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Sample records for rational genome mining

  1. Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins.

    PubMed

    Begley, Máire; Cotter, Paul D; Hill, Colin; Ross, R Paul

    2009-09-01

    Lantibiotics are ribosomally synthesized peptide antimicrobials which contain considerable posttranslational modifications. Given their usually broad host range and their highly stable structures, there have been renewed attempts to identify and characterize novel members of the lantibiotic family in recent years. The increasing availability of bacterial genome sequences means that in addition to traditional microbiological approaches, in silico screening strategies may now be employed to the same end. Taking advantage of the highly conserved nature of lantibiotic biosynthetic enzymes, we screened publicly available microbial genome sequences for genes encoding LanM proteins, which are required for the posttranslational modification of type 2 lantibiotics. By using this approach, 89 LanM homologs, including 61 in strains not known to be lantibiotic producers, were identified. Of these strains, five (Streptococcus pneumoniae SP23-BS72, Bacillus licheniformis ATCC 14580, Anabaena variabilis ATCC 29413, Geobacillus thermodenitrificans NG80-2, and Herpetosiphon aurantiacus ATCC 23779) were subjected to a more detailed bioinformatic analysis. Four of the strains possessed genes potentially encoding a structural peptide in close proximity to the lanM determinants, while two, S. pneumoniae SP23-BS72 and B. licheniformis ATCC 14580, possess two potential structural genes. The B. licheniformis strain was selected for a proof-of-concept exercise, which established that a two-peptide lantibiotic, lichenicidin, which exhibits antimicrobial activity against all Listeria monocytogenes, methicillin-resistant Staphylococcus aureus, and vancomycin-resistant enterococcus strains tested, was indeed produced, thereby confirming the benefits of such a bioinformatic approach when screening for novel lantibiotic producers. PMID:19561184

  2. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

    PubMed Central

    Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.; Unni, Deepak R.; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  3. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

    PubMed

    Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  4. The case for a rational genome-based vaccine against malaria

    PubMed Central

    Proietti, Carla; Doolan, Denise L.

    2015-01-01

    Historically, vaccines have been designed to mimic the immunity induced by natural exposure to the target pathogen, but this approach has not been effective for any parasitic pathogen of humans or complex pathogens that cause chronic disease in humans, such as Plasmodium. Despite intense efforts by many laboratories around the world on different aspects of Plasmodium spp. molecular and cell biology, epidemiology and immunology, progress towards the goal of an effective malaria vaccine has been disappointing. The premise of rational vaccine design is to induce the desired immune response against the key pathogen antigens or epitopes targeted by protective immune responses. We advocate that development of an optimally efficacious malaria vaccine will need to improve on nature, and that this can be accomplished by rational vaccine design facilitated by mining genomic, proteomic and transcriptomic datasets in the context of relevant biological function. In our opinion, modern genome-based rational vaccine design offers enormous potential above and beyond that of whole-organism vaccines approaches established over 200 years ago where immunity is likely suboptimal due to the many genetic and immunological host-parasite adaptations evolved to allow the Plasmodium parasite to coexist in the human host, and which are associated with logistic and regulatory hurdles for production and delivery. PMID:25657640

  5. DGIdb - Mining the druggable genome

    PubMed Central

    Coffman, Adam C.; Weible, James V.; McMichael, Josh F.; Spies, Nicholas C.; Koval, James; Das, Indraniel; Callaway, Matthew B.; Eldred, James M.; Miller, Christopher A.; Subramanian, Janakiraman; Govindan, Ramaswamy; Kumar, Runjun D.; Bose, Ron; Ding, Li; Walker, Jason R.; Larson, David E.; Dooling, David J.; Smith, Scott M.; Ley, Timothy J.; Mardis, Elaine R.; Wilson, Richard K.

    2013-01-01

    The Drug-Gene Interaction database (DGIdb) mines existing resources that generate hypotheses about how mutated genes might be targeted therapeutically or prioritized for drug development. It provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially druggable genes. DGIdb can be accessed at dgidb.org. PMID:24122041

  6. Rationality.

    PubMed

    Sosis, Clifford; Bishop, Michael A

    2014-01-01

    A theory of rationality is a theory that evaluates instances of reasoning as rational, irrational, or (ir)rational to some degree. Theories can be categorized as rule-based or consequentialist. Rule-based theories say that rational reasoning accords with certain rules (e.g., of logic or probability). Consequentialist theories say that rational reasoning tends to produce good consequences. For instance, the reliabilist takes rationality to be reasoning that tends to produce mostly true beliefs. The pragmatist takes it to be reasoning that tends to produce mostly useful beliefs. This article reviews some of the features and the challenges of rule-based, reliabilist, and pragmatist theories of rationality. WIREs Cogn Sci 2014, 5:27-37. doi: 10.1002/wcs.1263 CONFLICT OF INTEREST: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website. PMID:26304295

  7. Genomic mining for Aspergillus natural products.

    PubMed

    Bok, Jin Woo; Hoffmeister, Dirk; Maggio-Hall, Lori A; Murillo, Renato; Glasner, Jeremy D; Keller, Nancy P

    2006-01-01

    The genus Aspergillus is renowned for its ability to produce a myriad of bioactive secondary metabolites. Although the propensity of biosynthetic genes to form contiguous clusters greatly facilitates assignment of putative secondary metabolite genes in the completed Aspergillus genomes, such analysis cannot predict gene expression and, ultimately, product formation. To circumvent this deficiency, we have examined Aspergillus nidulans microarrays for expressed secondary metabolite gene clusters by using the transcriptional regulator LaeA. Deletion or overexpression of laeA clearly identified numerous secondary metabolite clusters. A gene deletion in one of the clusters eliminated the production of the antitumor compound terrequinone A, a metabolite not described, from A. nidulans. In this paper, we highlight that LaeA-based genome mining helps decipher the secondary metabolome of Aspergilli and provides an unparalleled view to assess secondary metabolism gene regulation. PMID:16426969

  8. Genome Mining for Ribosomally Synthesized Natural Products

    PubMed Central

    Velásquez, Juan E.; van der Donk, Wilfred

    2011-01-01

    In recent years, the number of known peptide natural products that are synthesized via the ribosomal pathway has rapidly grown. Taking advantage of sequence homology among genes encoding precursor peptides or biosynthetic proteins, in silico mining of genomes combined with molecular biology approaches has guided the discovery of a large number of new ribosomal natural products, including lantipeptides, cyanobactins, linear thiazole/oxazole-containing peptides, microviridins, lasso peptides, amatoxins, cyclotides, and conopeptides. In this review, we describe the strategies used for the identification of these ribosomally-synthesized and posttranslationally modified peptides (RiPPs) and the structures of newly identified compounds. The increasing number of chemical entities and their remarkable structural and functional diversity may lead to novel pharmaceutical applications. PMID:21095156

  9. The evolution of genome mining in microbes - a review.

    PubMed

    Ziemert, Nadine; Alanjary, Mohammad; Weber, Tilmann

    2016-08-27

    Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology. PMID:27272205

  10. Mining the genome for lipid genes.

    PubMed

    Kuivenhoven, Jan Albert; Hegele, Robert A

    2014-10-01

    Mining of the genome for lipid genes has since the early 1970s helped to shape our understanding of how triglycerides are packaged (in chylomicrons), repackaged (in very low density lipoproteins; VLDL), and hydrolyzed, and also how remnant and low-density lipoproteins (LDL) are cleared from the circulation. Gene discoveries have also provided insights into high-density lipoprotein (HDL) biogenesis and remodeling. Interestingly, at least half of these key molecular genetic studies were initiated with the benefit of prior knowledge of relevant proteins. In addition, multiple important findings originated from studies in mouse, and from other types of non-genetic approaches. Although it appears by now that the main lipid pathways have been uncovered, and that only modulators or adaptor proteins such as those encoded by LDLRAP1, APOA5, ANGPLT3/4, and PCSK9 are currently being discovered, genome wide association studies (GWAS) in particular have implicated many new loci based on statistical analyses; these may prove to have equally large impacts on lipoprotein traits as gene products that are already known. On the other hand, since 2004 - and particularly since 2010 when massively parallel sequencing has become de rigeur - no major new insights into genes governing lipid metabolism have been reported. This is probably because the etiologies of true Mendelian lipid disorders with overt clinical complications have been largely resolved. In the meantime, it has become clear that proving the importance of new candidate genes is challenging. This could be due to very low frequencies of large impact variants in the population. It must further be emphasized that functional genetic studies, while necessary, are often difficult to accomplish, making it hazardous to upgrade a variant that is simply associated to being definitively causative. Also, it is clear that applying a monogenic approach to dissect complex lipid traits that are mostly of polygenic origin is the wrong way to

  11. Highlights of recent articles on data mining in genomics & proteomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This editorial elaborates on investigations consisting of different “OMICS” technologies and their application to biological sciences. In addition, advantages and recent development of the proteomic, genomic and data mining technologies are discussed. This information will be useful to scientists ...

  12. WormBase: methods for data mining and comparative genomics.

    PubMed

    Harris, Todd W; Stein, Lincoln D

    2006-01-01

    WormBase is a comprehensive repository for information on Caenorhabditis elegans and related nematodes. Although the primary web-based interface of WormBase (http:// www.wormbase.org/) is familiar to most C. elegans researchers, WormBase also offers powerful data-mining features for addressing questions of comparative genomics, genome structure, and evolution. In this chapter, we focus on data mining at WormBase through the use of flexible web interfaces, custom queries, and scripts. The intended audience includes users wishing to query the database beyond the confines of the web interface or fetch data en masse. No knowledge of programming is necessary or assumed, although users with intermediate skills in the Perl scripting language will be able to utilize additional data-mining approaches. PMID:16988424

  13. Nature-oriented open coal mining technologies using mined-out space in an open-pit. Part II: A method for selecting rational sequence of mining flat dipping stratified deposits

    SciTech Connect

    Molotilov, S.G.; Norri, V.K.; Cheskidov, V.I.; Mattis, A.R.

    2007-01-15

    A method is proposed for selecting a rational mining sequence with internal dumping for flat stratified deposits, using new principles of the open-pit process-space formation and development. The main criteria for substantiating the mining sequence are geometrical form and development direction of the open-pit space, structure of the working wall and transportation network, internal dumping capacities and mining earthworks volumes.

  14. Microbial genome mining for accelerated natural products discovery: is a renaissance in the making?

    PubMed Central

    Bachmann, Brian O; Van Lanen, Steven G; Baltz, Richard H

    2014-01-01

    Microbial genome mining is a rapidly developing approach to discover new and novel secondary metabolites for drug discovery. Many advances have been made in the past decade to facilitate genome mining, and these are reviewed in this Special Issue of the Journal of Industrial Microbiology and Biotechnology. In this Introductory Review, we discuss the concept of genome mining and why it is important for the revitalization of natural product discovery; what microbes show the most promise for focused genome mining; how microbial genomes can be mined; how genome mining can be leveraged with other technologies; how progress on genome mining can be accelerated; and who should fund future progress in this promising field. We direct interested readers to more focused reviews on the individual topics in this Special Issue for more detailed summaries on the current state-of-the-art. PMID:24342967

  15. Large-scale data mining pilot project in human genome

    SciTech Connect

    Musick, R.; Fidelis, R.; Slezak, T.

    1997-05-01

    This whitepaper briefly describes a new, aggressive effort in large- scale data Livermore National Labs. The implications of `large- scale` will be clarified Section. In the short term, this effort will focus on several @ssion-critical questions of Genome project. We will adapt current data mining techniques to the Genome domain, to quantify the accuracy of inference results, and lay the groundwork for a more extensive effort in large-scale data mining. A major aspect of the approach is that we will be fully-staffed data warehousing effort in the human Genome area. The long term goal is strong applications- oriented research program in large-@e data mining. The tools, skill set gained will be directly applicable to a wide spectrum of tasks involving a for large spatial and multidimensional data. This includes applications in ensuring non-proliferation, stockpile stewardship, enabling Global Ecology (Materials Database Industrial Ecology), advancing the Biosciences (Human Genome Project), and supporting data for others (Battlefield Management, Health Care).

