the successive biotechnology programmes, compared to the more informal-yet visionary-role of key individuals upstream to any legislative decision. Examples of success stories and of the role of the biotechnology programmes in addressing societal issues and industrial competitiveness are also presented. Finally, an outline of Horizon 2020, the successor of FP7, is described, together with the role of biotechnology in building the bioeconomy. Copyright © 2012 Elsevier B.V. All rights reserved.

SeedStor: A Germplasm Information Management System and Public Database

PubMed Central

Horler, RSP; Turner, AS; Fretter, P; Ambrose, M

2018-01-01

Abstract SeedStor (https://www.seedstor.ac.uk) acts as the publicly available database for the seed collections held by the Germplasm Resources Unit (GRU) based at the John Innes Centre, Norwich, UK. The GRU is a national capability supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The GRU curates germplasm collections of a range of temperate cereal, legume and Brassica crops and their associated wild relatives, as well as precise genetic stocks, near-isogenic lines and mapping populations. With >35,000 accessions, the GRU forms part of the UK’s plant conservation contribution to the Multilateral System (MLS) of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA) for wheat, barley, oat and pea. SeedStor is a fully searchable system that allows our various collections to be browsed species by species through to complicated multipart phenotype criteria-driven queries. The results from these searches can be downloaded for later analysis or used to order germplasm via our shopping cart. The user community for SeedStor is the plant science research community, plant breeders, specialist growers, hobby farmers and amateur gardeners, and educationalists. Furthermore, SeedStor is much more than a database; it has been developed to act internally as a Germplasm Information Management System that allows team members to track and process germplasm requests, determine regeneration priorities, handle cost recovery and Material Transfer Agreement paperwork, manage the Seed Store holdings and easily report on a wide range of the aforementioned tasks. PMID:29228298

Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE).

PubMed

Schmedes, Sarah E; King, Jonathan L; Budowle, Bruce

2015-01-01

Whole-genome data are invaluable for large-scale comparative genomic studies. Current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. More than 3,000 bacterial genomes have been sequenced and are available at the finished status. Publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained within the download and to identify errors and inconsistencies that may be present within the organizational data content and metadata. AutoCurE, an automated tool for bacterial genome database curation in Excel, was developed to facilitate local database curation of supporting data that accompany downloaded genomes from the National Center for Biotechnology Information. AutoCurE provides an automated approach to curate local genomic databases by flagging inconsistencies or errors by comparing the downloaded supporting data to the genome reports to verify genome name, RefSeq accession numbers, the presence of archaea, BioProject/UIDs, and sequence file descriptions. Flags are generated for nine metadata fields if there are inconsistencies between the downloaded genomes and genomes reports and if erroneous or missing data are evident. AutoCurE is an easy-to-use tool for local database curation for large-scale genome data prior to downstream analyses.

Complementary DNA sequencing and identification of mRNAs from the venomous gland of Agkistrodon piscivorus leucostoma.

PubMed

Jia, Ying; Cantu, Bruno A; Sánchez, Elda E; Pérez, John C

2008-06-15

To advance our knowledge on the snake venom composition and transcripts expressed in venom gland at the molecular level, we constructed a cDNA library from the venom gland of Agkistrodon piscivorus leucostoma for the generation of expressed sequence tags (ESTs) database. From the randomly sequenced 2112 independent clones, we have obtained ESTs for 1309 (62%) cDNAs, which showed significant deduced amino acid sequence similarity (scores >80) to previously characterized proteins in National Center for Biotechnology Information (NCBI) database. Ribosomal proteins make up 47 clones (2%) and the remaining 756 (36%) cDNAs represent either unknown identity or show BLASTX sequence identity scores of <80 with known GenBank accessions. The most highly expressed gene encoding phospholipase A(2) (PLA(2)) accounting for 35% of A. p. leucostoma venom gland cDNAs was identified and further confirmed by crude venom applied to sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) electrophoresis and protein sequencing. A total of 180 representative genes were obtained from the sequence assemblies and deposited to EST database. Clones showing sequence identity to disintegrins, thrombin-like enzymes, hemorrhagic toxins, fibrinogen clotting inhibitors and plasminogen activators were also identified in our EST database. These data can be used to develop a research program that will help us identify genes encoding proteins that are of medical importance or proteins involved in the mechanisms of the toxin venom.

Development and Validation of an Instrument to Measure University Students' Biotechnology Attitude

NASA Astrophysics Data System (ADS)

Erdogan, Mehmet; Özel, Murat; Uşak, Muhammet; Prokop, Pavol

2009-06-01

The impact of biotechnologies on peoples' everyday lives continuously increases. Measuring young peoples' attitudes toward biotechnologies is therefore very important and its results are useful not only for science curriculum developers and policy makers, but also for producers and distributors of genetically modified products. Despite of substantial number of instruments which focused on measuring student attitudes toward biotechnology, a majority of them were not rigorously validated. This study deals with the development and validation of an attitude questionnaire toward biotechnology. Detailed information on development and validation process of the instrument is provided. Data gathered from 326 university students provided evidence for the validity and reliability of the new instrument which consists of 28 attitude items on a five point likert type scale. It is believed that the instrument will serve as a valuable tool for both instructors and researchers in science education to assess students' biotechnology attitudes.

Termites as targets and models for biotechnology.

PubMed

Scharf, Michael E

2015-01-07

Termites have many unique evolutionary adaptations associated with their eusocial lifestyles. Recent omics research has created a wealth of new information in numerous areas of termite biology (e.g., caste polyphenism, lignocellulose digestion, and microbial symbiosis) with wide-ranging applications in diverse biotechnological niches. Termite biotechnology falls into two categories: (a) termite-targeted biotechnology for pest management purposes, and (b) termite-modeled biotechnology for use in various industrial applications. The first category includes several candidate termiticidal modes of action such as RNA interference, digestive inhibition, pathogen enhancement, antimicrobials, endocrine disruption, and primer pheromone mimicry. In the second category, termite digestomes are deep resources for host and symbiont lignocellulases and other enzymes with applications in a variety of biomass, industrial, and processing applications. Moving forward, one of the most important approaches for accelerating advances in both termite-targeted and termite-modeled biotechnology will be to consider host and symbiont together as a single functional unit.

Biotechnology Program Guide.

ERIC Educational Resources Information Center

Georgia Univ., Athens. Dept. of Vocational Education.

This program quide presents the biotechnology curriculum for technical institutes in Georgia. The general information section contains the following: purpose and objectives; program description, including admissions, typical job titles, and accreditation and certification; and curriculum model, including standard curriculum sequence and lists of…

Cloud-based adaptive exon prediction for DNA analysis.

PubMed

Putluri, Srinivasareddy; Zia Ur Rahman, Md; Fathima, Shaik Yasmeen

2018-02-01

Cloud computing offers significant research and economic benefits to healthcare organisations. Cloud services provide a safe place for storing and managing large amounts of such sensitive data. Under conventional flow of gene information, gene sequence laboratories send out raw and inferred information via Internet to several sequence libraries. DNA sequencing storage costs will be minimised by use of cloud service. In this study, the authors put forward a novel genomic informatics system using Amazon Cloud Services, where genomic sequence information is stored and accessed for processing. True identification of exon regions in a DNA sequence is a key task in bioinformatics, which helps in disease identification and design drugs. Three base periodicity property of exons forms the basis of all exon identification techniques. Adaptive signal processing techniques found to be promising in comparison with several other methods. Several adaptive exon predictors (AEPs) are developed using variable normalised least mean square and its maximum normalised variants to reduce computational complexity. Finally, performance evaluation of various AEPs is done based on measures such as sensitivity, specificity and precision using various standard genomic datasets taken from National Center for Biotechnology Information genomic sequence database.

High-School Students' Informal Reasoning and Argumentation about Biotechnology: An Indicator of Scientific Literacy?

ERIC Educational Resources Information Center

Dawson, Vaille; Venville, Grady Jane

2009-01-01

The aim of this research was to explore Australian high-school students' argumentation and informal reasoning about biotechnology. Data were obtained from semi-structured interviews with 10 Year-8 students (12-13 years old), 14 Year-10 students (14-15 years old) and 6 Year-12 students (16-17 years old) from six metropolitan high schools in Perth,…

Characterization of a feruloyl esterase from Aspergillus terreus facilitates the division of fungal enzymes from Carbohydrate Esterase family 1 of the carbohydrate-active enzymes (CAZy) database.

PubMed

Mäkelä, Miia R; Dilokpimol, Adiphol; Koskela, Salla M; Kuuskeri, Jaana; de Vries, Ronald P; Hildén, Kristiina

2018-04-26

Feruloyl esterases (FAEs) are accessory enzymes for plant biomass degradation, which catalyse hydrolysis of carboxylic ester linkages between hydroxycinnamic acids and plant cell-wall carbohydrates. They are a diverse group of enzymes evolved from, e.g. acetyl xylan esterases (AXEs), lipases and tannases, thus complicating their classification and prediction of function by sequence similarity. Recently, an increasing number of fungal FAEs have been biochemically characterized, owing to their potential in various biotechnological applications and multitude of candidate FAEs in fungal genomes. However, only part of the fungal FAEs are included in Carbohydrate Esterase family 1 (CE1) of the carbohydrate-active enzymes (CAZy) database. In this work, we performed a phylogenetic analysis that divided the fungal members of CE1 into five subfamilies of which three contained characterized enzymes with conserved activities. Conservation within one of the subfamilies was confirmed by characterization of an additional CE1 enzyme from Aspergillus terreus. Recombinant A. terreus FaeD (AtFaeD) showed broad specificity towards synthetic methyl and ethyl esters, and released ferulic acid from plant biomass substrates, demonstrating its true FAE activity and interesting features as potential biocatalyst. The subfamily division of the fungal CE1 members enables more efficient selection of candidate enzymes for biotechnological processes. © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

'Click chemistry' for diagnosis: a patent review on exploitation of its emerging trends.

PubMed

Mandhare, Anita; Banerjee, Paromita; Bhutkar, Smita; Hirwani, Rajkumar

2014-12-01

Click chemistry is the novel synthetic approach towards developing reactions with large thermodynamic driving forces to give almost complete conversion of new molecular reagents to a single product. Thus, click chemistry describes the chemistry for making carbon-heteroatom-carbon bonds in benign solvents, especially in water, and having a plethora of chemical and biological applications. This has played an important role in early detection of diseases, real-time monitoring of drug delivery and investigating the biomolecular functions in vivo. This review aims at highlighting the research advancements in click chemistry published in the patent literature and categorizing the patents according to the technological progress. An extensive search was carried out to collect and analyze the patent information claiming the use of click chemistry in biotechnology, especially for diagnosis. The study further concentrates on licensing of the click chemistry patents and defining the recent breakthroughs. Different databases like Espacenet, ISI Web of Science, Patbase and Thomson Innovation are used to compile the relevant literature. In recent years, considerable development in the click concept has encouraged researchers in using click reactions in almost every branch of industry that uses chemistry. Click chemistry for chemical ligation has been immensely explored in the field of biotechnology especially for detection, diagnosis and therapeutics.

SeqHound: biological sequence and structure database as a platform for bioinformatics research

PubMed Central

2002-01-01

Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit. PMID:12401134

Biotechnology and Open University Science.

ERIC Educational Resources Information Center

Grobstein, Clifford

1985-01-01

Discusses whether biotechnology commercial application will significantly inhibit the free flow of information traditional in academic environments. Background factors, crux of the concern, assessment, and current options are given. Although little evidence that industry-university collaboration has impaired academic molecular genetics exists,…

The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

PubMed

Marenco, Luis; Ascoli, Giorgio A; Martone, Maryann E; Shepherd, Gordon M; Miller, Perry L

2008-09-01

This paper describes the NIF LinkOut Broker (NLB) that has been built as part of the Neuroscience Information Framework (NIF) project. The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related to entries in the National Center for Biotechnology Information's (NCBI's) Entrez system. The NLB collects these links from each resource and passes them to the NCBI which incorporates them into its Entrez LinkOut service. In this way, an Entrez user looking at a specific Entrez entry can LinkOut directly to related neuroscience information. The information stored in the NLB can also be utilized in other ways. A second approach, which is operational on a pilot basis, is for the NLB Web server to create dynamically its own Web page of LinkOut links for each NCBI identifier in the NLB database. This approach can allow other resources (in addition to the NCBI Entrez) to LinkOut to related neuroscience information. The paper describes the current NLB system and discusses certain design issues that arose during its implementation.

Diseases and Molecular Diagnostics: A Step Closer to Precision Medicine.

PubMed

Dwivedi, Shailendra; Purohit, Purvi; Misra, Radhieka; Pareek, Puneet; Goel, Apul; Khattri, Sanjay; Pant, Kamlesh Kumar; Misra, Sanjeev; Sharma, Praveen

2017-10-01

The current advent of molecular technologies together with a multidisciplinary interplay of several fields led to the development of genomics, which concentrates on the detection of pathogenic events at the genome level. The structural and functional genomics approaches have now pinpointed the technical challenge in the exploration of disease-related genes and the recognition of their structural alterations or elucidation of gene function. Various promising technologies and diagnostic applications of structural genomics are currently preparing a large database of disease-genes, genetic alterations etc., by mutation scanning and DNA chip technology. Further the functional genomics also exploring the expression genetics (hybridization-, PCR- and sequence-based technologies), two-hybrid technology, next generation sequencing with Bioinformatics and computational biology. Advances in microarray "chip" technology as microarrays have allowed the parallel analysis of gene expression patterns of thousands of genes simultaneously. Sequence information collected from the genomes of many individuals is leading to the rapid discovery of single nucleotide polymorphisms or SNPs. Further advances of genetic engineering have also revolutionized immunoassay biotechnology via engineering of antibody-encoding genes and the phage display technology. The Biotechnology plays an important role in the development of diagnostic assays in response to an outbreak or critical disease response need. However, there is also need to pinpoint various obstacles and issues related to the commercialization and widespread dispersal of genetic knowledge derived from the exploitation of the biotechnology industry and the development and marketing of diagnostic services. Implementation of genetic criteria for patient selection and individual assessment of the risks and benefits of treatment emerges as a major challenge to the pharmaceutical industry. Thus this field is revolutionizing current era and further it may open new vistas in the field of disease management.

Fungal genome resources at NCBI.

PubMed

Robbertse, B; Tatusova, T

2011-09-01

The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

NCBI GEO: archive for functional genomics data sets—10 years on

PubMed Central

Barrett, Tanya; Troup, Dennis B.; Wilhite, Stephen E.; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F.; Tomashevsky, Maxim; Marshall, Kimberly A.; Phillippy, Katherine H.; Sherman, Patti M.; Muertter, Rolf N.; Holko, Michelle; Ayanbule, Oluwabukunmi; Yefanov, Andrey; Soboleva, Alexandra

2011-01-01

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/. PMID:21097893

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

Lushbough, Carol M.; Jennewein, Douglas M.; Brendel, Volker P.

2011-01-01

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. PMID:21546552

Why do the biotechnology and the climate change debates hardly mix? Evidence from a global stakeholder survey.

PubMed

Aerni, Philipp

2013-05-25

Despite its potential to address climate change problems, the role of biotechnology is hardly ever touched upon in the global sustainability debate. We wanted to know why. For that purpose, we conducted a global online stakeholder survey on biotechnology and climate change. The relevant stakeholders and their representatives were selected by means of key informants that were familiar with either of the two debates. A self-assessment showed that a majority of respondents felt more familiar with the climate change than the biotechnology debate. Even though the survey results reveal that most respondents consider the potential of modern biotechnology to address climate change to be substantial, the policy network analysis revealed that one stakeholder who is not just considered to be relevant in both debates but also crucial in the formation of global public opinion, strongly rejects the view that biotechnology is a climate-friendly and therefore clean technology. This influential opposition seems to ensure that the biotechnology and the climate change debates do not mix. Copyright © 2012 Elsevier B.V. All rights reserved.

Identification and Analysis of Jasmonate Pathway Genes in Coffea canephora (Robusta Coffee) by In Silico Approach.

PubMed

Bharathi, Kosaraju; Sreenath, H L

2017-07-01

Coffea canephora is the commonly cultivated coffee species in the world along with Coffea arabica . Different pests and pathogens affect the production and quality of the coffee. Jasmonic acid (JA) is a plant hormone which plays an important role in plants growth, development, and defense mechanisms, particularly against insect pests. The key enzymes involved in the production of JA are lipoxygenase, allene oxide synthase, allene oxide cyclase, and 12-oxo-phytodienoic reductase. There is no report on the genes involved in JA pathway in coffee plants. We made an attempt to identify and analyze the genes coding for these enzymes in C. canephora . First, protein sequences of jasmonate pathway genes from model plant Arabidopsis thaliana were identified in the National Center for Biotechnology Information (NCBI) database. These protein sequences were used to search the web-based database Coffee Genome Hub to identify homologous protein sequences in C. canephora genome using Basic Local Alignment Search Tool (BLAST). Homologous protein sequences for key genes were identified in the C. canephora genome database. Protein sequences of the top matches were in turn used to search in NCBI database using BLAST tool to confirm the identity of the selected proteins and to identify closely related genes in species. The protein sequences from C. canephora database and the top matches in NCBI were aligned, and phylogenetic trees were constructed using MEGA6 software and identified the genetic distance of the respective genes. The study identified the four key genes of JA pathway in C. canephora , confirming the conserved nature of the pathway in coffee. The study expected to be useful to further explore the defense mechanisms of coffee plants. JA is a plant hormone that plays an important role in plant defense against insect pests. Genes coding for the 4 key enzymes involved in the production of JA viz., LOX, AOS, AOC, and OPR are identified in C. canephora (robusta coffee) by bioinformatic approaches confirming the conserved nature of the pathway in coffee. The findings are useful to understand the defense mechanisms of C. canephora and coffee breeding in the long run. JA is a plant hormone that plays an important role in plant defense against insect pests. Genes coding for the 4 key enzymes involved in the production of JA viz., LOX, AOS, AOC and OPR were identified and analyzed in C. canephora (robusta coffee) by in silico approach. The study has confirmed the conserved nature of JA pathway in coffee; the findings are useful to further explore the defense mechanisms of coffee plants. Abbreviations used: C. canephora : Coffea canephora ; C. arabica : Coffea arabica ; JA: Jasmonic acid; CGH: Coffee Genome Hub; NCBI: National Centre for Biotechnology Information; BLAST: Basic Local Alignment Search Tool; A. thaliana : Arabidopsis thaliana ; LOX: Lipoxygenase, AOS: Allene oxide synthase; AOC: Allene oxide cyclase; OPR: 12 oxo phytodienoic reductase.

The rise of health biotechnology research in Latin America: A scientometric analysis of health biotechnology production and impact in Argentina, Brazil, Chile, Colombia, Cuba and Mexico

PubMed Central

2018-01-01

This paper analyzes the patterns of health biotechnology publications in six Latin American countries from 2001 to 2015. The countries studied were Argentina, Brazil, Chile, Colombia, Cuba and Mexico. Before our study, there were no data available on HBT development in half of the Latin-American countries we studied, i.e., Argentina, Colombia and Chile. To include these countries in a scientometric analysis of HBT provides fuller coverage of HBT development in Latin America. The scientometric study used the Web of Science database to identify health biotechnology publications. The total amount of health biotechnology production in the world during the period studied was about 400,000 papers. A total of 1.2% of these papers, were authored by the six Latin American countries in this study. The results show a significant growth in health biotechnology publications in Latin America despite some of the countries having social and political instability, fluctuations in their gross domestic expenditure in research and development or a trade embargo that limits opportunities for scientific development. The growth in the field of some of the Latin American countries studied was larger than the growth of most industrialized nations. Still, the visibility of the Latin American research (measured in the number of citations) did not reach the world average, with the exception of Colombia. The main producers of health biotechnology papers in Latin America were universities, except in Cuba were governmental institutions were the most frequent producers. The countries studied were active in international research collaboration with Colombia being the most active (64% of papers co-authored internationally), whereas Brazil was the least active (35% of papers). Still, the domestic collaboration was even more prevalent, with Chile being the most active in such collaboration (85% of papers co-authored domestically) and Argentina the least active (49% of papers). We conclude that the Latin American countries studied are increasing their health biotechnology publishing. This strategy could contribute to the development of innovations that may solve local health problems in the region. PMID:29415003

The rise of health biotechnology research in Latin America: A scientometric analysis of health biotechnology production and impact in Argentina, Brazil, Chile, Colombia, Cuba and Mexico.

PubMed

León-de la O, Dante Israel; Thorsteinsdóttir, Halla; Calderón-Salinas, José Víctor

2018-01-01

This paper analyzes the patterns of health biotechnology publications in six Latin American countries from 2001 to 2015. The countries studied were Argentina, Brazil, Chile, Colombia, Cuba and Mexico. Before our study, there were no data available on HBT development in half of the Latin-American countries we studied, i.e., Argentina, Colombia and Chile. To include these countries in a scientometric analysis of HBT provides fuller coverage of HBT development in Latin America. The scientometric study used the Web of Science database to identify health biotechnology publications. The total amount of health biotechnology production in the world during the period studied was about 400,000 papers. A total of 1.2% of these papers, were authored by the six Latin American countries in this study. The results show a significant growth in health biotechnology publications in Latin America despite some of the countries having social and political instability, fluctuations in their gross domestic expenditure in research and development or a trade embargo that limits opportunities for scientific development. The growth in the field of some of the Latin American countries studied was larger than the growth of most industrialized nations. Still, the visibility of the Latin American research (measured in the number of citations) did not reach the world average, with the exception of Colombia. The main producers of health biotechnology papers in Latin America were universities, except in Cuba were governmental institutions were the most frequent producers. The countries studied were active in international research collaboration with Colombia being the most active (64% of papers co-authored internationally), whereas Brazil was the least active (35% of papers). Still, the domestic collaboration was even more prevalent, with Chile being the most active in such collaboration (85% of papers co-authored domestically) and Argentina the least active (49% of papers). We conclude that the Latin American countries studied are increasing their health biotechnology publishing. This strategy could contribute to the development of innovations that may solve local health problems in the region.

The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers

PubMed Central

Ascoli, Giorgio A.; Martone, Maryann E.; Shepherd, Gordon M.; Miller, Perry L.

2009-01-01

This paper describes the NIF LinkOut Broker (NLB) that has been built as part of the Neuroscience Information Framework (NIF) project. The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related to entries in the National Center for Biotechnology Information’s (NCBI’s) Entrez system. The NLB collects these links from each resource and passes them to the NCBI which incorporates them into its Entrez LinkOut service. In this way, an Entrez user looking at a specific Entrez entry can LinkOut directly to related neuroscience information. The information stored in the NLB can also be utilized in other ways. A second approach, which is operational on a pilot basis, is for the NLB Web server to create dynamically its own Web page of LinkOut links for each NCBI identifier in the NLB database. This approach can allow other resources (in addition to the NCBI Entrez) to LinkOut to related neuroscience information. The paper describes the current NLB system and discusses certain design issues that arose during its implementation. PMID:18975149

Contamination of sequence databases with adaptor sequences

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

Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D.

Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable ofmore » transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.« less

An Exploration of High School (12 17 Year Old) Students' Understandings of, and Attitudes Towards Biotechnology Processes

NASA Astrophysics Data System (ADS)

Dawson, Vaille

2007-03-01

The products of modern biotechnology processes such as genetic engineering, DNA testing and cloning will increasingly impact on society. It is essential that young people have a well-developed scientific understanding of biotechnology and associated processes so that they are able to contribute to public debate and make informed personal decisions. The aim of this study was to examine the development of understandings and attitudes about biotechnology processes as students progress through high school. In a cross-sectional case study, data was obtained from student interviews and written surveys of students aged 12 to 17 years. The results indicate that students' ability to provide a generally accepted definition and examples of biotechnology, cloning and genetically modified foods was relatively poor amongst 12 13 year old students but improved in older students. Most students approved of the use of biotechnology processes involving micro-organisms, plants and humans and disapproved of the use of animals. Overall, 12 13 year old students' attitudes were less favourable than older students regardless of the context. An awareness of the development and range of students' understandings and attitudes may lead to a more appropriate use of biotechnology curriculum materials and thus improved biotechnology education in schools.

NCBI GEO: archive for high-throughput functional genomic data.

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Rudnev, Dmitry; Evangelista, Carlos; Kim, Irene F; Soboleva, Alexandra; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Muertter, Rolf N; Edgar, Ron

2009-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as 'Minimum Information About a Microarray Experiment' (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Gene Expression Omnibus (GEO): Microarray data storage, submission, retrieval, and analysis

PubMed Central

Barrett, Tanya

2006-01-01

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of both unprocessed and processed data in a MIAME- (Minimum Information About a Microarray Experiment) supportive infrastructure that promotes fully annotated submissions. GEO currently stores about a billion individual gene expression measurements, derived from over 100 organisms, submitted by over 1,500 laboratories, addressing a wide range of biological phenomena. To maximize the utility of these data, several user-friendly Web-based interfaces and applications have been implemented that enable effective exploration, query, and visualization of these data, at the level of individual genes or entire studies. This chapter describes how the data are stored, submission procedures, and mechanisms for data retrieval and query. GEO is publicly accessible at http://www.ncbi.nlm.nih.gov/projects/geo/. PMID:16939800

Advances in yeast systematics and phylogeny and their use as predictors of biotechnologically important metabolic pathways

USDA-ARS?s Scientific Manuscript database

Detection, identification, and classification of yeasts have undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of t...

SeedStor: A Germplasm Information Management System and Public Database.

PubMed

Horler, R S P; Turner, A S; Fretter, P; Ambrose, M

2018-01-01

SeedStor (https://www.seedstor.ac.uk) acts as the publicly available database for the seed collections held by the Germplasm Resources Unit (GRU) based at the John Innes Centre, Norwich, UK. The GRU is a national capability supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The GRU curates germplasm collections of a range of temperate cereal, legume and Brassica crops and their associated wild relatives, as well as precise genetic stocks, near-isogenic lines and mapping populations. With >35,000 accessions, the GRU forms part of the UK's plant conservation contribution to the Multilateral System (MLS) of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA) for wheat, barley, oat and pea. SeedStor is a fully searchable system that allows our various collections to be browsed species by species through to complicated multipart phenotype criteria-driven queries. The results from these searches can be downloaded for later analysis or used to order germplasm via our shopping cart. The user community for SeedStor is the plant science research community, plant breeders, specialist growers, hobby farmers and amateur gardeners, and educationalists. Furthermore, SeedStor is much more than a database; it has been developed to act internally as a Germplasm Information Management System that allows team members to track and process germplasm requests, determine regeneration priorities, handle cost recovery and Material Transfer Agreement paperwork, manage the Seed Store holdings and easily report on a wide range of the aforementioned tasks. © The Author(s) 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Workflow and web application for annotating NCBI BioProject transcriptome data

PubMed Central

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A.; Barrero, Luz S.; Landsman, David

2017-01-01

Abstract The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/ PMID:28605765

Recovery of biotechnological products using aqueous two phase systems.

PubMed

Phong, Win Nee; Show, Pau Loke; Chow, Yin Hui; Ling, Tau Chuan

2018-04-16

Aqueous two-phase system (ATPS) has been suggested as a promising separation tool in the biotechnological industry. This liquid-liquid extraction technique represents an interesting advance in downstream processing due to several advantages such as simplicity, rapid separation, efficiency, economy, flexibility and biocompatibility. Up to date, a range of biotechnological products have been successfully recovered from different sources with high yield using ATPS-based strategy. In view of the important potential contribution of the ATPS in downstream processing, this review article aims to provide latest information about the application of ATPS in the recovery of various biotechnological products in the past 7 years (2010-2017). Apart from that, the challenges as well as the possible future work and outlook of the ATPS-based recovery method have also been presented in this review article. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Understanding public perceptions of biotechnology through the "Integrative Worldview Framework".

PubMed

De Witt, Annick; Osseweijer, Patricia; Pierce, Robin

2015-07-03

Biotechnological innovations prompt a range of societal responses that demand understanding. Research has shown such responses are shaped by individuals' cultural worldviews. We aim to demonstrate how the Integrative Worldview Framework (IWF) can be used for analyzing perceptions of biotechnology, by reviewing (1) research on public perceptions of biotechnology and (2) analyses of the stakeholder-debate on the bio-based economy, using the Integrative Worldview Framework (IWF) as analytical lens. This framework operationalizes the concept of worldview and distinguishes between traditional, modern, and postmodern worldviews, among others. Applied to these literatures, this framework illuminates how these worldviews underlie major societal responses, thereby providing a unifying understanding of the literature on perceptions of biotechnology. We conclude the IWF has relevance for informing research on perceptions of socio-technical changes, generating insight into the paradigmatic gaps in social science, and facilitating reflexive and inclusive policy-making and debates on these timely issues. © The Author(s) 2015.

Needs and means for education and training in biotechnology: perspectives from developing countries and Europe.

PubMed

Grainger, J M

1996-09-01

A plenary discussion session on 'Biotechnology education and training programs' at the Xth International Conference on The global Impacts of Applied Microbiology in 1995 gave an opportunity to identify current priorities for biotechnology in developing countries. The discussion focused on three major areas: the nature of the skills required; education and training for the various categories of staff; the role of the scientific community in informing the decision makers about biotechnology and its prospects. Comparable discussions are taking place in Europe and elsewhere in the industrialized world. They are exemplified by developments arising from a White Paper on 'Growth, Competitiveness, Employment' published by the European Commission in 1993 which included a reinforcement of the work of the European Initiative for Biotechnology Education (EIBE) for teachers in schools. There are also widespread anxieties about the effects of deficiencies in the amount of attention being given to microbiology in undergraduate courses.

Medical biotechnology trends and achievements in iran.

PubMed

Mahboudi, Fereidoun; Hamedifar, Haleh; Aghajani, Hamideh

2012-10-01

A healthcare system has been the most important priority for all governments worldwide. Biotechnology products have affected the promotion of health care over the last thirty years. During the last several decades, Iran has achieved significant success in extending healthcare to the rural areas and in reducing the rates of infant mortality and increasing population growth. Biomedical technology as a converging technology is considered a helpful tool to fulfill the Iranian healthcare missions. The number of biotechnology products has reached 148 in 2012. The total sales have increased to 98 billion USD without considering vaccines and plasma derived proteins in 2012. Iran is one of the leading countries in the Middle East and North Africa in the area of Medical biotechnology. The number of biotechnology medicines launched in Iran is 13 products until 2012. More than 15 products are in pipelines now. Manufacturers are expecting to receive the market release for more than 8 products by the end of 2012. Considering this information, Iran will lead the biotechnology products especially in area of biosimilars in Asia after India in next three years. The present review will discuss leading policy, decision makers' role, human resource developing system and industry development in medical biotechnology.

Medical Biotechnology Trends and Achievements in Iran

PubMed Central

Mahboudi, Fereidoun; Hamedifar, Haleh; Aghajani, Hamideh

2012-01-01

A healthcare system has been the most important priority for all governments worldwide. Biotechnology products have affected the promotion of health care over the last thirty years. During the last several decades, Iran has achieved significant success in extending healthcare to the rural areas and in reducing the rates of infant mortality and increasing population growth. Biomedical technology as a converging technology is considered a helpful tool to fulfill the Iranian healthcare missions. The number of biotechnology products has reached 148 in 2012. The total sales have increased to 98 billion USD without considering vaccines and plasma derived proteins in 2012. Iran is one of the leading countries in the Middle East and North Africa in the area of Medical biotechnology. The number of biotechnology medicines launched in Iran is 13 products until 2012. More than 15 products are in pipelines now. Manufacturers are expecting to receive the market release for more than 8 products by the end of 2012. Considering this information, Iran will lead the biotechnology products especially in area of biosimilars in Asia after India in next three years. The present review will discuss leading policy, decision makers’ role, human resource developing system and industry development in medical biotechnology. PMID:23407888

Biotechnology and Consumer Decision-Making.

PubMed

Sax, Joanna K

Society is facing major challenges in climate change, health care and overall quality of life. Scientific advances to address these areas continue to grow, with overwhelming evidence that the application of highly tested forms of biotechnology is safe and effective. Despite scientific consensus in these areas, consumers appear reluctant to support their use. Research that helps to understand consumer decision-making and the public’s resistance to biotechnologies such as vaccines, fluoridated water programs and genetically engineered food, will provide great social value. This article is forward-thinking in that it suggests that important research in behavioral decision-making, specifically affect and ambiguity, can be used to help consumers make informed choices about major applications of biotechnology. This article highlights some of the most controversial examples: vaccinations, genetically engineered food, rbST treated dairy cows, fluoridated water, and embryonic stem cell research. In many of these areas, consumers perceive the risks as high, but the experts calculate the risks as low. Four major thematic approaches are proposed to create a roadmap for policymakers to consider for policy design and implementation in controversial areas of biotechnology. This article articulates future directions for studies that implement decision-making research to allow consumers to appropriately assign risk to their options and make informed decisions.

Genebanks: a comparison of eight proposed international genetic databases.

PubMed

Austin, Melissa A; Harding, Sarah; McElroy, Courtney

2003-01-01

To identify and compare population-based genetic databases, or "genebanks", that have been proposed in eight international locations between 1998 and 2002. A genebank can be defined as a stored collection of genetic samples in the form of blood or tissue, that can be linked with medical and genealogical or lifestyle information from a specific population, gathered using a process of generalized consent. Genebanks were identified by searching Medline and internet search engines with key words such as "genetic database" and "biobank" and by reviewing literature on previously identified databases such as the deCode project. Collection of genebank characteristics was by an electronic and literature search, augmented by correspondence with informed individuals. The proposed genebanks are located in Iceland, the United Kingdom, Estonia, Latvia, Sweden, Singapore, the Kingdom of Tonga, and Quebec, Canada. Comparisons of the genebanks were based on the following criteria: genebank location and description of purpose, role of government, commercial involvement, consent and confidentiality procedures, opposition to the genebank, and current progress. All of the groups proposing the genebanks plan to search for susceptibility genes for complex diseases while attempting to improve public health and medical care in the region and, in some cases, stimulating the local economy through expansion of the biotechnology sector. While all of the identified plans share these purposes, they differ in many aspects, including funding, subject participation, and organization. The balance of government and commercial involvement in the development of each project varies. Genetic samples and health information will be collected from participants and coded in all of the genebanks, but consent procedures range from presumed consent of the entire eligible population to recruitment of volunteers with informed consent. Issues regarding confidentiality and consent have resulted in opposition to some of the more publicized projects. None of the proposed databases are currently operational and at least one project was terminated due to opposition. Ambitious genebank projects have been proposed in numerous countries and provinces. The characteristics of the projects vary, but all intend to map genes for common diseases and hope to improve the health of the populations involved. The impact of these projects on understanding genetic susceptibility to disease will be increasingly apparent if the projects become operational. The ethical, legal, and social implications of the projects should be carefully considered during their development. Copyright 2003 S. Karger AG, Basel

The life of family trees and the Book of Icelanders.

PubMed

Pálsson, Gísli

2002-01-01

This article discusses the tracing of family histories and competing assumptions about identities and relatedness in the era of biotechnology and biopower. Although the fascination with genealogical trees and family histories is common throughout the West, in Iceland this attraction is extreme. A genealogical database for most of the Icelandic population, the so-called Book of Icelanders, is being constructed as part of a larger biogenetic enterprise that seeks to establish the presumed genetic causes of common diseases for the purpose of developing pharmaceutical products. The discussion explores the changing implications of family trees as they become enmeshed in biomedical projects and political debates. Genealogical records, I suggest, are never innocent phenomena; this is because they have a social life of their own, a biography informed by the contours of the cultural landscapes to which they belong.

Biotechnology in Switzerland: high on the public agenda, but only moderate support.

PubMed

Bonfadelli, Heinz; Dahinden, Urs; Leonarz, Martina

2002-04-01

In Switzerland, there have been intensive public debates about biotechnology because of the specific Swiss political system of direct democracy that led, in 1992 and 1998, to two national referenda on biotechnology regulation. As a result, the Swiss population is well informed but skeptical about this technology. These findings contrast with the deficit model of public understanding of science, which predicts a positive correlation between knowledge of, and support for, a specific technology. What role did the media play in the development of public opinion? This question is discussed because of a content analysis (time series) of national newspapers. In addition, representative surveys and focus groups yield insights into the public perception of biotechnology and the influence of mass communication for opinion formation.

Biotechnology awareness study, Part 2: Meeting the information needs of biotechnologists.

PubMed Central

Cunningham, D; Grefsheim, S; Simon, M; Lansing, P S

1991-01-01

The second part of the biotechnology awareness study focused on health sciences libraries and how well they are meeting the needs of biotechnologists working in the study's nine medical centers. A survey was conducted over a three-month period to assess the demand for biotechnology-related reference services at nine libraries and the sources the librarians used to answer the questions. Data on monographic and current serial holdings were also collected. At the end of the survey period, librarians were asked for their perceptions about biotechnology research at their institutions and in their geographic areas. Their responses were compared to the responses the scientists at the nine schools gave to the same or similar questions. Results showed few biotechnology-related reference questions were asked of the librarians. The recorded questions dealt with a range of biotechnology subjects. MEDLINE was used to answer 77% of the questions received during the survey period. More detailed notes in MeSH and a guide to online searching for biotechnology topics were suggested by the librarians as ways to improve reference service to this group of researchers. Journal collections were generally strong, with libraries owning from 50% to 87% of the titles on a core list of biotechnology journals compiled for this study. All libraries subscribed to the five titles most often cited by the scientists surveyed. Generally, librarians were unaware of the biotechnology-related research being done on their campuses or in their geographic areas. PMID:1998819

Educational awareness of biotechnology issues among undergraduate students at the United Arab Emirates University.

PubMed

AbuQamar, Synan; Alshannag, Qasim; Sartawi, Abdelaziz; Iratni, Rabah

2015-01-01

Due to its valuable benefits and potential risks, there is a progressing debate among opponents and proponents of biotechnology in recent decades. Previous studies have shown that lack of knowledge about biotechnology remains the concern about genetically modified organisms/food (GMO/GMF). This study assessed levels of educational awareness perceptions and attitudes of United Arab Emirates University (UAEU) students towards biotechnology. An electronic survey including literacy, environmental, social, and economic domains associated with biotechnology was administered to obtain data from undergraduate students in different colleges of the university. Responses from students (n = 1,104) were gathered and statistically analyzed. Results indicated that educational awareness in biotechnology literacy and environmental domains were significantly different according to the enrolled college and the academic achievement of the student. In general, a poor overall performance of our students' understanding was concluded. Aware groups most likely accepted accurate biotechnology information delivered by reliable sources from internet or lectures; they grasped their knowledge from surrounding people as a secondary source. Since UAEU students have several concept misunderstandings of biotechnology and its ethics, our results suggest that awareness plays a crucial role in forming a "clear-cut" opinion about this technology. Because education can shape public attitudes toward biotechnology, priorities on university curricula and teaching strategies should be extensively given, and therefore, improve in respect to this topic. Ultimately, this promotes the students' perception in understanding the new technology. © 2015 The International Union of Biochemistry and Molecular Biology.

Cloud-based adaptive exon prediction for DNA analysis

PubMed Central

Putluri, Srinivasareddy; Fathima, Shaik Yasmeen

2018-01-01

Cloud computing offers significant research and economic benefits to healthcare organisations. Cloud services provide a safe place for storing and managing large amounts of such sensitive data. Under conventional flow of gene information, gene sequence laboratories send out raw and inferred information via Internet to several sequence libraries. DNA sequencing storage costs will be minimised by use of cloud service. In this study, the authors put forward a novel genomic informatics system using Amazon Cloud Services, where genomic sequence information is stored and accessed for processing. True identification of exon regions in a DNA sequence is a key task in bioinformatics, which helps in disease identification and design drugs. Three base periodicity property of exons forms the basis of all exon identification techniques. Adaptive signal processing techniques found to be promising in comparison with several other methods. Several adaptive exon predictors (AEPs) are developed using variable normalised least mean square and its maximum normalised variants to reduce computational complexity. Finally, performance evaluation of various AEPs is done based on measures such as sensitivity, specificity and precision using various standard genomic datasets taken from National Center for Biotechnology Information genomic sequence database. PMID:29515813

Post-Genome Era Pedagogy: How a BS Biotechnology Program Benefits the Liberal Arts Institution

ERIC Educational Resources Information Center

Eden, Peter

2005-01-01

Genomics profoundly affects society, because genome sequence information is widely used in such areas as genetic testing, genomic medicine/vaccine development, and so forth. Therefore, a responsibility to modernize science curricula exists for "post-genome era" educators. At my university, we developed a BS biotechnology program within a…

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.

PubMed

Rimet, Frédéric; Chaumeil, Philippe; Keck, François; Kermarrec, Lenaïg; Vasselon, Valentin; Kahlert, Maria; Franc, Alain; Bouchez, Agnès

2016-01-01

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/. © The Author(s) 2016. Published by Oxford University Press.

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

PubMed Central

Rimet, Frédéric; Chaumeil, Philippe; Keck, François; Kermarrec, Lenaïg; Vasselon, Valentin; Kahlert, Maria; Franc, Alain; Bouchez, Agnès

2016-01-01

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/ PMID:26989149

Technological Innovations from NASA

NASA Technical Reports Server (NTRS)

Pellis, Neal R.

2006-01-01

The challenge of human space exploration places demands on technology that push concepts and development to the leading edge. In biotechnology and biomedical equipment development, NASA science has been the seed for numerous innovations, many of which are in the commercial arena. The biotechnology effort has led to rational drug design, analytical equipment, and cell culture and tissue engineering strategies. Biomedical research and development has resulted in medical devices that enable diagnosis and treatment advances. NASA Biomedical developments are exemplified in the new laser light scattering analysis for cataracts, the axial flow left ventricular-assist device, non contact electrocardiography, and the guidance system for LASIK surgery. Many more developments are in progress. NASA will continue to advance technologies, incorporating new approaches from basic and applied research, nanotechnology, computational modeling, and database analyses.

Agenda 21: biotechnology at the United Nations Conference on Environment and Development.

PubMed

Taylhardat, A R; Zilinskas, R A

1992-04-01

Preparation has yet to be completed for the 1992 Earth Summit, UN Conference on Environment and Development (UNCED), in Rio de Janeiro, Brazil. Nonetheless, it has been planned as a forum in which recommendations will be made to governments and international organizations on how to alleviate environmental damage caused by human activities and how to prevent future damage without retarding development in the Third World. It will declare basic principles for national and individual conduct regarding environmental preservation and sustainable development; adopt international conventions to protect biodiversity and manage climatic change; lay out Agenda 21 activities as specified by UNCED; provide an agenda to help Third World governments manage environmental matters; and provide an agenda for improving the transfer of technology to developing countries. Where biotechnology is concerned, scientists and policy makers in developing countries have shown their interest. Limited resources and capabilities, however, constrain their abilities to engage in serious research and development. International organizations such as the UN Industrial Development Organization (UNIDO) may help UNCED and developing countries with biotechnology. Since 1986, UNIDO has held the International Centre for Genetic Engineering and Biotechnology (ICGEB) as a special project. The ICGEB conducts research and development (R&D) on high priority topics in developing countries; trains scientific and technical personnel from member countries in advanced biotechnology techniques; helps member countries implement and operate ICGEB-affiliated R&D and training centers; and manages an information exchange for internationally affiliated centers. To maximize the potential of biotechnology to help Third World nations clear their environments of pollutants while safely exploiting natural resources, organizations should promote full use of available training resources; promote biosafety and the dissemination of information on risk assessment and risk management; increase funding to support existing information networks; help make equipment and supplies available to developing countries; help bridge the gap between research and applications by encouraging universities and research institutions to market their research; and promote entrepreneurship in developing countries.

Functional Genomics Analysis of Singapore Grouper Iridovirus: Complete Sequence Determination and Proteomic Analysis

PubMed Central

Song, Wen Jun; Qin, Qi Wei; Qiu, Jin; Huang, Can Hua; Wang, Fan; Hew, Choy Leong

2004-01-01

Here we report the complete genome sequence of Singapore grouper iridovirus (SGIV). Sequencing of the random shotgun and restriction endonuclease genomic libraries showed that the entire SGIV genome consists of 140,131 nucleotide bp. One hundred sixty-two open reading frames (ORFs) from the sense and antisense DNA strands, coding for lengths varying from 41 to 1,268 amino acids, were identified. Computer-assisted analyses of the deduced amino acid sequences revealed that 77 of the ORFs exhibited homologies to known virus genes, 23 of which matched functional iridovirus proteins. Forty-two putative conserved domains or signatures were detected in the National Center for Biotechnology Information CD-Search database and PROSITE database. An assortment of enzyme activities involved in DNA replication, transcription, nucleotide metabolism, cell signaling, etc., were identified. Viruses were cultured on a cell line derived from the embryonated egg of the grouper Epinephelus tauvina, isolated, and purified by sucrose gradient ultracentrifugation. The protein extract from the purified virions was analyzed by polyacrylamide gel electrophoresis followed by in-gel digestion of protein bands. Matrix-assisted laser desorption ionization-time of flight mass spectrometry and database searching led to identification of 26 proteins. Twenty of these represented novel or previously unidentified genes, which were further confirmed by reverse transcription-PCR (RT-PCR) and DNA sequencing of their respective RT-PCR products. PMID:15507645

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

PubMed

Schoch, Conrad L; Robbertse, Barbara; Robert, Vincent; Vu, Duong; Cardinali, Gianluigi; Irinyi, Laszlo; Meyer, Wieland; Nilsson, R Henrik; Hughes, Karen; Miller, Andrew N; Kirk, Paul M; Abarenkov, Kessy; Aime, M Catherine; Ariyawansa, Hiran A; Bidartondo, Martin; Boekhout, Teun; Buyck, Bart; Cai, Qing; Chen, Jie; Crespo, Ana; Crous, Pedro W; Damm, Ulrike; De Beer, Z Wilhelm; Dentinger, Bryn T M; Divakar, Pradeep K; Dueñas, Margarita; Feau, Nicolas; Fliegerova, Katerina; García, Miguel A; Ge, Zai-Wei; Griffith, Gareth W; Groenewald, Johannes Z; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Gueidan, Cécile; Guo, Liangdong; Hambleton, Sarah; Hamelin, Richard; Hansen, Karen; Hofstetter, Valérie; Hong, Seung-Beom; Houbraken, Jos; Hyde, Kevin D; Inderbitzin, Patrik; Johnston, Peter R; Karunarathna, Samantha C; Kõljalg, Urmas; Kovács, Gábor M; Kraichak, Ekaphan; Krizsan, Krisztina; Kurtzman, Cletus P; Larsson, Karl-Henrik; Leavitt, Steven; Letcher, Peter M; Liimatainen, Kare; Liu, Jian-Kui; Lodge, D Jean; Luangsa-ard, Janet Jennifer; Lumbsch, H Thorsten; Maharachchikumbura, Sajeewa S N; Manamgoda, Dimuthu; Martín, María P; Minnis, Andrew M; Moncalvo, Jean-Marc; Mulè, Giuseppina; Nakasone, Karen K; Niskanen, Tuula; Olariaga, Ibai; Papp, Tamás; Petkovits, Tamás; Pino-Bodas, Raquel; Powell, Martha J; Raja, Huzefa A; Redecker, Dirk; Sarmiento-Ramirez, J M; Seifert, Keith A; Shrestha, Bhushan; Stenroos, Soili; Stielow, Benjamin; Suh, Sung-Oui; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M Teresa; Udayanga, Dhanushka; Untereiner, Wendy A; Diéguez Uribeondo, Javier; Subbarao, Krishna V; Vágvölgyi, Csaba; Visagie, Cobus; Voigt, Kerstin; Walker, Donald M; Weir, Bevan S; Weiß, Michael; Wijayawardene, Nalin N; Wingfield, Michael J; Xu, J P; Yang, Zhu L; Zhang, Ning; Zhuang, Wen-Ying; Federhen, Scott

2014-01-01

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353. Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.

NEMiD: a web-based curated microbial diversity database with geo-based plotting.

PubMed

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

PubMed Central

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/. PMID:24714636

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

Experimental and early investigational drugs for androgenetic alopecia.

PubMed

Guo, Hongwei; Gao, Wendi Victor; Endo, Hiromi; McElwee, Kevin John

2017-08-01

Treatments for androgenetic alopecia constitute a multi-billion-dollar industry, however, currently available therapeutic options have variable efficacy. Consequently, in recent years small biotechnology companies and academic research laboratories have begun to investigate new or improved treatment methods. Research and development approaches include improved formulations and modes of application for current drugs, new drug development, development of cell-based treatments, and medical devices for modulation of hair growth. Areas covered: Here we review the essential pathways of androgenetic alopecia pathogenesis and collate the current and emerging therapeutic strategies using journal publications databases and clinical trials databases to gather information about active research on new treatments. Expert opinion: We propose that topically applied medications, or intra-dermal injected or implanted materials, are preferable treatment modalities, minimizing side effect risks as compared to systemically applied treatments. Evidence in support of new treatments is limited. However, we suggest therapeutics which reverse the androgen-driven inhibition of hair follicle signaling pathways, such as prostaglandin analogs and antagonists, platelet-rich plasma (PRP), promotion of skin angiogenesis and perfusion, introduction of progenitor cells for hair regeneration, and more effective ways of transplanting hair, are the likely near future direction of androgenetic alopecia treatment development.

Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection.

PubMed

Ramos, Vitor; Morais, João; Castelo-Branco, Raquel; Pinheiro, Ângela; Martins, Joana; Regueiras, Ana; Pereira, Ana L; Lopes, Viviana R; Frazão, Bárbara; Gomes, Dina; Moreira, Cristiana; Costa, Maria Sofia; Brûle, Sébastien; Faustino, Silvia; Martins, Rosário; Saker, Martin; Osswald, Joana; Leão, Pedro N; Vasconcelos, Vitor M

2018-01-01

Cyanobacteria are a well-known source of bioproducts which renders culturable strains a valuable resource for biotechnology purposes. We describe here the establishment of a cyanobacterial culture collection (CC) and present the first version of the strain catalog and its online database (http://lege.ciimar.up.pt/). The LEGE CC holds 386 strains, mainly collected in coastal (48%), estuarine (11%), and fresh (34%) water bodies, for the most part from Portugal (84%). By following the most recent taxonomic classification, LEGE CC strains were classified into at least 46 genera from six orders (41% belong to the Synechococcales), several of them are unique among the phylogenetic diversity of the cyanobacteria. For all strains, primary data were obtained and secondary data were surveyed and reviewed, which can be reached through the strain sheets either in the catalog or in the online database. An overview on the notable biodiversity of LEGE CC strains is showcased, including a searchable phylogenetic tree and images for all strains. With this work, 80% of the LEGE CC strains have now their 16S rRNA gene sequences deposited in GenBank. Also, based in primary data, it is demonstrated that several LEGE CC strains are a promising source of extracellular polymeric substances (EPS). Through a review of previously published data, it is exposed that LEGE CC strains have the potential or actual capacity to produce a variety of biotechnologically interesting compounds, including common cyanotoxins or unprecedented bioactive molecules. Phylogenetic diversity of LEGE CC strains does not entirely reflect chemodiversity. Further bioprospecting should, therefore, account for strain specificity of the valuable cyanobacterial holdings of LEGE CC.

[The public perception of information about the potential risks of genetically modified crops in the food chain].

PubMed

Furnival, Ariadne Chloë; Pinheiro, Sônia Maria

2008-01-01

At a time when genetically modified (GM) crops are entering the Brazilian food chain, we present the findings of a study that makes use of a qualitative technique involving focal groups to look into the public's interpretation of the information available about this biotechnological innovation. This methodology produced results that revealed the interconnections drawn by the research subjects between this form of biotechnology, changes to the environment, and food production in general. The mistrust expressed about GM crops was particularly attributed by the participants to the non-availability of comprehensible information in the mass media or on product labels.

High Quality Unigenes and Microsatellite Markers from Tissue Specific Transcriptome and Development of a Database in Clusterbean (Cyamopsis tetragonoloba, L. Taub)

PubMed Central

Rawal, Hukam C.; Kumar, Shrawan; Mithra S.V., Amitha; Solanke, Amolkumar U.; Saxena, Swati; Tyagi, Anshika; V., Sureshkumar; Yadav, Neelam R.; Kalia, Pritam; Singh, Narendra Pratap; Singh, Nagendra Kumar; Sharma, Tilak Raj; Gaikwad, Kishor

2017-01-01

Clusterbean (Cyamopsis tetragonoloba L. Taub), is an important industrial, vegetable and forage crop. This crop owes its commercial importance to the presence of guar gum (galactomannans) in its endosperm which is used as a lubricant in a range of industries. Despite its relevance to agriculture and industry, genomic resources available in this crop are limited. Therefore, the present study was undertaken to generate RNA-Seq based transcriptome from leaf, shoot, and flower tissues. A total of 145 million high quality Illumina reads were assembled using Trinity into 127,706 transcripts and 48,007 non-redundant high quality (HQ) unigenes. We annotated 79% unigenes against Plant Genes from the National Center for Biotechnology Information (NCBI), Swiss-Prot, Pfam, gene ontology (GO) and KEGG databases. Among the annotated unigenes, 30,020 were assigned with 116,964 GO terms, 9984 with EC and 6111 with 137 KEGG pathways. At different fragments per kilobase of transcript per millions fragments sequenced (FPKM) levels, genes were found expressed higher in flower tissue followed by shoot and leaf. Additionally, we identified 8687 potential simple sequence repeats (SSRs) with an average frequency of one SSR per 8.75 kb. A total of 28 amplified SSRs in 21 clusterbean genotypes resulted in polymorphism in 13 markers with average polymorphic information content (PIC) of 0.21. We also constructed a database named ‘ClustergeneDB’ for easy retrieval of unigenes and the microsatellite markers. The tissue specific genes identified and the molecular marker resources developed in this study is expected to aid in genetic improvement of clusterbean for its end use. PMID:29120386

COREMIC: a web-tool to search for a niche associated CORE MICrobiome.

PubMed

Rodrigues, Richard R; Rodgers, Nyle C; Wu, Xiaowei; Williams, Mark A

2018-01-01

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool "COREMIC" meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the "core microbiome" associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q -val <0.05% for Fisher's exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp , and Chitinophagaceae . These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

COREMIC: a web-tool to search for a niche associated CORE MICrobiome

PubMed Central

Rodgers, Nyle C.; Wu, Xiaowei; Williams, Mark A.

2018-01-01

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val <0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software. PMID:29473009

78 FR 70617 - In the Matter of Pure H20 Bio-Technologies, Inc.; Order of Suspension of Trading

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-26

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] In the Matter of Pure H20 Bio-Technologies, Inc.; Order of Suspension of Trading November 22, 2013. It appears to the Securities and Exchange Commission that there is a lack of current and accurate information concerning the securities of Pure H20 Bio...

A Regulatory Framework for Nanotechnology

DTIC Science & Technology

informed by a map of the regulatory landscape of nanotechnology and a review of the regulatory frameworks for the aviation and biotechnology industries...aviation and biotechnology and maps the regulatory landscape in the United States by examining stakeholders, regulatory entities, and applicable legislation...state of nanotechnology if the limitations of technical expertise are addressed. This expertise can be provided by advisory committees of technical

Biotechnology in the Treatment of Sensorineural Hearing Loss: Foundations and Future of Hair Cell Regeneration

PubMed Central

Parker, Mark A.

2011-01-01

Purpose To provide an overview of the methodologies involved in the field of hair cell regeneration. First, a tutorial on the biotechnological foundations of this field will be provided in order to assist the reader in the comprehension and interpretation of the research involved in hair cell regeneration. Next, a review of stem cell and gene therapy will be presented and a critical appraisal of their application to hair cell regeneration will be provided. The methodologies used in these approaches will be highlighted. Method Narrative review of the fields of cellular, molecular, and developmental biology, tissue engineering, and stem cell and gene therapy using the PubMed database. Results The use of biotechnological approaches to the treatment of hearing loss, such as stem cell and gene therapy, has led to new methods of regenerating cochlear hair cells in mammals. Conclusions There have been incredible strides made in assembling important pieces of the puzzle that comprise hair cell regeneration. However, mammalian hair cell regeneration using stem cell and gene therapy are years if not decades away from being clinically feasible. If the goals of the biological approaches are met, these therapies may represent the future treatments for hearing loss. PMID:21386039

How Japanese students reason about agricultural biotechnology.

PubMed

Maekawa, Fumi; Macer, Darryl

2004-10-01

Many have claimed that education of the ethical issues raised by biotechnology is essential in universities, but there is little knowledge of its effectiveness. The focus of this paper is to investigate how university students assess the information given in class to make their own value judgments and decisions relating to issues of agricultural biotechnology, especially over genetically modified organisms (GMOs). Analysis of homework reports related with agricultural biotechnology after identification of key concepts and ideas in each student report is presented. The ideas were sorted into different categories. The ideas were compared with those in the reading materials using the same categories. These categories included: concern about affects on humans, affects on the environment, developing countries and starvation, trust in industry, responsibility of scientists, risk perception, media influence, need for (international) organizations or third parties, and information dissemination. What was consistent through the different years was that more than half of the students took a "neutral" position. A report was scored as "neutral" when the report included both the positive and negative side of an issue, or when the student could not make a definite decision about the use of GMOs and GM food. While it may be more difficult to defend a strong ''for" or "against" position, some students used logical arguments successfully in doing so. Sample comments are presented to depict how Japanese students see agricultural technology, and how they value its application, with comparisons to the general social attitudes towards biotechnology.

Expression of glutathione S-transferases in poplar trees (Populus trichocarpa) exposed to 2,4,6-trinitrotoluene (TNT).

PubMed

Brentner, Laura B; Mukherji, Sachiyo T; Merchie, Kate M; Yoon, Jong Moon; Schnoor, Jerald L; Van Aken, Benoit

2008-10-01

Twelve Populus genes were identified from Arabidopsis thaliana sequences previously shown to be induced by exposure to 2,4,6-trinitrotoluene (TNT). Using the resources of the Poplar Genome Project and National Center for Biotechnology Information databases, Populus conserved domains were identified and used to design gene specific primers. RNA extracted from root tissues of TNT-exposed hydroponic poplar plants was used to quantify the expression of genes by reverse-transcriptase real-time polymerase chain reaction. Cyclophilin and 18S ribosomal DNA genes were used as internal standards. Exposure to TNT resulted in a significant increase of gene expression of two glutathione S-transferases (GST), peaking at levels of 25.0 +/- 13.1 and 10 +/- 0.7 fold the expression level of non-exposed plants after 24 h for each of the GST genes, respectively. This paper demonstrates the use of functional genomics information from the model plant species, Arabidopsis, to identify genes which may be important in detoxification of TNT in the model phytoremediation species, Populus trichocarpa.

Gene Graphics: a genomic neighborhood data visualization web application.

PubMed

Harrison, Katherine J; Crécy-Lagard, Valérie de; Zallot, Rémi

2018-04-15

The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be customized for many parameters including gene and genome names, colors and sizes. Gene attributes can be copied and pasted for rapid and user-friendly customization of homologous genes between species. In addition to Portable Network Graphics and Scalable Vector Graphics, produced representations can be exported as Tagged Image File Format or Encapsulated PostScript, formats that are standard for publication. Hands-on tutorials with real life examples inspired from publications are available for training. Gene Graphics is freely available at https://katlabs.cc/genegraphics/ and source code is hosted at https://github.com/katlabs/genegraphics. katherinejh@ufl.edu or remizallot@ufl.edu. Supplementary data are available at Bioinformatics online.

How can developing countries harness biotechnology to improve health?

PubMed Central

Daar, Abdallah S; Berndtson, Kathryn; Persad, Deepa L; Singer, Peter A

2007-01-01

Background The benefits of genomics and biotechnology are concentrated primarily in the industrialized world, while their potential to combat neglected diseases in the developing world has been largely untapped. Without building developing world biotechnology capacity to address local health needs, this disparity will only intensify. To assess the potential of genomics to address health needs in the developing world, the McLaughlin-Rotman Centre for Global Health, along with local partners, organized five courses on Genomics and Public Health Policy in the developing world. The overall objective of the courses was to collectively explore how to best harness genomics to improve health in each region. This article presents and analyzes the recommendations from all five courses. Discussion In this paper we analyze recommendations from 232 developing world experts from 58 countries who sought to answer how best to harness biotechnology to improve health in their regions. We divide their recommendations into four categories: science; finance; ethics, society and culture; and politics. Summary The Courses' recommendations can be summarized across the four categories listed above: Science - Collaborate through national, regional, and international networks - Survey and build capacity based on proven models through education, training, and needs assessments Finance - Develop regulatory and intellectual property frameworks for commercialization of biotechnology - Enhance funding and affordability of biotechnology - Improve the academic-industry interface and the role of small and medium enterprise Ethics, Society, Culture - Develop public engagement strategies to inform and educate the public about developments in genomics and biotechnology - Develop capacity to address ethical, social and cultural issues - Improve accessibility and equity Politics - Strengthen understanding, leadership and support at the political level for biotechnology - Develop policies outlining national biotechnology strategy These recommendations provide guidance for all those interested in supporting science, technology, and innovation to improve health in the developing world. Applying these recommendations broadly across sectors and regions will empower developing countries themselves to harness the benefits of biotechnology and genomics for billions who have long been excluded. PMID:18053180

How can developing countries harness biotechnology to improve health?

PubMed

Daar, Abdallah S; Berndtson, Kathryn; Persad, Deepa L; Singer, Peter A

2007-12-03

The benefits of genomics and biotechnology are concentrated primarily in the industrialized world, while their potential to combat neglected diseases in the developing world has been largely untapped. Without building developing world biotechnology capacity to address local health needs, this disparity will only intensify. To assess the potential of genomics to address health needs in the developing world, the McLaughlin-Rotman Centre for Global Health, along with local partners, organized five courses on Genomics and Public Health Policy in the developing world. The overall objective of the courses was to collectively explore how to best harness genomics to improve health in each region. This article presents and analyzes the recommendations from all five courses. In this paper we analyze recommendations from 232 developing world experts from 58 countries who sought to answer how best to harness biotechnology to improve health in their regions. We divide their recommendations into four categories: science; finance; ethics, society and culture; and politics. The Courses' recommendations can be summarized across the four categories listed above: SCIENCE: - Collaborate through national, regional, and international networks- Survey and build capacity based on proven models through education, training, and needs assessments FINANCE: - Develop regulatory and intellectual property frameworks for commercialization of biotechnology- Enhance funding and affordability of biotechnology- Improve the academic-industry interface and the role of small and medium enterprise ETHICS, SOCIETY, CULTURE: - Develop public engagement strategies to inform and educate the public about developments in genomics and biotechnology- Develop capacity to address ethical, social and cultural issues- Improve accessibility and equity POLITICS: - Strengthen understanding, leadership and support at the political level for biotechnology- Develop policies outlining national biotechnology strategyThese recommendations provide guidance for all those interested in supporting science, technology, and innovation to improve health in the developing world. Applying these recommendations broadly across sectors and regions will empower developing countries themselves to harness the benefits of biotechnology and genomics for billions who have long been excluded.

Biotransformation of lignocellulosic materials into value-added products-A review.

PubMed

Bilal, Muhammad; Asgher, Muhammad; Iqbal, Hafiz M N; Hu, Hongbo; Zhang, Xuehong

2017-05-01

In the past decade, with the key biotechnological advancements, lignocellulosic materials have gained a particular importance. In serious consideration of global economic, environmental and energy issues, research scientists have been re-directing their interests in (re)-valorizing naturally occurring lignocellulosic-based materials. In this context, lignin-modifying enzymes (LMEs) have gained considerable attention in numerous industrial and biotechnological processes. However, their lower catalytic efficiencies and operational stabilities limit their practical and multipurpose applications in various sectors. Therefore, to expand the range of natural industrial biocatalysts e.g. LMEs, significant progress related to the enzyme biotechnology has appeared. Owing to the abundant lignocellulose availability along with LMEs in combination with the scientific advances in the biotechnological era, solid-phase biocatalysts can be economically tailored on a large scale. This review article outlines first briefly on the lignocellulose materials as a potential source for biotransformation into value-added products including composites, fine chemicals, nutraceutical, delignification, and enzymes. Comprehensive information is also given on the purification and characterization of LMEs to present their potential for the industrial and biotechnological sector. Copyright © 2017 Elsevier B.V. All rights reserved.

Re-Framing Biotechnology Regulation.

PubMed

Peck, Alison

Biotechnology is about to spill the banks of federal regulation. New genetic engineering techniques like CRISPR-Cas9 promise revolutionary breakthroughs in medicine, agriculture, and public health—but those techniques would not be regulated under the terms of the Coordinated Framework for Regulation of Biotechnology. This revolutionary moment in biotechnology offers an opportunity to correct the flaws in the framework, which was hastily patched together at the advent of the technology. The framework has never captured all relevant technologies, has never satisfied the public that risk is being effectively managed, and has never been accessible to small companies and publicly-funded labs that increasingly are positioned to make radical, life-saving innovations. This Article offers a proposal for new legislation that would reshape biotechnology regulation to better meet these goals. Key reforms include tying regulation to risk rather than technology category; consolidating agency review; capturing distinct regulatory expertise through inter-agency consultations; creating a clearinghouse to help guide applicants and disseminate information; setting up more comprehensive monitoring of environmental effects; and providing federal leadership to fill key data gaps and address socio-economic impacts.

The future of biotechnology testing in the next decade: a perspective.

PubMed

Johnson, D E

2001-01-01

The power of genomics in transforming the biotechnology industry will be evident in all areas of drug discovery and development. This will be particularly true in safety evaluation, where the field will be forced to adapt to new schemes of e-R&D and e-business in general. Toxicologists will be required to create information-rich, real-time systems that can be used for decisions in the earliest phases of discovery and throughout development. The largest growth area in specific product types will be those that can move genomics information from the laboratory to the clinic the fastest.

Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL).

PubMed

Hooper, Cornelia M; Castleden, Ian R; Aryamanesh, Nader; Jacoby, Richard P; Millar, A Harvey

2016-01-01

Barley, wheat, rice and maize provide the bulk of human nutrition and have extensive industrial use as agricultural products. The genomes of these crops each contains >40,000 genes encoding proteins; however, the major genome databases for these species lack annotation information of protein subcellular location for >80% of these gene products. We address this gap, by constructing the compendium of crop protein subcellular locations called crop Proteins with Annotated Locations (cropPAL). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in subcellular purifications, but can also be predicted from amino acid sequence or protein expression patterns. The cropPAL database collates 556 published studies, from >300 research institutes in >30 countries that have been previously published, as well as compiling eight pre-computed subcellular predictions for all Hordeum vulgare, Triticum aestivum, Oryza sativa and Zea mays protein sequences. The data collection including metadata for proteins and published studies can be accessed through a search portal http://crop-PAL.org. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

An emerging interface between life science and nanotechnology: present status and prospects of reproductive healthcare aided by nano-biotechnology

PubMed Central

Jha, Rakhi K.; Jha, Pradeep K.; Chaudhury, Koel; Rana, Suresh V.S.; Guha, Sujoy K.

2014-01-01

Among the various applications of nano-biotechnology, healthcare is considered one of the most significant domains. For that possibility to synthesize various kind of nanoparticles (NPs) and the ever-increasing ability to control their size as well as structure, to improve surface characteristics and binding NPs with other desired curing agents has played an important role. In this paper, a brief sketch of various kinds of nanomaterials and their biomedical applications is given. Despite claims of bio-nanotechnology about to touch all areas of medical science, information pertaining to the role of nanotechnology for the betterment of reproductive healthcare is indeed limited. Therefore, the various achievements of nano-biotechnology for healthcare in general have been illustrated while giving special insight into the role of nano-biotechnology for the future of reproductive healthcare betterment as well as current achievements of nanoscience and nanotechnology in this arena. PMID:24600516

An emerging interface between life science and nanotechnology: present status and prospects of reproductive healthcare aided by nano-biotechnology.

PubMed

Jha, Rakhi K; Jha, Pradeep K; Chaudhury, Koel; Rana, Suresh V S; Guha, Sujoy K

2014-01-01

Among the various applications of nano-biotechnology, healthcare is considered one of the most significant domains. For that possibility to synthesize various kind of nanoparticles (NPs) and the ever-increasing ability to control their size as well as structure, to improve surface characteristics and binding NPs with other desired curing agents has played an important role. In this paper, a brief sketch of various kinds of nanomaterials and their biomedical applications is given. Despite claims of bio-nanotechnology about to touch all areas of medical science, information pertaining to the role of nanotechnology for the betterment of reproductive healthcare is indeed limited. Therefore, the various achievements of nano-biotechnology for healthcare in general have been illustrated while giving special insight into the role of nano-biotechnology for the future of reproductive healthcare betterment as well as current achievements of nanoscience and nanotechnology in this arena.

[Biotechnology's macroeconomic impact].

PubMed

Dones Tacero, Milagros; Pérez García, Julián; San Román, Antonio Pulido

2008-12-01

This paper tries to yield an economic valuation of biotechnological activities in terms of aggregated production and employment. This valuation goes beyond direct estimation and includes the indirect effects derived from sectorial linkages between biotechnological activities and the rest of economic system. To deal with the proposed target several sources of data have been used, including official data from National Statistical Office (INE) such us national accounts, input-output tables, and innovation surveys, as well as, firms' level balance sheets and income statements and also specific information about research projects compiled by Genoma Spain Foundation. Methodological approach is based on the estimation of a new input-output table which includes the biotechnological activities as a specific branch. This table offers both the direct impact of these activities and the main parameters to obtain the induced effects over the rest of the economic system. According to the most updated available figures, biotechnological activities would have directly generated almost 1,600 millions of euros in 2005, and they would be employed more than 9,000 workers. But if we take into account the full linkages with the rest of the system, the macroeconomic impact of Biotechnological activities would reach around 5,000 millions euros in production terms (0.6% of total GDP) and would be responsible, directly or indirectly, of more than 44,000 employments.

Epistemic Beliefs and Conceptual Understanding in Biotechnology: A Case Study

NASA Astrophysics Data System (ADS)

Rebello, Carina M.; Siegel, Marcelle A.; Witzig, Stephen B.; Freyermuth, Sharyn K.; McClure, Bruce A.

2012-04-01

The purpose of this investigation was to explore students' epistemic beliefs and conceptual understanding of biotechnology. Epistemic beliefs can influence reasoning, how individuals evaluate information, and informed decision making abilities. These skills are important for an informed citizenry that will participate in debates regarding areas in science such as biotechnology. We report on an in-depth case study analysis of three undergraduate, non-science majors in a biotechnology course designed for non-biochemistry majors. We selected participants who performed above average and below average on the first in-class exam. Data from multiple sources—interviews, exams, and a concept instrument—were used to construct (a) individual profiles and (b) a cross-case analysis of our participants' conceptual development and epistemic beliefs from two different theoretical perspectives—Women's Ways of Knowing and the Reflective Judgment Model. Two independent trained researchers coded all case records independently for both theoretical perspectives, with resultant initial Cohen's kappa values above .715 (substantial agreement), and then reached consensus on the codes. Results indicate that a student with more sophisticated epistemology demonstrated greater conceptual understandings at the end of the course than a student with less sophisticated epistemology, even though the latter performed higher initially. Also a student with a less sophisticated epistemology and low initial conceptual performance does not demonstrate gains in their overall conceptual understanding. Results suggest the need for instructional interventions fostering epistemological development of learners in order to facilitate their conceptual growth.

7 CFR 372.3 - Information and assistance.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 5 2012-01-01 2012-01-01 false Information and assistance. 372.3 Section 372.3... Information and assistance. Information, including the status of studies, and the availability of reference..., will be made available upon request to Environmental Analysis and Documentation, Biotechnology...

Ocular gene transfer in the spotlight: implications of newspaper content for clinical communications

PubMed Central

2014-01-01

Background Ocular gene transfer clinical trials are raising hopes for blindness treatments and attracting media attention. News media provide an accessible health information source for patients and the public, but are often criticized for overemphasizing benefits and underplaying risks of novel biomedical interventions. Overly optimistic portrayals of unproven interventions may influence public and patient expectations; the latter may cause patients to downplay risks and over-emphasize benefits, with implications for informed consent for clinical trials. We analyze the news media communications landscape about ocular gene transfer and make recommendations for improving communications between clinicians and potential trial participants in light of media coverage. Methods We analyzed leading newspaper articles about ocular gene transfer (1990-2012) from United States (n = 55), Canada (n = 26), and United Kingdom (n = 77) from Factiva and Canadian Newsstand databases using pre-defined coding categories. We evaluated the content of newspaper articles about ocular gene transfer for hereditary retinopathies, exploring representations of framing techniques, research design, risks/benefits, and translational timelines. Results The dominant frame in 61% of stories was a celebration of progress, followed by human-interest in 30% of stories. Missing from the positive frames were explanations of research design; articles conflated clinical research with treatment. Conflicts-of-interest and funding sources were similarly omitted. Attention was directed to the benefits of gene transfer, while risks were only reported in 43% of articles. A range of visual outcomes was described from slowing vision loss to cure, but the latter was the most frequently represented even though it is clinically infeasible. Despite the prominence of visual benefit portrayals, 87% of the articles failed to provide timelines for the commencement of clinical trials or for clinical implementation. Conclusions Our analysis confirms that despite many initiatives to improve media communications about experimental biotechnologies, media coverage remains overly optimistic and omits important information. In light of these findings, our recommendations focus on the need for clinicians account for media coverage in their communications with patients, especially in the context of clinical trial enrolment. The development of evidence-based communication strategies will facilitate informed consent and promote the ethical translation of this biotechnology. PMID:25027482

Ocular gene transfer in the spotlight: implications of newspaper content for clinical communications.