  16. Genomic Mining Reveals Deep Evolutionary Relationships between Bornaviruses and Bats

    PubMed Central

    Cui, Jie; Wang, Lin-Fa

    2015-01-01

    Bats globally harbor viruses in order Mononegavirales, such as lyssaviruses and henipaviruses; however, little is known about their relationships with bornaviruses. Previous studies showed that viral fossils of bornaviral origin are embedded in the genomes of several mammalian species such as primates, indicative of an ancient origin of exogenous bornaviruses. In this study, we mined the available 10 bat genomes and recreated a clear evolutionary relationship of endogenous bornaviral elements and bats. Comparative genomics showed that endogenization of bornaviral elements frequently occurred in vesper bats, harboring EBLLs (endogenous bornavirus-like L elements) in their genomes. Molecular dating uncovered a continuous bornavirus-bat interaction spanning 70 million years. We conclude that better understanding of modern exogenous bornaviral circulation in bat populations is warranted. PMID:26569285

  17. Chapter 13: Mining electronic health records in the genomics era.

    PubMed

    Denny, Joshua C

    2012-01-01

    The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical genomic knowledge in the last decade. Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR) systems that not only can improve health care, but also contain a vast repository of disease and treatment data that could be mined for genomic research. Indeed, institutions are creating EHR-linked DNA biobanks to enable genomic and pharmacogenomic research, using EHR data for phenotypic information. However, EHRs are designed primarily for clinical care, not research, so reuse of clinical EHR data for research purposes can be challenging. Difficulties in use of EHR data include: data availability, missing data, incorrect data, and vast quantities of unstructured narrative text data. Structured information includes billing codes, most laboratory reports, and other variables such as physiologic measurements and demographic information. Significant information, however, remains locked within EHR narrative text documents, including clinical notes and certain categories of test results, such as pathology and radiology reports. For relatively rare observations, combinations of simple free-text searches and billing codes may prove adequate when followed by manual chart review. However, to extract the large cohorts necessary for genome-wide association studies, natural language processing methods to process narrative text data may be needed. Combinations of structured and unstructured textual data can be mined to generate high-validity collections of cases and controls for a given condition. Once high-quality cases and controls are identified, EHR-derived cases can be used for genomic discovery and validation. Since EHR data includes a broad sampling of clinically-relevant phenotypic information, it may enable multiple genomic investigations upon a single set of genotyped individuals. This

  18. Chapter 13: Mining Electronic Health Records in the Genomics Era

    PubMed Central

    Denny, Joshua C.

    2012-01-01

    Abstract: The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical genomic knowledge in the last decade. Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR) systems that not only can improve health care, but also contain a vast repository of disease and treatment data that could be mined for genomic research. Indeed, institutions are creating EHR-linked DNA biobanks to enable genomic and pharmacogenomic research, using EHR data for phenotypic information. However, EHRs are designed primarily for clinical care, not research, so reuse of clinical EHR data for research purposes can be challenging. Difficulties in use of EHR data include: data availability, missing data, incorrect data, and vast quantities of unstructured narrative text data. Structured information includes billing codes, most laboratory reports, and other variables such as physiologic measurements and demographic information. Significant information, however, remains locked within EHR narrative text documents, including clinical notes and certain categories of test results, such as pathology and radiology reports. For relatively rare observations, combinations of simple free-text searches and billing codes may prove adequate when followed by manual chart review. However, to extract the large cohorts necessary for genome-wide association studies, natural language processing methods to process narrative text data may be needed. Combinations of structured and unstructured textual data can be mined to generate high-validity collections of cases and controls for a given condition. Once high-quality cases and controls are identified, EHR-derived cases can be used for genomic discovery and validation. Since EHR data includes a broad sampling of clinically-relevant phenotypic information, it may enable multiple genomic investigations upon a single set of genotyped

  19. Mining bacterial genomes for novel arylesterase activity

    PubMed Central

    Wang, Lijun; Mavisakalyan, Valentina; Tillier, Elisabeth R. M.; Clark, Greg W.; Savchenko, Alexei V.; Yakunin, Alexander F.; Master, Emma R.

    2010-01-01

    Summary One hundred and seventy‐one genes encoding potential esterases from 11 bacterial genomes were cloned and overexpressed in Escherichia coli; 74 of the clones produced soluble proteins. All 74 soluble proteins were purified and screened for esterase activity; 36 proteins showed carboxyl esterase activity on short‐chain esters, 17 demonstrated arylesterase activity, while 38 proteins did not exhibit any activity towards the test substrates. Esterases from Rhodopseudomonas palustris (RpEST‐1, RpEST‐2 and RpEST‐3), Pseudomonas putida (PpEST‐1, PpEST‐2 and PpEST‐3), Pseudomonas aeruginosa (PaEST‐1) and Streptomyces avermitilis (SavEST‐1) were selected for detailed biochemical characterization. All of the enzymes showed optimal activity at neutral or alkaline pH, and the half‐life of each enzyme at 50°C ranged from < 5 min to over 5 h. PpEST‐3, RpEST‐1 and RpEST‐2 demonstrated the highest specific activity with pNP‐esters; these enzymes were also among the most stable at 50°C and in the presence of detergents, polar and non‐polar organic solvents, and imidazolium ionic liquids. Accordingly, these enzymes are particularly interesting targets for subsequent application trials. Finally, biochemical and bioinformatic analyses were compared to reveal sequence features that could be correlated to enzymes with arylesterase activity, facilitating subsequent searches for new esterases in microbial genome sequences. PMID:21255363

  20. Data mining and the human genome

    SciTech Connect

    Abarbanel, Henry; Callan, Curtis; Dally, William; Dyson, Freeman; Hwa, Terence; Koonin, Steven; Levine, Herbert; Rothaus, Oscar; Schwitters, Roy; Stubbs, Christopher; Weinberger, Peter

    2000-01-07

    As genomics research moves from an era of data acquisition to one of both acquisition and interpretation, new methods are required for organizing and prioritizing the data. These methods would allow an initial level of data analysis to be carried out before committing resources to a particular genetic locus. This JASON study sought to delineate the main problems that must be faced in bioinformatics and to identify information technologies that can help to overcome those problems. While the current influx of data greatly exceeds what biologists have experienced in the past, other scientific disciplines and the commercial sector have been handling much larger datasets for many years. Powerful datamining techniques have been developed in other fields that, with appropriate modification, could be applied to the biological sciences.

  1. Applying negative rule mining to improve genome annotation

    PubMed Central

    Artamonova, Irena I; Frishman, Goar; Frishman, Dmitrij

    2007-01-01

    Background Unsupervised annotation of proteins by software pipelines suffers from very high error rates. Spurious functional assignments are usually caused by unwarranted homology-based transfer of information from existing database entries to the new target sequences. We have previously demonstrated that data mining in large sequence annotation databanks can help identify annotation items that are strongly associated with each other, and that exceptions from strong positive association rules often point to potential annotation errors. Here we investigate the applicability of negative association rule mining to revealing erroneously assigned annotation items. Results Almost all exceptions from strong negative association rules are connected to at least one wrong attribute in the feature combination making up the rule. The fraction of annotation features flagged by this approach as suspicious is strongly enriched in errors and constitutes about 0.6% of the whole body of the similarity-transferred annotation in the PEDANT genome database. Positive rule mining does not identify two thirds of these errors. The approach based on exceptions from negative rules is much more specific than positive rule mining, but its coverage is significantly lower. Conclusion Mining of both negative and positive association rules is a potent tool for finding significant trends in protein annotation and flagging doubtful features for further inspection. PMID:17659089

  2. A web server for mining Comparative Genomic Hybridization (CGH) data

    NASA Astrophysics Data System (ADS)

    Liu, Jun; Ranka, Sanjay; Kahveci, Tamer

    2007-11-01

    Advances in cytogenetics and molecular biology has established that chromosomal alterations are critical in the pathogenesis of human cancer. Recurrent chromosomal alterations provide cytological and molecular markers for the diagnosis and prognosis of disease. They also facilitate the identification of genes that are important in carcinogenesis, which in the future may help in the development of targeted therapy. A large amount of publicly available cancer genetic data is now available and it is growing. There is a need for public domain tools that allow users to analyze their data and visualize the results. This chapter describes a web based software tool that will allow researchers to analyze and visualize Comparative Genomic Hybridization (CGH) datasets. It employs novel data mining methodologies for clustering and classification of CGH datasets as well as algorithms for identifying important markers (small set of genomic intervals with aberrations) that are potentially cancer signatures. The developed software will help in understanding the relationships between genomic aberrations and cancer types.

  3. Data mining approaches for information retrieval from genomic databases

    NASA Astrophysics Data System (ADS)

    Liu, Donglin; Singh, Gautam B.

    2000-04-01

    Sequence retrieval in genomic databases is used for finding sequences related to a query sequence specified by a user. Comparison is the main part of the retrieval system in genomic databases. An efficient sequence comparison algorithm is critical in bioinformatics. There are several different algorithms to perform sequence comparison, such as the suffix array based database search, divergence measurement, methods that rely upon the existence of a local similarity between the query sequence and sequences in the database, or common mutual information between query and sequences in DB. In this paper we have described a new method for DNA sequence retrieval based on data mining techniques. Data mining tools generally find patterns among data and have been successfully applied in industries to improve marketing, sales, and customer support operations. We have applied the descriptive data mining techniques to find relevant patterns that are significant for comparing genetic sequences. Relevance feedback score based on common patterns is developed and employed to compute distance between sequences. The contigs of human chromosomes are used to test the retrieval accuracy and the experimental results are presented.

  4. JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

    PubMed Central

    Richter, Michael; Lombardot, Thierry; Kostadinov, Ivaylo; Kottmann, Renzo; Duhaime, Melissa Beth; Peplies, Jörg; Glöckner, Frank Oliver

    2008-01-01

    Background Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions. Results The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets. Conclusion JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage. PMID:18380896

  5. Automated genome mining of ribosomal peptide natural products

    SciTech Connect

    Mohimani, Hosein; Kersten, Roland; Liu, Wei; Wang, Mingxun; Purvine, Samuel O.; Wu, Si; Brewer, Heather M.; Pasa-Tolic, Ljiljana; Bandeira, Nuno; Moore, Bradley S.; Pevzner, Pavel A.; Dorrestein, Pieter C.

    2014-07-31

    Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity (1). In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic datasets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs and apply it for lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connection of multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 as the first natural product to be identified in an automated fashion by genome mining. The presented tool is available at cy-clo.ucsd.edu.

  6. Event-based text mining for biology and functional genomics.

    PubMed

    Ananiadou, Sophia; Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B

    2015-05-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. PMID:24907365

  7. Event-based text mining for biology and functional genomics

    PubMed Central

    Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B.

    2015-01-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. PMID:24907365

  8. TCGA4U: A Web-Based Genomic Analysis Platform To Explore And Mine TCGA Genomic Data For Translational Research.

    PubMed

    Huang, Zhenzhen; Duan, Huilong; Li, Haomin

    2015-01-01

    Large-scale human cancer genomics projects, such as TCGA, generated large genomics data for further study. Exploring and mining these data to obtain meaningful analysis results can help researchers find potential genomics alterations that intervene the development and metastasis of tumors. We developed a web-based gene analysis platform, named TCGA4U, which used statistics methods and models to help translational investigators explore, mine and visualize human cancer genomic characteristic information from the TCGA datasets. Furthermore, through Gene Ontology (GO) annotation and clinical data integration, the genomic data were transformed into biological process, molecular function, cellular component and survival curves to help researchers identify potential driver genes. Clinical researchers without expertise in data analysis will benefit from such a user-friendly genomic analysis platform. PMID:26262133

  9. The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.

    PubMed

    Cherry, J Michael

    2015-12-01

    At the core of the Saccharomyces Genome Database (SGD) are chromosomal features that encode a product. These include protein-coding genes and major noncoding RNA genes, such as tRNA and rRNA genes. The basic entry point into SGD is a gene or open-reading frame name that leads directly to the locus summary information page. A keyword describing function, phenotype, selective condition, or text from abstracts will also provide a door into the SGD. A DNA or protein sequence can be used to identify a gene or a chromosomal region using BLAST. Protein and DNA sequence identifiers, PubMed and NCBI IDs, author names, and function terms are also valid entry points. The information in SGD has been gathered and is maintained by a group of scientific biocurators and software developers who are devoted to providing researchers with up-to-date information from the published literature, connections to all the major research resources, and tools that allow the data to be explored. All the collected information cannot be represented or summarized for every possible question; therefore, it is necessary to be able to search the structured data in the database. This protocol describes the YeastMine tool, which provides an advanced search capability via an interactive tool. The SGD also archives results from microarray expression experiments, and a strategy designed to explore these data using the SPELL (Serial Pattern of Expression Levels Locator) tool is provided. PMID:26631124