PubMed

Benjaminy, Shelly; Bubela, Tania

2014-07-16

Ocular gene transfer clinical trials are raising hopes for blindness treatments and attracting media attention. News media provide an accessible health information source for patients and the public, but are often criticized for overemphasizing benefits and underplaying risks of novel biomedical interventions. Overly optimistic portrayals of unproven interventions may influence public and patient expectations; the latter may cause patients to downplay risks and over-emphasize benefits, with implications for informed consent for clinical trials. We analyze the news media communications landscape about ocular gene transfer and make recommendations for improving communications between clinicians and potential trial participants in light of media coverage. We analyzed leading newspaper articles about ocular gene transfer (1990-2012) from United States (n = 55), Canada (n = 26), and United Kingdom (n = 77) from Factiva and Canadian Newsstand databases using pre-defined coding categories. We evaluated the content of newspaper articles about ocular gene transfer for hereditary retinopathies, exploring representations of framing techniques, research design, risks/benefits, and translational timelines. The dominant frame in 61% of stories was a celebration of progress, followed by human-interest in 30% of stories. Missing from the positive frames were explanations of research design; articles conflated clinical research with treatment. Conflicts-of-interest and funding sources were similarly omitted. Attention was directed to the benefits of gene transfer, while risks were only reported in 43% of articles. A range of visual outcomes was described from slowing vision loss to cure, but the latter was the most frequently represented even though it is clinically infeasible. Despite the prominence of visual benefit portrayals, 87% of the articles failed to provide timelines for the commencement of clinical trials or for clinical implementation. Our analysis confirms that despite many initiatives to improve media communications about experimental biotechnologies, media coverage remains overly optimistic and omits important information. In light of these findings, our recommendations focus on the need for clinicians account for media coverage in their communications with patients, especially in the context of clinical trial enrolment. The development of evidence-based communication strategies will facilitate informed consent and promote the ethical translation of this biotechnology.

Draft Genome Sequence of Leptolyngbya sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes

PubMed Central

Kim, Ji Hyung

2016-01-01

Here, we report the draft genome of cyanobacterium Leptolyngbya sp. KIOST-1 isolated from a microalgal culture pond in South Korea. The genome consists of 13 contigs containing 6,320,172 bp, and a total of 5,327 coding sequences were predicted. This genomic information will allow further exploitation of its biotechnological potential for alimentary purposes. PMID:27635005

[Current estate of biotechnology in Costa Rica].

PubMed

Valdez, Marta; López, Rebeca; Jiménez, Luis

2004-09-01

A study was carried out on the construction of indicators in biotechnology in Costa Rica as part of the project "SYMBIOSIS, Cooperative Program for the Construction of Indicators in Biotechnology adapted to Latin American and Caribbean countries, to motivate the application and transference of industrial technologies". The study focused on two units: researchers and research projects developed in Costa Rica, between 1998 and 2002. For researchers, information was collected about indicators related to sex, age, teaching activities, number of projects, academic degree, area of speciality and number of publications. For research projects we obtained information about: speciality, sector of application, duration of projects and number of researchers per project. Very interesting results include the high participation of the women in this area of investigation (54%); the low participation of young researchers (13% younger than 30), and a high proportion of the investigators that are responsible for 4 or more projects (42%). With relation to the specialities of the projects, the majority are in the category Bio-Agro (39%) whereas in Acuaculture only 1% was found. The sectors of application with the most number of projects are: Agriculture and Livestock (37%) and Human Health (35%). The main strengthts and limitatations for the development of biotechnology in Costa Rica are discussed.

Harnessing genomics to improve health in the Eastern Mediterranean Region – an executive course in genomics policy

PubMed Central

Acharya, Tara; Rab, Mohammed Abdur; Singer, Peter A; Daar, Abdallah S

2005-01-01

Background While innovations in medicine, science and technology have resulted in improved health and quality of life for many people, the benefits of modern medicine continue to elude millions of people in many parts of the world. To assess the potential of genomics to address health needs in EMR, the World Health Organization's Eastern Mediterranean Regional Office and the University of Toronto Joint Centre for Bioethics jointly organized a Genomics and Public Health Policy Executive Course, held September 20th–23rd, 2003, in Muscat, Oman. The 4-day course was sponsored by WHO-EMRO with additional support from the Canadian Program in Genomics and Global Health. The overall objective of the course was to collectively explore how to best harness genomics to improve health in the region. This article presents the course findings and recommendations for genomics policy in EMR. Methods The course brought together senior representatives from academia, biotechnology companies, regulatory bodies, media, voluntary, and legal organizations to engage in discussion. Topics covered included scientific advances in genomics, followed by innovations in business models, public sector perspectives, ethics, legal issues and national innovation systems. Results A set of recommendations, summarized below, was formulated for the Regional Office, the Member States and for individuals. • Advocacy for genomics and biotechnology for political leadership; • Networking between member states to share information, expertise, training, and regional cooperation in biotechnology; coordination of national surveys for assessment of health biotechnology innovation systems, science capacity, government policies, legislation and regulations, intellectual property policies, private sector activity; • Creation in each member country of an effective National Body on genomics, biotechnology and health to: - formulate national biotechnology strategies - raise biotechnology awareness - encourage teaching and training of biotechnology - devise integration of biotechnology within national health systems. Conclusion The recommendations provide the basis for a road map for EMR to take steps to harness biotechnology for better and more equitable health. As a result of these recommendations, health ministers from the region, at the 50th Regional Committee Meeting held in October 2003, have urged Member States to establish national bodies of biotechnology to formulate a strategic vision for developing biotechnology in the service of the region's health. These efforts promise to raise the profile of genomics in EMR and increase regional cooperation in this exciting new field. PMID:15663786

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards

PubMed Central

2015-01-01

Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for “Reporting” and “Serving” data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7th Framework Programme “Ocean of Tomorrow”, and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science. PMID:26203332

Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T.

PubMed

Diken, Elif; Ozer, Tugba; Arikan, Muzaffer; Emrence, Zeliha; Oner, Ebru Toksoy; Ustek, Duran; Arga, Kazim Yalcin

2015-01-01

Halomonas smyrnensis AAD6T is a gram negative, aerobic, and moderately halophilic bacterium, and is known to produce high levels of levan with many potential uses in foods, feeds, cosmetics, pharmaceutical and chemical industries due to its outstanding properties. Here, the whole-genome analysis was performed to gain more insight about the biological mechanisms, and the whole-genome organization of the bacterium. Industrially crucial genes, including the levansucrase, were detected and the genome-scale metabolic model of H. smyrnensis AAD6T was reconstructed. The bacterium was found to have many potential applications in biotechnology not only being a levan producer, but also because of its capacity to produce Pel exopolysaccharide, polyhydroxyalkanoates, and osmoprotectants. The genomic information presented here will not only provide additional information to enhance our understanding of the genetic and metabolic network of halophilic bacteria, but also accelerate the research on systematical design of engineering strategies for biotechnology applications.

SIDECACHE: Information access, management and dissemination framework for web services.

PubMed

Doderer, Mark S; Burkhardt, Cory; Robbins, Kay A

2011-06-14

Many bioinformatics algorithms and data sets are deployed using web services so that the results can be explored via the Internet and easily integrated into other tools and services. These services often include data from other sites that is accessed either dynamically or through file downloads. Developers of these services face several problems because of the dynamic nature of the information from the upstream services. Many publicly available repositories of bioinformatics data frequently update their information. When such an update occurs, the developers of the downstream service may also need to update. For file downloads, this process is typically performed manually followed by web service restart. Requests for information obtained by dynamic access of upstream sources is sometimes subject to rate restrictions. SideCache provides a framework for deploying web services that integrate information extracted from other databases and from web sources that are periodically updated. This situation occurs frequently in biotechnology where new information is being continuously generated and the latest information is important. SideCache provides several types of services including proxy access and rate control, local caching, and automatic web service updating. We have used the SideCache framework to automate the deployment and updating of a number of bioinformatics web services and tools that extract information from remote primary sources such as NCBI, NCIBI, and Ensembl. The SideCache framework also has been used to share research results through the use of a SideCache derived web service.

Patents and patent office resources in biotechnology.

PubMed

Koniarek, J P; Coleman, K D

1988-02-01

Patents play an increasingly important role in the dissemination of information in many fast moving fields such as biotechnology and semiconductors. Quite a few new developments are introduced as patents, and only later, if at all, do they find their way into the scientific literature. In spite of this, patents lack wide acceptance as a source of information among scientists in academia and, to a lesser degree, industry. Patents share many similarities with scientific papers. They both are organized in a similar way and are carefully reviewed by experts in the field. Both can be effective and timely sources of information. Patents can be accessed through data bases, library collections, the "Official Gazette of the Patent and Trademark Office," or directly in the Patent and Trademark Office. This article is designed to serve as a guide to the type of information which can be found in patents, and alternatives for obtaining this information.

De novo assembly and transcriptomic profiling of the grazing response in Stipa grandis.

PubMed

Wan, Dongli; Wan, Yongqing; Hou, Xiangyang; Ren, Weibo; Ding, Yong; Sa, Rula

2015-01-01

Stipa grandis (Poaceae) is one of the dominant species in a typical steppe of the Inner Mongolian Plateau. However, primarily due to heavy grazing, the grasslands have become seriously degraded, and S. grandis has developed a special growth-inhibition phenotype against the stressful habitat. Because of the lack of transcriptomic and genomic information, the understanding of the molecular mechanisms underlying the grazing response of S. grandis has been prohibited. Using the Illumina HiSeq 2000 platform, two libraries prepared from non-grazing (FS) and overgrazing samples (OS) were sequenced. De novo assembly produced 94,674 unigenes, of which 65,047 unigenes had BLAST hits in the National Center for Biotechnology Information (NCBI) non-redundant (nr) database (E-value < 10-5). In total, 47,747, 26,156 and 40,842 unigenes were assigned to the Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. A total of 13,221 unigenes showed significant differences in expression under the overgrazing condition, with a threshold false discovery rate ≤ 0.001 and an absolute value of log2Ratio ≥ 1. These differentially expressed genes (DEGs) were assigned to 43,257 GO terms and were significantly enriched in 32 KEGG pathways (q-value ≤ 0.05). The alterations in the wound-, drought- and defense-related genes indicate that stressors have an additive effect on the growth inhibition of this species. This first large-scale transcriptome study will provide important information for further gene expression and functional genomics studies, and it facilitated our investigation of the molecular mechanisms of the S. grandis grazing response and the associated morphological and physiological characteristics.

De novo Assembly and Transcriptomic Profiling of the Grazing Response in Stipa grandis

PubMed Central

Hou, Xiangyang; Ren, Weibo; Ding, Yong; Sa, Rula

2015-01-01

Background Stipa grandis (Poaceae) is one of the dominant species in a typical steppe of the Inner Mongolian Plateau. However, primarily due to heavy grazing, the grasslands have become seriously degraded, and S. grandis has developed a special growth-inhibition phenotype against the stressful habitat. Because of the lack of transcriptomic and genomic information, the understanding of the molecular mechanisms underlying the grazing response of S. grandis has been prohibited. Results Using the Illumina HiSeq 2000 platform, two libraries prepared from non-grazing (FS) and overgrazing samples (OS) were sequenced. De novo assembly produced 94,674 unigenes, of which 65,047 unigenes had BLAST hits in the National Center for Biotechnology Information (NCBI) non-redundant (nr) database (E-value < 10-5). In total, 47,747, 26,156 and 40,842 unigenes were assigned to the Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. A total of 13,221 unigenes showed significant differences in expression under the overgrazing condition, with a threshold false discovery rate ≤ 0.001 and an absolute value of log2Ratio ≥ 1. These differentially expressed genes (DEGs) were assigned to 43,257 GO terms and were significantly enriched in 32 KEGG pathways (q-value ≤ 0.05). The alterations in the wound-, drought- and defense-related genes indicate that stressors have an additive effect on the growth inhibition of this species. Conclusions This first large-scale transcriptome study will provide important information for further gene expression and functional genomics studies, and it facilitated our investigation of the molecular mechanisms of the S. grandis grazing response and the associated morphological and physiological characteristics. PMID:25875617

Biotechnology and the developing world. Finding ways to bridge the agricultural technology gap.

PubMed

Platais, K W; Collinson, M P

1992-03-01

Biotechnology is a controversial subject that involves a range of scientific principles from basic tissue culture to genetic manipulation. Proponents include private sector capitalists, public sector researchers, and developing nation governments. Opponents include environmental organizations and social organizations involved in protecting the rights of developing nations. Biotechnology is being presented as the next step after the Green Revolution and the only way that the people of the developing world will be able to feed themselves in the next half century. Research by industrialized nations world wide total an estimated $11 billion with 66% being contributed by the private sector. Biotechnology represents somewhat of a dilemma. Since the majority of the work is being done by the private sector the interests of shareholders and profit are greater done by the private sector the interests of shareholders and profit are greater than that of public welfare or safety. The Consultative Group on International Agricultural Research (CGIAR) is one public sector group that is concerned about this problem. The countries of the developing world fall into 2 categories in relation to use of biotechnology: (1) those that have the potential to adapt imported biotechnologies to local conditions; (2) those that have little or no applied research capacity to effectively use biotechnologies. Currently only Brazil, China, India, and Thailand belong in the 1st category, all other developing countries fall into the 2nd. CGIAR believes it can help in 2 ways: (1) it can provide a bridge for needed information and germplasm between developed and developing countries; (2) it can help to ensure that the agricultural needs of developing countries are not lost. In 1990 CGIAR's plant and animal biotechnology research totaled $14.5 million which was less than 5% of the total CGIAR budget. Networking and institutions building are areas that CGIAR focuses on in an attempt to increase its affect. Looking ahead the 2 major issue of biotechnology that still have to be worked out are biosafety and intellectual property management.

INTEGRATED TAXONOMIC INFORMATION SYSTEM (ITIS) - BACILLARIOPHYTA

EPA Science Inventory

Access to consistent, scientifically credible taxomonic information is essential to many governmental activities. These activities include natural resource management for sustained use, land owner assistance, environmental regulation, and biotechnology development. As part of the...

Getting the most out of parasitic helminth transcriptomes using HelmDB: implications for biology and biotechnology.

PubMed

Mangiola, Stefano; Young, Neil D; Korhonen, Pasi; Mondal, Alinda; Scheerlinck, Jean-Pierre; Sternberg, Paul W; Cantacessi, Cinzia; Hall, Ross S; Jex, Aaron R; Gasser, Robin B

2013-12-01

Compounded by a massive global food shortage, many parasitic diseases have a devastating, long-term impact on animal and human health and welfare worldwide. Parasitic helminths (worms) affect the health of billions of animals. Unlocking the systems biology of these neglected pathogens will underpin the design of new and improved interventions against them. Currently, the functional annotation of genomic and transcriptomic sequence data for socio-economically important parasitic worms relies almost exclusively on comparative bioinformatic analyses using model organism- and other databases. However, many genes and gene products of parasitic helminths (often >50%) cannot be annotated using this approach, because they are specific to parasites and/or do not have identifiable homologs in other organisms for which sequence data are available. This inability to fully annotate transcriptomes and predicted proteomes is a major challenge and constrains our understanding of the biology of parasites, interactions with their hosts and of parasitism and the pathogenesis of disease on a molecular level. In the present article, we compiled transcriptomic data sets of key, socioeconomically important parasitic helminths, and constructed and validated a curated database, called HelmDB (www.helmdb.org). We demonstrate how this database can be used effectively for the improvement of functional annotation by employing data integration and clustering. Importantly, HelmDB provides a practical and user-friendly toolkit for sequence browsing and comparative analyses among divergent helminth groups (including nematodes and trematodes), and should be readily adaptable and applicable to a wide range of other organisms. This web-based, integrative database should assist 'systems biology' studies of parasitic helminths, and the discovery and prioritization of novel drug and vaccine targets. This focus provides a pathway toward developing new and improved approaches for the treatment and control of parasitic diseases, with the potential for important biotechnological outcomes. Copyright © 2012 Elsevier Inc. All rights reserved.

Draft Genome Sequence of Leptolyngbya sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes.

PubMed

Kim, Ji Hyung; Kang, Do-Hyung

2016-09-15

Here, we report the draft genome of cyanobacterium Leptolyngbya sp. KIOST-1 isolated from a microalgal culture pond in South Korea. The genome consists of 13 contigs containing 6,320,172 bp, and a total of 5,327 coding sequences were predicted. This genomic information will allow further exploitation of its biotechnological potential for alimentary purposes. Copyright © 2016 Kim and Kang.

Transgenic barley: a prospective tool for biotechnology and agriculture.

PubMed

Mrízová, Katarína; Holasková, Edita; Öz, M Tufan; Jiskrová, Eva; Frébort, Ivo; Galuszka, Petr

2014-01-01

Barley (Hordeum vulgare L.) is one of the founder crops of agriculture, and today it is the fourth most important cereal grain worldwide. Barley is used as malt in brewing and distilling industry, as an additive for animal feed, and as a component of various food and bread for human consumption. Progress in stable genetic transformation of barley ensures a potential for improvement of its agronomic performance or use of barley in various biotechnological and industrial applications. Recently, barley grain has been successfully used in molecular farming as a promising bioreactor adapted for production of human therapeutic proteins or animal vaccines. In addition to development of reliable transformation technologies, an extensive amount of various barley genetic resources and tools such as sequence data, microarrays, genetic maps, and databases has been generated. Current status on barley transformation technologies including gene transfer techniques, targets, and progeny stabilization, recent trials for improvement of agricultural traits and performance of barley, especially in relation to increased biotic and abiotic stress tolerance, and potential use of barley grain as a protein production platform have been reviewed in this study. Overall, barley represents a promising tool for both agricultural and biotechnological transgenic approaches, and is considered an ancient but rediscovered crop as a model industrial platform for molecular farming. © 2013 Elsevier Inc. All rights reserved.

Advanced health biotechnologies in Thailand: redefining policy directions.

PubMed

Velasco, Román Pérez; Chaikledkaew, Usa; Myint, Chaw Yin; Khampang, Roongnapa; Tantivess, Sripen; Teerawattananon, Yot

2013-01-02

Thailand faces a significant burden in terms of treating and managing degenerative and chronic diseases. Moreover, incidences of rare diseases are rising. Many of these-such as diabetes, cancer, and inherited inborn metabolic diseases-have no definite treatments or cure. Meanwhile, advanced health biotechnology has been found, in principle, to be an effective solution for these health problems. Qualitative approaches were employed to analyse the current situation and examine existing public policies related to advanced health biotechnologies in Thailand. The results of this analysis were then used to formulate policy recommendations. Our research revealed that the system in Thailand in relation to advanced health biotechnologies is fragmented, with multiple unaddressed gaps, underfunding of research and development (R&D), and a lack of incentives for the private sector. In addition, there are no clear definitions of advanced health biotechnologies, and coverage pathways are absent. Meanwhile, false advertising and misinformation are prevalent, with no responsible bodies to actively and effectively provide appropriate information and education (I&E). The establishment of a specialised institution to fill the gaps in this area is warranted. The development and implementation of a comprehensive national strategic plan related to advanced health biotechnologies, greater investment in R&D and I&E for all stakeholders, collaboration among agencies, harmonisation of reimbursement across public health schemes, and provision of targeted I&E are specifically recommended.

Indian Biotech Bazaar: a swot analysis.

PubMed

Kumar, Abhishek

2007-05-01

Biotechnology is a life science-based technique especially used in agriculture, medicine and food sciences. It is generally defined as the manipulation in organisms to generate products for the welfare of the world. Biotechnology combines disciplines such as genetics, biochemistry, microbiology, and cell biology along with information technology, chemical engineering, robotics etc. It includes basic industries such as food processing, tissue culture, plant development and other sophisticated ones such as recombinant therapeutics and diagnostics. Biotechnology, globally recognized as a rapidly emerging and far-reaching technology, is aptly described as the "technology of hope" for its promise of food, health and environmental sustainability. In India, biotechnology employs more than 10 000 people and generates roughly US$ 500 million in revenue annually. The biotechnology market has increased its sales from Rs. 50 billion in 1997 to Rs.70 billion in 2000, and is expected to cross Rs. 240 billion by the year 2010. In India, the human health biotech products account for 60% of the total market; agribiotech and veterinary 25%, medical devices, contract research and development (R&D), reagents and supplies constitute the remaining 15% Moreover, to facilitate foreign investment, capital and government policies are being revised. Other important industries include industrial enzyme manufacture, bioinformatics, and medical devices. Biotechnology has had limited appeal so far on our capital markets, and we have less then a dozen biotech companies listed on the public markets.

Advanced health biotechnologies in Thailand: redefining policy directions

PubMed Central

2013-01-01

Background Thailand faces a significant burden in terms of treating and managing degenerative and chronic diseases. Moreover, incidences of rare diseases are rising. Many of these—such as diabetes, cancer, and inherited inborn metabolic diseases—have no definite treatments or cure. Meanwhile, advanced health biotechnology has been found, in principle, to be an effective solution for these health problems. Methods Qualitative approaches were employed to analyse the current situation and examine existing public policies related to advanced health biotechnologies in Thailand. The results of this analysis were then used to formulate policy recommendations. Results Our research revealed that the system in Thailand in relation to advanced health biotechnologies is fragmented, with multiple unaddressed gaps, underfunding of research and development (R&D), and a lack of incentives for the private sector. In addition, there are no clear definitions of advanced health biotechnologies, and coverage pathways are absent. Meanwhile, false advertising and misinformation are prevalent, with no responsible bodies to actively and effectively provide appropriate information and education (I&E). The establishment of a specialised institution to fill the gaps in this area is warranted. Conclusion The development and implementation of a comprehensive national strategic plan related to advanced health biotechnologies, greater investment in R&D and I&E for all stakeholders, collaboration among agencies, harmonisation of reimbursement across public health schemes, and provision of targeted I&E are specifically recommended. PMID:23281771

The first GCC Marine Biotechnology Symposium: Emerging Opportunities and Future Perspectives.

PubMed

Goddard, Stephen; Delghandi, Madjid; Dobretsov, Sergey; Al-Oufi, Hamed; Al-Habsi, Saoud; Burgess, J Grant

2015-06-01

With its diverse, living marine resources and rapidly growing educational and research infrastructure, the Sultanate of Oman is well-positioned to take advantage of the commercial opportunities presented by marine biotechnology. In recognition of potential development, an international symposium, Marine Biotechnology-Emerging Opportunities and Future Perspectives, was held in Muscat, November 12-13, 2013. Three keynote addresses were given, 23 oral presentations made, and a poster exhibition held. The final session reviewed national and regional issues, and the delegates agreed informally on a number of future actions. The potential for future development of marine biotechnology was recognized by all delegates, and following the symposium, they were surveyed for their views on how best to sustain and develop new activities. One hundred percent of respondents found the meeting useful and would support future symposia in the region. Fifty-one percent of Omani respondents recognized major organizational challenges and obstacles to the development of marine biotechnology compared with 23 % of overseas respondents. The need for greater collaboration between research institutions within the GCC region was recognized by 98 % of all respondents. The presentations and survey outcomes are reviewed in this paper.

Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications.

PubMed

Martin, Marjolaine; Portetelle, Daniel; Michel, Gurvan; Vandenbol, Micheline

2014-04-01

Marine microorganisms play key roles in every marine ecological process, hence the growing interest in studying their populations and functions. Microbial communities on algae remain underexplored, however, despite their huge biodiversity and the fact that they differ markedly from those living freely in seawater. The study of this microbiota and of its relationships with algal hosts should provide crucial information for ecological investigations on algae and aquatic ecosystems. Furthermore, because these microorganisms interact with algae in multiple, complex ways, they constitute an interesting source of novel bioactive compounds with biotechnological potential, such as dehalogenases, antimicrobials, and alga-specific polysaccharidases (e.g., agarases, carrageenases, and alginate lyases). Here, to demonstrate the huge potential of alga-associated organisms and their metabolites in developing future biotechnological applications, we first describe the immense diversity and density of these microbial biofilms. We further describe their complex interactions with algae, leading to the production of specific bioactive compounds and hydrolytic enzymes of biotechnological interest. We end with a glance at their potential use in medical and industrial applications.

Geothermal Program Review XI: proceedings. Geothermal Energy - The Environmental Responsible Energy Technology for the Nineties

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

Not Available

1993-10-01

These proceedings contain papers pertaining to current research and development of geothermal energy in the USA. The seven sections of the document are: Overview, The Geysers, Exploration and Reservoir Characterization, Drilling, Energy Conversion, Advanced Systems, and Potpourri. The Overview presents current DOE energy policy and industry perspectives. Reservoir studies, injection, and seismic monitoring are reported for the geysers geothermal field. Aspects of geology, geochemistry and models of geothermal exploration are described. The Drilling section contains information on lost circulation, memory logging tools, and slim-hole drilling. Topics considered in energy conversion are efforts at NREL, condensation on turbines and geothermal materials.more » Advanced Systems include hot dry rock studies and Fenton Hill flow testing. The Potpourri section concludes the proceedings with reports on low-temperature resources, market analysis, brines, waste treatment biotechnology, and Bonneville Power Administration activities. Selected papers have been indexed separately for inclusion in the Energy Science and Technology Database.« less

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.

PubMed

Deck, John; Gaither, Michelle R; Ewing, Rodney; Bird, Christopher E; Davies, Neil; Meyer, Christopher; Riginos, Cynthia; Toonen, Robert J; Crandall, Eric D

2017-08-01

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.

A composite molecular phylogeny of living lemuroid primates.

PubMed

DelPero, Massimiliano; Pozzi, Luca; Masters, Judith C

2006-01-01

Lemuroid phylogeny is a source of lively debate among primatologists. Reconstructions based on morphological, physiological, behavioural and molecular data have yielded a diverse array of tree topologies with few nodes in common. In the last decade, molecular phylogenetic studies have grown in popularity, and a wide range of sequences has been brought to bear on the problem, but consensus has remained elusive. We present an analysis based on a composite molecular data set of approx. 6,400 bp assembled from the National Center for Biotechnology Information (NCBI) database, including both mitochondrial and nuclear genes, and diverse analytical methods. Our analysis consolidates some of the nodes that were insecure in previous reconstructions, but is still equivocal on the placement of some taxa. We conducted a similar analysis of a composite data set of approx. 3,600 bp to investigate the controversial relationships within the family Lemuridae. Here our analysis was more successful; only the position of Eulemur coronatus remained uncertain. Copyright 2006 S. Karger AG, Basel.

Finding similar nucleotide sequences using network BLAST searches.

PubMed

Ladunga, Istvan

2009-06-01

The Basic Local Alignment Search Tool (BLAST) is a keystone of bioinformatics due to its performance and user-friendliness. Beginner and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNA, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez, PUBMED, structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge.

Flexitarian Diets and Health: A Review of the Evidence-Based Literature

PubMed Central

Derbyshire, Emma J.

2017-01-01

A flexitarian or semi-vegetarian diet (SVD) is one that is primarily vegetarian with the occasional inclusion of meat or fish. Of late, there appears to be an increasing movement toward this practice. There has not been a recent update on these diets from a health perspective. Using the National Centre for Biotechnology Information PubMed database, a search was made for all studies published between 2000 and 2016 that met defined inclusion criteria. A total of 25 studies were located with 12 focusing on body weight and diet quality. There was emerging evidence suggestive of benefits for body weight, improved markers of metabolic health, blood pressure, and reduced risk of type 2 diabetes. SVD may also have a role to play in the treatment of inflammatory bowel diseases, such as Crohn’s disease. Given that there is a higher tendency for females to be flexitarian yet males are more likely to overconsume meat, there is a clear need to communicate the potential health benefits of these diets to males. PMID:28111625

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

PubMed

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

2016-04-01

Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g. genes, compounds, pathways-that lead to interesting correlations. Normally, they must refer to additional public databases in order to enrich the information about the identified entities-e.g. scientific literature, published clinical trial results, etc. While semantic integration techniques have traditionally focused on providing homogeneous access to private datasets-thus helping automate the first part of the research, and there exist different solutions for browsing public data, there is still a need for tools that facilitate merging public repositories with private datasets. This paper presents a framework that automatically locates public data of interest to the researcher and semantically integrates it with existing private datasets. The framework has been designed as an extension of traditional data integration systems, and has been validated with an existing data integration platform from a European research project by integrating a private biological dataset with data from the National Center for Biotechnology Information (NCBI). Copyright © 2016 Elsevier Inc. All rights reserved.

Workflow and web application for annotating NCBI BioProject transcriptome data.

PubMed

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A; Barrero, Luz S; Landsman, David; Mariño-Ramírez, Leonardo

2017-01-01

The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. URL: http://www.ncbi.nlm.nih.gov/projects/physalis/. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Biotechnology regulation: is policy transfer an appropriate answer?

PubMed

Cárdenas-Gómez, Olga Carolina; Létourneau, Lyne

2010-01-01

In the world of biotechnology regulation, one often encounters the suggestion that the legislation of other countries should be consulted. Known as "policy transfer" in the field of public policy analysis, the purpose of such a recommendation is for policymakers to use the experiences of other States as a basis for developing appropriate regulatory frameworks in a timely manner. This paper examines whether policy transfer is relevant as an instrument for biotechnology regulation, and if it is, to what extent. Our analysis uses the example of Assisted Reproductive Technologies (ART), and unfolds according to the following argumentative steps. We will begin by discussing policy transfer as a recognized feature of policymaking in the literature pertaining to public policy analysis. We will then introduce a distinction between the technical dimension of policymaking and its political component. We will refer to "morality policy" as an illustration of policymaking directed toward its political component. We will show that, in the case of morality policy, States have moved away from a policy transfer approach. We will then establish that ART qualifies as morality policy, suggesting that policy transfer is most likely not the optimal policymaking tool for dealing with biotechnology regulation. Moving beyond the issue of ART in order to expand our reasoning to biotechnology regulation as a whole, we will conclude that, although the experiences of other States may be useful, policy transfer does not suffice in terms of informing policymaking in the case of biotechnology advances.

GGDonto ontology as a knowledge-base for genetic diseases and disorders of glycan metabolism and their causative genes.

PubMed

Solovieva, Elena; Shikanai, Toshihide; Fujita, Noriaki; Narimatsu, Hisashi

2018-04-18

Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides information about these diseases and disorders as well as their causative genes, has been developed by the Research Center for Medical Glycoscience (RCMG) and released in April 2010. GDGDB currently provides information on about 80 genetic diseases and disorders caused by single-gene mutations in glyco-related genes. Many biomedical resources provide information about genetic disorders and genes involved in their pathogenesis, but resources focused on genetic disorders known to be related to glycan metabolism are lacking. With the aim of providing more comprehensive knowledge on genetic diseases and disorders of glycan biosynthesis and degradation, we enriched the content of the GDGDB database and improved the methods for data representation. We developed the Genetic Glyco-Diseases Ontology (GGDonto) and a RDF/SPARQL-based user interface using Semantic Web technologies. In particular, we represented the GGDonto content using Semantic Web languages, such as RDF, RDFS, SKOS, and OWL, and created an interactive user interface based on SPARQL queries. This user interface provides features to browse the hierarchy of the ontology, view detailed information on diseases and related genes, and find relevant background information. Moreover, it provides the ability to filter and search information by faceted and keyword searches. Focused on the molecular etiology, pathogenesis, and clinical manifestations of genetic diseases and disorders of glycan metabolism and developed as a knowledge-base for this scientific field, GGDonto provides comprehensive information on various topics, including links to aid the integration with other scientific resources. The availability and accessibility of this knowledge will help users better understand how genetic defects impact the metabolism of glycans as well as how this impaired metabolism affects various biological functions and human health. In this way, GGDonto will be useful in fields related to glycoscience, including cell biology, biotechnology, and biomedical, and pharmaceutical research.

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.

PubMed

Putman, Tim E; Burgstaller-Muehlbacher, Sebastian; Waagmeester, Andra; Wu, Chunlei; Su, Andrew I; Good, Benjamin M

2016-01-01

The last 20 years of advancement in sequencing technologies have led to sequencing thousands of microbial genomes, creating mountains of genetic data. While efficiency in generating the data improves almost daily, applying meaningful relationships between taxonomic and genetic entities on this scale requires a structured and integrative approach. Currently, knowledge is distributed across a fragmented landscape of resources from government-funded institutions such as National Center for Biotechnology Information (NCBI) and UniProt to topic-focused databases like the ODB3 database of prokaryotic operons, to the supplemental table of a primary publication. A major drawback to large scale, expert-curated databases is the expense of maintaining and extending them over time. No entity apart from a major institution with stable long-term funding can consider this, and their scope is limited considering the magnitude of microbial data being generated daily. Wikidata is an openly editable, semantic web compatible framework for knowledge representation. It is a project of the Wikimedia Foundation and offers knowledge integration capabilities ideally suited to the challenge of representing the exploding body of information about microbial genomics. We are developing a microbial specific data model, based on Wikidata's semantic web compatibility, which represents bacterial species, strains and the gene and gene products that define them. Currently, we have loaded 43,694 gene and 37,966 protein items for 21 species of bacteria, including the human pathogenic bacteriaChlamydia trachomatis.Using this pathogen as an example, we explore complex interactions between the pathogen, its host, associated genes, other microbes, disease and drugs using the Wikidata SPARQL endpoint. In our next phase of development, we will add another 99 bacterial genomes and their gene and gene products, totaling ∼900,000 additional entities. This aggregation of knowledge will be a platform for community-driven collaboration, allowing the networking of microbial genetic data through the sharing of knowledge by both the data and domain expert. © The Author(s) 2016. Published by Oxford University Press.

Position of the American Dietetic Association: Agricultural and food biotechnology.

PubMed

Bruhn, Christine; Earl, Robert

2006-02-01

It is the position of the American Dietetic Association that agricultural and food biotechnology techniques can enhance the quality, safety, nutritional value, and variety of food available for human consumption and increase the efficiency of food production, food processing, food distribution, and environmental and waste management. The American Dietetic Association encourages the government, food manufacturers, food commodity groups, and qualified food and nutrition professionals to work together to inform consumers about this new technology and encourage the availability of these products in the marketplace.

Software for rapid prototyping in the pharmaceutical and biotechnology industries.

PubMed

Kappler, Michael A

2008-05-01

The automation of drug discovery methods continues to develop, especially techniques that process information, represent workflow and facilitate decision-making. The magnitude of data and the plethora of questions in pharmaceutical and biotechnology research give rise to the need for rapid prototyping software. This review describes the advantages and disadvantages of three solutions: Competitive Workflow, Taverna and Pipeline Pilot. Each of these systems processes large amounts of data, integrates diverse systems and assists novice programmers and human experts in critical decision-making steps.

Young people's awareness on biobanking and DNA profiling: results of a questionnaire administered to Italian university students.

PubMed

Tozzo, Pamela; Fassina, Antonio; Caenazzo, Luciana

2017-12-01

Current policy approaches to social and ethical issues surrounding biobanks manifest lack of public information given by researchers and government, despite the evidence that Italian citizens are well informed about technical and other public perspectives of biotechnologies. For this reason, the focus of our survey was to interview our University's students on these aspects. The sample consisted of Padua University students (N = 959), who were administered a questionnaire comprising eight questions covering their knowledge about biobanks, their perception of the related benefits and risks, their willingness to donate samples to a biobank for research purposes, their attitude to having their own DNA profile included in a forensic DNA database, and the reasons behind their answers. The vast majority of the students invited to take part in the survey completed the questionnaire, and the number of participants sufficed to be considered representative of the target population. Despite the respondents' unfamiliarity with the topics explored, suggested by the huge group of respondents answering "I don't know" to the questions regarding Itaian regulation and reality, their answers demonstrate a general agreement to participate in a biobanking scheme for research purposes, as expressed by the 91% of respondents who were reportedly willing to donate their samples. As for the idea of a forensic DNA database, 35% of respondents said they would agree to having their profile included in such a database, even if they were not fully aware of the benefits and risks of such action.This study shows that Italian people with a higher education take a generally positive attitude to the idea of donating biological samples. It contributes to empirical evidence of what Italy's citizens understand about biobanking, and of their willingness to donate samples for research purposes, and also to have their genetic profiles included in a national forensic DNA database. Our findings may have clear implications for the policy discussion on biobanks in Italy, in particular it is important to take into account the Italian population's poor consciousness of forensic DNA database, in order to ensure a better interaction between policy makers and citizens and to make them more aware of the need to balance the individual's rights and the security of society.

Novel and transgenic food crops: overview of scientific versus public perception.

PubMed

Ruibal-Mendieta, N L; Lints, F A

1998-09-01

Recombinant DNA technology offers opportunities to develop new products in many different fields, including agriculture and the agro-food area. Transgenic plants with improved agronomic traits currently grow in field trials and a few varieties have already reached the European market. By and large, new technologies raise both concerns and expectations and modern biotechnology is no exception. Indeed, a voluntary moratorium on experiments involving recombinant DNA molecules was called for in 1974. At the present time, although a majority of academic and industrial scientists agree that transgenic food crops pose no risk for the environment or human health, some others believe that certain applications of modern plant biotechnology are hazardous. In particular, deliberate releases of genetically modified plants are regarded as risky. There is also a disparity between expert and lay perception of r-DNA technology applications to food crops, which makes public information a difficult task. This paper aims at exposing these conflicting points of view on the agricultural applications of modern biotechnology. We also propose some recommendations pertaining to public information in Europe. It appears that consensus conferences might be a good approach to stimulate public information and public debate in Europe, although this approach has to be adapted to the cultural context of each country.

The fifth international conference on microbial enhanced oil recovery and related biotechnology for solving environmental problems: 1995 Conference proceedings

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

Bryant, R.

1995-12-31

This volume contains 41 papers covering the following topics: field trials of microbial enhanced recovery of oil; control and treatment of sour crudes and natural gas with microorganisms; bioremediation of hydrocarbon contamination in soils; microbial plugging processes; microbial waste water treatment; the use of microorganisms as biological indicators of oils; and characterization and behavior of microbial systems. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

A metabolomics guided exploration of marine natural product chemical space.

PubMed

Floros, Dimitrios J; Jensen, Paul R; Dorrestein, Pieter C; Koyama, Nobuhiro

2016-09-01

Natural products from culture collections have enormous impact in advancing discovery programs for metabolites of biotechnological importance. These discovery efforts rely on the metabolomic characterization of strain collections. Many emerging approaches compare metabolomic profiles of such collections, but few enable the analysis and prioritization of thousands of samples from diverse organisms while delivering chemistry specific read outs. In this work we utilize untargeted LC-MS/MS based metabolomics together with molecular networking to. This approach annotated 76 molecular families (a spectral match rate of 28 %), including clinically and biotechnologically important molecules such as valinomycin, actinomycin D, and desferrioxamine E. Targeting a molecular family produced primarily by one microorganism led to the isolation and structure elucidation of two new molecules designated maridric acids A and B. Molecular networking guided exploration of large culture collections allows for rapid dereplication of know molecules and can highlight producers of uniques metabolites. These methods, together with large culture collections and growing databases, allow for data driven strain prioritization with a focus on novel chemistries.

Career Development: Revolution, Reform, and Renaissance.

ERIC Educational Resources Information Center

Patterson, John

1985-01-01

Discusses elements to be considered by career counselors, including robotics, fiber optics, biotechnology, space industry, transition from industry to information, expected labor shortage in the 1990s, population trends, and entrepreneurial explosion. Also describes four basic skills of the information society. (CT)

7 CFR 3415.13 - Availability of information.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 15 2010-01-01 2010-01-01 false Availability of information. 3415.13 Section 3415.13 Agriculture Regulations of the Department of Agriculture (Continued) COOPERATIVE STATE RESEARCH, EDUCATION, AND EXTENSION SERVICE, DEPARTMENT OF AGRICULTURE BIOTECHNOLOGY RISK ASSESSMENT RESEARCH GRANTS PROGRAM...

Workshop Summary for Maintaining Innovation and Security in Biotechnology: Lessons Learned from Nuclear, Chemical, and Informational Technologies

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

Althouse, Paris

In the fast-paced field of biotechnology where innovation has such far-reaching impacts on human health and the environment, dealing with the implications of possible illicit activities, accidents or unintended research consequences with potential detrimental societal impacts tends to remain in the background. While controls may be inevitable for the biotech industry, workshop attendees agreed that the way in which controls are implemented will play a major role in the agility and innovation of the biotechnology industry. There is little desire to slow down the pace of the gains while dealing with the security issues that arise. As was seen frommore » the brief examinations of the Nuclear, Chemical, and Information Technology sectors explored in this workshop, establishing a regulatory regime needs to be a partnership between the public, corporate interests, scientists, and the government. Regulation is often written to combat perceived risk rather than actual risk—the public’s perceptions (occasionally even fictional portrayals) can spur regulatory efforts. This leads to the need for a thorough and continuing assessment of the risks posed by modern biotechnology. Inadequate or minimal risk assessment might expedite development in the short term but has potential negative long-term security and economic consequences. Industry and the technical community also often have a large role in setting regulatory policy, especially when well-crafted incentives are incorporated into the regulations. Such incentives might actually lead to enhanced innovation while poorly designed incentives can actually reduce safety and security. Any regulations should be as agile and flexible as the technology they regulate and when applied to biotechnologies they will need a new framework for thinking and implementing. The new framework should consider biotechnology as a technology and not simply a science since it is an extremely complex and adaptive system. This suggests the need to invest in social and political systems, rather than exclusively in technology, as a part of maintaining not only robust, but agile regulation. Modeling and simulations to illustrate how the biotech ecosystem might respond to new policies may be a promising approach to crafting regulations.« less

Effectiveness of a cloning and sequencing exercise on student learning with subsequent publication in the National Center for Biotechnology Information GenBank.

PubMed

Lau, Joann M; Robinson, David L

2009-01-01

With rapid advances in biotechnology and molecular biology, instructors are challenged to not only provide undergraduate students with hands-on experiences in these disciplines but also to engage them in the "real-world" scientific process. Two common topics covered in biotechnology or molecular biology courses are gene-cloning and bioinformatics, but to provide students with a continuous laboratory-based research experience in these techniques is difficult. To meet these challenges, we have partnered with Bio-Rad Laboratories in the development of the "Cloning and Sequencing Explorer Series," which combines wet-lab experiences (e.g., DNA extraction, polymerase chain reaction, ligation, transformation, and restriction digestion) with bioinformatics analysis (e.g., evaluation of DNA sequence quality, sequence editing, Basic Local Alignment Search Tool searches, contig construction, intron identification, and six-frame translation) to produce a sequence publishable in the National Center for Biotechnology Information GenBank. This 6- to 8-wk project-based exercise focuses on a pivotal gene of glycolysis (glyceraldehyde-3-phosphate dehydrogenase), in which students isolate, sequence, and characterize the gene from a plant species or cultivar not yet published in GenBank. Student achievement was evaluated using pre-, mid-, and final-test assessments, as well as with a survey to assess student perceptions. Student confidence with basic laboratory techniques and knowledge of bioinformatics tools were significantly increased upon completion of this hands-on exercise.

Regulation of animal biotechnology: research needs.

PubMed

Rexroad, C E; Green, R D; Wall, R J

2007-09-01

Livestock that result from biotechnology have been a part of agricultural science for over 30 years but have not entered the market place as food or fiber. Two biotechnologies are at the forefront as challenges to the world's systems for regulating the market place: animal clones and transgenic animals. Both technologies have come before the Food and Drug Administration in the United States and it appears that action is imminent for clones. The FDA has asserted principles for evaluation of clones and asserts that "... remaining hazard(s) from cloning are likely to be subtle in nature." The science-based principles recognize that in some areas related to developmental biology and gene expression in clones, additional scientific information would be useful. The role of science then is to use the genomic tools that we have available to answer questions about epigenetic regulation of development and reprogramming of genes to the state found in germ cells. Transgenics pose additional challenges to regulators. If the transgenics are produced using cloning from modified cells then the additional scientific information needed will be related to the effects of insertion and expression of the transgenes. Other approaches such as retrovirally vectored transgenesis will elicit additional questions. These questions will be challenging because the science will have to be related to the expression and function of each gene or class of genes. For the promises of animal biotechnology to be fulfilled, scientists will have to resolve many questions for regulators and the public but tools to answer those questions are rapidly becoming available.

Discovering the Deregulated Molecular Functions Involved in Malignant Transformation of Endometriosis to Endometriosis-Associated Ovarian Carcinoma Using a Data-Driven, Function-Based Analysis

PubMed Central

Chang, Chia-Ming; Yang, Yi-Ping; Chuang, Jen-Hua; Chuang, Chi-Mu; Lin, Tzu-Wei; Wang, Peng-Hui; Yu, Mu-Hsien

2017-01-01

The clinical characteristics of clear cell carcinoma (CCC) and endometrioid carcinoma EC) are concomitant with endometriosis (ES), which leads to the postulation of malignant transformation of ES to endometriosis-associated ovarian carcinoma (EAOC). Different deregulated functional areas were proposed accounting for the pathogenesis of EAOC transformation, and there is still a lack of a data-driven analysis with the accumulated experimental data in publicly-available databases to incorporate the deregulated functions involved in the malignant transformation of EOAC. We used the microarray gene expression datasets of ES, CCC and EC downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) database. Then, we investigated the pathogenesis of EAOC by a data-driven, function-based analytic model with the quantified molecular functions defined by 1454 Gene Ontology (GO) term gene sets. This model converts the gene expression profiles to the functionome consisting of 1454 quantified GO functions, and then, the key functions involving the malignant transformation of EOAC can be extracted by a series of filters. Our results demonstrate that the deregulated oxidoreductase activity, metabolism, hormone activity, inflammatory response, innate immune response and cell-cell signaling play the key roles in the malignant transformation of EAOC. These results provide the evidence supporting the specific molecular pathways involved in the malignant transformation of EAOC. PMID:29113136

Genetic Testing: MedlinePlus Health Topic

MedlinePlus

... Disease Control and Prevention) Glossary (National Center for Biotechnology Information) Talking Glossary of Genetic Terms (National Human Genome Research Institute) Also in Spanish Find an Expert ...

Food biotechnology's challenge to cultural integrity and individual consent.

PubMed

Thompson, P B

1997-01-01

Consumer response to genetically altered foods has been mixed in the United States. While transgenic crops have entered the food supply with little comment, other foods, such as the bioengineered tomato, have caused considerable controversy. Objections to genetically engineered food are varied, ranging from the religious to the aesthetic. One need not endorse these concerns to conclude that food biotechnology violates procedural protections of consumer sovereignty and religious liberty. Consumer sovereignty, a principle especially valued in this country, requires that information be made available so each individual or group may make food choices based on their own values. And as yet, there is no policy provision for informing consumers about the degree to which food has been genetically engineered.

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management.

PubMed

Burgarella, Sarah; Cattaneo, Dario; Pinciroli, Francesco; Masseroli, Marco

2005-12-01

Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.

7 CFR 3415.13 - Availability of information.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 15 2011-01-01 2011-01-01 false Availability of information. 3415.13 Section 3415.13 Agriculture Regulations of the Department of Agriculture (Continued) NATIONAL INSTITUTE OF FOOD AND AGRICULTURE BIOTECHNOLOGY RISK ASSESSMENT RESEARCH GRANTS PROGRAM Scientific Peer Review of Research Grant...

Biotechnology stock prices before public announcements: evidence of insider trading?

PubMed

Overgaard, C B; van den Broek, R A; Kim, J H; Detsky, A S

2000-03-01

Unique financial challenges faced by biotechnology companies developing therapeutics have contributed to the creation of a highly sensitive market, where stock prices are capable of great fluctuation. The potential for significant financial reward and the nature of the scientific review process make this industry susceptible to illegal share trading on nonpublic information. We examined stock prices of biotechnology products before and after announcement of Phase III clinical trial and Food and Drug Administration (FDA) Advisory Panel results for indirect evidence of insider trading. Biotechnology stock prices were recorded for 98 products undergoing Phase III clinical trials and 49 products undergoing FDA Advisory Panel review between 1990 and 1998. Prices were recorded for 120 consecutive trading days before and after public announcement of these two events. We compared the average change in stock price of successful products ('winners') with unsuccessful products ('losers') before the public announcement of results for both critical events. The difference between average stock price change from 120 to 3 days before public announcement of results of Phase III clinical trial winners (+27%) and losers (-4%) was highly significant (P = 0.0007). A similar but non-significant difference was observed between the average stock price of winning (+27%) and losing products (+13%) before FDA Advisory Panel review announcements (P = 0.25). Our results provide indirect evidence that insider trading may be common in the biotechnology industry. Clinical investigators may wish to consider this issue before participating in any equity position in the biotechnology industry, especially if they are going to perform research for those companies.

Case studies on the use of biotechnologies and on biosafety provisions in four African countries.

PubMed

Black, Robert; Fava, Fabio; Mattei, Niccolo; Robert, Vincent; Seal, Susan; Verdier, Valerie

2011-12-20

This review is based on a study commissioned by the European Commission on the evaluation of scientific, technical and institutional challenges, priorities and bottlenecks for biotechnologies and regional harmonisation of biosafety in Africa. Biotechnology was considered within four domains: agricultural biotechnologies ('Green'), industrial biotechnologies and biotechnologies for environmental remediation ('White'), biotechnologies in aquaculture ('Blue') and biotechnologies for healthcare ('Red'). An important consideration was the decline in partnerships between the EU and developing countries because of the original public antipathy to some green biotechnologies, particularly genetically modified organisms (GMOs) and food from GM crops in Europe. The study focus reported here was West Africa (Ghana, Senegal, Mali and Burkina Faso). The overall conclusion was that whereas high-quality research was proceeding in the countries visited, funding is not sustained and there is little evidence of practical application of biotechnology and benefit to farmers and the wider community. Research and development that was being carried out on genetically modified crop varieties was concentrating on improving food security and therefore unlikely to have significant impact on EU markets and consumers. However, there is much non-controversial green biotechnology such as molecular diagnostics for plant and animal disease and marker-assisted selection for breeding that has great potential application. Regarding white biotechnology, it is currently occupying only a very small industrial niche in West Africa, basically in the sole sector of the production of liquid biofuels (i.e., bio-ethanol) from indigenous and locally planted biomass (very often non-food crops). The presence of diffused small-scale fish production is the basis to develop and apply new (Blue) aquaculture technologies and, where the research conditions and the production sector can permit, to increase this type of production and the economy of this depressed areas. However, the problems bound to environmental protection must not be forgotten; priority should be given to monitor the risks of introduction of foreign species. Red biotechnologies potentially bring a vast domain of powerful tools and processes to achieve better human health, most notably improved diagnostics by molecular techniques, better targeting of pathogens and a better knowledge of their sensitivities to drugs to permit better treatment. Biosafety regulatory frameworks had been initiated in several countries, starting with primary biosafety law. However, disparate attitudes to the purpose of biosafety regulation (e.g., fostering informed decision-making versus 'giving the green-light for a flood of GMOs') currently prevent a needed consensus for sub-regional harmonisation. To date, most R&D funding has come from North America with some commercial interests from Asia, but African biotechnology workers expressed strong desire for (re-)engagement with interested parties from the European Union. Although in some of the visited countries there are very well qualified personnel in molecular biology and biosafety/regulation, the main message received is that human resources and capacity building in-house are still needed. This could be achieved through home-based courses and capacity-building including funds for post-degree research to motivate and retain trained staff. Copyright © 2011 Elsevier B.V. All rights reserved.

Analysis of the Genome and Chromium Metabolism-Related Genes of Serratia sp. S2.

PubMed

Dong, Lanlan; Zhou, Simin; He, Yuan; Jia, Yan; Bai, Qunhua; Deng, Peng; Gao, Jieying; Li, Yingli; Xiao, Hong

2018-05-01

This study is to investigate the genome sequence of Serratia sp. S2. The genomic DNA of Serratia sp. S2 was extracted and the sequencing library was constructed. The sequencing was carried out by Illumina 2000 and complete genomic sequences were obtained. Gene function annotation and bioinformatics analysis were performed by comparing with the known databases. The genome size of Serratia sp. S2 was 5,604,115 bp and the G+C content was 57.61%. There were 5373 protein coding genes, and 3732, 3614, and 3942 genes were respectively annotated into the GO, KEGG, and COG databases. There were 12 genes related to chromium metabolism in the Serratia sp. S2 genome. The whole genome sequence of Serratia sp. S2 is submitted to the GenBank database with gene accession number of LNRP00000000. Our findings may provide theoretical basis for the subsequent development of new biotechnology to repair environmental chromium pollution.

Blood and Lymph Diseases

MedlinePlus

... Support Center External link. Please review our privacy policy . NLM NIH DHHS USA.gov National Center for Biotechnology Information , U.S. National Library of Medicine 8600 Rockville Pike , Bethesda MD , 20894 ...

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

PubMed Central

Onwubiko, J.; Zaru, R.; Rosanoff, S.; Antunes, R.; Bingley, M.; Watkins, X.; O'Donovan, C.; Martin, M. J.

2017-01-01

Abstract Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al., (2013), BMC Bioinformatics, 14 (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al., Nucleic Acids Res.2016; 44, D385–D395) Rhea—a database of enzyme-catalysed reactions (Morgat, A., et al., Nucleic Acids Res. 2015; 43, D459-D464), Reactome—a database of biochemical pathways (Fabregat, A., et al., Nucleic Acids Res. 2016; 44, D481–D487), IntEnz—a resource with enzyme nomenclature information (Fleischmann, A., et al., Nucleic Acids Res. 2004 32, D434–D437) and ChEBI (Hastings, J., et al., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al., Nucleic Acids Res. 201442, 1083–1090)—resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration. PMID:28158609

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.

PubMed

Pundir, S; Onwubiko, J; Zaru, R; Rosanoff, S; Antunes, R; Bingley, M; Watkins, X; O'Donovan, C; Martin, M J

2017-03-01

Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al. , (2013), BMC Bioinformatics , (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al ., Nucleic Acids Res. 2016; , D385-D395) Rhea-a database of enzyme-catalysed reactions (Morgat, A., et al .,  Nucleic Acids Res.  2015; , D459-D464), Reactome-a database of biochemical pathways (Fabregat, A., et al ., Nucleic Acids Res. 2016;  , D481-D487), IntEnz-a resource with enzyme nomenclature information (Fleischmann, A., et al ., Nucleic Acids Res.  2004 , D434-D437) and ChEBI (Hastings, J., et al .,  Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al ., Nucleic Acids Res.  2014 , 1083-1090)-resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Space Biotechnology and Commercial Applications University of Florida

NASA Technical Reports Server (NTRS)

Phillips, Winfred; Evanich, Peggy L.

2004-01-01

The Space Biotechnology and Commercial Applications grant was funded by NASA's Kennedy Space Center in FY 2002 to provide dedicated biotechnology and agricultural research focused on the regeneration of space flight environments with direct parallels in Earth-based applications for solving problems in the environment, advances in agricultural science, and other human support issues amenable to targeted biotechnology solutions. This grant had three project areas, each with multiple tasks. They are: 1) Space Agriculture and Biotechnology Research and Education, 2) Integrated Smart Nanosensors for Space Biotechnology Applications, and 3) Commercial Applications. The Space Agriculture and Biotechnology Research and Education (SABRE) Center emphasized the fundamental biology of organisms involved in space flight applications, including those involved in advanced life support environments because of their critical role in the long-term exploration of space. The SABRE Center supports research at the University of Florida and at the Space Life Sciences Laboratory (SLSL) at the Kennedy Space Center. The Integrated Smart Nanosensors for Space Biotechnology Applications component focused on developing and applying sensor technologies to space environments and agricultural systems. The research activities in nanosensors were coordinated with the SABRE portions of this grant and with the research sponsored by the NASA Environmental Systems Commercial Space Technology Center located in the Department of Environmental Engineering Sciences. Initial sensor efforts have focused on air and water quality monitoring essential to humans for living and working permanently in space, an important goal identified in NASA's strategic plan. The closed environment of a spacecraft or planetary base accentuates cause and effect relationships and environmental impacts. The limited available air and water resources emphasize the need for reuse, recycling, and system monitoring. It is essential to collect real-time information from these systems to ensure crew safety. This new class of nanosensors will be critical to monitoring the space flight environment in future NASA space systems. The Commercial Applications component of this program pursued industry partnerships to develop products for terrestrial use of NASA sponsored technologies, and in turn to stimulate growth in the biotechnology industry. For technologies demonstrating near term commercial potential, the objective is to include industry partners on or about the time of proof of concept that will not only co-invest in the technology but also take the resultant technology to the commercial market.

Protecting Privacy of Genomic Information.

PubMed

Delgado, Jaime; Llorente, Silvia; Naro, Daniel

2017-01-01

The ISO/IEC committee in charge of standardizing the well-known MPEG audiovisual standards has launched, in cooperation with the ISO committee on Biotechnology, a new activity for efficient compressed storage and transmission of genomic information. The paper presents proposals for adding privacy and security to such in-progress standards.

ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome

PubMed Central

Carmona, Rosario; Zafra, Adoración; Seoane, Pedro; Castro, Antonio J.; Guerrero-Fernández, Darío; Castillo-Castillo, Trinidad; Medina-García, Ana; Cánovas, Francisco M.; Aldana-Montes, José F.; Navas-Delgado, Ismael; Alché, Juan de Dios; Claros, M. Gonzalo

2015-01-01

Plant reproductive transcriptomes have been analyzed in different species due to the agronomical and biotechnological importance of plant reproduction. Here we presented an olive tree reproductive transcriptome database with samples from pollen and pistil at different developmental stages, and leaf and root as control vegetative tissues http://reprolive.eez.csic.es). It was developed from 2,077,309 raw reads to 1,549 Sanger sequences. Using a pre-defined workflow based on open-source tools, sequences were pre-processed, assembled, mapped, and annotated with expression data, descriptions, GO terms, InterPro signatures, EC numbers, KEGG pathways, ORFs, and SSRs. Tentative transcripts (TTs) were also annotated with the corresponding orthologs in Arabidopsis thaliana from TAIR and RefSeq databases to enable Linked Data integration. It results in a reproductive transcriptome comprising 72,846 contigs with average length of 686 bp, of which 63,965 (87.8%) included at least one functional annotation, and 55,356 (75.9%) had an ortholog. A minimum of 23,568 different TTs was identified and 5,835 of them contain a complete ORF. The representative reproductive transcriptome can be reduced to 28,972 TTs for further gene expression studies. Partial transcriptomes from pollen, pistil, and vegetative tissues as control were also constructed. ReprOlive provides free access and download capability to these results. Retrieval mechanisms for sequences and transcript annotations are provided. Graphical localization of annotated enzymes into KEGG pathways is also possible. Finally, ReprOlive has included a semantic conceptualisation by means of a Resource Description Framework (RDF) allowing a Linked Data search for extracting the most updated information related to enzymes, interactions, allergens, structures, and reactive oxygen species. PMID:26322066

Whole Transcriptome Analysis Provides Insights into Molecular Mechanisms for Molting in Litopenaeus vannamei

PubMed Central

Gao, Yi; Zhang, Xiaojun; Wei, Jiankai; Sun, Xiaoqing; Yuan, Jianbo; Li, Fuhua; Xiang, Jianhai

2015-01-01

Molting is one of the most important biological processes in shrimp growth and development. All shrimp undergo cyclic molting periodically to shed and replace their exoskeletons. This process is essential for growth, metamorphosis, and reproduction in shrimp. However, the molecular mechanisms underlying shrimp molting remain poorly understood. In this study, we investigated global expression changes in the transcriptomes of the Pacific white shrimp, Litopenaeus vannamei, the most commonly cultured shrimp species worldwide. The transcriptome of whole L. vannamei was investigated by RNA-sequencing (RNA-seq) throughout the molting cycle, including the inter-molt (C), pre-molt (D0, D1, D2, D3, D4), and post-molt (P1 and P2) stages, and 93,756 unigenes were identified. Among these genes, we identified 5,117 genes differentially expressed (log2ratio ≥1 and FDR ≤0.001) in adjacent molt stages. The results were compared against the National Center for Biotechnology Information (NCBI) non-redundant protein/nucleotide sequence database, Swiss-Prot, PFAM database, the Gene Ontology database, and the Kyoto Encyclopedia of Genes and Genomes database in order to annotate gene descriptions, associate them with gene ontology terms, and assign them to pathways. The expression patterns for genes involved in several molecular events critical for molting, such as hormone regulation, triggering events, implementation phases, skelemin, immune responses were characterized and considered as mechanisms underlying molting in L. vannamei. Comparisons with transcriptomic analyses in other arthropods were also performed. The characterization of major transcriptional changes in genes involved in the molting cycle provides candidates for future investigation of the molecular mechanisms. The data generated in this study will serve as an important transcriptomic resource for the shrimp research community to facilitate gene and genome annotation and to characterize key molecular processes underlying shrimp development. PMID:26650402

Literature and patent analysis of the cloning and identification of human functional genes in China.

PubMed

Xia, Yan; Tang, LiSha; Yao, Lei; Wan, Bo; Yang, XianMei; Yu, Long

2012-03-01

The Human Genome Project was launched at the end of the 1980s. Since then, the cloning and identification of functional genes has been a major focus of research across the world. In China too, the potentially profound impact of such studies on the life sciences and on human health was realized, and relevant studies were initiated in the 1990s. To advance China's involvement in the Human Genome Project, in the mid-1990s, Committee of Experts in Biology from National High Technology Research and Development Program of China (863 Program) proposed the "two 1%" goal. This goal envisaged China contributing 1% of the total sequencing work, and cloning and identifying 1% of the total human functional genes. Over the past 20 years, tremendous achievement has been accomplished by Chinese scientists. It is well known that scientists in China finished the 1% of sequencing work of the Human Genome Project, whereas, there is no comprehensive report about "whether China had finished cloning and identifying 1% of human functional genes". In the present study, the GenBank database at the National Center of Biotechnology Information, the PubMed search tool, and the patent database of the State Intellectual Property Office, China, were used to retrieve entries based on two screening standards: (i) Were the newly cloned and identified genes first reported by Chinese scientists? (ii) Were the Chinese scientists awarded the gene sequence patent? Entries were retrieved from the databases up to the cut-off date of 30 June 2011 and the obtained data were analyzed further. The results showed that 589 new human functional genes were first reported by Chinese scientists and 159 gene sequences were patented (http://gene.fudan.sh.cn/introduction/database/chinagene/chinagene.html). This study systematically summarizes China's contributions to human functional genomics research and answers the question "has China finished cloning and identifying 1% of human functional genes?" in the affirmative.

Ethical limitations in patenting biotechnological inventions.

PubMed

Lugagnani, V

1999-01-01

In order to connect ethical considerations with practical limits to patentability, the moral judgement should possibly move from the exploitation of the invention to the nature and/or objectives of Research and Development (R&D) projects which have produced it: in other words, it appears quite reasonable and logical that Society is not rewarding unethical R&D activities by granting intellectual property rights. As far as biotechnology R&D is concerned, ethical guidance can be derived from the 1996 Council of EuropeOs OConvention for the protection of human rights and dignity of the human being with regard to the application of biology and medicineO, whose Chapter V - Scientific research - provides guidelines on: i. protection of persons undergoing research (e.g. informed consent); ii. protection of persons not able to consent to research; iii. research on embryos in vitro. As far as the specific point of patenting biotechnology inventions is concerned, the four exclusions prescribed by Directive 98/44/EC (i.e. human cloning, human germ-line gene therapy, use of human embryos for commercial purposes, unjustified animal suffering for medical purposes) are all we have in Europe in terms of ethical guidance to patentability. In Italy, in particular, we certainly need far more comprehensive legislation, expressing SocietyOs demand to provide ethical control of modern biotechnology. However it is quite difficult to claim that ethical concerns are being raised by currently awarded biotechnology patents related to living organisms and material thereof; they largely deal with the results of genomic R&D, purposely and usefully oriented toward improving health-care and agri-food processes, products and services. ONo patents on lifeOO can be an appealing slogan of militants against modern biotechnology, but it is far too much of an over-simplified abstraction to become the Eleventh Commandment our Society.

POLLUX: a program for simulated cloning, mutagenesis and database searching of DNA constructs.

PubMed

Dayringer, H E; Sammons, S A

1991-04-01

Computer support for research in biotechnology has developed rapidly and has provided several tools to aid the researcher. This report describes the capabilities of new computer software developed in this laboratory to aid in the documentation and planning of experiments in molecular biology. The program, POLLUX, provides a graphical medium for the entry, edit and manipulation of DNA constructs and a textual format for display and edit of construct descriptive data. Program operation and procedures are designed to mimic the actual laboratory experiments with respect to capability and the order in which they are performed. Flexible control over the content of the computer-generated displays and program facilities is provided by a mouse-driven menu interface. Programmed facilities for mutagenesis, simulated cloning and searching of the database from networked workstations are described.

Genes and Disease: Prader-Willi Syndrome

MedlinePlus

... Support Center External link. Please review our privacy policy . NLM NIH DHHS USA.gov National Center for Biotechnology Information , U.S. National Library of Medicine 8600 Rockville Pike , Bethesda MD , 20894 ...

Bioethical Considerations of Advancing the Application of Marine Biotechnology and Aquaculture

PubMed Central

Harrell, Reginal M.

2017-01-01

Normative ethical considerations of growth of the marine biotechnology and aquaculture disciplines in biopharming, food production, and marine products commercialization from a bioethical perspective have been limited. This paucity of information begs the question of what constitutes a bioethical approach (i.e., respect for individuals or autonomy; beneficence, nonmaleficence, and justice) to marine biotechnology and aquaculture, and whether it is one that is appropriate for consideration. Currently, thoughtful discussion on the bioethical implications of use, development, and commercialization of marine organisms or their products, as well as potential environmental effects, defaults to human biomedicine as a model. One must question the validity of using human bioethical principlism moral norms for appropriating a responsible marine biotechnology and aquaculture ethic. When considering potential impacts within these disciplines, deference must be given to differing value systems in order to find common ground to advance knowledge and avoid emotive impasses that can hinder the science and its application. The import of bioethical considerations when conducting research and/or production is discussed. This discussion is directed toward applying bioethical principles toward technology used for food, biomedical development (e.g., biopharming), or as model species for advancement of knowledge for human diseases. PMID:28672802

Bioethical Considerations of Advancing the Application of Marine Biotechnology and Aquaculture.

PubMed

Harrell, Reginal M

2017-06-24

Normative ethical considerations of growth of the marine biotechnology and aquaculture disciplines in biopharming, food production, and marine products commercialization from a bioethical perspective have been limited. This paucity of information begs the question of what constitutes a bioethical approach (i.e., respect for individuals or autonomy; beneficence, nonmaleficence, and justice) to marine biotechnology and aquaculture, and whether it is one that is appropriate for consideration. Currently, thoughtful discussion on the bioethical implications of use, development, and commercialization of marine organisms or their products, as well as potential environmental effects, defaults to human biomedicine as a model. One must question the validity of using human bioethical principlism moral norms for appropriating a responsible marine biotechnology and aquaculture ethic. When considering potential impacts within these disciplines, deference must be given to differing value systems in order to find common ground to advance knowledge and avoid emotive impasses that can hinder the science and its application. The import of bioethical considerations when conducting research and/or production is discussed. This discussion is directed toward applying bioethical principles toward technology used for food, biomedical development (e.g., biopharming), or as model species for advancement of knowledge for human diseases.

Ethnopharmacological uses, phytochemistry, biological activities, and biotechnological applications of Eclipta prostrata.

PubMed

Chung, Ill-Min; Rajakumar, Govindasamy; Lee, Ji-Hee; Kim, Seung-Hyun; Thiruvengadam, Muthu

2017-07-01

Eclipta prostrata belongs to a family of medicinal plants (Asteraceae) and plays a role in the treatment of several diseases, including infectious hepatitis, snake venom poisoning, gastritis, and respiratory diseases such as a cough and asthma. A number of compounds, including thiophene derivatives, steroids, triterpenes, flavonoids, polyacetylenes, polypeptides, and coumestans, have been isolated from E. prostrata. The plant functional compounds can act as reducing agent in the field of nanoparticle synthesis. The extracts of E. prostrata are widely used for green biosynthesis of various metal and metal oxide nanoparticles, nanoparticles, which showed a potential for pharmaceutical, biotechnological, and biomedical applications. Establishment of a efficient in vitro regeneration and genetic transformation method of E. prostrata is a vital prerequisite for application of biotechnology in order to improve secondary metabolite yields. The present mini-review discusses its pharmacological profile, chemical constituents, biotechnological, and ethnomedical uses, mainly focusing on antimyotoxic, antihemorrhagic, antiproliferative, antioxidant, antitumor, antihyperglycemic, antidementia, antimicrobial, antihyperlipidemic, antivenom, anti-HIV, and larvicidal activities, so that the pharmaceutical potential of the plant can be better evaluated. The mini review, providing up-to-date phytochemical and other information on E. prostrata, will serve a reference for further studies.

Communication Strategy: Proper Structure Necessary but not Sufficient

DTIC Science & Technology

2010-12-01

Information, (1998), http://www.ncbi.nlm.nih.gov/ bookshelf /br.fcgi?book=nap6200&part=a20006484ddd00073 (accessed November 12, 2010). “The multidimensional...Biotechnology Information (1998). http://www.ncbi.nlm.nih.gov/ bookshelf /br.fcgi?book=nap6200&part=a20006484ddd000 73 (accessed November 12, 2010

Communication Strategy: Proper Structure Necessary But Not Sufficient

DTIC Science & Technology

2010-01-01

Information, (1998), http://www.ncbi.nlm.nih.gov/ bookshelf /br.fcgi?book=nap6200&part=a20006484ddd00073 (accessed November 12, 2010). “The multidimensional...Biotechnology Information (1998). http://www.ncbi.nlm.nih.gov/ bookshelf /br.fcgi?book=nap6200&part=a20006484ddd000 73 (accessed November 12, 2010

cDNAs from Nylanderia sp nr pubens (Hymenoptera: Formicidae)

USDA-ARS?s Scientific Manuscript database

7 new gene sequences were identified from workers of Rasberry crazy ant, Nylanderia sp.nr. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are HQ636472-HQ636478. This information will provide scientists with genetic tools to study the pop...

Research in the Biotech Age: Can Informational Privacy Compete?

ERIC Educational Resources Information Center

Peekhaus, Wilhelm

2008-01-01

This article examines the privacy of personal medical information in the health research context. Arguing that biomedical research in Canada has been caught up in the government's broader neoliberal policy agenda that has positioned biotechnology as a strategic driver of economic growth, the author discusses the tension between informational…

Cyborgs, biotechnologies, and informatics in health care - new paradigms in nursing sciences.

PubMed

Monteiro, Ana Paula Teixeira de Almeida Vieira

2016-01-01

Nursing Sciences are at a moment of paradigmatic transition. The aim of this paper is to reflect on the new epistemological paradigms of nursing science from a critical approach. In this paper, we identified and analysed some new research lines and trends which anticipate the reorganization of nursing sciences and the paradigms emerging from nursing care: biotechnology-centred knowledge; the interface between nursing knowledge and new information technologies; body care centred knowledge; the human body as a cyborg body; and the rediscovery of an aesthetic knowledge in nursing care. © 2015 John Wiley & Sons Ltd.

Virus-Based RNA Silencing Agents and Virus-Derived Expression Vectors as Gene Therapy Vehicles.

PubMed

Venkataraman, Srividhya; Ahmad, Tauqeer; AbouHaidar, Mounir G; Hefferon, Kathleen L

2017-01-01

In consideration of recent developments in understanding the genomics and proteomics of viruses, the use of viral DNA / RNA sequences as well as their gene expression schemes, have found new in-roads towards the prognosis and therapy of diseases. Correspondingly, the sphere of the patenting scenario has expanded significantly. The current review addresses patented inventions concerning the use of virus sequences as gene silencing machineries and inventions concerning the generation and application of viral sequences as expression vectors. Furthermore, this review also discusses the employment of these patents for clinical, agricultural and biotechnological applications. Considering these objectives, the Delphion Research Intellectual Property Network database was searched using keywords such as "gene silencing", "engineered viruses" and "expression vectors" and descriptions of recent patents on the said topics were discussed. Despite several recent advances in the use of viruses as disease therapy vehicles and biotechnological vectors, these developments have yet to be proven effective in practice, in clinical and field trials. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Synergy between Competitive Intelligence (CI), Knowledge Management (KM) and Technological Foresight (TF) as a strategic model of prospecting--the use of biotechnology in the development of drugs against breast cancer.

PubMed

Canongia, Claudia

2007-01-01

The aim of this paper is to demonstrate the synergy between Competitive Intelligence, Knowledge Management and Technological Foresight, and to emphasize the proposal of a strategic model of data prospecting as a mechanism to support decision-making in regard to three approaches for sustainable development and innovation: technological, social and economic. The use of biotechnology in the development of drugs against breast cancer is the case study. The article shows the results of data and text mining in specialized medical and patent databases, identifying the most frequently cited drugs, as well as the authors of research, and the inventors of new technology at the beginning of the 21st century. In addition, the study includes reference to Brazilian competence in breast cancer area, the international trends in drugs for treatment of this cancer, leading international institutions and Brazilian competencies. A framework is presented, which could serve as a guide and support for the decision-making process.

Molecular Diagnostics in Pathology: Time for a Next-Generation Pathologist?

PubMed

Fassan, Matteo

2018-03-01

- Comprehensive molecular investigations of mainstream carcinogenic processes have led to the use of effective molecular targeted agents in most cases of solid tumors in clinical settings. - To update readers regarding the evolving role of the pathologist in the therapeutic decision-making process and the introduction of next-generation technologies into pathology practice. - Current literature on the topic, primarily sourced from the PubMed (National Center for Biotechnology Information, Bethesda, Maryland) database, were reviewed. - Adequate evaluation of cytologic-based and tissue-based predictive diagnostic biomarkers largely depends on both proper pathologic characterization and customized processing of biospecimens. Moreover, increased requests for molecular testing have paralleled the recent, sharp decrease in tumor material to be analyzed-material that currently comprises cytology specimens or, at minimum, small biopsies in most cases of metastatic/advanced disease. Traditional diagnostic pathology has been completely revolutionized by the introduction of next-generation technologies, which provide multigene, targeted mutational profiling, even in the most complex of clinical cases. Combining traditional and molecular knowledge, pathologists integrate the morphological, clinical, and molecular dimensions of a disease, leading to a proper diagnosis and, therefore, the most-appropriate tailored therapy.

The ORNL Chemical Technology Division, 1950-1994

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

Jolley, R.L.; Genung, R.K.; McNeese, L.E.