  10. Investigating the Control of Chlorophyll Degradation by Genomic Correlation Mining.

    PubMed

    Ghandchi, Frederick P; Caetano-Anolles, Gustavo; Clough, Steven J; Ort, Donald R

    2016-01-01

    Chlorophyll degradation is an intricate process that is critical in a variety of plant tissues at different times during the plant life cycle. Many of the photoactive chlorophyll degradation intermediates are exceptionally cytotoxic necessitating that the pathway be carefully coordinated and regulated. The primary regulatory step in the chlorophyll degradation pathway involves the enzyme pheophorbide a oxygenase (PAO), which oxidizes the chlorophyll intermediate pheophorbide a, that is eventually converted to non-fluorescent chlorophyll catabolites. There is evidence that PAO is differentially regulated across different environmental and developmental conditions with both transcriptional and post-transcriptional components, but the involved regulatory elements are uncertain or unknown. We hypothesized that transcription factors modulate PAO expression across different environmental conditions, such as cold and drought, as well as during developmental transitions to leaf senescence and maturation of green seeds. To test these hypotheses, several sets of Arabidopsis genomic and bioinformatic experiments were investigated and re-analyzed using computational approaches. PAO expression was compared across varied environmental conditions in the three separate datasets using regression modeling and correlation mining to identify gene elements co-expressed with PAO. Their functions were investigated as candidate upstream transcription factors or other regulatory elements that may regulate PAO expression. PAO transcript expression was found to be significantly up-regulated in warm conditions, during leaf senescence, and in drought conditions, and in all three conditions significantly positively correlated with expression of transcription factor Arabidopsis thaliana activating factor 1 (ATAF1), suggesting that ATAF1 is triggered in the plant response to these processes or abiotic stresses and in result up-regulates PAO expression. The proposed regulatory network includes the

  11. Mining Genomes of Three Marine Sponge-Associated Actinobacterial Isolates for Secondary Metabolism

    PubMed Central

    Horn, Hannes; Hentschel, Ute

    2015-01-01

    Here, we report the draft genome sequences of three actinobacterial isolates, Micromonospora sp. RV43, Rubrobacter sp. RV113, and Nocardiopsis sp. RV163 that had previously been isolated from Mediterranean sponges. The draft genomes were analyzed for the presence of gene clusters indicative of secondary metabolism using antiSMASH 3.0 and NapDos pipelines. Our findings demonstrated the chemical richness of sponge-associated actinomycetes and the efficacy of genome mining in exploring the genomic potential of sponge-derived actinomycetes. PMID:26430030

  12. The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes

    PubMed Central

    Hamilton, John P.; Neeno-Eckwall, Eric C.; Adhikari, Bishwo N.; Perna, Nicole T.; Tisserat, Ned; Leach, Jan E.; Lévesque, C. André; Buell, C. Robin

    2011-01-01

    The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera. Database URL: http://cpgr.plantbiology.msu.edu. PMID:22120664

  13. Expanding the computational toolbox for mining cancer genomes

    PubMed Central

    Ding, Li; Wendl, Michael C.; McMichael, Joshua F.; Raphael, Benjamin J.

    2014-01-01

    High-throughput DNA sequencing has revolutionized cancer genomics with numerous discoveries relevant to cancer diagnosis and treatment. The latest sequencing and analysis methods have successfully identified somatic alterations including single nucleotide variants (SNVs), insertions and deletions (indels), structural aberrations, and gene fusions. Additional computational techniques have proved useful to define those mutations, genes, and molecular networks that drive diverse cancer phenotypes as well as determine clonal architectures in tumour samples. Collectively, these tools have advanced the study of genomic, transcriptomic, epigenomic alterations and their association to clinical properties. Here, we review cancer genomics software and the insights that have been gained from their application. PMID:25001846

  14. Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome.

    PubMed

    Pinto, Ameet J; Sharp, Jonathan O; Yoder, Michael J; Almstrand, Robert

    2016-01-01

    Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in heavy metal-contaminated acidic environments. However, their phylogenetic and metabolic diversity is poorly resolved. We present draft genome sequences of two novel and phylogenetically distinct Acidimicrobiaceae members assembled from an acid mine drainage biofilm metagenome. PMID:26769942

  15. Imaging mass spectrometry and genome mining reveal highly antifungal virulence factor of mushroom soft rot pathogen.

    PubMed

    Graupner, Katharina; Scherlach, Kirstin; Bretschneider, Tom; Lackner, Gerald; Roth, Martin; Gross, Harald; Hertweck, Christian

    2012-12-21

    Caught in the act: imaging mass spectrometry of a button mushroom infected with the soft rot pathogen Janthinobacterium agaricidamnosum in conjunction with genome mining revealed jagaricin as a highly antifungal virulence factor that is not produced under standard cultivation conditions. The structure of jagaricin was rigorously elucidated by a combination of physicochemical analyses, chemical derivatization, and bioinformatics. PMID:23161559

  16. Discovery of novel phosphonate natural products and their biosynthetic pathways by large-scale genome mining

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome mining has revolutionized the field of natural products, providing hope that new antibiotics can be discovered in time before all remainders are rendered useless against multidrug resistant pathogens. While this approach has been successful in academic settings focused on small collections or...

  17. Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome

    PubMed Central

    Pinto, Ameet J.; Sharp, Jonathan O.; Yoder, Michael J.

    2016-01-01

    Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in heavy metal-contaminated acidic environments. However, their phylogenetic and metabolic diversity is poorly resolved. We present draft genome sequences of two novel and phylogenetically distinct Acidimicrobiaceae members assembled from an acid mine drainage biofilm metagenome. PMID:26769942

  18. VirSorter: mining viral signal from microbial genomic data.

    PubMed

    Roux, Simon; Enault, Francois; Hurwitz, Bonnie L; Sullivan, Matthew B

    2015-01-01

    Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter's prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in "reverse" to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the i

  19. VirSorter: mining viral signal from microbial genomic data

    PubMed Central

    Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.

    2015-01-01

    Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the i

  20. The next generation of literature analysis: integration of genomic analysis into text mining.

    PubMed

    Scherf, Matthias; Epple, Anton; Werner, Thomas

    2005-09-01

    Text-mining systems are indispensable tools to reduce the increasing flux of information in scientific literature to topics pertinent to a particular interest in focus. Most of the scientific literature is published as unstructured free text, complicating the development of data processing tools, which rely on structured information. To overcome the problems of free text analysis, structured, hand-curated information derived from literature is integrated in text-mining systems to improve precision and recall. In this paper several text-mining approaches are reviewed and the next step in development of text-mining systems, which is based on a concept of multiple lines of evidence, is described: results from literature analysis are combined with evidence from experiments and genome analysis to improve the accuracy of results and to generate additional knowledge beyond what is known solely from literature. PMID:16212776

  1. Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining.

    PubMed

    Tang, Xiaoyu; Li, Jie; Millán-Aguiñaga, Natalie; Zhang, Jia Jia; O'Neill, Ellis C; Ugalde, Juan A; Jensen, Paul R; Mantovani, Simone M; Moore, Bradley S

    2015-12-18

    Recent genome sequencing efforts have led to the rapid accumulation of uncharacterized or "orphaned" secondary metabolic biosynthesis gene clusters (BGCs) in public databases. This increase in DNA-sequenced big data has given rise to significant challenges in the applied field of natural product genome mining, including (i) how to prioritize the characterization of orphan BGCs and (ii) how to rapidly connect genes to biosynthesized small molecules. Here, we show that by correlating putative antibiotic resistance genes that encode target-modified proteins with orphan BGCs, we predict the biological function of pathway specific small molecules before they have been revealed in a process we call target-directed genome mining. By querying the pan-genome of 86 Salinispora bacterial genomes for duplicated house-keeping genes colocalized with natural product BGCs, we prioritized an orphan polyketide synthase-nonribosomal peptide synthetase hybrid BGC (tlm) with a putative fatty acid synthase resistance gene. We employed a new synthetic double-stranded DNA-mediated cloning strategy based on transformation-associated recombination to efficiently capture tlm and the related ttm BGCs directly from genomic DNA and to heterologously express them in Streptomyces hosts. We show the production of a group of unusual thiotetronic acid natural products, including the well-known fatty acid synthase inhibitor thiolactomycin that was first described over 30 years ago, yet never at the genetic level in regards to biosynthesis and autoresistance. This finding not only validates the target-directed genome mining strategy for the discovery of antibiotic producing gene clusters without a priori knowledge of the molecule synthesized but also paves the way for the investigation of novel enzymology involved in thiotetronic acid natural product biosynthesis. PMID:26458099

  2. Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine.

    PubMed

    Megaw, Julianne; Gilmore, Brendan F

    2016-01-01

    Here, we report the draft genome sequence of Staphylococcus succinus strain CSM-77. This moderately halophilic bacterium was isolated from the surface of a halite sample obtained from a Triassic salt mine. PMID:27284152

  3. Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine

    PubMed Central

    Gilmore, Brendan F.

    2016-01-01

    Here, we report the draft genome sequence of Staphylococcus succinus strain CSM-77. This moderately halophilic bacterium was isolated from the surface of a halite sample obtained from a Triassic salt mine. PMID:27284152

  4. Genome-Wide Mining, Characterization, and Development of Microsatellite Markers in Gossypium Species

    PubMed Central

    Wang, Qiong; Fang, Lei; Chen, Jiedan; Hu, Yan; Si, Zhanfeng; Wang, Sen; Chang, Lijing; Guo, Wangzhen; Zhang, Tianzhen

    2015-01-01

    Although much research has been conducted to characterize microsatellites and develop markers, the distribution of microsatellites remains ambiguous and the use of microsatellite markers in genomic studies and marker-assisted selection is limited. To identify microsatellites for cotton research, we mined 100,290, 83,160, and 56,937 microsatellites with frequencies of 41.2, 49.1, and 74.8 microsatellites per Mb in the recently sequenced Gossypium species: G. hirsutum, G. arboreum, and G. raimondii, respectively. The distributions of microsatellites in their genomes were non-random and were positively and negatively correlated with genes and transposable elements, respectively. Of the 77,996 developed microsatellite markers, 65,498 were physically anchored to the 26 chromosomes of G. hirsutum with an average marker density of 34 markers per Mb. We confirmed 67,880 (87%) universal and 7,705 (9.9%) new genic microsatellite markers. The polymorphism was estimated in above three species by in silico PCR and validated with 505 markers in G. hirsutum. We further predicted 8,825 polymorphic microsatellite markers within G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. In our study, genome-wide mining and characterization of microsatellites, and marker development were very useful for the saturation of the allotetraploid genetic linkage map, genome evolution studies and comparative genome mapping. PMID:26030481

  5. Systematic Association of Genes to Phenotypes by Genome and Literature Mining

    PubMed Central

    2005-01-01

    One of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. So far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. Here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. We first mine the MEDLINE literature database for terms that reflect phenotypic similarities of species. Subsequently we predict the likely genomic determinants: genes specifically present in the respective genomes. In a global analysis involving 92 prokaryotic genomes we retrieve 323 clusters containing a total of 2,700 significant gene–phenotype associations. Some clusters contain mostly known relationships, such as genes involved in motility or plant degradation, often with additional hypothetical proteins associated with those phenotypes. Other clusters comprise unexpected associations; for example, a group of terms related to food and spoilage is linked to genes predicted to be involved in bacterial food poisoning. Among the clusters, we observe an enrichment of pathogenicity-related associations, suggesting that the approach reveals many novel genes likely to play a role in infectious diseases. PMID:15799710

  6. Recent advances in genome mining of secondary metabolites in Aspergillus terreus

    PubMed Central

    Guo, Chun-Jun; Wang, Clay C. C.

    2014-01-01

    Filamentous fungi are rich resources of secondary metabolites (SMs) with a variety of interesting biological activities. Recent advances in genome sequencing and techniques in genetic manipulation have enabled researchers to study the biosynthetic genes of these SMs. Aspergillus terreus is the well-known producer of lovastatin, a cholesterol-lowering drug. This fungus also produces other SMs, including acetylaranotin, butyrolactones, and territram, with interesting bioactivities. This review will cover recent progress in genome mining of SMs identified in this fungus. The identification and characterization of the gene cluster for these SMs, as well as the proposed biosynthetic pathways, will be discussed in depth. PMID:25566227

  7. Mining the pig genome to investigate the domestication process

    PubMed Central

    Ramos-Onsins, S E; Burgos-Paz, W; Manunza, A; Amills, M

    2014-01-01

    Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication. PMID:25074569

  8. Genome mining offers a new starting point for parasitology research.

    PubMed

    Lv, Zhiyue; Wu, Zhongdao; Zhang, Limei; Ji, Pengyu; Cai, Yifeng; Luo, Shiqi; Wang, Hongxi; Li, Hao

    2015-02-01

    Parasites including helminthes, protozoa, and medical arthropod vectors are a major cause of global infectious diseases, affecting one-sixth of the world's population, which are responsible for enormous levels of morbidity and mortality important and remain impediments to economic development especially in tropical countries. Prevalent drug resistance, lack of highly effective and practical vaccines, as well as specific and sensitive diagnostic markers are proving to be challenging problems in parasitic disease control in most parts of the world. The impressive progress recently made in genome-wide analysis of parasites of medical importance, including trematodes of Clonorchis sinensis, Opisthorchis viverrini, Schistosoma haematobium, S. japonicum, and S. mansoni; nematodes of Brugia malayi, Loa loa, Necator americanus, Trichinella spiralis, and Trichuris suis; cestodes of Echinococcus granulosus, E. multilocularis, and Taenia solium; protozoa of Babesia bovis, B. microti, Cryptosporidium hominis, Eimeria falciformis, E. histolytica, Giardia intestinalis, Leishmania braziliensis, L. donovani, L. major, Plasmodium falciparum, P. vivax, Trichomonas vaginalis, Trypanosoma brucei and T. cruzi; and medical arthropod vectors of Aedes aegypti, Anopheles darlingi, A. sinensis, and Culex quinquefasciatus, have been systematically covered in this review for a comprehensive understanding of the genetic information contained in nuclear, mitochondrial, kinetoplast, plastid, or endosymbiotic bacterial genomes of parasites, further valuable insight into parasite-host interactions and development of promising novel drug and vaccine candidates and preferable diagnostic tools, thereby underpinning the prevention and control of parasitic diseases. PMID:25563615

  9. metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.