1994-10-01

This document attempts to reconstruct the role played by the Chemical Technology Division (Chem Tech) of the Oak Ridge National Laboratory (ORNL) in the atomic era since the 1940`s related to the development and production of nuclear weapons and power reactors. Chem Tech`s early contributions were landmark pioneering studies. Unknown and dimly perceived problems like chemical hazards, radioactivity, and criticality had to be dealt with. New chemical concepts and processes had to be developed to test the new theories being developed by physicists. New engineering concepts had to be developed and demonstrated in order to build facilities and equipment thatmore » had never before been attempted. Chem Tech`s role was chemical separations, especially uranium and plutonium, and nuclear fuel reprocessing. With diversification of national and ORNL missions, Chem Tech undertook R&D studies in many areas including biotechnology; clinical and environmental chemistry; nuclear reactors; safety regulations; effective and safe waste management and disposal; computer modeling and informational databases; isotope production; and environmental control. The changing mission of Chem Tech are encapsulated in the evolving activities.« less

Application of GIS in public health in India: A literature-based review, analysis, and recommendations.

PubMed

Ruiz, Marilyn O'Hara; Sharma, Arun Kumar

2016-01-01

The implementation of geospatial technologies and methods for improving health has become widespread in many nations, but India's adoption of these approaches has been fairly slow. With a large population, ongoing public health challenges, and a growing economy with an emphasis on innovative technologies, the adoption of spatial approaches to disease surveillance, spatial epidemiology, and implementation of health policies in India has great potential for both success and efficacy. Through our evaluation of scientific papers selected through a structured key phrase review of the National Center for Biotechnology Information on the database PubMed, we found that current spatial approaches to health research in India are fairly descriptive in nature, but the use of more complex models and statistics is increasing. The institutional home of the authors is skewed regionally, with Delhi and South India more likely to show evidence of use. The need for scientists engaged in spatial health analysis to first digitize basic data, such as maps of road networks, hydrological features, and land use, is a strong impediment to efficiency, and their work would certainly advance more quickly without this requirement.

Bombyx mori Serpin6 regulates prophenoloxidase activity and the expression of antimicrobial proteins.

PubMed

Li, Bing; Yu, Hai-Zhong; Ye, Chong-Jun; Ma, Yan; Li, Xing; Fan, Tao; Chen, Fu-Sheng; Xu, Jia-Ping

2017-04-30

Serpins are a family of serine protease inhibitors that are found widely in insects. They play an important role in insect physiological responses, such as innate immunity and development. In this study, we obtained the Bombyx mori serpin6 (BmSerpin6) sequence from National Center for Biotechnology Information (NCBI) and the silkworm genome database (SilkDB). Reverse transcription PCR (RT-PCR) results showed that BmSerpin6 was expressed highly in hemocytes, the midgut, and the fat body. After challenging with Micrococcus luteus (Mi) and Serratia marcescens (Sm), the BmSerpin6 expression level was induced significantly. Transcript levels of gloverin2 and prophenoloxidase (PPO) activity were reduced significantly in the fat body and hemocytes after injecting the recombinant BmSerpin6 protein into silkworm larvae. A BmSerpin6 recombinant plasmid (BmSerpin6-pAC 5.1) was constructed successfully and transfected into Drosophila S2 cells, which resulted in significantly reduced expression of the drosomycin protein. These results indicated that BmSerpin6 might regulate silkworm immune responses. Copyright © 2017 Elsevier B.V. All rights reserved.

Protecting genetic privacy.

PubMed

Roche, P A; Annas, G J

2001-05-01

This article outlines the arguments for and against new rules to protect genetic privacy. We explain why genetic information is different to other sensitive medical information, why researchers and biotechnology companies have opposed new rules to protect genetic privacy (and favour anti-discrimination laws instead), and discuss what can be done to protect privacy in relation to genetic-sequence information and to DNA samples themselves.

Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes

PubMed Central

Li, Ben; Sun, Zhaonan; He, Qing; Zhu, Yu; Qin, Zhaohui S.

2016-01-01

Motivation: Modern high-throughput biotechnologies such as microarray are capable of producing a massive amount of information for each sample. However, in a typical high-throughput experiment, only limited number of samples were assayed, thus the classical ‘large p, small n’ problem. On the other hand, rapid propagation of these high-throughput technologies has resulted in a substantial collection of data, often carried out on the same platform and using the same protocol. It is highly desirable to utilize the existing data when performing analysis and inference on a new dataset. Results: Utilizing existing data can be carried out in a straightforward fashion under the Bayesian framework in which the repository of historical data can be exploited to build informative priors and used in new data analysis. In this work, using microarray data, we investigate the feasibility and effectiveness of deriving informative priors from historical data and using them in the problem of detecting differentially expressed genes. Through simulation and real data analysis, we show that the proposed strategy significantly outperforms existing methods including the popular and state-of-the-art Bayesian hierarchical model-based approaches. Our work illustrates the feasibility and benefits of exploiting the increasingly available genomics big data in statistical inference and presents a promising practical strategy for dealing with the ‘large p, small n’ problem. Availability and implementation: Our method is implemented in R package IPBT, which is freely available from https://github.com/benliemory/IPBT. Contact: yuzhu@purdue.edu; zhaohui.qin@emory.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26519502

Biotech Information-Sharing Memorandum of Understanding

EPA Pesticide Factsheets

EPA, FDA, and the U.S. Department of Agriculture's Animal and Plant Health Inspection Service/Biotechnology Regulatory Services share the regulatory oversight over genetically engineered plants and the foods derived from such plants.

FDA perspective on specifications for biotechnology products--from IND to PLA.

PubMed

Murano, G

1997-01-01

Quality standards are obligatory throughout development, approval and post-marketing phases of biotechnology-derived products, thus assuring product identity, purity, and potency/strength. The process of developing and setting specifications should be based on sound science and should represent a logical progression of actions based on the use of experiential data spanning manufacturing process validation, consistency in production, and characterization of relevant product properties/attributes, by multiple analytical means. This interactive process occurs in phases, varying in rigour. It is best described as encompassing a framework which starts with the implementation of realistic/practical operational quality limits, progressing to the establishment/adoption of more stringent specifications. The historical database is generated from preclinical, toxicology and early clinical lots. This supports the clinical development programme which, as it progresses, allows for further assay method validation/refinement, adoption/addition due to relevant or newly recognized product attributes or rejection due to irrelevance. In the next phase, (licensing/approval) specifications are set through extended experience and validation of both the preparative and analytical processes, to include availability of suitable reference standards and extensive product characterization throughout its proposed dating period. Subsequent to product approval, the incremental database of test results serves as a natural continuum for further evolving/refining specifications. While there is considerable latitude in the kinds of testing modalities finally adopted to establish product quality on a routine basis, for both drugs and drug products, it is important that the selection takes into consideration relevant (significant) product characteristics that appropriately reflect on identity, purity and potency.

Genetics Home Reference: factor V Leiden thrombophilia

MedlinePlus

... Additional NIH Resources (3 links) National Center for Biotechnology Information: Mutations and Blood Clots National Heart, Lung, and Blood Institute: Deep Vein Thrombosis National Human Genome Research Institute Educational Resources (3 links) Factor V ...

Towards PubMed 2.0.

PubMed

Fiorini, Nicolas; Lipman, David J; Lu, Zhiyong

2017-10-30

Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called PubMed Labs.

Interactions between drugs and drug-nutrient in enteral nutrition: a review based on evidences.

PubMed

Ferreira Silva, Renata; Rita Carvalho Garbi Novaes, Maria

2014-09-01

Enteral nutrition (EN) provides calories, macronutrients and micronutrients in adequate quantity and quality to meet the patient's needs. Some drugs when crushed and diluted may have their properties altered, including the reduction of bioavailability causing the reduction of the serum concentration of the drug; tube obstruction; drug-drug interaction or drug-nutrient interaction. The study was conducted through review of submitted articles in the databases of the Virtual Health Library (VHL): MEDLINE (National Library of Medicine, USA), Lilacs (Latin American and Caribbean Literature on Health Sciences) PUBMED - NCBI (National Center for Biotechnology Information) and COCHRANE. For this survey, 42 articles were identified during database searching. After applying the inclusion and exclusion criteria, 08 articles were selected, obtained from the MEDLINE and Lilacs. Some interactions were found such as the aluminium hydroxide and lactulose with the enteral nutrition, which may result in a precipitation and reduction of drug bioavailability. Mineral oil will alter the absorption of fat-soluble vitamins and reduces the tube light. Others results were found as phenytoin, warfarin, captopril and furosemide with enteral nutrition may reduce the maximum serum concentration. Drug interactions are more common in day-to-day activities than health professionals may suppose. Knowledge on the matter may also assist in reducing cases of obstruction of tubes, through which enteral nutrition and medications are administered. Thus, the multidisciplinary team, acting together, may have more beneficial effects to the patient. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Molecular cloning and expression of the CRISP family of proteins in the boar.

PubMed

Vadnais, Melissa L; Foster, Douglas N; Roberts, Kenneth P

2008-12-01

The family of mammalian cysteine-rich secretory proteins (CRISP) have been well characterized in the rat, mouse, and human. Here we report the molecular cloning and expression analysis of CRISP1, CRISP2, and CRISP3 in the boar. A partial sequence published in the National Center for Biotechnology Information (NCBI) database was used to derive the full-length sequences for CRISP1 and CRISP2 using rapid amplification of cDNA ends. RT-PCR confirmed the expression of these mRNAs in the boar reproductive tract, and real time RT-PCR showed CRISP1 to be highly expressed throughout the epididymis, with CRISP2 highly expressed in the testis. A search of the porcine genomic sequence in the NCBI database identified a BAC (CH242-199E6) encoding the CRISP1 gene. This BAC is derived from porcine Chromosome 7 and is syntenic with the regions of the mouse, rat, and human genomes encoding the CRISP gene family. This BAC was found to encode a third CRISP protein with a predicted amino acid sequence of high similarity to human CRISP3. Using RT-PCR we show that CRISP3 expression in the boar reproductive tract is confined to the prostate. Recombinant porcine (rp) CRISP2 protein was produced and purified. When incubated with capacitated boar sperm, rpCRISP2 induced an acrosome reaction, consistent with its demonstrated ability to alter the activity of calcium channels.

Key genes and pathways in measles and their interaction with environmental chemicals.

PubMed

Zhang, Rongqiang; Jiang, Hualin; Li, Fengying; Su, Ning; Ding, Yi; Mao, Xiang; Ren, Dan; Wang, Jing

2018-06-01

The aim of the present study was to explore key genes that may have a role in the pathology of measles virus infection and to clarify the interaction networks between environmental factors and differentially expressed genes (DEGs). After screening the database of the Gene Expression Omnibus of the National Center for Biotechnology Information, the dataset GSE5808 was downloaded and analyzed. A global normalization method was performed to minimize data inconsistencies and heterogeneity. DEGs during different stages of measles virus infection were explored using R software (v3.4.0). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs were performed using Cytoscape 3.4.0 software. A protein-protein interaction (PPI) network of the DEGs was obtained from the STRING database v9.05. A total of 43 DEGs were obtained from four analyzed sample groups, including 10 highly expressed genes and 33 genes with decreased expression. The most enriched pathways based on KEGG analysis were fatty acid elongation, cytokine-cytokine receptor interaction and RNA degradation. The genes mentioned in the PPI network were mainly associated with protein binding and chemokine activity. A total of 219 chemicals were identified that may, jointly or on their own, interact with the 6 DEGs between the control group and patients with measles (at hospital entry), including benzo(a)pyrene (BaP) and tetrachlorodibenzodioxin (TCDD). In conclusion, the present study revealed that chemokines and environmental chemicals, e.g. BaP and TCDD, may affect the development of measles.

Considerations on patent valuation based on patent classification and citation in biotechnological field

NASA Astrophysics Data System (ADS)

Mihara, Kenji

Regarding innovation measurement utilizing patent information, a number of researchers are making great efforts to measure a "patent value (patent quality)." For patent valuation, patent classification and citation are often utilized as patent information. Also, biotechnological field is attracting attention from the viewpoint of application to environmental or medical study, and considerable researches on patent valuation are ongoing in this technical field. However, it is not enough recognized that researchers cannot be too careful when they deal with classification information in the biotech field because patent classification structure in this field is not well-established. And also, it is not known enough that citation patterns of both academic papers and patent documents are so complicated that the patterns cannot be easily generalized. In this article, the issues above were verified from a position based on working experiences of biotech patent examiner at Japan Patent Office, and considerations and implications were given on what patent valuation should be.

Ethics in biotechnology and biosecurity.

PubMed

Jameel, S

2011-01-01

Great advances in technology produce unique challenges. Every technology also has a dual use, which needs to be understood and managed to extract maximum benefits for mankind and the development of civilization. The achievements of physicists in the mid-20th century resulted in the nuclear technology, which gave us the destructive power of the atomic bomb as also a source of energy. Towards the later part of the 20th century, information technology empowered us with fast, easy and cheap access to information, but also led to intrusions into our privacy. Today, biotechnology is yielding life- saving and life-enhancing advances at a fast pace. But, the same tools can also give rise to fiercely destructive forces. How do we construct a security regime for biology? What have we learnt from the management of earlier technological advances? How much information should be in the public domain? Should biology, or more broadly science, be regulated? Who should regulate it? These and many other ethical questions need to be addressed.

Bacterial and Fungal Proteolytic Enzymes: Production, Catalysis and Potential Applications.

PubMed

da Silva, Ronivaldo Rodrigues

2017-09-01

Submerged and solid-state bioprocesses have been extensively explored worldwide and employed in a number of important studies dealing with microbial cultivation for the production of enzymes. The development of these production technologies has facilitated the generation of new enzyme-based products with applications in pharmaceuticals, food, bioactive peptides, and basic research studies, among others. The applicability of microorganisms in biotechnology is potentiated because of their various advantages, including large-scale production, short time of cultivation, and ease of handling. Currently, several studies are being conducted to search for new microbial peptidases with peculiar biochemical properties for industrial applications. Bioprospecting, being an important prerequisite for research and biotechnological development, is based on exploring the microbial diversity for enzyme production. Limited information is available on the production of specific proteolytic enzymes from bacterial and fungal species, especially on the subgroups threonine and glutamic peptidases, and the seventh catalytic type, nonhydrolytic asparagine peptide lyase. This gap in information motivated the present study about these unique biocatalysts. In this study, the biochemical and biotechnological aspects of the seven catalytic types of proteolytic enzymes, namely aspartyl, cysteine, serine, metallo, glutamic, and threonine peptidase, and asparagine peptide lyase, are summarized, with an emphasis on new studies, production, catalysis, and application of these enzymes.

Complete cDNAs from Solenopsis invicta (Hymenoptera: Formicidae). --GenBank accession numbers: HM130684-HM130685.

USDA-ARS?s Scientific Manuscript database

2 new gene sequences were identified from workers of Solenopsis invicta, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are HM130684-HM130685. This information will provide scientists with genetic tools to study the populations of this ant....

Complete cDNAs from Brachymyrmex patagonicus (Hymenoptera: Formicidae). --GenBank accession numbers: GU582126-GU582140.

USDA-ARS?s Scientific Manuscript database

15 new gene sequences were identified from workers of Brachymyrmex patagonicus, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU582126-GU582140. This information will provide scientists with genetic tools to study the development and the p...

Turkish university students' knowledge of biotechnology and attitudes toward biotechnological applications.

PubMed

Öztürk-Akar, Ebru

2017-03-04

This study questions the presumed relation between formal schooling and scientific literacy about biotechnologies. Comparing science and nonscience majors' knowledge of and attitudes toward biotechnological applications, conclusions are drawn if their formal learnings improve pupils' understandings of and attitudes toward biotechnology applications. Sample of the study consists of 403 undergraduate and graduate students, 198 nonscience, and 205 science majors. The Biotechnology Knowledge Questionnaire and the Biotechnology Attitude Questionnaire were administered. Descriptive statistics (mean and percentages), t test, and correlations were used to examine the participants' knowledge of biotechnology and attitudes toward biotechnological applications and differences as regards their majors. Although the science majors had higher knowledge and attitude scores than the nonscience majors, it is not possible to say that they have sufficient knowledge of biotechnologies. Besides, the participants' attitudes toward biotechnological applications were not considerably related to their knowledge of biotechnology. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(2):115-125, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

Industrial College of the Armed Forces Industry Studies 2004: Biotechnology

DTIC Science & Technology

2004-01-01

life over the next two decades, in much the same way information technology did during the previous two decades. Seminar Members: CDR Paul...American Chamber of Commerce, Hong Kong American Embassy, Tokyo, Japan American Embassy, Singapore Asia Technology Information Program...before. At the same time, scientists are experiencing a rapid acceleration of product development as they exploit the power of information technology

www.studentthink.molecularbiology.

ERIC Educational Resources Information Center

Morvillo, Nancy; Schmidt, Matthew; Carlson, Albert

2000-01-01

Describes a microbiology exercise that is designed to expose students to the world wide web. Introduces a molecular biology quiz site and National Center for Biotechnology Information (NCBI). Provides a list of molecular biology sites on the Internet. (YDS)

Towards PubMed 2.0

PubMed Central

Fiorini, Nicolas; Lipman, David J; Lu, Zhiyong

2017-01-01

Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called PubMed Labs. PMID:29083299

BIOTECHNOLOGY/ECORISK

EPA Science Inventory

This research effort is designed to provide the risk assessment community with modern genetic tools for evaluating long-term risks of genetically modified (GM) crops. Molecular population genetic data can potentially reveal information about long-term trends in both pest populat...

Filing a Biotechnology Submission under TSCA

EPA Pesticide Factsheets

Section 5 of the Toxic Substances Control Act (TSCA) requires the submission of certain information to EPA if a person wishes to commercialize an intergeneric microorganism or Introduce such microorganisms into the environment for research purposes.

Genetics Experts Unite to I.D. Unknown Katrina Victims

MedlinePlus

... News From NIH Genetics Experts Unite to I.D. Unknown Katrina Victims Past Issues / Summer 2006 Table ... and genetics," says team member Stephen Sherry, Ph.D., of NLM's National Center for Biotechnology Information, "is ...

Bridging the gap between fluxomics and industrial biotechnology.

PubMed

Feng, Xueyang; Page, Lawrence; Rubens, Jacob; Chircus, Lauren; Colletti, Peter; Pakrasi, Himadri B; Tang, Yinjie J

2010-01-01

Metabolic flux analysis is a vital tool used to determine the ultimate output of cellular metabolism and thus detect biotechnologically relevant bottlenecks in productivity. ¹³C-based metabolic flux analysis (¹³C-MFA) and flux balance analysis (FBA) have many potential applications in biotechnology. However, noteworthy hurdles in fluxomics study are still present. First, several technical difficulties in both ¹³C-MFA and FBA severely limit the scope of fluxomics findings and the applicability of obtained metabolic information. Second, the complexity of metabolic regulation poses a great challenge for precise prediction and analysis of metabolic networks, as there are gaps between fluxomics results and other omics studies. Third, despite identified metabolic bottlenecks or sources of host stress from product synthesis, it remains difficult to overcome inherent metabolic robustness or to efficiently import and express nonnative pathways. Fourth, product yields often decrease as the number of enzymatic steps increases. Such decrease in yield may not be caused by rate-limiting enzymes, but rather is accumulated through each enzymatic reaction. Fifth, a high-throughput fluxomics tool hasnot been developed for characterizing nonmodel microorganisms and maximizing their application in industrial biotechnology. Refining fluxomics tools and understanding these obstacles will improve our ability to engineer highly efficient metabolic pathways in microbial hosts.

Agricultural biotechnology and its contribution to the global knowledge economy.

PubMed

Aerni, Philipp

2007-01-01

The theory of neoclassical welfare economics largely shaped international and national agricultural policies during the Cold War period. It treated technology as an exogenous factor that could boost agricultural productivity but not necessarily sustainable agriculture. New growth theory, the economic theory of the new knowledge economy, treats technological change as endogenous and argues that intangible assets such as human capital and knowledge are the drivers of sustainable economic development. In this context, the combined use of agricultural biotechnology and information technology has a great potential, not just to boost economic growth but also to empower people in developing countries and improve the sustainable management of natural resources. This article outlines the major ideas behind new growth theory and explains why agricultural economists and agricultural policy-makers still tend to stick to old welfare economics. Finally, the article uses the case of the Cassava Biotechnology Network (CBN) to illustrate an example of how new growth theory can be applied in the fight against poverty. CBN is a successful interdisciplinary crop research network that makes use of the new knowledge economy to produce new goods that empower the poor and improve the productivity and nutritional quality of cassava. It shows that the potential benefits of agricultural biotechnology go far beyond the already known productivity increases and pesticide use reductions of existing GM crops.

Biotechnology essay competition: biotechnology and sustainable food practices.

PubMed

Peng, Judy; Schoeb, Helena; Lee, Gina

2013-06-01

Biotechnology Journal announces our second biotechnology essay competition with the theme "biotechnology and sustainable food practices", open to all undergraduate students. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PmiRExAt: plant miRNA expression atlas database and web applications

PubMed Central

Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S.

2016-01-01

High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database. Database URL: http://pmirexat.nabi.res.in. PMID:27081157

Biotechnological Trends in Spider and Scorpion Antivenom Development

PubMed Central

Laustsen, Andreas Hougaard; Solà, Mireia; Jappe, Emma Christine; Oscoz, Saioa; Lauridsen, Line Præst; Engmark, Mikael

2016-01-01

Spiders and scorpions are notorious for their fearful dispositions and their ability to inject venom into prey and predators, causing symptoms such as necrosis, paralysis, and excruciating pain. Information on venom composition and the toxins present in these species is growing due to an interest in using bioactive toxins from spiders and scorpions for drug discovery purposes and for solving crystal structures of membrane-embedded receptors. Additionally, the identification and isolation of a myriad of spider and scorpion toxins has allowed research within next generation antivenoms to progress at an increasingly faster pace. In this review, the current knowledge of spider and scorpion venoms is presented, followed by a discussion of all published biotechnological efforts within development of spider and scorpion antitoxins based on small molecules, antibodies and fragments thereof, and next generation immunization strategies. The increasing number of discovery and development efforts within this field may point towards an upcoming transition from serum-based antivenoms towards therapeutic solutions based on modern biotechnology. PMID:27455327

Host cell proteins in biotechnology-derived products: A risk assessment framework.

PubMed

de Zafra, Christina L Zuch; Quarmby, Valerie; Francissen, Kathleen; Vanderlaan, Martin; Zhu-Shimoni, Judith

2015-11-01

To manufacture biotechnology products, mammalian or bacterial cells are engineered for the production of recombinant therapeutic human proteins including monoclonal antibodies. Host cells synthesize an entire repertoire of proteins which are essential for their own function and survival. Biotechnology manufacturing processes are designed to produce recombinant therapeutics with a very high degree of purity. While there is typically a low residual level of host cell protein in the final drug product, under some circumstances a host cell protein(s) may copurify with the therapeutic protein and, if it is not detected and removed, it may become an unintended component of the final product. The purpose of this article is to enumerate and discuss factors to be considered in an assessment of risk of residual host cell protein(s) detected and identified in the drug product. The consideration of these factors and their relative ranking will lead to an overall risk assessment that informs decision-making around how to control the levels of host cell proteins. © 2015 Wiley Periodicals, Inc.

The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas.

PubMed

Bonomo, Melia E; Deem, Michael W

2018-04-30

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used to recognize and interfere with subsequent invasions from the same genetic elements. This versatile prokaryotic tool has also been used to advance applications in biotechnology. Here we review a large body of CRISPR-Cas research to explore themes of evolution and selection, population dynamics, horizontal gene transfer, specific and cross-reactive interactions, cost and regulation, non-immunological CRISPR functions that boost host cell robustness, as well as applicable mechanisms for efficient and specific genetic engineering. We offer future directions that can be addressed by the physics community. Physical understanding of the CRISPR-Cas system will advance uses in biotechnology, such as developing cell lines and animal models, cell labeling and information storage, combatting antibiotic resistance, and human therapeutics.

Experiences from the implementation of a biosafety system in Slovenia.

PubMed

Milavec, Mojca; Racman, Darja Stanic

2007-09-01

The development and implementation of an effective national biosafety system is important for several key reasons: to ensure safe access to products of modern biotechnology, to build public confidence, to encourage the growth of domestic modern biotechnology, and to comply with international standards and agreements. There is no single best approach in the development and implementation of a national biosafety system and each country is faced with unique challenges. Slovenia is a small country and a new EU Member State. However, it has developed and implemented an efficient national biosafety system. The key elements of this system are administrative procedure, risk assessment, enforcement, and public participation and information.

Microgravity Materials and Biotechnology Experiments

NASA Technical Reports Server (NTRS)

Vlasse, Marcus

1998-01-01

Presentation will deal with an overview of the Materials Science and Biotechnology/Crystal Growth flight experiments and their requirements for a successful execution. It will also deal with the hardware necessary to perform these experiments as well as the hardware requirements. This information will serve as a basis for the Abstract: workshop participants to review the poss7ibilifies for a low cost unmanned carrier and the simple automation to carry-out experiments in a microgravity environment with little intervention from the ground. The discussion will include what we have now and what will be needed to automate totally the hardware and experiment protocol at relatively low cost.

Learning about Trimethylaminuria

MedlinePlus

... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers ... ncbi.nlm.nih.gov] An electronic catalog of human genes and genetic ... Center for Biotechnology Information (NCBI). The language on this page about ...

Human Values and Biotechnology

ERIC Educational Resources Information Center

Seibert, M. Angelice; Jacob, Martha Ann

1976-01-01

The response that this generation and the next generation gives to that most basic question of all, "What is man?," was the focus of this article. It attempted to make us aware of and informed of the topic. (Author/RK)

PubMed and beyond: a survey of web tools for searching biomedical literature

PubMed Central

Lu, Zhiyong

2011-01-01

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search PMID:21245076

Systems architecture: a new model for sustainability and the built environment using nanotechnology, biotechnology, information technology, and cognitive science with living technology.

PubMed

Armstrong, Rachel

2010-01-01

This report details a workshop held at the Bartlett School of Architecture, University College London, to initiate interdisciplinary collaborations for the practice of systems architecture, which is a new model for the generation of sustainable architecture that combines the discipline of the study of the built environment with the scientific study of complexity, or systems science, and adopts the perspective of systems theory. Systems architecture offers new perspectives on the organization of the built environment that enable architects to consider architecture as a series of interconnected networks with embedded links into natural systems. The public workshop brought together architects and scientists working with the convergence of nanotechnology, biotechnology, information technology, and cognitive science and with living technology to investigate the possibility of a new generation of smart materials that are implied by this approach.

Information Sharing from 9-1-1 Centers

DTIC Science & Technology

2014-09-01

Police Chief, 2014, http://www.policechiefmagazine.org/ magazine /index.cfm?fuseaction=display_arch&article_id=1199&issue _id=62007. 2 “9-1-1 History...Homeland Security Magazine ,51 discusses the pros and cons of using social media to 49 Jennifer E...Information Dilemmas in Biotechnology : Organizational Boundaries As Trust Production, NBER WorkingPaper No. 5199, National Bureau of Economic

Complete cDNAs from Nylanderia cf. pubens (Hymenoptera: Formicidae). --GenBank accession numbers: JF815100-JF815104

USDA-ARS?s Scientific Manuscript database

5 new gene sequences were identified from workers of Caribbean crazy ant, Nylanderia cf. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are JF815100-JF815104. This information will provide scientists with genetic tools to study the popu...

Complete cDNAs from Nylanderia sp. nr. pubens (Hymenoptera: Formicidae). GenBank GU980916-GU980928.

USDA-ARS?s Scientific Manuscript database

13 new gene sequences were identified from workers of Rasberry crazy ant, Nylanderia sp.nr. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU980916-GU980928. This information will provide scientists with genetic tools to study the p...

TECHNOLOGICAL INFORMATION REGARDING PREBIOTICS AND PROBIOTICS NUTRITION VERSUS THE PATENT REGISTERS: WHAT IS NEW?

PubMed

Reis, José Maciel Caldas Dos; Pinheiro, Maurício Fortuna; Oti, André Takashi; Feitosa-Junior, Denilson José Silva; Pantoja, Mauro de Souza; Barros, Rui Sérgio Monteiro

2016-01-01

Food is a key factor both in prevention and in promoting human health. Among the functional food are highlighted probiotics and prebiotics. Patent databases are the main source of technological information about innovation worldwide, providing extensive library for research sector. Perform mapping in the main patent databases about pre and probiotics, seeking relevant information regarding the use of biotechnology, nanotechnology and genetic engineering in the production of these foods. Electronic consultation was conducted (online) in the main public databases of patents in Brazil (INPI), United States (USPTO) and the European Patent Bank (EPO). The research involved the period from January 2014 to July 2015, being used in the title fields and summary of patents, the following descriptors in INPI "prebiotic", "prebiotic" "probiotics", "probiotic" and the USPTO and EPO: "prebiotic", "prebiotics", "probiotic", "probiotics". This search haven't found any deposit at the brazilian patents website (INPI) in this period; US Patent &Trademark Office had registered 60 titles in patents and the European Patent Office (EPO) showed 10 documents on the issue. Information technology offered by genetic engineering, biotechnology and nanotechnology deposited in the form of titles and abstracts of patents in relation to early nutritional intervention as functional foods, has increasingly required to decrease the risks and control the progression of health problems. But, the existing summaries, although attractive and promising in this sense, are still incipient to recommend them safely as a therapeutic tool. Therefore, they should be seen more as diet elements and healthy lifestyles. A alimentação é fator primordial tanto na prevenção quanto na promoção para a saúde humana. Dentre os alimentos funcionais destacam-se os probióticos e prebióticos. Os bancos de dados de patentes representam a maior fonte de informação tecnológica acerca de inovação em nível mundial, provendo vasta biblioteca para o setor de pesquisa. Realizar mapeamento nas principais bases de dados de patentes relacionada aos pré e probióticos buscando informações relevantes com relação ao uso da biotecnologia, nanotecnologia e engenharia genética na produção desses alimentos. Foi realizada consulta eletrônica (online) nas principais bases de dados públicas de patentes do Brasil (INPI), Estados Unidos da América (USPTO) e o Banco de Patentes Europeu (EPO). A pesquisa envolveu o período de janeiro de 2014 a julho 2015, sendo utilizado nos campos de título e resumo das patentes, os seguintes descritores no INPI: "prebiótico", "prebióticos" "probiótico", "probióticos" e no USPTO e EPO: "prebiotic", "prebiotics", "probiotic", "probiotics". Não foram observados, no INPI, depósitos de residentes (empresas ou universidades). Já no USPTO foram detectados 60 depósitos e no EPO 10 títulos de interesse à pesquisa. A tecnologia da informação ofertada pela engenharia genética, biotecnologia e nanotecnologia depositada na forma de títulos e resumos das patentes em relação à intervenção nutricional precoce como alimentos funcionais, tem cada vez mais pretendido diminuir os riscos e controlar a progressão de agravos à saúde. Mas, os resumos existentes, embora atraentes e promissores neste sentido, ainda são incipientes para recomendá-los de forma segura como ferramenta terapêutica. Portanto, devem ser encarados mais como integrantes de dieta e estilos de vida saudáveis.

Sharing Malaysian experience with the development of biotechnology-derived food crops.

PubMed

Abu Bakar, Umi K; Pillai, Vilasini; Hashim, Marzukhi; Daud, Hassan Mat

2005-12-01

Biotechnology-derived food crops are currently being developed in Malaysia mainly for disease resistance and improved post harvest quality. The modern biotechnology approach is adopted because of its potential to overcome constraints faced by conventional breeding techniques. Research on the development of biotechnology-derived papaya, pineapple, chili, passion fruit, and citrus is currently under way. Biotechnology-derived papaya developed for resistance to papaya ringspot virus (PRSV) and improved postharvest qualities is at the field evaluation stage. Pineapple developed for resistance to fruit black heart disorder is also being evaluated for proof-of-concept. Other biotechnology-derived food crops are at early stages of gene cloning and transformation. Activities and products involving biotechnology-derived crops will be fully regulated in the near future under the Malaysian Biosafety Law. At present they are governed only by guidelines formulated by the Genetic Modification Advisory Committee (GMAC), Malaysia. Commercialization of biotechnology-derived crops involves steps that require GMAC approval for all field evaluations and food-safety assessments before the products are placed on the market. Public acceptance of the biotechnology product is another important factor for successful commercialization. Understanding of biotechnology is generally low among Malaysians, which may lead to low acceptance of biotechnology-derived products. Initiatives are being taken by local organizations to improve public awareness and acceptance of biotechnology. Future research on plant biotechnology will focus on the development of nutritionally enhanced biotechnology-derived food crops that can provide more benefits to consumers.

Biotechnology worldwide and the 'European Biotechnology Thematic Network' Association (EBTNA).

PubMed

Bruschi, F; Dundar, M; Gahan, P B; Gartland, K; Szente, M; Viola-Magni, M P; Akbarova, Y

2011-09-01

The European Biotechnology Congress 2011 held under the auspices of the European Biotechnology Thematic Network Association (EBTNA) in conjunction with the Turkish Medical Genetics Association brings together a broad spectrum of biotechnologists from around the world. The subsequent abstracts indicate the manner in which biotechnology has permeated all aspects of research from the basic sciences through to small and medium enterprises and major industries. The brief statements before the presentation of the abstracts aim to introduce not only Biotechnology in general and its importance around the world, but also the European Biotechnology Thematic Network Association and its aims especially within the framework of education and ethics in biotechnology. Copyright © 2011 Elsevier Ltd. All rights reserved.

75 FR 41798 - Solicitation of Letters of Interest to Participate in Biotechnology Quality Management System...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-19

...] Solicitation of Letters of Interest to Participate in Biotechnology Quality Management System Program AGENCY... participate in the APHIS Biotechnology Quality Management System Program. The Biotechnology Quality Management..., audit-based compliance assistance program known as the Biotechnology Quality Management System Program...

[The past 30 years of Chinese Journal of Biotechnology].

PubMed

Jiang, Ning

2015-06-01

This review addresses the association of "Chinese Journal of Biotechnology" and the development of biotechnology in China in the past 30 years. Topics include relevant awards and industrialization, development of the biotechnology discipline, and well know scientists in biotechnology, as well as perspectives on the journal.

Disclosing Biology Teachers' Beliefs about Biotechnology and Biotechnology Education

ERIC Educational Resources Information Center

Fonseca, Maria Joao; Costa, Patricio; Lencastre, Leonor; Tavares, Fernando

2012-01-01

Teachers have been shown to frequently avoid addressing biotechnology topics. Aiming to understand the extent to which teachers' scarce engagement in biotechnology teaching is influenced by their beliefs and/or by extrinsic constraints, such as practical limitations, this study evaluates biology teachers' beliefs about biotechnology and…

The rise (and decline?) of biotechnology.

PubMed

Kinch, Michael S

2014-11-01

Since the 1970s, biotechnology has been a key innovator in drug development. An analysis of FDA-approved therapeutics demonstrates pharmaceutical companies outpace biotechs in terms of new approvals but biotechnology companies are now responsible for earlier-stage activities (patents, INDs or clinical development). The number of biotechnology organizations that contributed to an FDA approval began declining in the 2000s and is at a level not seen since the 1980s. Whereas early biotechnology companies had a decade from first approval until acquisition, the average acquisition of a biotechnology company now occurs months before their first FDA approval. The number of hybrid organizations that arise when pharmaceutical companies acquire biotechnology is likewise declining, raising questions about the sustainability of biotechnology. Copyright © 2014 Elsevier Ltd. All rights reserved.

A virtual computer lab for distance biomedical technology education.

PubMed

Locatis, Craig; Vega, Anibal; Bhagwat, Medha; Liu, Wei-Li; Conde, Jose

2008-03-13

The National Library of Medicine's National Center for Biotechnology Information offers mini-courses which entail applying concepts in biochemistry and genetics to search genomics databases and other information sources. They are highly interactive and involve use of 3D molecular visualization software that can be computationally taxing. Methods were devised to offer the courses at a distance so as to provide as much functionality of a computer lab as possible, the venue where they are normally taught. The methods, which can be employed with varied videoconferencing technology and desktop sharing software, were used to deliver mini-courses at a distance in pilot applications where students could see demonstrations by the instructor and the instructor could observe and interact with students working at their remote desktops. Student ratings of the learning experience and comments to open ended questions were similar to those when the courses are offered face to face. The real time interaction and the instructor's ability to access student desktops from a distance in order to provide individual assistance and feedback were considered invaluable. The technologies and methods mimic much of the functionality of computer labs and may be usefully applied in any context where content changes frequently, training needs to be offered on complex computer applications at a distance in real time, and where it is necessary for the instructor to monitor students as they work.

Tobacco industry sponsorship of a book and conflict of interest.

PubMed

Hong, Mi-Kyung; Bero, Lisa A

2006-08-01

The tobacco industry has hidden its involvement in the design, conduct and publication of scientific research articles and has used the articles to argue against tobacco regulation. The objective of this study is to examine tobacco industry involvement in the development of scientific books. Qualitative analysis of previously secret internal tobacco industry documents retrieved from the Legacy Tobacco Documents Library (http://legacy.library.ucsf.edu). Information from the documents was supplemented with material from Internet searches, the National Center for Biotechnology Information Pubmed database and interviews with individuals involved in book publication. Between 1997 and 1999 the tobacco industry sponsored a monograph, entitled 'Analytical Determination of Nicotine and Related Compounds and their Metabolites', that examined the measurement and metabolism of nicotine. The tobacco industry recruited Elsevier Science to publish the monograph. Tobacco industry executives, lawyers and scientists reviewed the chapters. One use of the monograph was to stimulate collaborative efforts between academic and tobacco industry scientists. Another was to provide the book to a government regulatory agency reviewing the teratogenic effects of nicotine. Our findings show the breadth of tobacco industry engagement in scientific knowledge production and dissemination, and its motives for sponsoring scientific literature. The industry's effort to gain credibility through collaboration with academic scientists raises questions regarding the ethics of accepting tobacco industry funding for publication. Scientists who collaborate on publications sponsored by the tobacco industry must consider the full implications of these joint efforts.

Determinants of public attitudes to genetically modified salmon.

PubMed

Amin, Latifah; Azad, Md Abul Kalam; Gausmian, Mohd Hanafy; Zulkifli, Faizah

2014-01-01

The objective of this paper is to assess the attitude of Malaysian stakeholders to genetically modified (GM) salmon and to identify the factors that influence their acceptance of GM salmon using a structural equation model. A survey was carried out on 434 representatives from various stakeholder groups in the Klang Valley region of Malaysia. Public attitude towards GM salmon was measured using self-developed questionnaires with seven-point Likert scales. The findings of this study have confirmed that public attitudes towards GM salmon is a complex issue and should be seen as a multi-faceted process. The most important direct predictors for the encouragement of GM salmon are the specific application-linked perceptions about religious acceptability of GM salmon followed by perceived risks and benefits, familiarity, and general promise of modern biotechnology. Encouragement of GM salmon also involves the interplay among other factors such as general concerns of biotechnology, threatening the natural order of things, the need for labeling, the need for patenting, confidence in regulation, and societal values. The research findings can serve as a database that will be useful for understanding the social construct of public attitude towards GM foods in a developing country.

Pharmacological and biotechnological advances with Rosmarinus officinalis L.

PubMed

Neves, Josynaria Araújo; Neves, Josyanne Araújo; Oliveira, Rita de Cassia Meneses

2018-05-01

Rosmarinus officinalis L. is an aromatic plant with a number of biological properties. Recently, has been studied regarding its therapeutic potential. The objective of this study was to perform a systematic review on R. officinalis essential oil for its pharmacological properties and biotechnological applications. Areas covered: The databases were searched for articles (Science Direct, Pub Med and Web of Science) and patents (INPI, WIPO and EPO) with publications on R. officinalis and associations with essential oil (EO-Ro), cardiovascular system, hypertension and cyclodextrin. We selected 305 articles on EO-Ro in the most diverse subjects and six articles with of R. officinalis associated with hypertension. 59 patents were analyzed. The results demonstrate how extensive the studies are on the biological activities with the extract and EO-Ro. These have shown effects antibacterial, antifungal, anti-inflammatory, antitumor and other. The properties exhibited by EO-Ro reinforce the use of this plant as a phytotherapeutic agent. Expert opinion: Although there are several pharmacological properties, studies on the prevention or treatment of cardiovascular diseases with EO-Ro are scarce, especially to evaluate the antihypertensive activity of EO-Ro. It has also become clear that EO-Ro can be exploited in different commercial products as supplement, cosmetics and new formulations.

Determinants of Public Attitudes to Genetically Modified Salmon

PubMed Central

Amin, Latifah; Azad, Md. Abul Kalam; Gausmian, Mohd Hanafy; Zulkifli, Faizah

2014-01-01

The objective of this paper is to assess the attitude of Malaysian stakeholders to genetically modified (GM) salmon and to identify the factors that influence their acceptance of GM salmon using a structural equation model. A survey was carried out on 434 representatives from various stakeholder groups in the Klang Valley region of Malaysia. Public attitude towards GM salmon was measured using self-developed questionnaires with seven-point Likert scales. The findings of this study have confirmed that public attitudes towards GM salmon is a complex issue and should be seen as a multi-faceted process. The most important direct predictors for the encouragement of GM salmon are the specific application-linked perceptions about religious acceptability of GM salmon followed by perceived risks and benefits, familiarity, and general promise of modern biotechnology. Encouragement of GM salmon also involves the interplay among other factors such as general concerns of biotechnology, threatening the natural order of things, the need for labeling, the need for patenting, confidence in regulation, and societal values. The research findings can serve as a database that will be useful for understanding the social construct of public attitude towards GM foods in a developing country. PMID:24489695

Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9A gene of Clostridium thermocellum.

PubMed

Schwarz, Wolfgang H; Brunecky, Roman; Broeker, Jannis; Liebl, Wolfgang; Zverlov, Vladimir V

2018-02-26

An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with a respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.

Biotechnology: Impact on sugarcane agriculture and industry

USDA-ARS?s Scientific Manuscript database

Of the nine key technology issues that affect the sustainability of the sugar- or bio-energy- cane industry, namely: land, fertility, water, variety, planting density, crop protection, cultural practices, harvesting and processing, and lately, information technology, growing the right varieties rema...

7 CFR 3406.16 - Scope of a research proposal.

Code of Federal Regulations, 2010 CFR

2010-01-01

... of nutrition, housing, and life-style choices, and of community strategies for meeting the changing..., sustainable agriculture, biotechnology, agribusiness management and marketing, and aquaculture. (b... systems for nutrition information or for resource management assistance for low-income families and...

Impact of biotechnology on sugarcane agriculture and industry

USDA-ARS?s Scientific Manuscript database

There are nine key issues that can influence the productivity and sustainability of the sugarcane industry. These include land, soil fertility, water, variety, planting density, crop protection, cultural practices, harvesting and processing, and information technology. To all sugarcane farmers, it r...

Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1987

1987-01-01

Contains 21 articles ranging from instructional experiments to topical information. Deals with investigation of plant rust diseases, using computers to teach biology, plant roots, a biotechnology curriculum, the corrosion of oxides, electrochemical simulations, the Reimer-Tiemann reaction, the oxidation of aldehydes, and the extraction of iodine…

Editorial: Biotechnology Journal brings more than biotechnology.

PubMed

Jungbauer, Alois; Lee, Sang Yup

2015-09-01

Biotechnology Journal always brings the state-of-the-art biotechnologies to our readers. Different from other topical issues, this issue of Biotechnology Journal is complied with a series of exiting reviews and research articles from spontaneous submissions, again, addressing society's actual problems and needs. The progress is a real testimony how biotechnology contributes to achievements in healthcare, better utilization of resources, and a bio-based economy. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biosafety considerations for selectable and scorable markers used in cassava (Manihot esculenta Crantz) biotechnology.

PubMed

Petersen, William; Umbeck, Paul; Hokanson, Karen; Halsey, Mark

2005-01-01

Cassava is an important subsistence crop grown only in the tropics, and represents a major source of calories for many people in developing countries. Improvements in the areas of resistance to insects and viral diseases, enhanced nutritional qualities, reduced cyanogenic content and modified starch characteristics are urgently needed. Traditional breeding is hampered by the nature of the crop, which has a high degree of heterozygosity, irregular flowering, and poor seed set. Biotechnology has the potential to enhance crop improvement efforts, and genetic engineering techniques for cassava have thus been developed over the past decade. Selectable and scorable markers are critical to efficient transformation technology, and must be evaluated for biosafety, as well as efficiency and cost-effectiveness. In order to facilitate research planning and regulatory submission, the literature on biosafety aspects of the selectable and scorable markers currently used in cassava biotechnology is surveyed. The source, mode of action and current use of each marker gene is described. The potential for toxicity, allergenicity, pleiotropic effects, horizontal gene transfer, and the impact of these on food or feed safety and environmental safety is evaluated. Based on extensive information, the selectable marker genes nptII, hpt, bar/pat, and manA, and the scorable marker gene uidA, all have little risk in terms of biosafety. These appear to represent the safest options for use in cassava biotechnology available at this time.

Biotechnology for Non-biology Majors: An Activity Using a Commercial Biotechnology Laboratory.

ERIC Educational Resources Information Center

Wray, Francis P.; Fox, Mary C.; Huether, Carl A.; Schurdak, Eric R.

2001-01-01

Presents an inexpensive activity to stimulate student interest in biotechnology that was developed in partnership with a biotechnology company. Focuses on the use of DNA by a commercial laboratory; describing the analysis procedure; important uses of DNA technology in modern society; and ethical, social, and legal issues related to biotechnology.…

Biotechnology, nanotechnology, and pharmacogenomics and pharmaceutical compounding, Part 1.

PubMed

Allen, Loyd V

2015-01-01

The world of pharmaceuticals is changing rapidly as biotechnology continues to grow and nanotechnology appears on the horizon. Biotechnology is gaining in importance in extemporaneous pharmaceutical compounding, and nanotechnology and pharmacogenomics could drastically change the practice of pharmacy. This article discusses biotechnology and the factors to consider when compounding biotechnology drugs.

Bioart.

PubMed

Yetisen, Ali K; Davis, Joe; Coskun, Ahmet F; Church, George M; Yun, Seok Hyun

2015-12-01

Bioart is a creative practice that adapts scientific methods and draws inspiration from the philosophical, societal, and environmental implications of recombinant genetics, molecular biology, and biotechnology. Some bioartists foster inter- disciplinary relationships that blur distinctions between art and science. Others emphasize critical responses to emerging trends in the life sciences. Since bioart can be combined with realistic views of scientific developments, it may help inform the public about science. Artistic responses to biotechnology also integrate cultural commentary resembling political activism. Art is not only about ‘responses’, however. Bioart can also initiate new science and engineer- ing concepts, foster openness to collaboration and increasing scientific literacy, and help to form the basis of artists’ future relationships with the communities of biology and the life sciences.

A systematic review of the need for MRI for the clearance of cervical spine injury in obtunded blunt trauma patients after normal cervical spine CT.

PubMed

James, Iyore Ao; Moukalled, Ahmad; Yu, Elizabeth; Tulman, David B; Bergese, Sergio D; Jones, Christian D; Stawicki, Stanislaw Pa; Evans, David C

2014-10-01

Clearance of cervical spine injury (CSI) in the obtunded or comatose blunt trauma patient remains controversial. In patients with unreliable physical examination and no evidence of CSI on computed tomography (CT), magnetic resonance imaging of the cervical spine (CS-MRI) is the typical follow-up study. There is a growing body of evidence suggesting that CS-MRI is unnecessary with negative findings on a multi-detector CT (MDCT) scan. This review article systematically analyzes current literature to address the controversies surrounding clearance of CSI in obtunded blunt trauma patients. A literature search through MEDLINE database was conducted using all databases on the National Center for Biotechnology Information (NCBI) website (www.ncbi.nlm.nih.gov) for keywords: "cervical spine injury," "obtunded," and "MRI." The search was limited to studies published within the last 10 years and with populations of patients older than 18 years old. Eleven studies were included in the analysis yielding data on 1535 patients. CS-MRI detected abnormalities in 256 patients (16.6%). The abnormalities reported on CS-MRI resulted in prolonged rigid c-collar immobilization in 74 patients (4.9%). Eleven patients (0.7%) had unstable injury detected on CS-MRI alone that required surgical intervention. In the obtunded blunt trauma patient with unreliable clinical examination and a normal CT scan, there is still a role for CS-MRI in detecting clinically significant injuries when MRI resources are available. However, when a reliable clinical exam reveals intact gross motor function, CS-MRI may be unnecessary.

Key genes and pathways in measles and their interaction with environmental chemicals

PubMed Central

Zhang, Rongqiang; Jiang, Hualin; Li, Fengying; Su, Ning; Ding, Yi; Mao, Xiang; Ren, Dan; Wang, Jing

2018-01-01

The aim of the present study was to explore key genes that may have a role in the pathology of measles virus infection and to clarify the interaction networks between environmental factors and differentially expressed genes (DEGs). After screening the database of the Gene Expression Omnibus of the National Center for Biotechnology Information, the dataset GSE5808 was downloaded and analyzed. A global normalization method was performed to minimize data inconsistencies and heterogeneity. DEGs during different stages of measles virus infection were explored using R software (v3.4.0). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs were performed using Cytoscape 3.4.0 software. A protein-protein interaction (PPI) network of the DEGs was obtained from the STRING database v9.05. A total of 43 DEGs were obtained from four analyzed sample groups, including 10 highly expressed genes and 33 genes with decreased expression. The most enriched pathways based on KEGG analysis were fatty acid elongation, cytokine-cytokine receptor interaction and RNA degradation. The genes mentioned in the PPI network were mainly associated with protein binding and chemokine activity. A total of 219 chemicals were identified that may, jointly or on their own, interact with the 6 DEGs between the control group and patients with measles (at hospital entry), including benzo(a)pyrene (BaP) and tetrachlorodibenzodioxin (TCDD). In conclusion, the present study revealed that chemokines and environmental chemicals, e.g. BaP and TCDD, may affect the development of measles. PMID:29805511

Approaches to education of pharmaceutical biotechnology in faculties of pharmacy.

PubMed

Calis, S; Oner, F; Kas, S; Hincal, A A

2001-06-01

Pharmaceutical biotechnology is developing rapidly both in academic institutions and in the biopharmaceutical industry. For this reason, FIP Special Interest Group of Pharmaceutical Biotechnology decided to develop a questionnaire concerning pharmaceutical biotechnology education. After preliminary studies were completed, questionnaires were sent to the leading scientists in academia and research directors or senior managers of various Pharmaceutical Biotechnology Companies in order to gather their views about how to create a satisfactory program. The objectives of this study were as follows: -To review all of the graduate and undergraduate courses which are presently available worldwide on pharmaceutical biotechnology in Faculties of Pharmacy. -To review all of the text books, references and scientific sources available worldwide in the area of pharmaceutical biotechnology. When replying to the questionnaires, the respondents were asked to consider the present status of pharmaceutical biotechnology education in academia and future learning needs in collaboration with the biotechnology industry. The data from various pharmacy faculties and biotechnology industry representatives from Asia, Europe and America were evaluated and the outcome of the survey showed that educational efforts in training qualified staff in the rapidly growing field of pharmaceutical biotechnology is promising. Part of the results of this questionnaire study have already been presented at the 57th International Congress of FIP Vancouver, Canada in 1997.

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

PubMed Central

Jespersen, Martin Closter; Peters, Bjoern

2017-01-01

Abstract Antibodies have become an indispensable tool for many biotechnological and clinical applications. They bind their molecular target (antigen) by recognizing a portion of its structure (epitope) in a highly specific manner. The ability to predict epitopes from antigen sequences alone is a complex task. Despite substantial effort, limited advancement has been achieved over the last decade in the accuracy of epitope prediction methods, especially for those that rely on the sequence of the antigen only. Here, we present BepiPred-2.0 (http://www.cbs.dtu.dk/services/BepiPred/), a web server for predicting B-cell epitopes from antigen sequences. BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures. This new method was found to outperform other available tools for sequence-based epitope prediction both on epitope data derived from solved 3D structures, and on a large collection of linear epitopes downloaded from the IEDB database. The method displays results in a user-friendly and informative way, both for computer-savvy and non-expert users. We believe that BepiPred-2.0 will be a valuable tool for the bioinformatics and immunology community. PMID:28472356

Supervised Clustering Based on DPClusO: Prediction of Plant-Disease Relations Using Jamu Formulas of KNApSAcK Database

PubMed Central

Husnawati, Husnawati; Afendi, Farit Mochamad; Darusman, Latifah K.; Altaf-Ul-Amin, Md.; Sato, Tetsuo; Ono, Naoaki; Sugiura, Tadao; Kanaya, Shigehiko

2014-01-01

Indonesia has the largest medicinal plant species in the world and these plants are used as Jamu medicines. Jamu medicines are popular traditional medicines from Indonesia and we need to systemize the formulation of Jamu and develop basic scientific principles of Jamu to meet the requirement of Indonesian Healthcare System. We propose a new approach to predict the relation between plant and disease using network analysis and supervised clustering. At the preliminary step, we assigned 3138 Jamu formulas to 116 diseases of International Classification of Diseases (ver. 10) which belong to 18 classes of disease from National Center for Biotechnology Information. The correlation measures between Jamu pairs were determined based on their ingredient similarity. Networks are constructed and analyzed by selecting highly correlated Jamu pairs. Clusters were then generated by using the network clustering algorithm DPClusO. By using matching score of a cluster, the dominant disease and high frequency plant associated to the cluster are determined. The plant to disease relations predicted by our method were evaluated in the context of previously published results and were found to produce around 90% successful predictions. PMID:24804251

Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae)

PubMed Central

Vongsangnak, Wanwipa; Chumnanpuen, Pramote

2016-01-01

Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system. PMID:27761329

Microsatellite analysis in the genome of Acanthaceae: An in silico approach.

PubMed

Kaliswamy, Priyadharsini; Vellingiri, Srividhya; Nathan, Bharathi; Selvaraj, Saravanakumar

2015-01-01

Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future.

Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov.

PubMed

Bach, Evelise; Sant'Anna, Fernando Hayashi; Magrich Dos Passos, João Frederico; Balsanelli, Eduardo; de Baura, Valter Antonio; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Passaglia, Luciane Maria Pereira

2017-08-31

The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

PubMed

Salek, Reza M; Neumann, Steffen; Schober, Daniel; Hummel, Jan; Billiau, Kenny; Kopka, Joachim; Correa, Elon; Reijmers, Theo; Rosato, Antonio; Tenori, Leonardo; Turano, Paola; Marin, Silvia; Deborde, Catherine; Jacob, Daniel; Rolin, Dominique; Dartigues, Benjamin; Conesa, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; O'Hagan, Steve; Hao, Jie; van Vliet, Michael; Sysi-Aho, Marko; Ludwig, Christian; Bouwman, Jildau; Cascante, Marta; Ebbels, Timothy; Griffin, Julian L; Moing, Annick; Nikolski, Macha; Oresic, Matej; Sansone, Susanna-Assunta; Viant, Mark R; Goodacre, Royston; Günther, Ulrich L; Hankemeier, Thomas; Luchinat, Claudio; Walther, Dirk; Steinbeck, Christoph

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative 'coordination of standards in metabolomics' (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities' participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

The biotechnology innovation machine: a source of intelligent biopharmaceuticals for the pharma industry--mapping biotechnology's success.

PubMed

Evens, R P; Kaitin, K I

2014-05-01

The marriage of biotechnology and the pharmaceutical industry (pharma) is predicated on an evolution in technology and product innovation. It has come as a result of advances in both the science and the business practices of the biotechnology sector in the past 30 years. Biotechnology products can be thought of as "intelligent pharmaceuticals," in that they often provide novel mechanisms of action, new approaches to disease control, higher clinical success rates, improved patient care, extended patent protection, and a significant likelihood of reimbursement. Although the first biotechnology product, insulin, was approved just 32 years ago in 1982, today there are more than 200 biotechnology products commercially available. Research has expanded to include more than 900 biotechnology products in clinical trials. Pharma is substantially engaged in both the clinical development of these products and their commercialization.

Friends of the National Library of Medicine - How You Can Help the Library Extend Medical Knowledge

MedlinePlus

... Lipman (center), Director of the National Center for Biotechnology Information (NCBI) was among the hosts for the ... sponsorship and other charitable donations for NIH MedlinePlus magazine's publication and distribution, many more thousands of Americans ...

Raising Global Citizens: Focus on Cultural Competency

ERIC Educational Resources Information Center

Koprucu, Sirin

2009-01-01

Corporate leaders of high-growth initiative employment sectors, such as advanced manufacturing, aerospace, automotive, biotechnology, health care, hospitality, information technology, and homeland security, are not the only ones who list intercultural communication and management skills as business requisites. The entrepreneurs who are expected to…

Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology.

PubMed

Lee, Kang-Hoon; Lee, Young-Kwan; Kwon, Deug-Nam; Chiu, Sophia; Chew, Victoria; Rah, Hyungchul; Kujawski, Gregory; Melhem, Ramzi; Hsu, Karen; Chung, Cecilia; Greenhalgh, David G; Cho, Kiho

2011-06-01

Approximately 2% of the human genome is reported to be occupied by genes. Various forms of repetitive elements (REs), both characterized and uncharacterized, are presumed to make up the vast majority of the rest of the genomes of human and other species. In conjunction with a comprehensive annotation of genes, information regarding components of genome biology, such as gene polymorphisms, non-coding RNAs, and certain REs, is found in human genome databases. However, the genome-wide profile of unique RE arrangements formed by different groups of REs has not been fully characterized yet. In this study, the entire human genome was subjected to an unbiased RE survey to establish a whole-genome profile of REs and their arrangements. Due to the limitation in query size within the bl2seq alignment program (National Center for Biotechnology Information [NCBI]) utilized for the RE survey, the entire NCBI reference human genome was fragmented into 6206 units of 0.5M nucleotides. A number of RE arrangements with varying complexities and patterns were identified throughout the genome. Each chromosome had unique profiles of RE arrangements and density, and high levels of RE density were measured near the centromere regions. Subsequently, 175 complex RE arrangements, which were selected throughout the genome, were subjected to a comparison analysis using five different human genome sequences. Interestingly, three of the five human genome databases shared the exactly same arrangement patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 nucleotides). The findings from this study demonstrate that a substantial fraction of REs in the human genome are clustered into various forms of ordered structures. Further investigations are needed to examine whether some of these ordered RE arrangements contribute to the human pathobiology as a functional genome unit. Copyright © 2011 Elsevier Inc. All rights reserved.

Endo-cannabinoids system and the toxicity of cannabinoids with a biotechnological approach

PubMed Central

Niaz, Kamal; Khan, Fazlullah; Maqbool, Faheem; Momtaz, Saeideh; Ismail Hassan, Fatima; Nobakht-Haghighi, Navid; Rahimifard, Mahban; Abdollahi, Mohammad

2017-01-01

Cannabinoids have shown diverse and critical effects on the body systems, which alter the physiological functions. Synthetic cannabinoids are comparatively innovative misuse drugs with respect to their nature of synthesis. Synthetic cannabinoids therapy in healthy, chain smokers, and alcoholic individuals cause damage to the immune and nervous system, eventually leading to intoxication throughout the body. Relevant studies were retrieved using major electronic databases such as PubMed, EMBASE, Medline, Scopus, and Google Scholar. The extensive use of Cannabis Sativa L. (C. Sativa) and its derivatives/analogues such as the nonpsychoactive dimethyl heptyl homolog (CBG-DMH), and tetrahydrocannabivarin (THCV) amongst juveniles and adults have been enhanced in recent years. Cannabinoids play a crucial role in the induction of respiratory, reproductive, immune and carcinogenic effects; however, potential data about mutagenic and developmental effects are still insufficient. The possible toxicity associated with the prolong use of cannabinoids acts as a tumor promoter in animal models and humans. Particular synthetic cannabinoids and analogues have low affinity for CB1 or CB2 receptors, while some synthetic members like Δ9-THC have high affinity towards these receptors. Cannabinoids and their derivatives have a direct or indirect association with acute and long-term toxicity. To reduce/attenuate cannabinoids toxicity, pharmaceutical biotechnology and cloning methods have opened a new window to develop cannabinoids encoding the gene tetrahydrocannabinolic acid (THCA) synthase. Plant revolution and regeneration hindered genetic engineering in C. Sativa. The genetic culture suspension of C. Sativa can be transmuted by the use of Agrobacterium tumefaciens to overcome its toxicity. The main aim of the present review was to collect evidence of the endo-cannabinoid system (ECS), cannabinoids toxicity, and the potential biotechnological approach of cannabinoids synthesis. PMID:28827985

Engineering Pseudomonas for phenazine biosynthesis, regulation, and biotechnological applications: a review.

PubMed

Bilal, Muhammad; Guo, Shuqi; Iqbal, Hafiz M N; Hu, Hongbo; Wang, Wei; Zhang, Xuehong

2017-10-03

Pseudomonas strains are increasingly attracting considerable attention as a valuable bacterial host both for basic and applied research. It has been considered as a promising candidate to produce a variety of bioactive secondary metabolites, particularly phenazines. Apart from the biotechnological perspective, these aromatic compounds have the notable potential to inhibit plant-pathogenic fungi and thus are useful in controlling plant diseases. Nevertheless, phenazines production is quite low by the wild-type strains that necessitated its yield improvement for large-scale agricultural applications. Metabolic engineering approaches with the advent of plentiful information provided by systems-level genomic and transcriptomic analyses enabled the development of new biological agents functioning as potential cell factories for producing the desired level of value-added bioproducts. This study presents an up-to-date overview of recombinant Pseudomonas strains as the preferred choice of host organisms for the biosynthesis of natural phenazines. The biosynthetic pathway and regulatory mechanism involved in the phenazine biosynthesis are comprehensively discussed. Finally, a summary of biological functionalities and biotechnological applications of the phenazines is also provided.

Thermostable microbial xylanases for pulp and paper industries: trends, applications and further perspectives.

PubMed

Kumar, Vishal; Marín-Navarro, Julia; Shukla, Pratyoosh

2016-02-01

Xylanases are enzymes with biotechnological relevance in a number of fields, including food, feed, biofuel, and textile industries. Their most significant application is in the paper and pulp industry, where they are used as a biobleaching agent, showing clear economic and environmental advantages over chemical alternatives. Since this process requires high temperatures and alkali media, the identification of thermostable and alkali stable xylanases represents a major biotechnological goal in this field. Moreover, thermostability is a desirable property for many other applications of xylanases. The review makes an overview of xylanase producing microorganisms and their current implementation in paper biobleaching. Future perspectives are analyzed focusing in the efforts carried out to generate thermostable enzymes by means of modern biotechnological tools, including metagenomic analysis, enzyme molecular engineering and nanotechnology. Furthermore, structural and mutagenesis studies have revealed critical sites for stability of xylanases from glycoside hydrolase families GH10 and GH11, which constitute the main classes of these enzymes. The overall conclusions of these works are summarized here and provide relevant information about putative weak spots within xylanase structures to be targeted in future protein engineering approaches.

How is the Inquiry Skills of Biology Preservice Teachers in Biotechnology Lecture?

NASA Astrophysics Data System (ADS)

Hayat, M. S.; Rustaman, N. Y.

2017-09-01

This study was to investigate the inquiry skills of biology pre-service teachers in one teachers college in Central Java in biotechnology lecture. The method used is a case study of 29 biology preservice teacher. Data were collected using observation sheets, questionnaires, and interview guidelines. Research findings collected through questionnaires show that most students are accustomed to asking questions and formulating biotechnology issues; Skilled in conducting experiments; Skilled in obtaining relevant information from various sources; As well as skilled at processing, analyzing and interpreting data. Based on observation: lectures are not dominated by lecturers, students are able to solve problems encountered and conduct investigations. Based on the interview towards lecturers: students are always actively involved in questioning, investigation, inquiry, problem solving and experimenting in lectures. Why do most students show good inquiry skills? Because students are accustomed to invited inquiry in biology lectures. The impact, the students become more ready to be invited to do more advanced inquiry, such as real-world application inquiry, because the skill of inquiry is essentially trained.

Undisclosed conflicts of interest among biomedical textbook authors.

PubMed

Piper, Brian J; Lambert, Drew A; Keefe, Ryan C; Smukler, Phoebe U; Selemon, Nicolas A; Duperry, Zachary R

2018-02-05

Textbooks are a formative resource for health care providers during their education and are also an enduring reference for pathophysiology and treatment. Unlike the primary literature and clinical guidelines, biomedical textbook authors do not typically disclose potential financial conflicts of interest (pCoIs). The objective of this study was to evaluate whether the authors of textbooks used in the training of physicians, pharmacists, and dentists had appreciable undisclosed pCoIs in the form of patents or compensation received from pharmaceutical or biotechnology companies. The most recent editions of six medical textbooks, Harrison's Principles of Internal Medicine ( Har PIM), Katzung and Trevor's Basic and Clinical Pharmacology ( Kat BCP), the American Osteopathic Association's Foundations of Osteopathic Medicine ( AOA FOM), Remington: The Science and Practice of Pharmacy ( Rem SPP), Koda-Kimble and Young's Applied Therapeutics ( KKY AT), and Yagiela's Pharmacology and Therapeutics for Dentistry ( Yag PTD), were selected after consulting biomedical educators for evaluation. Author names (N = 1,152, 29.2% female) were submitted to databases to examine patents (Google Scholar) and compensation (ProPublica's Dollars for Docs [PDD]). Authors were listed as inventors on 677 patents (maximum/author = 23), with three-quarters (74.9%) to Har PIM authors. Females were significantly underrepresented among patent holders. The PDD 2009-2013 database revealed receipt of US$13.2 million, the majority to (83.9%) to Har PIM. The maximum compensation per author was $869,413. The PDD 2014 database identified receipt of $6.8 million, with 50.4% of eligible authors receiving compensation. The maximum compensation received by a single author was $560,021. Cardiovascular authors were most likely to have a PDD entry and neurologic disorders authors were least likely. An appreciable subset of biomedical authors have patents and have received remuneration from medical product companies and this information is not disclosed to readers. These findings indicate that full transparency of financial pCoI should become a standard practice among the authors of biomedical educational materials.

Students' Knowledge of, and Attitudes towards Biotechnology Revisited, 1995-2014: Changes in Agriculture Biotechnology but Not in Medical Biotechnology

ERIC Educational Resources Information Center

Chen, Shao-Yen; Chu, Yih-Ru; Lin, Chen-Yung; Chiang, Tzen-Yuh

2016-01-01

Modern biotechnology is one of the most important scientific and technological revolutions in the 21st century, with an increasing and measurable impact on society. Development of biotechnology curriculum has become important to high school bioscience classrooms. This study has monitored high school students in Taiwan on their knowledge of and…

Students' knowledge of, and attitudes towards biotechnology revisited, 1995-2014: Changes in agriculture biotechnology but not in medical biotechnology.

PubMed

Chen, Shao-Yen; Chu, Yih-Ru; Lin, Chen-Yung; Chiang, Tzen-Yuh

2016-09-10

Modern biotechnology is one of the most important scientific and technological revolutions in the 21st century, with an increasing and measurable impact on society. Development of biotechnology curriculum has become important to high school bioscience classrooms. This study has monitored high school students in Taiwan on their knowledge of and attitudes towards biotechnology for nearly two decades. Not surprisingly, knowledge of biotechnology of current students has increased significantly (p < 0.001) and most students have learned some definitions and examples of biotechnology. There was a positive correlation between biotechnology knowledge and attitudes toward biotechnology for current students who study Advanced Biology (AB). However, for current students who did not study AB, there was a negative correlation.The attitude results showed that students today expressed less favorable opinions toward agricultural biotechnology (p < 0.001) despite studying AB or not. However, there is no significant difference between students today and 18 years ago in opinions towards medical biotechnology. In addition, current students showed a greater concern involving environmental risks than former students. Interestingly, the high school curriculum did affect students' attitudes toward genetically engineered (GE) plants but not GE animals. Our current study also found that the students' attitude towards GE animals was influenced more by their limited knowledge than by their moral belief. On the basis of findings from this study, we suggest that more materials of emerging animal biotechnology should be included in high school curriculum and recommend that high school teachers and university faculty establish a collaborative framework in the near future. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(5):475-491, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Editorial: from plant biotechnology to bio-based products.

PubMed

Stöger, Eva

2013-10-01

From plant biotechnology to bio-based products - this Special Issue of Biotechnology Journal is dedicated to plant biotechnology and is edited by Prof. Eva Stöger (University of Natural Resources and Life Sciences, Vienna, Austria). The Special Issue covers a wide range of topics in plant biotechnology, including metabolic engineering of biosynthesis pathways in plants; taking advantage of the scalability of the plant system for the production of innovative materials; as well as the regulatory challenges and society acceptance of plant biotechnology. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Current state of biotechnology in Turkey.

PubMed

Dundar, Munis; Akbarova, Yagut

2011-09-01

Biotechnology is an interdisciplinary branch of science that encompasses a wide range of subjects like genetics, virology, microbiology, immunology, engineering to develop vaccines, and so on and plays a vital role in health systems, crop and seed management, yield improvement, agriculture, soil management, ecology, animal farming, cellular process, bio statistics, and so on. This article is about activities in medical and pharmaceutical biotechnology, environmental biotechnology, agricultural biotechnology and nanobiotechnology carried out in Turkey. Turkey has made some progress in biotechnology projects for research and development. Copyright © 2011 Elsevier Ltd. All rights reserved.

Space and biotechnology: An industry profile

NASA Technical Reports Server (NTRS)

Johnston, Richard S.; Norton, David J.; Tom, Baldwin H.

1988-01-01

The results of a study conducted by the Center for Space and Advanced Technology (CSAT) for NASA-JSC are presented. The objectives were to determine the interests and attitudes of the U.S. biotechnology industry toward space biotechnology and to prepare a concise review of the current activities of the biotechnology industry. In order to accomplish these objectives, two primary actions were taken. First, a questionnaire was designed, reviewed, and distributed to U.S. biotechnology companies. Second, reviews of the various biotechnology fields were prepared in several aspects of the industry. For each review, leading figures in the field were asked to prepare a brief review pointing out key trends and current industry technical problems. The result is a readable narrative of the biotechnology industry which will provide space scientists and engineers valuable clues as to where the space environment can be explored to advance the U.S. biotechnology industry.

"Othering" agricultural biotechnology: Slovenian media representation of agricultural biotechnology.

PubMed

Zajc, Jožica; Erjavec, Karmen

2014-08-01

While studies on media representations of agricultural biotechnology mostly analyse media texts, this work is intended to fill a research gap with an analysis of journalistic interpretations of media representations. The purpose of this project was to determine how news media represent agricultural biotechnology and how journalists interpret their own representations. A content and critical discourse analysis of news texts published in the Slovenian media over two years and in-depth interviews with their authors were conducted. News texts results suggest that most of the news posts were "othering" biotechnology and biotechnologists: biotechnology as a science and individual scientists are represented as "they," who are socially irresponsible, ignorant, arrogant, and "our" enemies who produce unnatural processes and work for biotechnology companies, whose greed is destroying people, animals, and the environment. Most journalists consider these representations to be objective because they have published the biotechnologists' opinions, despite their own negative attitudes towards biotechnology.

Integrated medical and behavioral laboratory measurement system engineering analysis and laboratory specification

NASA Technical Reports Server (NTRS)

Grave, C.; Margold, D. W.

1973-01-01

Site selection, program planning, cost and design studies for support of the IMBLMS program were investigated. Accomplishments are reported for the following areas: analysis of responses to site selection criteria, space-oriented biotechnology, life sciences payload definition, and program information transfer.

Governance Challenges of Technological Systems Convergence

ERIC Educational Resources Information Center

Whitman, Jim

2006-01-01

The convergence of several technological systems (especially nanotechnology, biotechnology, information technology, and robotics) has now been adopted as a strategic goal by several countries, most notably the United States and those of the European Union. The anticipated benefits and related fears of competitive disadvantage have brought together…

National Library of Medicine Celebrates 30 Years of Progress and Charts the Future | NIH MedlinePlus the Magazine

MedlinePlus

... described the genesis of the National Center for Biotechnology Information (NCBI); the Visible Human Project (a digital ... expand the publication and distribution of NIH MedlinePlus magazine, thousands and thousands more people will gain valuable, ...

77 FR 26725 - Advisory Committee on Biotechnology and 21st Century Agriculture Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-07

...; Fax (202) 690-4265; Email [email protected]ars.usda.gov . SUPPLEMENTARY INFORMATION: The next meeting of the AC21... Email at [email protected]ars.usda.gov at least 5 days prior to the meeting. Please provide your name...

Job Prospects for Agricultural Engineers.

ERIC Educational Resources Information Center

Basta, Nicholas

1986-01-01

Discusses the career outlook for agricultural engineers. Explains that the number of bachelor degrees awarded yearly continues to drop, and that the traditional industries that hire agricultural engineers are employing fewer each year. Suggests that future opportunities exist in the areas of information technology, biotechnology, and research. (TW)

Characterization of Botulinum Progenitor Toxins by Mass Spectrometry

DTIC Science & Technology

2005-08-01

and proteases by NTNH to HA-33 assistance in binding to and translocating progenitor toxin(s) through alimentary epithelial barriers (11, 12, 24...performed using peak list files generated by MassLynx (v3.5) and the following parameters: the National Center for Biotechnology Information

Designer cell signal processing circuits for biotechnology

PubMed Central

Bradley, Robert W.; Wang, Baojun

2015-01-01

Microorganisms are able to respond effectively to diverse signals from their environment and internal metabolism owing to their inherent sophisticated information processing capacity. A central aim of synthetic biology is to control and reprogramme the signal processing pathways within living cells so as to realise repurposed, beneficial applications ranging from disease diagnosis and environmental sensing to chemical bioproduction. To date most examples of synthetic biological signal processing have been built based on digital information flow, though analogue computing is being developed to cope with more complex operations and larger sets of variables. Great progress has been made in expanding the categories of characterised biological components that can be used for cellular signal manipulation, thereby allowing synthetic biologists to more rationally programme increasingly complex behaviours into living cells. Here we present a current overview of the components and strategies that exist for designer cell signal processing and decision making, discuss how these have been implemented in prototype systems for therapeutic, environmental, and industrial biotechnological applications, and examine emerging challenges in this promising field. PMID:25579192

Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining.