    PubMed

    Lyne, Mike; Smith, Richard N; Lyne, Rachel; Aleksic, Jelena; Hu, Fengyuan; Kalderimis, Alex; Stepan, Radek; Micklem, Gos

    2013-01-01

    Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first

  10. metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research

    PubMed Central

    Lyne, Mike; Smith, Richard N; Lyne, Rachel; Aleksic, Jelena; Hu, Fengyuan; Kalderimis, Alex; Stepan, Radek; Micklem, Gos

    2013-01-01

    Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first

  11. Study of Lateral Gene Transfer in an Acid Mine Drainage Community Enabled by Comparative Genomics

    NASA Astrophysics Data System (ADS)

    Hugenholtz, P.; Croft, L.; Tyson, G. W.; Baker, B. J.; Detter, C.; Richardson, P. M.; Banfield, J. F.

    2002-12-01

    Lateral gene transfer (LGT) is thought to play a crucial role in the ecology and evolution of prokaryotes. We are investigating the role of LGT in an acid mine drainage community hosted in a pyrite-dominated metal sulfide deposit at the Richmond mine at Iron Mountain, CA. Due to biologically-mediated pyrite dissolution, the prevailing conditions within the mine are extremely low pH (< 1.0), very high ionic concentrations (molar concentrations of iron sulfate and mM concentrations of arsenic, copper and zinc), and moderate to high temperatures (30 to >50 C). These conditions are thought to largely isolate the community from potential external gene donors since naked DNA, phage and prokaryotes native to neutral pH habitats do not persist at pH <1.0 precluding an external influx of genes by transformation, transduction and conjugation, respectively. Microbial communities exist in several distinct habitats within Richmond mine including biofilms (subaqueous slime streamers and subaerial slimes) and cells attached directly to pyrite granules. This, however, belies an unusual simplicity in community composition. All communities investigated to date comprise only a handful of phylogenetically distinct organisms, typically dominated by the iron-oxidizing genera Leptospirillum and Ferroplasma. We have undertaken a community genomics analysis of a subaerial biofilm dominated by a Leptospirillum population to facilitate the study of LGT in this type of environment. The genome of Ferroplasma acidarmanus fer1, a minor component of the target community (but a major component of other Richmond mine communities), has been sequenced. Comparative genome analyses indicate that F. acidarmanus and the ancestor of two acidophilic Thermoplasma species belonging to the Euryarchaeota have traded many genes with phylogenetically remote acidophilic Sulfolobus species (Crenarchaeota). The putatively transferred sets of Sulfolobus genes in Ferroplasma and the Thermoplasma ancestor are distinct

  12. Mining Genomes of Marine Cyanobacteria for Elements of Zinc Homeostasis

    PubMed Central

    Barnett, James P.; Millard, Andrew; Ksibe, Amira Z.; Scanlan, David J.; Schmid, Ralf; Blindauer, Claudia Andrea

    2012-01-01

    Zinc is a recognized essential element for the majority of organisms, and is indispensable for the correct function of hundreds of enzymes and thousands of regulatory proteins. In aquatic photoautotrophs including cyanobacteria, zinc is thought to be required for carbonic anhydrase and alkaline phosphatase, although there is evidence that at least some carbonic anhydrases can be cambialistic, i.e., are able to acquire in vivo and function with different metal cofactors such as Co2+ and Cd2+. Given the global importance of marine phytoplankton, zinc availability in the oceans is likely to have an impact on both carbon and phosphorus cycles. Zinc concentrations in seawater vary over several orders of magnitude, and in the open oceans adopt a nutrient-like profile. Most studies on zinc handling by cyanobacteria have focused on freshwater strains and zinc toxicity; much less information is available on marine strains and zinc limitation. Several systems for zinc homeostasis have been characterized in the freshwater species Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803, but little is known about zinc requirements or zinc handling by marine species. Comparative metallo-genomics has begun to explore not only the putative zinc proteome, but also specific protein families predicted to have an involvement in zinc homeostasis, including sensors for excess and limitation (SmtB and its homologs as well as Zur), uptake systems (ZnuABC), putative intracellular zinc chaperones (COG0523) and metallothioneins (BmtA), and efflux pumps (ZiaA and its homologs). PMID:22514551

  13. Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates

    PubMed Central

    Stanton, Brynne C.; Nielsen, Alec A.K.; Tamsir, Alvin; Clancy, Kevin; Peterson, Todd; Voigt, Christopher A.

    2014-01-01

    Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply “part mining” to build a library of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset were determined using an in vitro method and this information was used to build synthetic promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 were identified that both strongly repress their cognate promoter (5- to 207-fold) and do not interact with other promoters. Each repressor:promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOR gates, there are >1054 circuits that could be built by changing the pattern of input and output promoters. This represents a large set of compatible gates that can be used to construct user-defined circuits. PMID:24316737

  14. Genome Mining in Sorangium cellulosum So ce56

    PubMed Central

    Ewen, Kerstin Maria; Hannemann, Frank; Khatri, Yogan; Perlova, Olena; Kappl, Reinhard; Krug, Daniel; Hüttermann, Jürgen; Müller, Rolf; Bernhardt, Rita

    2009-01-01

    Myxobacteria, especially members of the genus Sorangium, are known for their biotechnological potential as producers of pharmaceutically valuable secondary metabolites. The biosynthesis of several of those myxobacterial compounds includes cytochrome P450 activity. Although class I cytochrome P450 enzymes occur wide-spread in bacteria and rely on ferredoxins and ferredoxin reductases as essential electron mediators, the study of these proteins is often neglected. Therefore, we decided to search in the Sorangium cellulosum So ce56 genome for putative interaction partners of cytochromes P450. In this work we report the investigation of eight myxobacterial ferredoxins and two ferredoxin reductases with respect to their activity in cytochrome P450 systems. Intriguingly, we found not only one, but two ferredoxins whose ability to sustain an endogenous So ce56 cytochrome P450 was demonstrated by CYP260A1-dependent conversion of nootkatone. Moreover, we could demonstrate that the two ferredoxins were able to receive electrons from both ferredoxin reductases. These findings indicate that S. cellulosum can alternate between different electron transport pathways to sustain cytochrome P450 activity. PMID:19696019

  15. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

    PubMed

    Bolser, Dan; Staines, Daniel M; Pritchard, Emily; Kersey, Paul

    2016-01-01

    Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ). PMID:26519403

  16. Mining and characterization of two amidase signature family amidases from Brevibacterium epidermidis ZJB-07021 by an efficient genome mining approach.

    PubMed

    Ruan, Li-Tao; Zheng, Ren-Chao; Zheng, Yu-Guo

    2016-10-01

    Amidases have received increasing attention for their significant potential in the production of valuable carboxylic acids. In this study, two amidases belonging to amidase signature family (BeAmi2 and BeAmi4) were identified and mined from genomic DNA of Brevibacterium epidermidis ZJB-07021 by an efficient strategy combining comparative analysis of genomes and identification of unknown region by high-efficiency thermal asymmetric interlaced PCR (HiTAIL-PCR). The deduced amino acid sequences of BeAmi2 and BeAmi4 showed low identity (< 40%) with other reported amidases. The two amidases displayed optimum activity toward a wide spectrum of substrates at a mild alkaline pH and 45 °C. Both of them were remarkably inactivated by serine-directed inhibitor and sulfhydryl-reducing agent. Kinetic analysis revealed that nicotinamide was the preferable substrate for both amidases and the chlorine substitutions on the pyridine ring had a negative effect on activity. The bioprocesses for hydrolysis of 100 mM nicotinamide, isonicotinamide, 2-chloronicotinamide and 5-chloronicotinamide with purified BeAmi2 (6 U mL(-1)) were complete in 60 min with full conversion except 2-chloronicotinamide. These results indicated BeAmi2 was an effective catalyst for hydrolysis of several nicotinamide derivatives. PMID:27180252

  17. Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes.

    PubMed

    Ju, Kou-San; Gao, Jiangtao; Doroghazi, James R; Wang, Kwo-Kwang A; Thibodeaux, Christopher J; Li, Steven; Metzger, Emily; Fudala, John; Su, Joleen; Zhang, Jun Kai; Lee, Jaeheon; Cioni, Joel P; Evans, Bradley S; Hirota, Ryuichi; Labeda, David P; van der Donk, Wilfred A; Metcalf, William W

    2015-09-29

    Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed "genome mining" as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N(5)-hydroxyarginine; valinophos, an N-acetyl l-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products. PMID:26324907

  18. Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica

    PubMed Central

    Kersten, Roland D.; Lane, Amy L.; Nett, Markus; Richter, Taylor K. S.; Duggan, Brendan M.; Dorrestein, Pieter C.

    2013-01-01

    The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico-chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo- and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB-440 by a DNA interference bioassay to isolate DNA-targeting enediyne polyketides. An organic extract of S. tropica showed DNA-interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA-interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction via a pathway related to the kinamycin monomer. PMID:23649992

  19. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway

    PubMed Central

    Mak, Wai Shun; Tran, Stephen; Marcheschi, Ryan; Bertolani, Steve; Thompson, James; Baker, David; Liao, James C.; Siegel, Justin B.

    2015-01-01

    The ability to biosynthetically produce chemicals beyond what is commonly found in Nature requires the discovery of novel enzyme function. Here we utilize two approaches to discover enzymes that enable specific production of longer-chain (C5–C8) alcohols from sugar. The first approach combines bioinformatics and molecular modelling to mine sequence databases, resulting in a diverse panel of enzymes capable of catalysing the targeted reaction. The median catalytic efficiency of the computationally selected enzymes is 75-fold greater than a panel of naively selected homologues. This integrative genomic mining approach establishes a unique avenue for enzyme function discovery in the rapidly expanding sequence databases. The second approach uses computational enzyme design to reprogramme specificity. Both approaches result in enzymes with >100-fold increase in specificity for the targeted reaction. When enzymes from either approach are integrated in vivo, longer-chain alcohol production increases over 10-fold and represents >95% of the total alcohol products. PMID:26598135

  20. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway.

    PubMed

    Mak, Wai Shun; Tran, Stephen; Marcheschi, Ryan; Bertolani, Steve; Thompson, James; Baker, David; Liao, James C; Siegel, Justin B

    2015-01-01

    The ability to biosynthetically produce chemicals beyond what is commonly found in Nature requires the discovery of novel enzyme function. Here we utilize two approaches to discover enzymes that enable specific production of longer-chain (C5-C8) alcohols from sugar. The first approach combines bioinformatics and molecular modelling to mine sequence databases, resulting in a diverse panel of enzymes capable of catalysing the targeted reaction. The median catalytic efficiency of the computationally selected enzymes is 75-fold greater than a panel of naively selected homologues. This integrative genomic mining approach establishes a unique avenue for enzyme function discovery in the rapidly expanding sequence databases. The second approach uses computational enzyme design to reprogramme specificity. Both approaches result in enzymes with >100-fold increase in specificity for the targeted reaction. When enzymes from either approach are integrated in vivo, longer-chain alcohol production increases over 10-fold and represents >95% of the total alcohol products. PMID:26598135

  1. Perspective: NanoMine: A material genome approach for polymer nanocomposites analysis and design

    NASA Astrophysics Data System (ADS)

    Zhao, He; Li, Xiaolin; Zhang, Yichi; Schadler, Linda S.; Chen, Wei; Brinson, L. Catherine

    2016-05-01

    Polymer nanocomposites are a designer class of materials where nanoscale particles, functional chemistry, and polymer resin combine to provide materials with unprecedented combinations of physical properties. In this paper, we introduce NanoMine, a data-driven web-based platform for analysis and design of polymer nanocomposite systems under the material genome concept. This open data resource strives to curate experimental and computational data on nanocomposite processing, structure, and properties, as well as to provide analysis and modeling tools that leverage curated data for material property prediction and design. With a continuously expanding dataset and toolkit, NanoMine encourages community feedback and input to construct a sustainable infrastructure that benefits nanocomposite material research and development.

  2. Genome mining of ascomycetous fungi reveals their genetic potential for ergot alkaloid production.

    PubMed

    Gerhards, Nina; Matuschek, Marco; Wallwey, Christiane; Li, Shu-Ming

    2015-06-01

    Ergot alkaloids are important as mycotoxins or as drugs. Naturally occurring ergot alkaloids as well as their semisynthetic derivatives have been used as pharmaceuticals in modern medicine for decades. We identified 196 putative ergot alkaloid biosynthetic genes belonging to at least 31 putative gene clusters in 31 fungal species by genome mining of the 360 available genome sequences of ascomycetous fungi with known proteins. Detailed analysis showed that these fungi belong to the families Aspergillaceae, Clavicipitaceae, Arthrodermataceae, Helotiaceae and Thermoascaceae. Within the identified families, only a small number of taxa are represented. Literature search revealed a large diversity of ergot alkaloid structures in different fungi of the phylum Ascomycota. However, ergot alkaloid accumulation was only observed in 15 of the sequenced species. Therefore, this study provides genetic basis for further study on ergot alkaloid production in the sequenced strains. PMID:25796201

  3. Culture-independent Community Genomics Study of Microogranisms Associated with Acid Mine Drainage

    NASA Astrophysics Data System (ADS)

    Tyson, G. W.; Hugenholtz, P.; Detter, C.; Richardson, P. M.; Banfield, J. F.

    2002-12-01

    Acid mine drainage (AMD) is a serious environmental problem that occurs when pyrite (FeS2)-rich rocks are exposed to air, water, and oxidizing agents. Pyrite dissolution is exothermic, yielding hot, metal-rich, extremely acidic solutions. Despite the hostile nature of AMD environments, microbial communities thrive, and are believed to control the rates of pyrite dissolution and acid generation. Previous studies of microbial communities within the Richmond Mine at Iron Mt., Redding, CA, revealed low species-level diversity and established close connections between metabolism and geochemistry. Thus, these communities are ideal candidates for culture-independent genomics-enabled analyses. Samples collected from the Richmond Mine in March 2002 were screened using quantitative fluorescence in situ hybridization to choose the most suitable target community for a genomics-enabled ecological study. The community selected (a pink subaerial biofilm) has low species complexity but high phylogenetic diversity, containing ~75% Leptospirillum group II (closely related to Leptospirillum ferriphilum), ~10% Leptospirillum group III, and ~10% archaea that fall into three distinct groups within the Thermoplasmatales order (Ferroplasma sp., for which genome data is already available, A-plasma and D-plasma). High throughput sequencing of four 16S rDNA clone libraries confirmed the low species-level diversity in this community and suggested that the extent of microheterogeneity within each of the five populations was limited. 17 unique Leptospirillum group II 16S rDNA phylotypes (defined by one or more base change) were resolved, with ~85% belonging to one phylotype. The remaining ~15% were very similar in sequence identity, only diverging by 1.2% in total. Similarly, 14 unique Leptospirillum group III phylotypes formed a tight cluster with < 0.8% sequence divergence. The limited inter-species, and significant intra-species variation in the populations should allow determination of the

  4. Discovery of pentangular polyphenols hexaricins A-C from marine Streptosporangium sp. CGMCC 4.7309 by genome mining.

    PubMed

    Tian, Jun; Chen, Haiyan; Guo, Zhengyan; Liu, Ning; Li, Jine; Huang, Ying; Xiang, Wensheng; Chen, Yihua

    2016-05-01

    Many novel microbial nature products were discovered from Actinobacteria by genome mining methods. However, only a few number of genome mining works were carried out in rare actinomycetes. An important reason precluding the genome mining efforts in rare actinomycetes is that most of them are recalcitrant to genetic manipulation. Herein, we chose the rare marine actinomycete Streptosporangium sp. CGMCC 4.7309 to explore its secondary metabolite diversity by genome mining. The genetic manipulation method has never been established for Streptosporangium strains. At first, we set up the genetic system of Streptosporangium sp. CGMCC 4.7309 unprecedentedly. The draft genome sequencing of Streptosporangium sp. CGMCC 4.7309 revealed that it contains more than 20 cryptic secondary metabolite biosynthetic clusters. A type II polyketide synthases-containing cluster (the hex cluster) was predicted to encode compounds with a pentangular polyphenol scaffold by in silico analysis. The products of the hex cluster were uncovered by comparing the metabolic profile of Streptosporangium sp. CGMCC 4.7309 with that of the hex30 inactivated mutant, in which a key ketoreductase gene was disrupted. Finally, three pentangular polyphenols were isolated and named as hexaricins A (1), B (2), and C (3). The inconsistency of the stereochemistry of C-15 in hexaricins A, B, and C indicates a branch point in their biosynthesis. Finally, the biosynthetic pathway of the hexaricins was proposed based on bioinformatics analysis. PMID:26754814

  5. Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes

    PubMed Central

    Ju, Kou-San; Gao, Jiangtao; Doroghazi, James R.; Wang, Kwo-Kwang A.; Thibodeaux, Christopher J.; Li, Steven; Metzger, Emily; Fudala, John; Su, Joleen; Zhang, Jun Kai; Lee, Jaeheon; Cioni, Joel P.; Evans, Bradley S.; Hirota, Ryuichi; Labeda, David P.; van der Donk, Wilfred A.; Metcalf, William W.

    2015-01-01

    Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed “genome mining” as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N5-hydroxyarginine; valinophos, an N-acetyl l-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products. PMID:26324907

  6. Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes.

    PubMed

    Aleti, Gajender; Sessitsch, Angela; Brader, Günter

    2015-01-01

    Bacillus and related genera in the Bacillales within the Firmicutes harbor a variety of secondary metabolite gene clusters encoding polyketide synthases and non-ribosomal peptide synthetases responsible for remarkable diverse number of polyketides (PKs) and lipopeptides (LPs). These compounds may be utilized for medical and agricultural applications. Here, we summarize the knowledge on structural diversity and underlying gene clusters of LPs and PKs in the Bacillales. Moreover, we evaluate by using published prediction tools the potential metabolic capacity of these bacteria to produce type I PKs or LPs. The huge sequence repository of bacterial genomes and metagenomes provides the basis for such genome-mining to reveal the potential for novel structurally diverse secondary metabolites. The otherwise cumbersome task to isolate often unstable PKs and deduce their structure can be streamlined. Using web based prediction tools, we identified here several novel clusters of PKs and LPs from genomes deposited in the database. Our analysis suggests that a substantial fraction of predicted LPs and type I PKs are uncharacterized, and their functions remain to be studied. Known and predicted LPs and PKs occurred in the majority of the plant associated genera, predominantly in Bacillus and Paenibacillus. Surprisingly, many genera from other environments contain no or few of such compounds indicating the role of these secondary metabolites in plant-associated niches. PMID:25893081

  7. Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes

    PubMed Central

    Aleti, Gajender; Sessitsch, Angela; Brader, Günter

    2015-01-01

    Bacillus and related genera in the Bacillales within the Firmicutes harbor a variety of secondary metabolite gene clusters encoding polyketide synthases and non-ribosomal peptide synthetases responsible for remarkable diverse number of polyketides (PKs) and lipopeptides (LPs). These compounds may be utilized for medical and agricultural applications. Here, we summarize the knowledge on structural diversity and underlying gene clusters of LPs and PKs in the Bacillales. Moreover, we evaluate by using published prediction tools the potential metabolic capacity of these bacteria to produce type I PKs or LPs. The huge sequence repository of bacterial genomes and metagenomes provides the basis for such genome-mining to reveal the potential for novel structurally diverse secondary metabolites. The otherwise cumbersome task to isolate often unstable PKs and deduce their structure can be streamlined. Using web based prediction tools, we identified here several novel clusters of PKs and LPs from genomes deposited in the database. Our analysis suggests that a substantial fraction of predicted LPs and type I PKs are uncharacterized, and their functions remain to be studied. Known and predicted LPs and PKs occurred in the majority of the plant associated genera, predominantly in Bacillus and Paenibacillus. Surprisingly, many genera from other environments contain no or few of such compounds indicating the role of these secondary metabolites in plant-associated niches. PMID:25893081

  8. Data Mining Approaches for Genome-Wide Association of Mood Disorders

    PubMed Central

    Pirooznia, Mehdi; Seifuddin, Fayaz; Judy, Jennifer; Mahon, Pamela B.; Potash, James B.; Zandi, Peter P.

    2012-01-01

    Mood disorders are highly heritable forms of major mental illness. A major breakthrough in elucidating the genetic architecture of mood disorders was anticipated with the advent of genome-wide association studies (GWAS). However, to date few susceptibility loci have been conclusively identified. The genetic etiology of mood disorders appears to be quite complex, and as a result, alternative approaches for analyzing GWAS data are needed. Recently, a polygenic scoring approach that captures the effects of alleles across multiple loci was successfully applied to the analysis of GWAS data in schizophrenia and bipolar disorder (BP). However, this method may be overly simplistic in its approach to the complexity of genetic effects. Data mining methods are available that may be applied to analyze the high dimensional data generated by GWAS of complex psychiatric disorders. We sought to compare the performance of five data mining methods, namely, Bayesian Networks (BN), Support Vector Machine (SVM), Random Forest (RF), Radial Basis Function network (RBF), and Logistic Regression (LR), against the polygenic scoring approach in the analysis of GWAS data on BP. The different classification methods were trained on GWAS datasets from the Bipolar Genome Study (2,191 cases with BP and 1,434 controls) and their ability to accurately classify case/control status was tested on a GWAS dataset from the Wellcome Trust Case Control Consortium. The performance of the classifiers in the test dataset was evaluated by comparing area under the receiver operating characteristic curves (AUC). BN performed the best of all the data mining classifiers, but none of these did significantly better than the polygenic score approach. We further examined a subset of SNPs in genes that are expressed in the brain, under the hypothesis that these might be most relevant to BP susceptibility, but all the classifiers performed worse with this reduced set of SNPs. The discriminative accuracy of all of these

  9. Draft Genome Sequence of Plant Growth-Promoting Rhizobium Mesorhizobium amorphae, Isolated from Zinc-Lead Mine Tailings

    PubMed Central

    Hao, Xiuli; Lin, Yanbing; Johnstone, Laurel; Baltrus, David A.; Miller, Susan J.

    2012-01-01

    Here, we describe the draft genome sequence of Mesorhizobium amorphae strain CCNWGS0123, isolated from nodules of Robinia pseudoacacia growing on zinc-lead mine tailings. A large number of metal(loid) resistance genes, as well as genes reported to promote plant growth, were identified, presenting a great future potential for aiding phytoremediation in metal(loid)-contaminated soil. PMID:22247533

  10. A Novel CalB-Type Lipase Discovered by Fungal Genomes Mining

    PubMed Central

    Vaquero, Maria E.; de Eugenio, Laura I.; Martínez, Maria J.; Barriuso, Jorge

    2015-01-01

    The fungus Pseudozyma antarctica produces a lipase (CalB) with broad substrate specificity, stability, high regio- and enantio-selectivity. It is active in non-aqueous organic solvents and at elevated temperatures. Hence, CalB is a robust biocatalyst for chemical conversions on an industrial scale. Here we report the in silico mining of public metagenomes and fungal genomes to discover novel lipases with high homology to CalB. The candidates were selected taking into account homology and conserved motifs criteria, as well as, phylogeny and 3D model analyses. The most promising candidate (PlicB) presented interesting structural properties. PlicB was expressed in a heterologous host, purified and partially characterized. Further experiments will allow finding novel catalytic properties with biotechnological interest. PMID:25898146

  11. A novel calb-type lipase discovered by fungal genomes mining.

    PubMed

    Vaquero, Maria E; de Eugenio, Laura I; Martínez, Maria J; Barriuso, Jorge

    2015-01-01

    The fungus Pseudozyma antarctica produces a lipase (CalB) with broad substrate specificity, stability, high regio- and enantio-selectivity. It is active in non-aqueous organic solvents and at elevated temperatures. Hence, CalB is a robust biocatalyst for chemical conversions on an industrial scale. Here we report the in silico mining of public metagenomes and fungal genomes to discover novel lipases with high homology to CalB. The candidates were selected taking into account homology and conserved motifs criteria, as well as, phylogeny and 3D model analyses. The most promising candidate (PlicB) presented interesting structural properties. PlicB was expressed in a heterologous host, purified and partially characterized. Further experiments will allow finding novel catalytic properties with biotechnological interest. PMID:25898146