PubMed

Schallmey, Marcus; Koopmeiners, Julia; Wells, Elizabeth; Wardenga, Rainer; Schallmey, Anett

2014-12-01

Halohydrin dehalogenases are very rare enzymes that are naturally involved in the mineralization of halogenated xenobiotics. Due to their catalytic potential and promiscuity, many biocatalytic reactions have been described that have led to several interesting and industrially important applications. Nevertheless, only a few of these enzymes have been made available through recombinant techniques; hence, it is of general interest to expand the repertoire of these enzymes so as to enable novel biocatalytic applications. After the identification of specific sequence motifs, 37 novel enzyme sequences were readily identified in public sequence databases. All enzymes that could be heterologously expressed also catalyzed typical halohydrin dehalogenase reactions. Phylogenetic inference for enzymes of the halohydrin dehalogenase enzyme family confirmed that all enzymes form a distinct monophyletic clade within the short-chain dehydrogenase/reductase superfamily. In addition, the majority of novel enzymes are substantially different from previously known phylogenetic subtypes. Consequently, four additional phylogenetic subtypes were defined, greatly expanding the halohydrin dehalogenase enzyme family. We show that the enormous wealth of environmental and genome sequences present in public databases can be tapped for in silico identification of very rare but biotechnologically important biocatalysts. Our findings help to readily identify halohydrin dehalogenases in ever-growing sequence databases and, as a consequence, make even more members of this interesting enzyme family available to the scientific and industrial community. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes.

PubMed

Li, Ben; Sun, Zhaonan; He, Qing; Zhu, Yu; Qin, Zhaohui S

2016-03-01

Modern high-throughput biotechnologies such as microarray are capable of producing a massive amount of information for each sample. However, in a typical high-throughput experiment, only limited number of samples were assayed, thus the classical 'large p, small n' problem. On the other hand, rapid propagation of these high-throughput technologies has resulted in a substantial collection of data, often carried out on the same platform and using the same protocol. It is highly desirable to utilize the existing data when performing analysis and inference on a new dataset. Utilizing existing data can be carried out in a straightforward fashion under the Bayesian framework in which the repository of historical data can be exploited to build informative priors and used in new data analysis. In this work, using microarray data, we investigate the feasibility and effectiveness of deriving informative priors from historical data and using them in the problem of detecting differentially expressed genes. Through simulation and real data analysis, we show that the proposed strategy significantly outperforms existing methods including the popular and state-of-the-art Bayesian hierarchical model-based approaches. Our work illustrates the feasibility and benefits of exploiting the increasingly available genomics big data in statistical inference and presents a promising practical strategy for dealing with the 'large p, small n' problem. Our method is implemented in R package IPBT, which is freely available from https://github.com/benliemory/IPBT CONTACT: yuzhu@purdue.edu; zhaohui.qin@emory.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Societal response to nanotechnology: converging technologies-converging societal response research?

NASA Astrophysics Data System (ADS)

Ronteltap, Amber; Fischer, Arnout R. H.; Tobi, Hilde

2011-10-01

Nanotechnology is an emerging technology particularly vulnerable to societal unrest, which may hinder its further development. With the increasing convergence of several technological domains in the field of nanotechnology, so too could convergence of social science methods help to anticipate societal response. This paper systematically reviews the current state of convergence in societal response research by first sketching the predominant approaches to previous new technologies, followed by an analysis of current research into societal response to nanotechnology. A set of 107 papers on previous new technologies shows that rational actor models have played an important role in the study of societal response to technology, in particular in the field of information technology and the geographic region of Asia. Biotechnology and nuclear power have, in contrast, more often been investigated through risk perception and other affective determinants, particularly in Europe and the USA. A set of 42 papers on societal response to nanotechnology shows similarities to research in biotechnology, as it also builds on affective variables such as risk perception. Although there is a tendency to extend the rational models with affective variables, convergence in social science approaches to response to new technologies still has a long way to go. The challenge for researchers of societal response to technologies is to converge to some shared principles by taking up the best parts from the rational actor models dominant in information technology, whilst integrating non-rational constructs from biotechnology research. The introduction of nanotechnology gives a unique opportunity to do so.

The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications.

PubMed

Park, Young-Kyoung; Nicaud, Jean-Marc; Ledesma-Amaro, Rodrigo

2018-03-01

Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism. This review focuses on recent engineering approaches in R. toruloides for bioproduction and explores its potential as a biotechnological chassis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Three Valuable Peptides from Bee and Wasp Venoms for Therapeutic and Biotechnological Use: Melittin, Apamin and Mastoparan

PubMed Central

Moreno, Miguel; Giralt, Ernest

2015-01-01

While knowledge of the composition and mode of action of bee and wasp venoms dates back 50 years, the therapeutic value of these toxins remains relatively unexploded. The properties of these venoms are now being studied with the aim to design and develop new therapeutic drugs. Far from evaluating the extensive number of monographs, journals and books related to bee and wasp venoms and the therapeutic effect of these toxins in numerous diseases, the following review focuses on the three most characterized peptides, namely melittin, apamin, and mastoparan. Here, we update information related to these compounds from the perspective of applied science and discuss their potential therapeutic and biotechnological applications in biomedicine. PMID:25835385

Biotechnological applications of transglutaminases.

PubMed

Rachel, Natalie M; Pelletier, Joelle N

2013-10-22

In nature, transglutaminases catalyze the formation of amide bonds between proteins to form insoluble protein aggregates. This specific function has long been exploited in the food and textile industries as a protein cross-linking agent to alter the texture of meat, wool, and leather. In recent years, biotechnological applications of transglutaminases have come to light in areas ranging from material sciences to medicine. There has also been a substantial effort to further investigate the fundamentals of transglutaminases, as many of their characteristics that remain poorly understood. Those studies also work towards the goal of developing transglutaminases as more efficient catalysts. Progress in this area includes structural information and novel chemical and biological assays. Here, we review recent achievements in this area in order to illustrate the versatility of transglutaminases.

Energy biotechnology in the CRISPR-Cas9 era.

PubMed

Estrela, Raissa; Cate, Jamie Harrison Doudna

2016-04-01

The production of bioenergy from plant biomass previously relied on using microorganisms that rapidly and efficiently convert simple sugars into fuels and chemicals. However, to exploit the far more abundant carbon fixed in plant cell walls, future industrial production hosts will need to be engineered to leverage the most efficient biochemical pathways and most robust traits that can be found in nature. The CRISPR-Cas9 genome editing technology now enables writing the genome at will, which will allow biotechnology to become an 'information science.' This review covers recent advances in using CRISPR-Cas9 to engineer the genomes of a wide variety of organisms that could be use in the industrial production of biofuels and renewable chemicals. Copyright © 2016 Elsevier Ltd. All rights reserved.

Social Science Research on Biotechnology and Agriculture: A Critique.

ERIC Educational Resources Information Center

Buttel, Frederick H.

1989-01-01

Examines trends in social science research on biotechnology and agriculture. Discusses role of private industry's biotechnology "hype" in defining social science research policy in universities. Suggests that widespread promotion of biotechnology as "revolutionary" contributed to lack of academic scrutiny. Examines social…

Alienation from the Objectives of the Patent System: How to Remedy the Situation of Biotechnology Patent.

PubMed

Jiang, Li

2018-03-12

Some fundamental biotechnologies hold unprecedented potential to eradicate many incurable diseases. However, in absence of regulations, the power of patent makes the future use of some important biotechnology in few institution's hands. The excessive patents restrict researcher access to the fundamental technologies. It generates concerns and complaints of deteriorating the public health and social welfare. Furthermore, intellectual curiosities, funding, respect among colleagues etc., rather than patents, are the real motivations driving a major ground-breaking discoveries in biotechnology. These phenomena reveal that some biotechnology patents are alienated from the purpose of patent system. Therefore, it is necessary to take some approaches to stop over-patenting these fundamental biotechnology inventions. This article proposes a model regulatory framework for controlling biotechnology patent alienating from the purpose of patent system.

The effect of biotechnology education on Australian high school students' understandings and attitudes about biotechnology processes

NASA Astrophysics Data System (ADS)

Dawson, Vaille; Soames, Christina

2006-11-01

Our education system aims to equip young people with the knowledge, problem-solving skills and values to cope with an increasingly technological society. The aim of this study was to determine the effect of biotechnology education on adolescents’ understanding and attitudes about processes associated with biotechnology. Data were drawn from teacher and student interviews and surveys in the context of innovative Year 10 biotechnology courses conducted in three Western Australian high schools. The results indicate that after completing a biotechnology course students’ understanding increased but their attitudes remained constant with the exception of their views about human uses of gene technology. The findings of this study have ramifications for the design and implementation of biotechnology education courses in high schools.

16 CFR 1102.6 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Background and Definitions... Product Safety Information Database. (2) Commission or CPSC means the Consumer Product Safety Commission... Information Database, also referred to as the Database, means the database on the safety of consumer products...

A Collaborative Assessment Among 11 Pharmaceutical Companies of Misinformation in Commonly Used Online Drug Information Compendia.

PubMed

Randhawa, Amarita S; Babalola, Olakiitan; Henney, Zachary; Miller, Michele; Nelson, Tanya; Oza, Meerat; Patel, Chandni; Randhawa, Anupma S; Riley, Joyce; Snyder, Scott; So, Sherri

2016-05-01

Online drug information compendia (ODIC) are valuable tools that health care professionals (HCPs) and consumers use to educate themselves on pharmaceutical products. Research suggests that these resources, although informative and easily accessible, may contain misinformation, posing risk for product misuse and patient harm. Evaluate drug summaries within ODIC for accuracy and completeness and identify product-specific misinformation. Between August 2014 and January 2015, medical information (MI) specialists from 11 pharmaceutical/biotechnology companies systematically evaluated 270 drug summaries within 5 commonly used ODIC for misinformation. Using a standardized approach, errors were identified; classified as inaccurate, incomplete, or omitted; and categorized per sections of the Full Prescribing Information (FPI). On review of each drug summary, content-correction requests were proposed and supported by the respective product's FPI. Across the 270 drug summaries reviewed within the 5 compendia, the median of the total number of errors identified was 782, with the greatest number of errors occurring in the categories of Dosage and Administration, Patient Education, and Warnings and Precautions. The majority of errors were classified as incomplete, followed by inaccurate and omitted. This analysis demonstrates that ODIC may contain misinformation. HCPs and consumers should be aware of the potential for misinformation and consider more than 1 drug information resource, including the FPI and Medication Guide as well as pharmaceutical/biotechnology companies' MI departments, to obtain unbiased, accurate, and complete product-specific drug information to help support the safe and effective use of prescription drug products. © The Author(s) 2016.

Global Adoption of Genetically Modified (GM) Crops: Challenges for the Public Sector.

PubMed

Huesing, Joseph E; Andres, David; Braverman, Michael P; Burns, Andrea; Felsot, Allan S; Harrigan, George G; Hellmich, Richard L; Reynolds, Alan; Shelton, Anthony M; Jansen van Rijssen, Wilna; Morris, E Jane; Eloff, Jacobus N

2016-01-20

Advances in biotechnology continue to drive the development of a wide range of insect-protected, herbicide-tolerant, stress-tolerant, and nutritionally enhanced genetically modified (GM) crops, yet societal and public policy considerations may slow their commercialization. Such restrictions may disproportionately affect developing countries, as well as smaller entrepreneurial and public sector initiatives. The 2014 IUPAC International Congress of Pesticide Chemistry (San Francisco, CA, USA; August 2014) included a symposium on "Challenges Associated with Global Adoption of Agricultural Biotechnology" to review current obstacles in promoting GM crops. Challenges identified by symposium presenters included (i) poor public understanding of GM technology and the need for enhanced communication strategies, (ii) nonharmonized and prescriptive regulatory requirements, and (iii) limited experience with regulations and product development within some public sector programs. The need for holistic resistance management programs to enable the most effective use of insect-protected crops was also a point of emphasis. This paper provides details on the symposium discussion and provides background information that can be used in support of further adoption of beneficial GM crops. Overall, it emphasizes that global adoption of modern agricultural biotechnology has not only provided benefits to growers and consumers but has great potential to provide solutions to an increasing global population and diminishing agricultural land. This potential will be realized by continued scientific innovation, harmonized regulatory systems, and broader communication of the benefits of the high-yielding, disease-resistant, and nutritionally enhanced crops attainable through modern biotechnology.

Biotechnology of temperate fruit trees and grapevines.

PubMed

Laimer, Margit; Mendonça, Duarte; Maghuly, Fatemeh; Marzban, Gorji; Leopold, Stephan; Khan, Mahmood; Balla, Ildiko; Katinger, Hermann

2005-01-01

Challenges concerning fruit trees and grapevines as long lived woody perennial crops require adapted biotechnological approaches, if solutions are to be found within a reasonable time frame. These challenges are represented by the need for correct identification of genetic resources, with the foreseen use either in conservation or in breeding programmes. Molecular markers provide most accurate information and will be the major solution for questions about plant breeders rights. Providing healthy planting material and rapid detection of newly introduced pathogens by reliable methods involving serological and molecular biological tools will be a future challenge of increases importance, given the fact that plant material travels freely in the entire European Union. But also new breeding goals and transgenic solutions are part of the biotechnological benefits, e.g. resistance against biotic and abiotic stress factors, modified growth habits, modified nutritional properties and altered processing and storage qualities. The successful characterization of transgenic grapevines and stone fruit trees carrying genes of viral origin in different vectors constructed under ecological consideration, will be presented. Beyond technical feasibility, efficiency of resistance, environmental safety and Intellectual Property Rights, also public acceptance needs consideration and has been addressed in a specific project. The molecular determination of internal quality parameters of food can also be addressed by the use of biotechnological tools. Patient independent detection tools for apple allergens have been developed and should allow to compare fruits from different production systems, sites, and genotypes for their content of health threatening compounds.

Tendencies of International Career of Romanian Researchers: Brain Drain?

ERIC Educational Resources Information Center

Popescu, Dan; Patrasca, Mihaela; Chivu, Iulia

2006-01-01

Recent economic and technological developments have led to a growing international demand for highly skilled human resources. The increased competition for human capital has determined numerous OECD countries to take special measures for attracting and retaining human capital in such fields as: information technology, biotechnology,…

75 FR 62549 - National Library of Medicine; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-12

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Library of Medicine... medical genetics area. Place: National Library of Medicine, Building 38, 2nd Floor, Board Room, 8600... Biotechnology Information, National Library of Medicine, Department of Health and Human Services, Building 38A...

78 FR 18358 - National Library of Medicine; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-26

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Library of Medicine.... Agenda: Review and Analysis of Systems. Place: National Library of Medicine, Building 38, 2nd Floor..., National Center for Biotechnology Information, National Library of Medicine, Building 38, Room 8N805...

Toward a Federal STEM Policy

ERIC Educational Resources Information Center

Brett, James T.

2007-01-01

Key New England industries including information technology, defense technology, biotechnology, environmental services, health care and university research rely upon people with skills in science, technology, engineering and math (STEM) fields. Yet, just 20 percent of New England high school students who took the SATs in 2005 indicated a desire to…

Characterization of adult transcriptomes from the omnivorous lady beetle Coleomegilla maculata fed pollen or insect Egg Diet

USDA-ARS?s Scientific Manuscript database

32 reference transcriptome sequences described herein are filed with the National Center for Biotechnology Information (NCBI), GenBank Bioproject PRJNA236444. Transcriptome Shotgun Assembly (TSA) will also be submitted when upload instructions are received from gb-admin....

Exploring Biotechnology Using Case-Based Multimedia

ERIC Educational Resources Information Center

Bergland, Mark; Lundeberg, Mary; Klyczek, Karen; Sweet, Jennifer; Emmons, Jean; Martin, Christine; Marsh, Katherine; Werner, Joy; Jarvis-Uetz, Michelle

2006-01-01

Today, teachers face more challenges than ever, and biology teachers face a special challenge. As technology continues to expand, biology teachers have a responsibility to keep students informed of technological and scientific advances. Biology teachers must also address ethical issues associated with these advances. In this paper, the authors…

The Challenge in Teaching Biotechnology

ERIC Educational Resources Information Center

Steele, F.; Aubusson, P.

2004-01-01

Agriculture, industry and medicine are being altered by new biotechnologies. Biotechnology education is important because today's students and citizens will make decisions about the development and application of these new molecular biologies. This article reports an investigation of the teaching of biotechnology in an Australian state, New South…

Turkish University Students' Knowledge of Biotechnology and Attitudes toward Biotechnological Applications

ERIC Educational Resources Information Center

Öztürk-Akar, Ebru

2017-01-01

This study questions the presumed relation between formal schooling and scientific literacy about biotechnologies. Comparing science and nonscience majors' knowledge of and attitudes toward biotechnological applications, conclusions are drawn if their formal learnings improve pupils' understandings of and attitudes toward biotechnology…

Construction Biotechnology: a new area of biotechnological research and applications.

PubMed

Stabnikov, Viktor; Ivanov, Volodymyr; Chu, Jian

2015-09-01

A new scientific and engineering discipline, Construction Biotechnology, is developing exponentially during the last decade. The major directions of this discipline are selection of microorganisms and development of the microbially-mediated construction processes and biotechnologies for the production of construction biomaterials. The products of construction biotechnologies are low cost, sustainable, and environmentally friendly microbial biocements and biogrouts for the construction ground improvement. The microbial polysaccharides are used as admixtures for cement. Microbially produced biodegradable bioplastics can be used for the temporarily constructions. The bioagents that are used in construction biotechnologies are either pure or enrichment cultures of microorganisms or activated indigenous microorganisms of soil. The applications of microorganisms in the construction processes are bioaggregation, biocementation, bioclogging, and biodesaturation of soil. The biotechnologically produced construction materials and the microbially-mediated construction technologies have a lot of advantages in comparison with the conventional construction materials and processes. Proper practical implementations of construction biotechnologies could give significant economic and environmental benefits.

Summary of the EMA Joint Regulators/Industry QbD workshop (London, UK; 28-29 January 2014).

PubMed

Cook, Graham; France, Georges; Holte, Øyvind; Lorenti, Giampiero; Tainsh, David

2016-01-01

This paper summarizes the discussions and insights gained from the key themes that emerged during the Quality by Design (QbD) Workshop held at the European Medicines Agency (EMA) offices in London, UK, on 28-29 January 2014. Industry and regulators shared practical experiences from six case studies (five approved small molecule products and one phase 3 biotechnological product) based on QbD submissions by five companies (AstraZeneca, GlaxoSmithKline, Novartis, NovoNordisk, and Pfizer).The case studies covered a range of different development, regulatory submission, and post-approval aspects of QbD and were developed through confidential discussions between the company representatives and regulators. Key themes that emerged from the workshop discussions were: 1. presentation of information in submissions (development story and the presentation of information in marketing authorization applications; risk assessment and criticality); 2. development aspects (design space; use of models; control strategy); and 3. post-approval aspects (lifecycle management; dossier-quality system interactions; handling of deviations). Many aspects of QbD for biotechnological products are similar to small molecules, but there are some important differences highlighted in this paper.The final section of the paper discusses some proposals for future developments to address the issues that were identified. This paper summarizes the discussions and insights gained from the key themes that emerged during the Quality by Design (QbD) Workshop held at the European Medicines Agency offices in London, UK, on 28-29 January 2014. Industry and regulators shared practical experiences from six case studies (five approved small-molecule products and one phase 3 biotechnological product) based on QbD submissions by five companies (AstraZeneca, GlaxoSmithKline, Novartis, NovoNordisk, and Pfizer).The case studies covered a range of different development, regulatory submission, and post-approval aspects of QbD and were developed through confidential discussions between the company representatives and regulators. Key themes that emerged from the workshop discussions were: 1. presentation of information in submissions (development story and the presentation of information in marketing authorization applications; risk assessment and criticality); 2. development aspects (design space; use of models; control strategy); and 3. post-approval aspects (lifecycle management; dossier-quality system interactions; handling of deviations). Many aspects of QbD for biotechnological products are similar to small molecules, but there are some important differences highlighted in this paper.The final section of the paper discusses some proposals for future developments to address the issues that were identified. © PDA, Inc. 2016.

The costly benefits of opposing agricultural biotechnology.

PubMed

Apel, Andrew

2010-11-30

Rigorous application of a simple definition of what constitutes opposition to agricultural biotechnology readily encompasses a wide array of key players in national and international systems of food production, distribution and governance. Even though the sum of political and financial benefits of opposing agricultural biotechnology appears vastly to outweigh the benefits which accrue to providers of agricultural biotechnology, technology providers actually benefit from this opposition. If these barriers to biotechnology were removed, subsistence farmers still would not represent a lucrative market for improved seed. The sum of all interests involved ensures that subsistence farmers are systematically denied access to agricultural biotechnology. Copyright © 2010 Elsevier B.V. All rights reserved.

75 FR 61413 - Notice of Availability of Biotechnology Quality Management System Audit Standard and Evaluation...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-05

...] Notice of Availability of Biotechnology Quality Management System Audit Standard and Evaluation of... Biotechnology Quality Management System Program (BQMS Program) to assist regulated entities in achieving and... customized biotechnology quality management system (BQMS) to improve their management of domestic research...

Crop Biotechnology. Where Now?

PubMed Central

Miflin, B. J.

2000-01-01

Abstract Nature Biotechnology organized a conference in London on Agbiotech 99: Biotechnology and World Agriculture (November 14-16, 1999). The conference focused entirely on crop biotechnology and covered both societal and scientific aspects. Below is an account of the more important issues raised by the speakers and the audience. PMID:10806221

Impact of Biotechnology on Pharmacy Practice.

ERIC Educational Resources Information Center

Black, Curtis D.; And Others

1990-01-01

Discussed is the role of schools of pharmacy in (1) preparing future practitioners to assimilate and shape the impact of biotechnology; (2) establish graduate and research programs to enhance and apply products of biotechnology; and (3) identify manpower needs to fully realize potential advances caused by biotechnology. (DB)

Undergraduate Biotechnology Students' Views of Science Communication

NASA Astrophysics Data System (ADS)

Edmondston, Joanne Elisabeth; Dawson, Vaille; Schibeci, Renato

2010-12-01

Despite rapid growth of the biotechnology industry worldwide, a number of public concerns about the application of biotechnology and its regulation remain. In response to these concerns, greater emphasis has been placed on promoting biotechnologists' public engagement. As tertiary science degree programmes form the foundation of the biotechnology sector by providing a pipeline of university graduates entering into the profession, it has been proposed that formal science communication training be introduced at this early stage of career development. The aim of the present study was to examine the views of biotechnology students towards science communication and science communication training. Using an Australian biotechnology degree programme as a case study, 69 undergraduates from all three years of the programme were administered a questionnaire that asked them to rank the importance of 12 components of a biotechnology curriculum, including two science communication items. The results were compared to the responses of 274 students enrolled in other science programmes. Additional questions were provided to the second year biotechnology undergraduates and semi-structured interviews were undertaken with 13 of these students to further examine their views of this area. The results of this study suggest that the biotechnology students surveyed do not value communication with non-scientists nor science communication training. The implications of these findings for the reform of undergraduate biotechnology courses yet to integrate science communication training into their science curriculum are discussed.

DESM: portal for microbial knowledge exploration systems.

PubMed

Salhi, Adil; Essack, Magbubah; Radovanovic, Aleksandar; Marchand, Benoit; Bougouffa, Salim; Antunes, Andre; Simoes, Marta Filipa; Lafi, Feras F; Motwalli, Olaa A; Bokhari, Ameerah; Malas, Tariq; Amoudi, Soha Al; Othum, Ghofran; Allam, Intikhab; Mineta, Katsuhiko; Gao, Xin; Hoehndorf, Robert; C Archer, John A; Gojobori, Takashi; Bajic, Vladimir B

2016-01-04

Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4,538,278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Strategies to improve reference databases for soil microbiomes

DOE PAGES

Choi, Jinlyung; Yang, Fan; Stepanauskas, Ramunas; ...

2016-12-09

A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 928 genomes of soil-associated organisms (888 bacteria, 34 archaea, and 6 fungi). Using this database as a representation of the current state of knowledge of soil microbes that are well-characterized, we evaluated its composition and compared it to broader microbial databases, specifically NCBI’s RefSeq,more » as well as 3,035 publicly available soil amplicon datasets. These comparisons identified phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. For example, RefSoil was observed to have increased representation of Firmicutes despite its low abundance in soil environments and also lacked representation of Acidobacteria and Verrucomicrobia, which are abundant in soils. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to recover 14 genomes from the "most wanted" list, which improved RefSoil's representation of EMP sequences by 7% by abundance. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps.« less

Strategies to improve reference databases for soil microbiomes

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

Choi, Jinlyung; Yang, Fan; Stepanauskas, Ramunas

A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 928 genomes of soil-associated organisms (888 bacteria, 34 archaea, and 6 fungi). Using this database as a representation of the current state of knowledge of soil microbes that are well-characterized, we evaluated its composition and compared it to broader microbial databases, specifically NCBI’s RefSeq,more » as well as 3,035 publicly available soil amplicon datasets. These comparisons identified phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. For example, RefSoil was observed to have increased representation of Firmicutes despite its low abundance in soil environments and also lacked representation of Acidobacteria and Verrucomicrobia, which are abundant in soils. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to recover 14 genomes from the "most wanted" list, which improved RefSoil's representation of EMP sequences by 7% by abundance. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps.« less

Progress towards the 'Golden Age' of biotechnology.

PubMed

Gartland, K M A; Bruschi, F; Dundar, M; Gahan, P B; Viola Magni, M p; Akbarova, Y

2013-07-01

Biotechnology uses substances, materials or extracts derived from living cells, employing 22 million Europeans in a € 1.5 Tn endeavour, being the premier global economic growth opportunity this century. Significant advances have been made in red biotechnology using pharmaceutically and medically relevant applications, green biotechnology developing agricultural and environmental tools and white biotechnology serving industrial scale uses, frequently as process feedstocks. Red biotechnology has delivered dramatic improvements in controlling human disease, from antibiotics to overcome bacterial infections to anti-HIV/AIDS pharmaceuticals such as azidothymidine (AZT), anti-malarial compounds and novel vaccines saving millions of lives. Green biotechnology has dramatically increased food production through Agrobacterium and biolistic genetic modifications for the development of 'Golden Rice', pathogen resistant crops expressing crystal toxin genes, drought resistance and cold tolerance to extend growth range. The burgeoning area of white biotechnology has delivered bio-plastics, low temperature enzyme detergents and a host of feedstock materials for industrial processes such as modified starches, without which our everyday lives would be much more complex. Biotechnological applications can bridge these categories, by modifying energy crops properties, or analysing circulating nucleic acid elements, bringing benefits for all, through increased food production, supporting climate change adaptation and the low carbon economy, or novel diagnostics impacting on personalized medicine and genetic disease. Cross-cutting technologies such as PCR, novel sequencing tools, bioinformatics, transcriptomics and epigenetics are in the vanguard of biotechnological progress leading to an ever-increasing breadth of applications. Biotechnology will deliver solutions to unimagined problems, providing food security, health and well-being to mankind for centuries to come. Copyright © 2013 Elsevier Ltd. All rights reserved.

78 FR 13302 - Syngenta Biotechnology, Inc.; Determination of Nonregulated Status of Corn Genetically Engineered...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-27

...] Syngenta Biotechnology, Inc.; Determination of Nonregulated Status of Corn Genetically Engineered for... are advising the public of our determination that a corn line developed by the Syngenta Biotechnology... evaluation of data submitted by Syngenta Biotechnology, Inc., in its petition for a determination of...

High School Students' Knowledge and Attitudes regarding Biotechnology Applications

ERIC Educational Resources Information Center

Ozel, Murat; Erdogan, Mehmet; Usak, Muhammet; Prokop, Pavol

2009-01-01

The purpose of this study was to investigate high school students' knowledge and attitudes regarding biotechnology and its various applications. In addition, whether students' knowledge and attitudes differed according to age and gender were also explored. The Biotechnology Knowledge Questionnaire (BKQ) with 16 items and the Biotechnology Attitude…

Student Content Knowledge Increases after Participation in a Hands-on Biotechnology Intervention

ERIC Educational Resources Information Center

Bigler, Amber M.; Hanegan, Nikki L.

2011-01-01

Implementing biotechnology education through hands-on teaching methods should be considered by secondary biology teachers. This study is an experimental research design to examine increased student content knowledge in biotechnology after a hands-on biotechnology intervention. The teachers from both school groups participated in, Project Crawfish,…

76 FR 3599 - Renewal of the Advisory Committee on Biotechnology and 21st Century Agriculture

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-20

... Service Renewal of the Advisory Committee on Biotechnology and 21st Century Agriculture AGENCY: Office of... of Agriculture intends to renew the Advisory Committee on Biotechnology and 21st Century Agriculture... responsible development and application of biotechnology within the global food and agricultural system...

75 FR 20560 - Syngenta Biotechnology, Inc.; Determination of Nonregulated Status for Corn Genetically...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-20

...] Syngenta Biotechnology, Inc.; Determination of Nonregulated Status for Corn Genetically Engineered for... are advising the public of our determination that a corn line developed by Syngenta Biotechnology, Inc... Biotechnology, Inc., in its petition for a determination of nonregulated status, our analysis of other...

Technology Teachers' Beliefs about Biotechnology and Its Instruction in South Korea

ERIC Educational Resources Information Center

Kwon, Hyuksoo; Chang, Mido

2009-01-01

The increased public awareness of the significance and necessity of biotechnology has encouraged educators to implement biotechnology instruction in various educational settings. One example is the great effort made by educational researchers and practitioners internationally to integrate biotechnology in technology education. Despite the gains in…

Nanotechnology Based Materials and Devices for Health Care

NASA Technical Reports Server (NTRS)

Srivastava, Deepaka; Cho, K.; Brenner, Don; Menon, Madhu; Andriotis, Antonis; Sagman, Uri; Biegel, Bryan A. (Technical Monitor)

2002-01-01

This viewgraph presentation provides information on trends in NASA nanotechnology research and development, and future biotechnological applications for that nanotechnology. The presentation covers nanoelectronics, nanosensors, and nanomaterials, biomimetics, devices and materials for health care, carbon nanotubes, biosensors for astrobiology, solid-state nanopores for DNA sequencing, and protein nanotubes.

After Years of Neglecting Academe, NASA Reaches Out to Universities.

ERIC Educational Resources Information Center

Southwick, Ron

2000-01-01

Reports that the National Aeronautics and Space Administration (NASA) is increasing its solicitation of university-based research on space missions, biotechnology, and information technology. Notes NASA's existing ties to institutions and the perception of a "closed community" of institutions with which NASA deals. Identifies the top 10 university…

78 FR 36555 - National Library of Medicine; Notice of Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-18

..., MD 20892. Open: 2:00 p.m. to 3:00 p.m. Agenda: Program Discussion. Place: National Library of... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Library of Medicine... Biotechnology Information. The meetings will be open to the public as indicated below, with attendance limited...

76 FR 51994 - National Library of Medicine Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-19

...: November 8, 2011. Open: 8:30 am to 12:00 pm. Agenda: Program Discussion. Place: National Library of... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Library of Medicine... Biotechnology Information. The meeting will be open to the public as indicated below, with attendance limited to...

76 FR 48797 - Notice of the Advisory Committee on Biotechnology and 21st Century Agriculture Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-09

...; E-mail [email protected]ars.usda.gov . SUPPLEMENTARY INFORMATION: The first meeting of the reconstituted AC21... Ms. Dianne Fowler at (202) 720-4074, by fax at (202) 720-3191 or by e- mail at [email protected]ars.usda...

77 FR 11064 - Notice of the Advisory Committee on Biotechnology and 21st Century Agriculture Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-24

...; Fax (202) 690-4265; Email [email protected]ars.usda.gov . SUPPLEMENTARY INFORMATION: The next meeting of the AC21... Fowler at (202) 720-4074 or by Email at [email protected]ars.usda.gov at least 5 days prior to the meeting...

"Nanoselves": NBIC and the Culture of Convergence

ERIC Educational Resources Information Center

Venkatesan, Priya

2010-01-01

The subject of this essay is NBIC convergence (nanotechnology, biotechnology, information technology and cognitive science convergence). NBIC convergence is a recurring trope that is dominated by the paradigm of integration of the sciences. It is largely influenced by the considerations of social and economic impact, and it assumes positivism in…

Current Trends in Biology Education.

ERIC Educational Resources Information Center

Wivagg, Daniel E.; Moore, Randy

1987-01-01

This newsletter reports on the status of biology education in the United States. It states that biology has entered its "golden age" because of the emergence of biotechnology, ecology, agricultural productivity, and human biology as major societal issues. This report discusses the status of the informal national curriculum of biology, involving…

77 FR 17488 - National Library of Medicine; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-26

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Library of Medicine...: Review and Analysis of Systems. Place: National Library of Medicine, Building 38, 2nd Floor, Board Room... Center for Biotechnology Information, National Library of Medicine, Building 38, Room 8N805, Bethesda, MD...

Socioscientific and Epistemic Dimensions of Support for Science: Associations with Science Education and Religiosity

ERIC Educational Resources Information Center

Stewart, Craig O.; McConnell, John R., III; Dickerson, Daniel L.

2017-01-01

This study investigated deference to scientific authority [Brossard, D., & Nisbet, M. C. (2007). "Deference to scientific authority among a low information public: Understanding U.S. opinion on agricultural biotechnology." "International Journal of Public Opinion Research," 19, 24-52] as it relates to support for science…

Challenges of Trainees in a Multidisciplinary Research Program: Nano-Biotechnology

ERIC Educational Resources Information Center

Kriegel, Christina; Koehne, Jessica; Tinkle, Sally; Maynard, Andrew D.; Hill, Rodney A.

2011-01-01

The breadth of knowledge required for the multidisciplinary field of nanotechnology challenges and extends traditional concepts of multidisciplinary graduate education. There is a paucity of information, both general reporting and peer-reviewed studies, on the challenges for graduate students working in this multidisciplinary paradigm, from the…

Financial Conflicts of Interest in the School Psychology Assessment Literature

ERIC Educational Resources Information Center

Truscott, Stephen D.; Baumgart, Mary B.; Rogers, Keba M.

2004-01-01

Recent scrutiny of medical and biotechnology research raises serious concerns about the potential for financial conflicts of interest (FCOIs) to bias research, impede the free flow of scientific information, and use scientific journals to influence consumers about the relative qualities of products produced for profit (e.g., pharmaceuticals).…

Computer Graphics and Metaphorical Elaboration for Learning Science Concepts.

ERIC Educational Resources Information Center

ChanLin, Lih-Juan; Chan, Kung-Chi

This study explores the instructional impact of using computer multimedia to integrate metaphorical verbal information into graphical representations of biotechnology concepts. The combination of text and graphics into a single metaphor makes concepts dual-coded, and therefore more comprehensible and memorable for the student. Visual stimuli help…

Handling Gene and Protein Names in the Age of Bioinformatics: The Special Challenge of Secreted Multimodular Bacterial Enzymes such as the cbhA/cbh9A Gene of Clostridium thermocellum

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

Brunecky, Roman; Schwarz, Wolfgang H.; Broeker, Jannis

An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with amore » respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.« less

Streptomyces spp. in the biocatalysis toolbox.

PubMed

Spasic, Jelena; Mandic, Mina; Djokic, Lidija; Nikodinovic-Runic, Jasmina

2018-04-01

About 20,100 research publications dated 2000-2017 were recovered searching the PubMed and Web of Science databases for Streptomyces, which are the richest known source of bioactive molecules. However, these bacteria with versatile metabolism are powerful suppliers of biocatalytic tools (enzymes) for advanced biotechnological applications such as green chemical transformations and biopharmaceutical and biofuel production. The recent technological advances, especially in DNA sequencing coupled with computational tools for protein functional and structural prediction, and the improved access to microbial diversity enabled the easier access to enzymes and the ability to engineer them to suit a wider range of biotechnological processes. The major driver behind a dramatic increase in the utilization of biocatalysis is sustainable development and the shift toward bioeconomy that will, in accordance to the UN policy agenda "Bioeconomy to 2030," become a global effort in the near future. Streptomyces spp. already play a significant role among industrial microorganisms. The intention of this minireview is to highlight the presence of Streptomyces in the toolbox of biocatalysis and to give an overview of the most important advances in novel biocatalyst discovery and applications. Judging by the steady increase in a number of recent references (228 for the 2000-2017 period), it is clear that biocatalysts from Streptomyces spp. hold promises in terms of valuable properties and applicative industrial potential.

White biotechnology: ready to partner and invest in.

PubMed

Kircher, Manfred

2006-01-01

It needs three factors to build an industry: market demand, product vision and capital. White biotechnology already produces high volume products such as feed additive amino acids and specialty products like enzymes for enantioselective biocatalysis. It serves large and diverse markets in the nutrition, wellness, pharmaceutical, agricultural and chemical industry. The total volume adds up to $ 50 billion worldwide. In spite of its proven track record, white biotechnology so far did not attract as much capital as red and even green biotechnology. However, the latest finance indicators confirm the continuously growing attractiveness of investment opportunities in white biotechnology. This article discusses white biotechnology's position and potential in the finance market and success factors.