  12. Epigenetic Genome Mining of an Endophytic Fungus Leads to Pleiotropic Biosynthesis of Natural Products

    PubMed Central

    Mao, Xu-Ming; Xu, Wei; Li, Dehai; Yin, Wen-Bing; Chooi, Yit-Heng; Li, Yong-Quan

    2015-01-01

    The small molecule biosynthetic potential of most filamentous fungi remains largely unexplored and represents an attractive source for new compound discovery. Genome sequencing of Calcarisporium arbuscula, a mushroom endophytic fungus, revealed 68 core genes that are involved in natural products biosynthesis. This is in sharp contrast to predominant production of the ATPase inhibitors aurovertin B (1) and D (2). Inactivation of a histone H3 deacetylase HdaA led to pleiotropic activation and overexpression of more than 75% of the biosynthetic genes. Sampling of the overproduced compounds led to isolation of ten compounds of which four contain new structures, including the cyclic peptides arbumycin (3) and arbumelin (4); the diterpenoid arbuscullic acid A (11); and a meroterpenoid arbuscullic acid B (12). Such epigenetic modification therefore provides a rapid and global approach to mine the chemical diversity of endophytic fungi. PMID:26013262

  13. Discovery of defense- and neuropeptides in social ants by genome-mining.

    PubMed

    Gruber, Christian W; Muttenthaler, Markus

    2012-01-01

    Natural peptides of great number and diversity occur in all organisms, but analyzing their peptidome is often difficult. With natural product drug discovery in mind, we devised a genome-mining approach to identify defense- and neuropeptides in the genomes of social ants from Atta cephalotes (leaf-cutter ant), Camponotus floridanus (carpenter ant) and Harpegnathos saltator (basal genus). Numerous peptide-encoding genes of defense peptides, in particular defensins, and neuropeptides or regulatory peptide hormones, such as allatostatins and tachykinins, were identified and analyzed. Most interestingly we annotated genes that encode oxytocin/vasopressin-related peptides (inotocins) and their putative receptors. This is the first piece of evidence for the existence of this nonapeptide hormone system in ants (Formicidae) and supports recent findings in Tribolium castaneum (red flour beetle) and Nasonia vitripennis (parasitoid wasp), and therefore its confinement to some basal holometabolous insects. By contrast, the absence of the inotocin hormone system in Apis mellifera (honeybee), another closely-related member of the eusocial Hymenoptera clade, establishes the basis for future studies on the molecular evolution and physiological function of oxytocin/vasopressin-related peptides (vasotocin nonapeptide family) and their receptors in social insects. Particularly the identification of ant inotocin and defensin peptide sequences will provide a basis for future pharmacological characterization in the quest for potent and selective lead compounds of therapeutic value. PMID:22448224

  14. Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules

    PubMed Central

    Kersten, Roland D.; Ziemert, Nadine; Gonzalez, David J.; Duggan, Brendan M.; Nizet, Victor; Dorrestein, Pieter C.; Moore, Bradley S.

    2013-01-01

    Glycosyl groups are an essential mediator of molecular interactions in cells and on cellular surfaces. There are very few methods that directly relate sugar-containing molecules to their biosynthetic machineries. Here, we introduce glycogenomics as an experiment-guided genome-mining approach for fast characterization of glycosylated natural products (GNPs) and their biosynthetic pathways from genome-sequenced microbes by targeting glycosyl groups in microbial metabolomes. Microbial GNPs consist of aglycone and glycosyl structure groups in which the sugar unit(s) are often critical for the GNP’s bioactivity, e.g., by promoting binding to a target biomolecule. GNPs are a structurally diverse class of molecules with important pharmaceutical and agrochemical applications. Herein, O- and N-glycosyl groups are characterized in their sugar monomers by tandem mass spectrometry (MS) and matched to corresponding glycosylation genes in secondary metabolic pathways by a MS-glycogenetic code. The associated aglycone biosynthetic genes of the GNP genotype then classify the natural product to further guide structure elucidation. We highlight the glycogenomic strategy by the characterization of several bioactive glycosylated molecules and their gene clusters, including the anticancer agent cinerubin B from Streptomyces sp. SPB74 and an antibiotic, arenimycin B, from Salinispora arenicola CNB-527. PMID:24191063

  15. Discovery of Defense- and Neuropeptides in Social Ants by Genome-Mining

    PubMed Central

    Gruber, Christian W.; Muttenthaler, Markus

    2012-01-01

    Natural peptides of great number and diversity occur in all organisms, but analyzing their peptidome is often difficult. With natural product drug discovery in mind, we devised a genome-mining approach to identify defense- and neuropeptides in the genomes of social ants from Atta cephalotes (leaf-cutter ant), Camponotus floridanus (carpenter ant) and Harpegnathos saltator (basal genus). Numerous peptide-encoding genes of defense peptides, in particular defensins, and neuropeptides or regulatory peptide hormones, such as allatostatins and tachykinins, were identified and analyzed. Most interestingly we annotated genes that encode oxytocin/vasopressin-related peptides (inotocins) and their putative receptors. This is the first piece of evidence for the existence of this nonapeptide hormone system in ants (Formicidae) and supports recent findings in Tribolium castaneum (red flour beetle) and Nasonia vitripennis (parasitoid wasp), and therefore its confinement to some basal holometabolous insects. By contrast, the absence of the inotocin hormone system in Apis mellifera (honeybee), another closely-related member of the eusocial Hymenoptera clade, establishes the basis for future studies on the molecular evolution and physiological function of oxytocin/vasopressin-related peptides (vasotocin nonapeptide family) and their receptors in social insects. Particularly the identification of ant inotocin and defensin peptide sequences will provide a basis for future pharmacological characterization in the quest for potent and selective lead compounds of therapeutic value. PMID:22448224

  16. Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.

    PubMed

    Medema, Marnix H; Paalvast, Yared; Nguyen, Don D; Melnik, Alexey; Dorrestein, Pieter C; Takano, Eriko; Breitling, Rainer

    2014-09-01

    Nonribosomally and ribosomally synthesized bioactive peptides constitute a source of molecules of great biomedical importance, including antibiotics such as penicillin, immunosuppressants such as cyclosporine, and cytostatics such as bleomycin. Recently, an innovative mass-spectrometry-based strategy, peptidogenomics, has been pioneered to effectively mine microbial strains for novel peptidic metabolites. Even though mass-spectrometric peptide detection can be performed quite fast, true high-throughput natural product discovery approaches have still been limited by the inability to rapidly match the identified tandem mass spectra to the gene clusters responsible for the biosynthesis of the corresponding compounds. With Pep2Path, we introduce a software package to fully automate the peptidogenomics approach through the rapid Bayesian probabilistic matching of mass spectra to their corresponding biosynthetic gene clusters. Detailed benchmarking of the method shows that the approach is powerful enough to correctly identify gene clusters even in data sets that consist of hundreds of genomes, which also makes it possible to match compounds from unsequenced organisms to closely related biosynthetic gene clusters in other genomes. Applying Pep2Path to a data set of compounds without known biosynthesis routes, we were able to identify candidate gene clusters for the biosynthesis of five important compounds. Notably, one of these clusters was detected in a genome from a different subphylum of Proteobacteria than that in which the molecule had first been identified. All in all, our approach paves the way towards high-throughput discovery of novel peptidic natural products. Pep2Path is freely available from http://pep2path.sourceforge.net/, implemented in Python, licensed under the GNU General Public License v3 and supported on MS Windows, Linux and Mac OS X. PMID:25188327

  17. RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

    PubMed

    Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart

    2009-01-01

    RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th. PMID:18820292

  18. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks

    PubMed Central

    2013-01-01

    Background The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of medical and scientific terms that is used by biomedical scientists to manually index articles in the PubMed literature database. We hypothesized that genome-wide gene-MeSH term associations from the PubMed literature database could be used to predict implicit gene-to-gene relationships and networks. While the gene-MeSH associations have been used to detect gene-gene interactions in some studies, different methods have not been well compared, and such a strategy has not been evaluated for a genome-wide literature analysis. Genome-wide literature mining of gene-to-gene interactions allows ranking of the best gene interactions and investigation of comprehensive biological networks at a genome level. Results The genome-wide GenoMesh literature mining algorithm was developed by sequentially generating a gene-article matrix, a normalized gene-MeSH term matrix, and a gene-gene matrix. The gene-gene matrix relies on the calculation of pairwise gene dissimilarities based on gene-MeSH relationships. An optimized dissimilarity score was identified from six well-studied functions based on a receiver operating characteristic (ROC) analysis. Based on the studies with well-studied Escherichia coli and less-studied Brucella spp., GenoMesh was found to accurately identify gene functions using weighted MeSH terms, predict gene-gene interactions not reported in the literature, and cluster all the genes studied from an organism using the MeSH-based gene-gene matrix. A web-based GenoMesh literature mining program is also available at: http://genomesh.hegroup.org. GenoMesh also predicts gene interactions and networks among genes associated with specific MeSH terms or user-selected gene lists. Conclusions The GenoMesh algorithm and web program provide the first genome

  19. OntoMate: a text-mining tool aiding curation at the Rat Genome Database.

    PubMed

    Liu, Weisong; Laulederkind, Stanley J F; Hayman, G Thomas; Wang, Shur-Jen; Nigam, Rajni; Smith, Jennifer R; De Pons, Jeff; Dwinell, Melinda R; Shimoyama, Mary

    2015-01-01

    The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu. PMID:25619558

  20. OntoMate: a text-mining tool aiding curation at the Rat Genome Database

    PubMed Central

    Liu, Weisong; Laulederkind, Stanley J. F.; Hayman, G. Thomas; Wang, Shur-Jen; Nigam, Rajni; Smith, Jennifer R.; De Pons, Jeff; Dwinell, Melinda R.; Shimoyama, Mary

    2015-01-01

    The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu PMID:25619558

  1. Mining the genome of Rhodococcus fascians, a plant growth-promoting bacterium gone astray.

    PubMed

    Francis, Isolde M; Stes, Elisabeth; Zhang, Yucheng; Rangel, Diana; Audenaert, Kris; Vereecke, Danny

    2016-09-25

    Rhodococcus fascians is a phytopathogenic Gram-positive Actinomycete with a very broad host range encompassing especially dicotyledonous herbaceous perennials, but also some monocots, such as the Liliaceae and, recently, the woody crop pistachio. The pathogenicity of R. fascians strain D188 is known to be encoded by the linear plasmid pFiD188 and to be dictated by its capacity to produce a mixture of cytokinins. Here, we show that D188-5, the nonpathogenic plasmid-free derivative of the wild-type strain D188 actually has a plant growth-promoting effect. With the availability of the genome sequence of R. fascians, the chromosome of strain D188 was mined for putative plant growth-promoting functions and the functionality of some of these activities was tested. This analysis together with previous results suggests that the plant growth-promoting activity of R. fascians is due to production of plant growth modulators, such as auxin and cytokinin, combined with degradation of ethylene through 1-amino-cyclopropane-1-carboxylic acid deaminase. Moreover, R. fascians has several functions that could contribute to efficient colonization and competitiveness, but there is little evidence for a strong impact on plant nutrition. Possibly, the plant growth promotion encoded by the D188 chromosome is imperative for the epiphytic phase of the life cycle of R. fascians and prepares the plant to host the bacteria, thus ensuring proper continuation into the pathogenic phase. PMID:26877150

  2. Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota.

    PubMed

    Rossi, Maddalena; Martínez-Martínez, Daniel; Amaretti, Alberto; Ulrici, Alessandro; Raimondi, Stefano; Moya, Andrés

    2016-06-01

    The genus Lactobacillus includes over 215 species that colonize plants, foods, sewage and the gastrointestinal tract (GIT) of humans and animals. In the GIT, Lactobacillus population can be made by true inhabitants or by bacteria occasionally ingested with fermented or spoiled foods, or with probiotics. This study longitudinally surveyed Lactobacillus species and strains in the feces of a healthy subject through whole genome sequencing (WGS) data-mining, in order to identify members of the permanent or transient populations. In three time-points (0, 670 and 700 d), 58 different species were identified, 16 of them being retrieved for the first time in human feces. L. rhamnosus, L. ruminis, L. delbrueckii, L. plantarum, L. casei and L. acidophilus were the most represented, with estimated amounts ranging between 6 and 8 Log (cells g(-1) ), while the other were detected at 4 or 5 Log (cells g(-1) ). 86 Lactobacillus strains belonging to 52 species were identified. 43 seemingly occupied the GIT as true residents, since were detected in a time span of almost 2 years in all the three samples or in 2 samples separated by 670 or 700 d. As a whole, a stable community of lactobacilli was disclosed, with wide and understudied biodiversity. PMID:27043715

  3. Recent Advances in Discovery, Biosynthesis and Genome Mining of Medicinally Relevant Polycyclic Tetramate Macrolactams.