Final Report: Northern Virginia Community College Training for Biotechnology Workers

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

Weiss, Johanna V

The intent of this project was to expand Northern Virginia Community College's capability to offer training to support the Biotechnology Industry in the northern Virginia region. The general goal of this project was to create a College Biotechnology Program; specific goals of the project were to a) design curricula/courses to prepare students to become entry-level lab technicians, b) redesign and equip lab space to better suit the needs of the program, c) develop partnerships with the local industry through outreach and the formation on an advisory board, d) recruit students into the program, and e) provide instructional support for localmore » high school teachers. At the end of the grant period, NOVA has successfully created two new curricula in biotechnology: an Associate of Applied Science (A.A.S.) in Biotechnology (initiated in Fall 2008) and a Career Studies Certificate for Biotechnology Lab Technicians (to be initiated in Fall 2010). These curricula were designed with advice from an external advisory committee which is comprised of representatives from industry, transfer institutions and high school administrators. To date, almost all courses have been designed and piloted; the equipment needed for the courses and the initial supplies were paid for by the grant as was the re-modeling of some lab space to be used for the biotech courses. In order to market the program, the NOVA Biotech Program has also established relationships with the local high schools. Presentations were given at several local high schools and on-site workshops were held for high school students and teachers. As a result, close to 1000 students have attended program open houses, presentations within the high schools, or workshops held in the summer. Over 100 teachers have received information and/or training in biotechnology. These outreach efforts as well as high quality curricula have started to attract a number of students to the program – for example, there are currently 70 students enrolled in the A.A.S. program. The first students in the biotech program are expected to graduate in Spring 2011; already, students enrolled in the biotech program/courses have obtained jobs or internships in several local companies. Our current goal continues to be to foster the formation of a regional biotech education pipeline into the local industry which includes the recruitment of individuals into the NOVA Biotech Program, the training and graduation of highly-skilled lab technicians, and the placement of graduates in local biotech industry jobs.« less

Knowledge management in a waste based biorefinery in the QbD paradigm.

PubMed

Rathore, Anurag S; Chopda, Viki R; Gomes, James

2016-09-01

Shifting resource base from fossil feedstock to renewable raw materials for production of chemical products has opened up an area of novel applications of industrial biotechnology-based process tools. This review aims to provide a concise and focused discussion on recent advances in knowledge management to facilitate efficient and optimal operation of a biorefinery. Application of quality by design (QbD) and process analytical technology (PAT) as tools for knowledge creation and management at different levels has been highlighted. Role of process integration, government policies, knowledge exchange through collaboration, and use of databases and computational tools have also been touched upon. Copyright © 2016 Elsevier Ltd. All rights reserved.

The command of biotechnology and merciful conquest in military opposition.

PubMed

Guo, Ji-Wei

2009-01-01

Biotechnology has an increasingly extensive use for military purposes. With the upcoming age of biotechnology, military operations are depending more on biotechnical methods. Judging from the evolving law of the theory of command, the command of biotechnology is feasible and inevitable. The report discusses some basic characteristics of modern theories of command, as well as the mature possibility of the command theory of military biotechnology. The evolution of the command theory is closely associated with the development of military medicine. This theory is expected to achieve successes in wars in an ultramicro, nonlethal, reversible, and merciful way and will play an important role in biotechnological identification and orientation, defense and attack, and the maintenance of fighting powers and biological monitoring. The command of military biotechnology has not become a part of the virtual military power yet, but it is an exigent strategic task to construct and perfect this theory.

Fungal biodiversity to biotechnology.

PubMed

Chambergo, Felipe S; Valencia, Estela Y

2016-03-01

Fungal habitats include soil, water, and extreme environments. With around 100,000 fungus species already described, it is estimated that 5.1 million fungus species exist on our planet, making fungi one of the largest and most diverse kingdoms of eukaryotes. Fungi show remarkable metabolic features due to a sophisticated genomic network and are important for the production of biotechnological compounds that greatly impact our society in many ways. In this review, we present the current state of knowledge on fungal biodiversity, with special emphasis on filamentous fungi and the most recent discoveries in the field of identification and production of biotechnological compounds. More than 250 fungus species have been studied to produce these biotechnological compounds. This review focuses on three of the branches generally accepted in biotechnological applications, which have been identified by a color code: red, green, and white for pharmaceutical, agricultural, and industrial biotechnology, respectively. We also discuss future prospects for the use of filamentous fungi in biotechnology application.

Evaluation of personal digital assistant drug information databases for the managed care pharmacist.

PubMed

Lowry, Colleen M; Kostka-Rokosz, Maria D; McCloskey, William W

2003-01-01

Personal digital assistants (PDAs) are becoming a necessity for practicing pharmacists. They offer a time-saving and convenient way to obtain current drug information. Several software companies now offer general drug information databases for use on hand held computers. PDAs priced less than 200 US dollars often have limited memory capacity; therefore, the user must choose from a growing list of general drug information database options in order to maximize utility without exceeding memory capacity. This paper reviews the attributes of available general drug information software databases for the PDA. It provides information on the content, advantages, limitations, pricing, memory requirements, and accessibility of drug information software databases. Ten drug information databases were subjectively analyzed and evaluated based on information from the product.s Web site, vendor Web sites, and from our experience. Some of these databases have attractive auxiliary features such as kinetics calculators, disease references, drug-drug and drug-herb interaction tools, and clinical guidelines, which may make them more useful to the PDA user. Not all drug information databases are equal with regard to content, author credentials, frequency of updates, and memory requirements. The user must therefore evaluate databases for completeness, currency, and cost effectiveness before purchase. In addition, consideration should be given to the ease of use and flexibility of individual programs.

Estimating economic gains for landowners due to time-dependent changes in biotechnology

Treesearch

John E. Wagner; Thomas P. Holmes

1998-01-01

This paper presents a model for examining the economic value of biotechnological research given time-dependent changes in biotechnology. Previous papers examined this issue assuming a time-neutral change in biotechnology. However, when analyzing the genetic improvements of increasing a tree's resistance to a pathogen, this assumption is untenable. The authors...

Biotechnology on the Battlefield: An Application of Agent-based Modelling for Emerging Technology Assessment

DTIC Science & Technology

2015-03-01

UNCLASSIFIED UNCLASSIFIED Biotechnology on the Battlefield: An Application of Agent-based Modelling for Emerging Technology Assessment...wounds might be treatable using advanced biotechnologies to control haemorrhaging and reduce blood-loss until medical evacuation can be completed. This...APPROVED FOR PUBLIC RELEASE UNCLASSIFIED UNCLASSIFIED Biotechnology on the Battlefield: An Application

75 FR 28811 - Office of Biotechnology Activities; Recombinant DNA Research: Proposed Actions Under the NIH...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-24

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Office of Biotechnology... Yersinia pestis has been submitted to the NIH Office of Biotechnology Activities (OBA) by the Institutional... Biotechnology Activities, National Institutes of Health. [FR Doc. 2010-12453 Filed 5-21-10; 8:45 am] BILLING...

75 FR 25282 - Office of the Director, Office of Biotechnology Activities; Notice of a Safety Symposium

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

..., Office of Biotechnology Activities; Notice of a Safety Symposium There will be a safety symposium... concerning this meeting contact Ms. Chezelle George, Administrative Assistant, Office of Biotechnology... Committee. Date: June 15, 2010. Time: 8 a.m. to 5:30 p.m. Agenda: The Office of Biotechnology Activities...

High School and University Students' Knowledge and Attitudes regarding Biotechnology: A Turkish Experience

ERIC Educational Resources Information Center

Usak, Muhammet; Erdogan, Mehmet; Prokop, Pavol; Ozel, Murat

2009-01-01

Biotechnology has a considerable importance in Turkish biology curriculum. This study was designed to explore or indicate Turkish high school and university students' knowledge and attitudes toward biotechnology. A total number of 352 high school and 276 university students were invited to the study. The Biotechnology Knowledge Questionnaire (BKQ)…

75 FR 69091 - Office of the Director, Office of Biotechnology Activities; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-10

..., Office of Biotechnology Activities; Notice of Meeting There will be a workshop entitled ``Retroviral and.... Time: 8 a.m. to 1 p.m. Agenda: The Office of Biotechnology Activities (OBA), NIH Recombinant DNA... Biotechnology Activities, National Institutes of Health, 6705 Rockledge Drive, Suite 750, Bethesda, MD 20892...

Are Students Prepared to Communicate? A Case Study of an Australian Degree Course in Biotechnology

ERIC Educational Resources Information Center

Edmondston, Joanne; Dawson, Vaille; Schibeci, Renato

2010-01-01

Public concerns about biotechnology have resulted in greater attention being paid to the mechanisms by which biotechnology is communicated with non-scientists, including the provision of science communication training. As undergraduate and postgraduate courses form the foundation of the biotechnology sector by providing a pipeline of university…

Healthcare biotechnology in India.

PubMed

Srivastava, L M

2005-01-01

Biotechnology in India has made great progress in the development of infrastructure, manpower, research and development and manufacturing of biological reagents, biodiagnostics, biotherapeutics, therapeutic and, prophylactic vaccines and biodevices. Many of these indigenous biological reagents, biodiagnostics, therapeutic and prophylactic vaccines and biodevices have been commercialized. Commercially when biotechnology revenue has reached $25 billions in the U.S. alone in 2000 excluding the revenues of biotech companies that were acquired by pharmaceutical companies, India has yet to register a measurable success. The conservative nature and craze of the Indian Industry for marketing imported biotechnology products, lack of Government support, almost non-existing national healthcare system and lack of trained managers for marketing biological and new products seem to be the important factors responsible for poor economic development of biotechnology in India. With the liberalization of Indian economy, more and more imported biotechnology products will enter into the Indian market. The conditions of internal development of biotechnology are not likely to improve in the near future and it is destined to grow only very slowly. Even today biotechnology in India may be called to be in its infancy.

Nanobiological studies on drug design using molecular mechanic method.

PubMed

Ghaheh, Hooria Seyedhosseini; Mousavi, Maryam; Araghi, Mahmood; Rasoolzadeh, Reza; Hosseini, Zahra

2015-01-01

Influenza H1N1 is very important worldwide and point mutations that occur in the virus gene are a threat for the World Health Organization (WHO) and druggists, since they could make this virus resistant to the existing antibiotics. Influenza epidemics cause severe respiratory illness in 30 to 50 million people and kill 250,000 to 500,000 people worldwide every year. Nowadays, drug design is not done through trial and error because of its cost and waste of time; therefore bioinformatics studies is essential for designing drugs. This paper, infolds a study on binding site of Neuraminidase (NA) enzyme, (that is very important in drug design) in 310K temperature and different dielectrics, for the best drug design. Information of NA enzyme was extracted from Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI) websites. The new sequences of N1 were downloaded from the NCBI influenza virus sequence database. Drug binding sites were assimilated and homologized modeling using Argus lab 4.0, HyperChem 6.0 and Chem. D3 softwares. Their stability was assessed in different dielectrics and temperatures. Measurements of potential energy (Kcal/mol) of binding sites of NA in different dielectrics and 310K temperature revealed that at time step size = 0 pSec drug binding sites have maximum energy level and at time step size = 100 pSec have maximum stability and minimum energy. Drug binding sites are more dependent on dielectric constants rather than on temperature and the optimum dielectric constant is 39/78.

The Challenge in Teaching Biotechnology

NASA Astrophysics Data System (ADS)

Steele, F.; Aubusson, P.

2004-08-01

Agriculture, industry and medicine are being altered by new biotechnologies. Biotechnology education is important because todays students and citizens will make decisions about the development and application of these new molecular biologies. This article reports an investigation of the teaching of biotechnology in an Australian state, New South Wales (NSW). In NSW few students were electing to answer examination questions related to biotechnology, suggesting that few students were studying the topic. This study looks at why electives relating to biotechnology are chosen or not chosen by students and teachers, with the intention of developing a greater understanding of the requirements for provision of a successful unit of study in this subject. Data was obtained through a survey of secondary science teachers, interviews with teachers and two case studies of the teaching of a biotechnology unit. Teachers reported a range of obstacles to the teaching of biotechnology including the difficulty of the subject matter and a lack of practical work that was suited to the content of the teaching unit. If biotechnology is worth learning in school science, then further research is needed to identify ways to promote the effective teaching of this topic, which teachers regard as important for, and interesting to, students but which most teachers choose not to teach.

Pharma Success in Product Development—Does Biotechnology Change the Paradigm in Product Development and Attrition.

PubMed

Evens, Ronald P

2016-01-01

The biotechnology segment of the overall biopharma industry has existed for only about 40–45 years, as a driver of new product development. This driving force was initiated with the FDA approval of recombinant human insulin in 1982, originating from the Genentech company. The pharma industry in the early years of 1970s and 1980s engaged with biotechnology companies only to a small extent with their in-licensing of a few recombinant molecules, led by Roche, Eli Lilly, and Johnson and Johnson. However, subsequently and dramatically over the last 25 years, biotechnology has become a primary driver of product and technology innovation and has become a cornerstone in new product development by all biopharma companies. This review demonstrates these evolutionary changes regarding approved products, product pipelines, novelty of the products, FDA approval rates, product sales, financial R&D investments in biotechnology, partnerships, mergers and acquisitions, and patent issues. We now have about 300 biotechnology products approved in USA covering 16 medical disciplines and about 250 indications, with the engagement of 25 pharma companies, along with their biotechnology company innovators and partners. The biotechnology pipeline involves over 1000 molecules in clinical trials, including over 300 molecules associated with the top 10 pharma companies. Product approval rates by the FDA for biotechnology products are over double the rate for drugs. Yes, the R&D paradigm has changed with biotechnology now as one of the major focuses for new product development with novel molecules by the whole biopharma industry.

Governing nanobiotechnology: lessons from agricultural biotechnology regulation

NASA Astrophysics Data System (ADS)

Johnson, Robbin S.

2011-04-01

This article uses lessons from biotechnology to help inform the design of oversight for nanobiotechnology. Those lessons suggest the following: first, oversight needs to be broadly defined, encompassing not just regulatory findings around safety and efficacy, but also public understanding and acceptance of the technology and its products. Second, the intensity of scrutiny and review should reflect not just risks but also perceptions of risk. Finally, a global marketplace argues for uniform standards or commercially practical solutions to differences in standards. One way of designing oversight to achieve these purposes is to think about it in three phases—precaution, prudence, and promotion. Precaution comes early in the technology or product's development and reflects real and perceived uncertainties. Prudence governs when risks and hazards have been identified, containment approaches established, and benefits broadly defined. Transparency and public participation rise to the fore. The promotional phase moves toward shaping public understanding and acceptance and involves marketing issues rather than safety ones. This flexible, three-phase approach to oversight would have avoided some of the early regulatory problems with agricultural biotechnology. It also would have led to a more risk-adjusted pathway to regulatory approval. Furthermore, it would avoid some of the arbitrary, disruptive marketing issues that have arisen.

The Role of Biotechnology for Conservation and Biologically Active Substances Production of Rhodiola rosea: Endangered Medicinal Species

PubMed Central

Tasheva, Krasimira; Kosturkova, Georgina

2012-01-01

At present, more than 50 000 plant species are used in phytotherapy and medicine. About 2/3 of them are harvested from nature leading to local extinction of many species or degradation of their habitats. Biotechnological methods offer possibilities not only for faster cloning and conservation of the genotype of the plants but for modification of their gene information, regulation, and expression for production of valuable substances in higher amounts or with better properties. Rhodiola rosea is an endangered medicinal species with limited distribution. It has outstanding importance for pharmaceutical industry for prevention and cure of cancer, heart and nervous system diseases, and so forth. Despite the great interest in golden root and the wide investigations in the area of phytochemistry, plant biotechnology remained less endeavoured and exploited. The paper presents research on initiation of in vitro cultures in Rhodiola rosea and some other Rhodiola species. Achievements in induction of organogenic and callus cultures, regeneration, and micropropagation varied but were a good basis for alternative in vitro synthesis of the desired metabolites and for the development of efficient systems for micropropagation for conservation of the species. PMID:22666097

Identification of new stress-induced microRNA and their targets in wheat using computational approach.

PubMed

Pandey, Bharati; Gupta, Om Prakash; Pandey, Dev Mani; Sharma, Indu; Sharma, Pradeep

2013-05-01

MicroRNAs (miRNAs) are a class of short endogenous non-coding small RNA molecules of about 18-22 nucleotides in length. Their main function is to downregulate gene expression in different manners like translational repression, mRNA cleavage and epigenetic modification. Computational predictions have raised the number of miRNAs in wheat significantly using an EST based approach. Hence, a combinatorial approach which is amalgamation of bioinformatics software and perl script was used to identify new miRNA to add to the growing database of wheat miRNA. Identification of miRNAs was initiated by mining the EST (Expressed Sequence Tags) database available at National Center for Biotechnology Information. In this investigation, 4677 mature microRNA sequences belonging to 50 miRNA families from different plant species were used to predict miRNA in wheat. A total of five abiotic stress-responsive new miRNAs were predicted and named Ta-miR5653, Ta-miR855, Ta-miR819k, Ta-miR3708 and Ta-miR5156. In addition, four previously identified miRNA, i.e., Ta-miR1122, miR1117, Ta-miR1134 and Ta-miR1133 were predicted in newly identified EST sequence and 14 potential target genes were subsequently predicted, most of which seems to encode ubiquitin carrier protein, serine/threonine protein kinase, 40S ribosomal protein, F-box/kelch-repeat protein, BTB/POZ domain-containing protein, transcription factors which are involved in growth, development, metabolism and stress response. Our result has increased the number of miRNAs in wheat, which should be useful for further investigation into the biological functions and evolution of miRNAs in wheat and other plant species.

RNA-Seq transcriptomic analysis of the Morus alba L. leaves exposed to high-level UVB with or without dark treatment.

PubMed

Guan, Qijie; Yu, Jiaojiao; Zhu, Wei; Yang, Bingxian; Li, Yaohan; Zhang, Lin; Tian, Jingkui

2018-03-01

Ultraviolet-B (UVB) irradiation induces oxidative stress in plant cells due to the generation of excessive reactive oxygen species. Morus alba L. (M. abla) is an important medicinal plant used for the treatment of human diseases. Also, its leaves are widely used as food for silkworms. In our previous research, we found that a high level of UVB irradiation with dark incubation led to the accumulation of secondary metabolites in M. abla leaf. The aim of the present study was to describe and compare M. alba leaf transcriptomics with different treatments (control, UVB, UVB+dark). Leaf transcripts from M. alba were sequenced using an Illumina Hiseq 2000 system, which produced 14.27Gb of data including 153,204,462 paired-end reads among the three libraries. We de novo assembled 133,002 transcripts with an average length of 1270bp and filtered 69,728 non-redundant unigenes. A similarity search was performed against the non-redundant National Center of Biotechnology Information (NCBI) protein database, which returned 41.08% hits. Among the 20,040 unigenes annotated in UniProtKB/SwissProt database, 16,683 unigenes were assigned 102,232 gene ontology terms and 6667 unigenes were identified in 287 known metabolic pathways. Results of differential gene expression analysis together with real-time quantitative PCR tests indicated that UVB irradiation with dark incubation enhanced the flavonoid biosynthesis in M. alba leaf. Our findings provided a valuable proof for a better understanding of the metabolic mechanism under abiotic stresses in M. alba leaf. Copyright © 2017 Elsevier B.V. All rights reserved.

Conserved and divergent rhythms of crassulacean acid metabolism-related and core clock gene expression in the cactus Opuntia ficus-indica.

PubMed

Mallona, Izaskun; Egea-Cortines, Marcos; Weiss, Julia

2011-08-01

The cactus Opuntia ficus-indica is a constitutive Crassulacean acid metabolism (CAM) species. Current knowledge of CAM metabolism suggests that the enzyme phosphoenolpyruvate carboxylase kinase (PPCK) is circadian regulated at the transcriptional level, whereas phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), NADP-malic enzyme (NADP-ME), and pyruvate phosphate dikinase (PPDK) are posttranslationally controlled. As little transcriptomic data are available from obligate CAM plants, we created an expressed sequence tag database derived from different organs and developmental stages. Sequences were assembled, compared with sequences in the National Center for Biotechnology Information nonredundant database for identification of putative orthologs, and mapped using Kyoto Encyclopedia of Genes and Genomes Orthology and Gene Ontology. We identified genes involved in circadian regulation and CAM metabolism for transcriptomic analysis in plants grown in long days. We identified stable reference genes for quantitative polymerase chain reaction and found that OfiSAND, like its counterpart in Arabidopsis (Arabidopsis thaliana), and OfiTUB are generally appropriate standards for use in the quantification of gene expression in O. ficus-indica. Three kinds of expression profiles were found: transcripts of OfiPPCK oscillated with a 24-h periodicity; transcripts of the light-active OfiNADP-ME and OfiPPDK genes adapted to 12-h cycles, while transcript accumulation patterns of OfiPEPC and OfiMDH were arrhythmic. Expression of the circadian clock gene OfiTOC1, similar to Arabidopsis, oscillated with a 24-h periodicity, peaking at night. Expression of OfiCCA1 and OfiPRR9, unlike in Arabidopsis, adapted best to a 12-h rhythm, suggesting that circadian clock gene interactions differ from those of Arabidopsis. Our results indicate that the evolution of CAM metabolism could be the result of modified circadian regulation at both the transcriptional and posttranscriptional levels.

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

PubMed Central

Aziz, Ramy K.; Devoid, Scott; Disz, Terrence; Edwards, Robert A.; Henry, Christopher S.; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Stevens, Rick L.; Vonstein, Veronika; Xia, Fangfang

2012-01-01

The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users. PMID:23110173

A Community Standard Format for the Representation of Protein Affinity Reagents*

PubMed Central

Gloriam, David E.; Orchard, Sandra; Bertinetti, Daniela; Björling, Erik; Bongcam-Rudloff, Erik; Borrebaeck, Carl A. K.; Bourbeillon, Julie; Bradbury, Andrew R. M.; de Daruvar, Antoine; Dübel, Stefan; Frank, Ronald; Gibson, Toby J.; Gold, Larry; Haslam, Niall; Herberg, Friedrich W.; Hiltke, Tara; Hoheisel, Jörg D.; Kerrien, Samuel; Koegl, Manfred; Konthur, Zoltán; Korn, Bernhard; Landegren, Ulf; Montecchi-Palazzi, Luisa; Palcy, Sandrine; Rodriguez, Henry; Schweinsberg, Sonja; Sievert, Volker; Stoevesandt, Oda; Taussig, Michael J.; Ueffing, Marius; Uhlén, Mathias; van der Maarel, Silvère; Wingren, Christer; Woollard, Peter; Sherman, David J.; Hermjakob, Henning

2010-01-01

Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site. PMID:19674966

Distinct profiles of expressed sequence tags during intestinal regeneration in the sea cucumber Holothuria glaberrima

PubMed Central

Rojas-Cartagena, Carmencita; Ortíz-Pineda, Pablo; Ramírez-Gómez, Francisco; Suárez-Castillo, Edna C.; Matos-Cruz, Vanessa; Rodríguez, Carlos; Ortíz-Zuazaga, Humberto; García-Arrarás, José E.

2010-01-01

Repair and regeneration are key processes for tissue maintenance, and their disruption may lead to disease states. Little is known about the molecular mechanisms that underline the repair and regeneration of the digestive tract. The sea cucumber Holothuria glaberrima represents an excellent model to dissect and characterize the molecular events during intestinal regeneration. To study the gene expression profile, cDNA libraries were constructed from normal, 3-day, and 7-day regenerating intestines of H. glaberrima. Clones were randomly sequenced and queried against the nonredundant protein database at the National Center for Biotechnology Information. RT-PCR analyses were made of several genes to determine their expression profile during intestinal regeneration. A total of 5,173 sequences from three cDNA libraries were obtained. About 46.2, 35.6, and 26.2% of the sequences for the normal, 3-days, and 7-days cDNA libraries, respectively, shared significant similarity with known sequences in the protein database of GenBank but only present 10% of similarity among them. Analysis of the libraries in terms of functional processes, protein domains, and most common sequences suggests that a differential expression profile is taking place during the regeneration process. Further examination of the expressed sequence tag dataset revealed that 12 putative genes are differentially expressed at significant level (R > 6). Experimental validation by RT-PCR analysis reveals that at least three genes (unknown C-4677-1, melanotransferrin, and centaurin) present a differential expression during regeneration. These findings strongly suggest that the gene expression profile varies among regeneration stages and provide evidence for the existence of differential gene expression. PMID:17579180

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission.

PubMed

Geib, Scott M; Hall, Brian; Derego, Theodore; Bremer, Forest T; Cannoles, Kyle; Sim, Sheina B

2018-04-01

One of the most overlooked, yet critical, components of a whole genome sequencing (WGS) project is the submission and curation of the data to a genomic repository, most commonly the National Center for Biotechnology Information (NCBI). While large genome centers or genome groups have developed software tools for post-annotation assembly filtering, annotation, and conversion into the NCBI's annotation table format, these tools typically require back-end setup and connection to an Structured Query Language (SQL) database and/or some knowledge of programming (Perl, Python) to implement. With WGS becoming commonplace, genome sequencing projects are moving away from the genome centers and into the ecology or biology lab, where fewer resources are present to support the process of genome assembly curation. To fill this gap, we developed software to assess, filter, and transfer annotation and convert a draft genome assembly and annotation set into the NCBI annotation table (.tbl) format, facilitating submission to the NCBI Genome Assembly database. This software has no dependencies, is compatible across platforms, and utilizes a simple command to perform a variety of simple and complex post-analysis, pre-NCBI submission WGS project tasks. The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline. The Genome Annotation Generator achieves the goal of providing a publicly available tool that will facilitate the submission of annotated genome assemblies to the NCBI. It is useful for any individual researcher or research group that wishes to submit a genome assembly of their study system to the NCBI.

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission

PubMed Central

Hall, Brian; Derego, Theodore; Bremer, Forest T; Cannoles, Kyle

2018-01-01

Abstract Background One of the most overlooked, yet critical, components of a whole genome sequencing (WGS) project is the submission and curation of the data to a genomic repository, most commonly the National Center for Biotechnology Information (NCBI). While large genome centers or genome groups have developed software tools for post-annotation assembly filtering, annotation, and conversion into the NCBI’s annotation table format, these tools typically require back-end setup and connection to an Structured Query Language (SQL) database and/or some knowledge of programming (Perl, Python) to implement. With WGS becoming commonplace, genome sequencing projects are moving away from the genome centers and into the ecology or biology lab, where fewer resources are present to support the process of genome assembly curation. To fill this gap, we developed software to assess, filter, and transfer annotation and convert a draft genome assembly and annotation set into the NCBI annotation table (.tbl) format, facilitating submission to the NCBI Genome Assembly database. This software has no dependencies, is compatible across platforms, and utilizes a simple command to perform a variety of simple and complex post-analysis, pre-NCBI submission WGS project tasks. Findings The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline Conclusions The Genome Annotation Generator achieves the goal of providing a publicly available tool that will facilitate the submission of annotated genome assemblies to the NCBI. It is useful for any individual researcher or research group that wishes to submit a genome assembly of their study system to the NCBI. PMID:29635297

Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment.

PubMed

Silva, Leslie P; Northen, Trent R

2015-08-01

Metabolism is at the heart of many biotechnologies from biofuels to medical diagnostics. Metabolomic methods that provide glimpses into cellular metabolism have rapidly developed into a critical component of the biotechnological development process. Most metabolomics methods have focused on what is happening inside the cell. Equally important are the biochemical transformations of the cell, and their effect on other cells and their environment; the exometabolome. Exometabolomics is therefore gaining popularity as a robust approach for obtaining rich phenotypic data, and being used in bioprocessing and biofuel development. Mass spectrometry imaging approaches, including several nanotechnologies, provide complimentary information by localizing metabolic processes within complex biological matrices. Together, the two technologies can provide new insights into the metabolism and interactions of cells. Published by Elsevier Ltd.

Novel biotechnology approaches in colorectal cancer diagnosis and therapy.

PubMed

Kavousipour, Soudabeh; Khademi, Fathemeh; Zamani, Mozhdeh; Vakili, Bahareh; Mokarram, Pooneh

2017-06-01

With ever-increasing molecular information about colorectal cancer (CRC), there is an expectation to detect more sensitive and specific molecular markers for new advanced diagnostic methods that can surpass the limitations of current screening tests. Moreover, enhanced molecular pathology knowledge about cancer has led to the development of targeted therapies, designed to interfere with specific aberrant biological pathways in cancer. Furthermore, biotechnology has opened a new window in CRC diagnosis and treatment by introducing different application of antibodies, antibody fragments, non-Ig scaffold proteins, and aptamers in targeted therapy and drug delivery. This review summarizes the molecular diagnostic and therapeutic approaches in CRC with a focus on genetic and epigenetic alterations, protein and metabolite markers as well as targeted therapy and drug delivery by Ig-scaffold proteins, non-Ig scaffold proteins, nanobodies, and aptamers.

[A web-based integrated clinical database for laryngeal cancer].

PubMed

E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

2014-08-01

To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

76 FR 53912 - FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-30

...] FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code Names... replaced non- informative code names with descriptive identifiers on its public database of products that... on our public database with non-informative code names. After careful consideration of this matter...

The Ohio Science Workbook: Biotechnology.

ERIC Educational Resources Information Center

Reames, Spencer E., Comp.

Because of the daily impact of biotechnology, it is important that students have some knowledge and experience with biotechnology in order to enable them to deal with the issues that arise as a result of its implementation. The purpose of this workbook is to assist in the efforts to expose students to the concepts of biotechnology through hands-on…

New Developments in Biotechnology: U.S. Investment in Biotechnology. Summary.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Office of Technology Assessment.

Since the discovery of recombinant DNA in the early 1970s, biotechnology has become an essential tool for many industries. The potential of biotechnology to improve the Nation's health, food supply, and the quality of the environment leads logically to questions of whether current levels of investment in research and development, human resources,…

The Effect of Biotechnology Education on Australian High School Students' Understandings and Attitudes about Biotechnology Processes

ERIC Educational Resources Information Center

Dawson, Vaille; Soames, Christina

2006-01-01

Our education system aims to equip young people with the knowledge, problem-solving skills and values to cope with an increasingly technological society. The aim of this study was to determine the effect of biotechnology education on adolescents' understanding and attitudes about processes associated with biotechnology. Data were drawn from…

New Developments in Biotechnology: U.S. Investment in Biotechnology. [Special Report.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Office of Technology Assessment.

Since the discovery of recombinant DNA in the early 1970s, biotechnology has become an essential tool for many industries. The potential of biotechnology to improve the Nation's health, food supply, and the quality of the environment leads logically to questions of whether current levels of investment in research and development, human resources,…

Current status of biotechnology in Slovakia.

PubMed

Stuchlík, Stanislav; Turna, Ján

2013-07-01

The United Nations Convention on Biological Diversity defines biotechnology as: 'Any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use.' In other words biotechnology is 'application of scientific and technical advances in life science to develop commercial products' or briefly 'the use of molecular biology for useful purposes'. This short overview is about different branches of biotechnology carried out in Slovakia and it shows that Slovakia has a good potential for further development of modern biotechnologies. Copyright © 2013 Elsevier Ltd. All rights reserved.

Drug development and nonclinical to clinical translational databases: past and current efforts.

PubMed

Monticello, Thomas M

2015-01-01

The International Consortium for Innovation and Quality (IQ) in Pharmaceutical Development is a science-focused organization of pharmaceutical and biotechnology companies. The mission of the Preclinical Safety Leadership Group (DruSafe) of the IQ is to advance science-based standards for nonclinical development of pharmaceutical products and to promote high-quality and effective nonclinical safety testing that can enable human risk assessment. DruSafe is creating an industry-wide database to determine the accuracy with which the interpretation of nonclinical safety assessments in animal models correctly predicts human risk in the early clinical development of biopharmaceuticals. This initiative aligns with the 2011 Food and Drug Administration strategic plan to advance regulatory science and modernize toxicology to enhance product safety. Although similar in concept to the initial industry-wide concordance data set conducted by International Life Sciences Institute's Health and Environmental Sciences Institute (HESI/ILSI), the DruSafe database will proactively track concordance, include exposure data and large and small molecules, and will continue to expand with longer duration nonclinical and clinical study comparisons. The output from this work will help identify actual human and animal adverse event data to define both the reliability and the potential limitations of nonclinical data and testing paradigms in predicting human safety in phase 1 clinical trials. © 2014 by The Author(s).

Learning Using Dynamic and Static Visualizations: Students' Comprehension, Prior Knowledge and Conceptual Status of a Biotechnological Method

ERIC Educational Resources Information Center

Yarden, Hagit; Yarden, Anat

2010-01-01

The importance of biotechnology education at the high-school level has been recognized in a number of international curriculum frameworks around the world. One of the most problematic issues in learning biotechnology has been found to be the biotechnological methods involved. Here, we examine the unique contribution of an animation of the…

Agriculture Breaks New Ground. How Biotechnology and Regrowing Materials Are Being Used in the Federal Republic of Germany. Sonderdienst Special Report SO1.

ERIC Educational Resources Information Center

Grimm, Fritz; Born, Sigrid

This document provides an overview of the major research priorities of biotechnology and the use of what is known as "regrowing raw materials" in agriculture in the Federal Republic of Germany. Following an introduction, section 2 addresses biotechnology in agriculture, including biotechnology and genetic engineering, the significance of…

Workshop proceedings: challenges and opportunities in evaluating protein allergenicity across biotechnology industries.

PubMed

Stagg, Nicola J; Ghantous, Hanan N; Ladics, Gregory S; House, Robert V; Gendel, Steven M; Hastings, Kenneth L

2013-01-01

A workshop entitled "Challenges and Opportunities in Evaluating Protein Allergenicity across Biotechnology Industries" was held at the 51st Annual Meeting of the Society of Toxicology (SOT) in San Francisco, California. The workshop was sponsored by the Biotechnology Specialty Section of SOT and was designed to present the science-based approaches used in biotechnology industries to evaluate and regulate protein allergenicity. A panel of experts from industry and government highlighted the allergenicity testing requirements and research in the agricultural, pharmaceutical/biopharma, and vaccine biotechnology industries and addressed challenges and opportunities for advancing the science of protein allergenicity. The main learning from the workshop was that immunoglobulin E-mediated allergenicity of biotechnology-derived products is difficult to assess without human data. The approaches currently being used to evaluate potential for allergenicity across biotechnology industries are very different and range from bioinformatics, in vitro serology, in vivo animal testing, in vitro and in vivo functional assays, and "biosimilar" assessments (ie, biotherapeutic equivalents to innovator products). The challenge remains with regard to the different or lack of regulatory requirements for allergenicity testing across industries, but the novel approaches being used with bioinformatics and biosimilars may lead to opportunities in the future to collaborate across biotechnology industries.

Path to bio-nano-information fusion.

PubMed

Chen, Jia Ming; Ho, Chih-Ming

2006-12-01

This article will discuss the challenges in a new convergent discipline created by the fusion of biotechnology, nanotechnology, and information technology. To illustrate the research challenges, we will begin with an introduction to the nanometer-scale environment in which biology resides, and point out the many important behaviors of matters at that scale. Then we will describe an ideal model system, the cell, for bio-nano-information fusion. Our efforts in advancing this field at the Institute of Cell Mimetic Space Exploration (CMISE) will be introduced here as an example to move toward achieving this goal.

Western Australian school students' understanding of biotechnology

NASA Astrophysics Data System (ADS)

Dawson, Vaille; Schibeci, Renato

2003-01-01

Are science educators providing secondary school students with the background to understand the science behind recent controversies such as the recently introduced compulsory labelling of genetically modified foods? Research from the UK suggests that many secondary school students do not understand the processes or implications of modern biotechnology. The situation in Australia is unclear. In this study, 1116 15-year-old students from eleven Western Australian schools were surveyed to determine their understanding of, and attitude towards, recent advances in modern biotechnology. The results indicate that approximately one third of students have little or no understanding of biotechnology. Many students over-estimate the use of biotechnology in our society by confusing current uses with possible future applications. The results provide a rationale for the inclusion of biotechnology, a cutting edge science, in the school science curriculum

Introduction to Pharmaceutical Biotechnology, Volume 1; Basic techniques and concepts

NASA Astrophysics Data System (ADS)

Bhatia, Saurabh; Goli, Divakar

2018-05-01

Animal biotechnology is a broad field including polarities of fundamental and applied research, as well as DNA science, covering key topics of DNA studies and its recent applications. In Introduction to Pharmaceutical Biotechnology, DNA isolation procedures followed by molecular markers and screening methods of the genomic library are explained. Interesting areas like isolation, sequencing and synthesis of genes, with the broader coverage on synthesis of genes, are also described. The book begins with an introduction to biotechnology and its main branches, explaining both the basic science and the applications of biotechnology-derived pharmaceuticals, with special emphasis on their clinical use. It then moves on to historical development and scope of biotechnology with an overall review of early applications that scientists employed long before the field was defined.

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 353)

NASA Technical Reports Server (NTRS)

1989-01-01

This bibliography lists 238 reports, articles, and other documents introduced into the NASA Scientific and Technical Information System in August 1991. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, biotechnology, human factors engineering, and flight crew behavior and performance.