    PubMed

    Zhang, Guangtao; Zhang, Wenjun; Saha, Subhasish; Zhang, Changsheng

    2016-01-01

    Polycyclic tetramate macrolactams (PTMs), a widely distributed class of structurally complex natural products exhibiting diverse biological activities, share a tetramate-containing macrocyclic lactam ring fused to a subset of carbocyclic rings. More than 30 naturally occurring PTM members have been reported. Representative members include ikarugamycin, HSAF, and alteramides. The emerging significance of PTMs in medicinal applications has raised attentions on their biosynthetic studies. These studies have unveiled the unexpected conservation of compact PTM biosynthetic loci in phylogenetically diverse bacteria and elucidated mechanisms for key steps in PTM biosynthesis. PTMs were demonstrated to be derived from the common origin of a hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) pathway, in which the PKS portion was iteratively used to generate two separate polyketide chains. A common tetramate-containing polyene intermediate was proposed to be the final product of all PTM PKS/NRPS assembly lines. Subsequently, a set of oxidoreductases acted in a not yet clearly understood way to dictate the manner of cyclizations to yield different polycycle ring systems in PTMs. The only well studied example was the formation of the inner fivemembered ring in ikarugamycin, which was catalyzed by an alcohol dehydrogenase via a [1 + 6] Michael addition. Nonetheless, these studies have illustrated the extraordinary simplicity of nature's art in the biosynthesis of PTMs with complex structures and paved the way to further expand the structural diversity of the family of medicinally relevant PTMs by genome mining and combinatorial biosynthesis. PMID:26456464

  4. Mining the human genome after Association for Molecular Pathology v. Myriad Genetics

    PubMed Central

    Evans, Barbara J

    2014-01-01

    The Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics portrays the human genome as a product of nature. This frames medical genetics as an extractive industry that mines a natural resource to produce valuable goods and services. Natural resource law offers insights into problems medical geneticists can expect after this decision and suggests possible solutions. Increased competition among clinical laboratories offers various benefits but threatens to increase fragmentation of genetic data resources, potentially causing waste in the form of lost opportunities to discover the clinical significance of particular gene variants. The solution lies in addressing legal barriers to appropriate data sharing. Sustainable discovery in the field of medical genetics can best be achieved through voluntary data sharing rather than command-and-control tactics, but voluntary mechanisms must be conceived broadly to include market-based approaches as well as donative and publicly funded data commons. The recently revised Health Insurance Portability and Accountability Act Privacy Rule offers an improved—but still imperfect—framework for market-oriented data sharing. This article explores strategies for addressing the Privacy Rule's remaining defects. America is close to having a legal framework that can reward innovators, protect privacy, and promote needed data sharing to advance medical genetics. Genet Med 16 7, 504–509. PMID:24357850

  5. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation.

    PubMed

    Farasat, Iman; Salis, Howard M

    2016-01-01

    The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical and engineering applications. The CRISPR/Cas9 (Type II) system binds and cuts DNA using guide RNAs, though the variables that control its on-target and off-target activity remain poorly characterized. Here, we develop and parameterize a system-wide biophysical model of Cas9-based genome editing and gene regulation to predict how changing guide RNA sequences, DNA superhelical densities, Cas9 and crRNA expression levels, organisms and growth conditions, and experimental conditions collectively control the dynamics of dCas9-based binding and Cas9-based cleavage at all DNA sites with both canonical and non-canonical PAMs. We combine statistical thermodynamics and kinetics to model Cas9:crRNA complex formation, diffusion, site selection, reversible R-loop formation, and cleavage, using large amounts of structural, biochemical, expression, and next-generation sequencing data to determine kinetic parameters and develop free energy models. Our results identify DNA supercoiling as a novel mechanism controlling Cas9 binding. Using the model, we predict Cas9 off-target binding frequencies across the lambdaphage and human genomes, and explain why Cas9's off-target activity can be so high. With this improved understanding, we propose several rules for designing experiments for minimizing off-target activity. We also discuss the implications for engineering dCas9-based genetic circuits. PMID:26824432

  6. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

    PubMed Central

    Farasat, Iman; Salis, Howard M.

    2016-01-01

    The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical and engineering applications. The CRISPR/Cas9 (Type II) system binds and cuts DNA using guide RNAs, though the variables that control its on-target and off-target activity remain poorly characterized. Here, we develop and parameterize a system-wide biophysical model of Cas9-based genome editing and gene regulation to predict how changing guide RNA sequences, DNA superhelical densities, Cas9 and crRNA expression levels, organisms and growth conditions, and experimental conditions collectively control the dynamics of dCas9-based binding and Cas9-based cleavage at all DNA sites with both canonical and non-canonical PAMs. We combine statistical thermodynamics and kinetics to model Cas9:crRNA complex formation, diffusion, site selection, reversible R-loop formation, and cleavage, using large amounts of structural, biochemical, expression, and next-generation sequencing data to determine kinetic parameters and develop free energy models. Our results identify DNA supercoiling as a novel mechanism controlling Cas9 binding. Using the model, we predict Cas9 off-target binding frequencies across the lambdaphage and human genomes, and explain why Cas9’s off-target activity can be so high. With this improved understanding, we propose several rules for designing experiments for minimizing off-target activity. We also discuss the implications for engineering dCas9-based genetic circuits. PMID:26824432

  7. Molecular Networking and Pattern-Based Genome Mining Improves discovery of biosynthetic gene clusters and their products from Salinispora species

    PubMed Central

    Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; Sarkar, Anindita; Li, Jie; Ziemert, Nadine; Wang, Mingxun; Bandeira, Nuno; Moore, Bradley S.; Dorrestein, Pieter C.; Jensen, Paul R.

    2015-01-01

    Summary Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches. PMID:25865308

  8. Draft Genome Sequence of Sinorhizobium meliloti CCNWSX0020, a Nitrogen-Fixing Symbiont with Copper Tolerance Capability Isolated from Lead-Zinc Mine Tailings

    PubMed Central

    Li, Zhefei; Ma, Zhanqiang; Hao, Xiuli

    2012-01-01

    Sinorhizobium meliloti CCNWSX0020 was isolated from Medicago lupulina plants growing in lead-zinc mine tailings, which can establish a symbiotic relationship with Medicago species. Also, the genome of this bacterium contains a number of protein-coding sequences related to metal tolerance. We anticipate that the genomic sequence provides valuable information to explore environmental bioremediation. PMID:22328762

  9. Draft Genome Sequence of the Mercury-Resistant Bacterium Acinetobacter idrijaensis Strain MII, Isolated from a Mine-Impacted Area, Idrija, Slovenia

    PubMed Central

    Caballero Pérez, Juan; Cruz Medina, Julio Alfonso; Molina Vera, Carlos; Salas Rosas, Luz María; Limpens Gutiérrez, Citlalli; García Salinas, Isaac; Hernández Ramírez, Miriam Rebeca; Soto Alonso, Gerardo; Cruz Hernández, Andrés; Saldaña Gutiérrez, Carlos; Romero Gómez, Sergio; Pastrana Martínez, Xóchitl; Álvarez Hidalgo, Erika; Gosar, Mateja; Dizdarevič, Tatjana

    2014-01-01

    We report here the first draft assembly for the genome of Acinetobacter idrijaensis strain MII, isolated from the Idrija mercury mine area (Slovenia). This strain shows a strikingly high tolerance to mercury, and the genome sequence shows genes involved in the mechanisms for heavy metal tolerance pathways and multidrug efflux pumps. PMID:25395645

  10. A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ARS Microbial Genome Sequence Database (http://199.133.98.43), a web-based database server, was established utilizing the BIGSdb (Bacterial Isolate Genomics Sequence Database) software package, developed at Oxford University, as a tool to manage multi-locus sequence data for the family Streptomy...

  11. Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

    NASA Astrophysics Data System (ADS)

    Lu, Xia; Luan, Sheng; Kong, Jie; Hu, Longyang; Mao, Yong; Zhong, Shengping

    2015-12-01

    The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identifi ed, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplifi ed with specifi c products and 24 (80.0%) were polymorphic. For the amplifi ed polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had signifi cant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identifi ed SSRs signifi cantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.

  12. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia

    PubMed Central

    Covell, David G.

    2015-01-01

    Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE) and Sanger Cancer Genome Project (CGP). The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a) evaluate drug responses of compounds with similar mechanism of action (MOA), b) examine measures of gene expression (GE), copy number (CN) and mutation status (MUT) biomarkers, combined with gene set enrichment analysis (GSEA), for hypothesizing biological processes important for drug response, c) conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d) assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions. PMID:26132924

  13. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

    PubMed

    Covell, David G

    2015-01-01

    Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE) and Sanger Cancer Genome Project (CGP). The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a) evaluate drug responses of compounds with similar mechanism of action (MOA), b) examine measures of gene expression (GE), copy number (CN) and mutation status (MUT) biomarkers, combined with gene set enrichment analysis (GSEA), for hypothesizing biological processes important for drug response, c) conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d) assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions. PMID:26132924

  14. Isolation and structure determination of a new lantibiotic cinnamycin B from Actinomadura atramentaria based on genome mining.

    PubMed

    Kodani, Shinya; Komaki, Hisayuki; Ishimura, Sho; Hemmi, Hikaru; Ohnishi-Kameyama, Mayumi

    2016-08-01

    New lantibiotic cinnamycin B was isolated from the extract of Actinomadura atramentaria NBRC 14695(T), based on genome mining and chemical investigation. The partial structure of cinnamycin B was established by 2D NMR experiments, which indicated that cinnamycin B had same methyl lanthionine bridging pattern with cinnamycin. The reduction with NaBH4-NiCl2 afforded the reduced cinnamycin B, and MS/MS experiment indicated the presence of hydroxy asparatic acid in the molecule. Cinnamycin B showed an antibacterial activity against Streptomyces antibioticus with dosage of 5 μg (0.5μL, 10 mg/mL solution) at spot-on-lawn testing method. The gene cluster of cinnamycin B on the genome of A. atramentaria was identified and discussed in comparison with that of cinnamycin. PMID:27255974

  15. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources

    PubMed Central

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/ PMID:26589635

  16. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

    PubMed

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. PMID:26589635

  17. Confucian Rationalism

    ERIC Educational Resources Information Center

    Lam, Chi-Ming

    2014-01-01

    Nowadays, there is still a widely held view that the Chinese and Western modes of thought are quite distinct from each other. In particular, the Chinese mode of thought derived from Confucianism is considered as comparatively less rational than the Western one. In this article, I first argue that although the analogical mode of argumentation,…

  18. Isolation and Identification of Rhizoxin Derivatives from Pseudomonas fluorescens Pf-5 using a Genomic Mining Strategy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The products synthesized from a hybrid polyketide synthase/nonribosomal peptide synthetase gene cluster in the genome of Pseudomonas fluorescens Pf-5 were identified using a genomics-guided strategy involving insertional mutagenesis and subsequent metabolite profiling. Five analogs of rhizoxin, a 1...

  19. Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although natural products have been a particularly rich source of human medicines, the rate at which new molecules are being discovered is declining precipitously. Based on the large number of natural product biosynthetic genes in microbial genomes, many have suggested “genome mining” as an approach...

  20. Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides

    PubMed Central

    2013-01-01

    Background Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters and share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or the secretion of peptides. In silico prediction of peptide structures according to NRPS architecture suggests eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas translucens and X. oryzae pv. oryzicola. Further genome mining revealed other novel NRPS

  1. CisMiner: Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining

    PubMed Central

    Navarro, Carmen; Lopez, Francisco J.; Cano, Carlos; Garcia-Alcalde, Fernando; Blanco, Armando

    2014-01-01

    Eukaryotic gene control regions are known to be spread throughout non-coding DNA sequences which may appear distant from the gene promoter. Transcription factors are proteins that coordinately bind to these regions at transcription factor binding sites to regulate gene expression. Several tools allow to detect significant co-occurrences of closely located binding sites (cis-regulatory modules, CRMs). However, these tools present at least one of the following limitations: 1) scope limited to promoter or conserved regions of the genome; 2) do not allow to identify combinations involving more than two motifs; 3) require prior information about target motifs. In this work we present CisMiner, a novel methodology to detect putative CRMs by means of a fuzzy itemset mining approach able to operate at genome-wide scale. CisMiner allows to perform a blind search of CRMs without any prior information about target CRMs nor limitation in the number of motifs. CisMiner tackles the combinatorial complexity of genome-wide cis-regulatory module extraction using a natural representation of motif combinations as itemsets and applying the Top-Down Fuzzy Frequent- Pattern Tree algorithm to identify significant itemsets. Fuzzy technology allows CisMiner to better handle the imprecision and noise inherent to regulatory processes. Results obtained for a set of well-known binding sites in the S. cerevisiae genome show that our method yields highly reliable predictions. Furthermore, CisMiner was also applied to putative in-silico predicted transcription factor binding sites to identify significant combinations in S. cerevisiae and D. melanogaster, proving that our approach can be further applied genome-wide to more complex genomes. CisMiner is freely accesible at: http://genome2.ugr.es/cisminer. CisMiner can be queried for the results presented in this work and can also perform a customized cis-regulatory module prediction on a query set of transcription factor binding sites provided by

  2. Draft Genome Sequence of "Acidibacillus ferrooxidans" ITV01, a Novel Acidophilic Firmicute Isolated from a Chalcopyrite Mine Drainage Site in Brazil.

    PubMed

    Dall'Agnol, Hivana; Ñancucheo, Ivan; Johnson, D Barrie; Oliveira, Renato; Leite, Laura; Pylro, Victor S; Holanda, Roseanne; Grail, Barry; Carvalho, Nelson; Nunes, Gisele Lopes; Tzotzos, George; Fernandes, Gabriel Rocha; Dutra, Julliane; Orellana, Sara Cuadros; Oliveira, Guilherme

    2016-01-01

    Here, we report the draft genome sequence of "Acidibacillus ferrooxidans" strain ITV01, a ferrous iron- and sulfide-mineral-oxidizing, obligate heterotrophic, and acidophilic bacterium affiliated with the phylum Firmicutes. Strain ITV01 was isolated from neutral drainage from a low-grade chalcopyrite from a mine in northern Brazil. PMID:26988062

  3. Draft Genome Sequence of “Acidibacillus ferrooxidans” ITV01, a Novel Acidophilic Firmicute Isolated from a Chalcopyrite Mine Drainage Site in Brazil

    PubMed Central

    Dall’Agnol, Hivana; Ñancucheo, Ivan; Johnson, D. Barrie; Oliveira, Renato; Leite, Laura; Holanda, Roseanne; Grail, Barry; Carvalho, Nelson; Nunes, Gisele Lopes; Tzotzos, George; Fernandes, Gabriel Rocha; Dutra, Julliane; Orellana, Sara Cuadros

    2016-01-01

    Here, we report the draft genome sequence of “Acidibacillus ferrooxidans” strain ITV01, a ferrous iron- and sulfide-mineral-oxidizing, obligate heterotrophic, and acidophilic bacterium affiliated with the phylum Firmicutes. Strain ITV01 was isolated from neutral drainage from a low-grade chalcopyrite from a mine in northern Brazil. PMID:26988062

  4. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

    PubMed Central

    Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong

    2016-01-01

    Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. PMID:27240697

  5. Rationalization: A Bibliography.

    ERIC Educational Resources Information Center

    Pedrini, D. T.; Pedrini, Bonnie C.

    Rationalization was studied by Sigmund Freud and was specifically labeled by Ernest Jones. Rationalization ought to be differentiated from rational, rationality, logical analysis, etc. On the one hand, rationalization is considered a defense mechanism, on the other hand, rationality is not. Haan has done much work with self-report inventories and…

  6. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

    PubMed

    Weber, Tilmann; Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko; Medema, Marnix H

    2015-07-01

    Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. PMID:25948579

  7. Genomic analyses of metal resistance genes in three plant growth promoting bacteria of legume plants in Northwest mine tailings, China.

    PubMed

    Xie, Pin; Hao, Xiuli; Herzberg, Martin; Luo, Yantao; Nies, Dietrich H; Wei, Gehong

    2015-01-01

    To better understand the diversity of metal resistance genetic determinant from microbes that survived at metal tailings in northwest of China, a highly elevated level of heavy metal containing region, genomic analyses was conducted using genome sequence of three native metal-resistant plant growth promoting bacteria (PGPB). It shows that: Mesorhizobium amorphae CCNWGS0123 contains metal transporters from P-type ATPase, CDF (Cation Diffusion Facilitator), HupE/UreJ and CHR (chromate ion transporter) family involved in copper, zinc, nickel as well as chromate resistance and homeostasis. Meanwhile, the putative CopA/CueO system is expected to mediate copper resistance in Sinorhizobium meliloti CCNWSX0020 while ZntA transporter, assisted with putative CzcD, determines zinc tolerance in Agrobacterium tumefaciens CCNWGS0286. The greenhouse experiment provides the consistent evidence of the plant growth promoting effects of these microbes on their hosts by nitrogen fixation and/or indoleacetic acid (IAA) secretion, indicating a potential in-site phytoremediation usage in the mining tailing regions of China. PMID:25597676

  8. Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics

    SciTech Connect

    Yang, Xiaohan; Ye, Chuyu; Bisaria, Anjali; Tuskan, Gerald A; Kalluri, Udaya C

    2011-01-01

    Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of ethanol from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidences supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional genomics in relation to cell wall biosynthesis.

  9. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

    PubMed Central

    Weber, Tilmann; Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A.; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko; Medema, Marnix H.

    2015-01-01

    Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. PMID:25948579

  10. antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

    PubMed Central

    Blin, Kai; Medema, Marnix H.; Kazempour, Daniyal; Fischbach, Michael A.; Breitling, Rainer; Takano, Eriko; Weber, Tilmann

    2013-01-01

    Microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals. Genome mining of their biosynthetic gene clusters has become a key method to accelerate their identification and characterization. In 2011, we developed antiSMASH, a web-based analysis platform that automates this process. Here, we present the highly improved antiSMASH 2.0 release, available at http://antismash.secondarymetabolites.org/. For the new version, antiSMASH was entirely re-designed using a plug-and-play concept that allows easy integration of novel predictor or output modules. antiSMASH 2.0 now supports input of multiple related sequences simultaneously (multi-FASTA/GenBank/EMBL), which allows the analysis of draft genomes comprising multiple contigs. Moreover, direct analysis of protein sequences is now possible. antiSMASH 2.0 has also been equipped with the capacity to detect additional classes of secondary metabolites, including oligosaccharide antibiotics, phenazines, thiopeptides, homo-serine lactones, phosphonates and furans. The algorithm for predicting the core structure of the cluster end product is now also covering lantipeptides, in addition to polyketides and non-ribosomal peptides. The antiSMASH ClusterBlast functionality has been extended to identify sub-clusters involved in the biosynthesis of specific chemical building blocks. The new features currently make antiSMASH 2.0 the most comprehensive resource for identifying and analyzing novel secondary metabolite biosynthetic pathways in microorganisms. PMID:23737449

  11. Machine learning and data mining in complex genomic data--a review on the lessons learned in Genetic Analysis Workshop 19.

    PubMed

    König, Inke R; Auerbach, Jonathan; Gola, Damian; Held, Elizabeth; Holzinger, Emily R; Legault, Marc-André; Sun, Rui; Tintle, Nathan; Yang, Hsin-Chou

    2016-01-01

    In the analysis of current genomic data, application of machine learning and data mining techniques has become more attractive given the rising complexity of the projects. As part of the Genetic Analysis Workshop 19, approaches from this domain were explored, mostly motivated from two starting points. First, assuming an underlying structure in the genomic data, data mining might identify this and thus improve downstream association analyses. Second, computational methods for machine learning need to be developed further to efficiently deal with the current wealth of data.In the course of discussing results and experiences from the machine learning and data mining approaches, six common messages were extracted. These depict the current state of these approaches in the application to complex genomic data. Although some challenges remain for future studies, important forward steps were taken in the integration of different data types and the evaluation of the evidence. Mining the data for underlying genetic or phenotypic structure and using this information in subsequent analyses proved to be extremely helpful and is likely to become of even greater use with more complex data sets. PMID:26866367

  12. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

    PubMed Central

    2013-01-01

    Background Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that

  13. Mining the Plasmodium genome database to define organellar function: what does the apicoplast do?

    PubMed Central

    Roos, David S; Crawford, Michael J; Donald, Robert G K; Fraunholz, Martin; Harb, Omar S; He, Cynthia Y; Kissinger, Jessica C; Shaw, Michael K; Striepen, Boris

    2002-01-01

    Apicomplexan species constitute a diverse group of parasitic protozoa, which are responsible for a wide range of diseases in many organisms. Despite differences in the diseases they cause, these parasites share an underlying biology, from the genetic controls used to differentiate through the complex parasite life cycle, to the basic biochemical pathways employed for intracellular survival, to the distinctive cell biology necessary for host cell attachment and invasion. Different parasites lend themselves to the study of different aspects of parasite biology: Eimeria for biochemical studies, Toxoplasma for molecular genetic and cell biological investigation, etc. The Plasmodium falciparum Genome Project contributes the first large-scale genomic sequence for an apicomplexan parasite. The Plasmodium Genome Database (http://PlasmoDB.org) has been designed to permit individual investigators to ask their own questions, even prior to formal release of the reference P. falciparum genome sequence. As a case in point, PlasmoDB has been exploited to identify metabolic pathways associated with the apicomplexan plastid, or 'apicoplast' - an essential organelle derived by secondary endosymbiosis of an alga, and retention of the algal plastid. PMID:11839180

  14. Genomic insights into a new acidophilic, copper-resistant Desulfosporosinus isolate from the oxidized tailings area of an abandoned gold mine.

    PubMed

    Mardanov, Andrey V; Panova, Inna A; Beletsky, Alexey V; Avakyan, Marat R; Kadnikov, Vitaly V; Antsiferov, Dmitry V; Banks, David; Frank, Yulia A; Pimenov, Nikolay V; Ravin, Nikolai V; Karnachuk, Olga V

    2016-08-01

    Microbial sulfate reduction in acid mine drainage is still considered to be confined to anoxic conditions, although several reports have shown that sulfate-reducing bacteria occur under microaerophilic or aerobic conditions. We have measured sulfate reduction rates of up to 60 nmol S cm(-3) day(-1) in oxidized layers of gold mine tailings in Kuzbass (SW Siberia). A novel, acidophilic, copper-tolerant Desulfosporosinus sp. I2 was isolated from the same sample and its genome was sequenced. The genomic analysis and physiological data indicate the involvement of transporters and additional mechanisms to tolerate metals, such as sequestration by polyphosphates. Desulfosporinus sp. I2 encodes systems for a metabolically versatile life style. The genome possessed a complete Embden-Meyerhof pathway for glycolysis and gluconeogenesis. Complete oxidation of organic substrates could be enabled by the complete TCA cycle. Genomic analysis found all major components of the electron transfer chain necessary for energy generation via oxidative phosphorylation. Autotrophic CO2 fixation could be performed through the Wood-Ljungdahl pathway. Multiple oxygen detoxification systems were identified in the genome. Taking into account the metabolic activity and genomic analysis, the traits of the novel isolate broaden our understanding of active sulfate reduction and associated metabolism beyond strictly anaerobic niches. PMID:27222219

  15. Novel Tn4371-ICE like element in Ralstonia pickettii and Genome mining for comparative elements

    PubMed Central

    2009-01-01

    Background Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements. A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element. Results Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several β and γ- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type. Conclusion All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water. PMID:19941653

  16. Mining clinical attributes of genomic variants through assisted literature curation in Egas.

    PubMed

    Matos, Sérgio; Campos, David; Pinho, Renato; Silva, Raquel M; Mort, Matthew; Cooper, David N; Oliveira, José Luís

    2016-01-01

    The veritable deluge of biological data over recent years has led to the establishment of a considerable number of knowledge resources that compile curated information extracted from the literature and store it in structured form, facilitating its use and exploitation. In this article, we focus on the curation of inherited genetic variants and associated clinical attributes, such as zygosity, penetrance or inheritance mode, and describe the use of Egas for this task. Egas is a web-based platform for text-mining assisted literature curation that focuses on usability through modern design solutions and simple user interactions. Egas offers a flexible and customizable tool that allows defining the concept types and relations of interest for a given annotation task, as well as the ontologies used for normalizing each concept type. Further, annotations may be performed on raw documents or on the results of automated concept identification and relation extraction tools. Users can inspect, correct or remove automatic text-mining results, manually add new annotations, and export the results to standard formats. Egas is compatible with the most recent versions of Google Chrome, Mozilla Firefox, Internet Explorer and Safari and is available for use at https://demo.bmd-software.com/egas/Database URL: https://demo.bmd-software.com/egas/. PMID:27278817

  17. Mining clinical attributes of genomic variants through assisted literature curation in Egas

    PubMed Central

    Matos, Sérgio; Campos, David; Pinho, Renato; Silva, Raquel M.; Mort, Matthew; Cooper, David N.; Oliveira, José Luís

    2016-01-01

    The veritable deluge of biological data over recent years has led to the establishment of a considerable number of knowledge resources that compile curated information extracted from the literature and store it in structured form, facilitating its use and exploitation. In this article, we focus on the curation of inherited genetic variants and associated clinical attributes, such as zygosity, penetrance or inheritance mode, and describe the use of Egas for this task. Egas is a web-based platform for text-mining assisted literature curation that focuses on usability through modern design solutions and simple user interactions. Egas offers a flexible and customizable tool that allows defining the concept types and relations of interest for a given annotation task, as well as the ontologies used for normalizing each concept type. Further, annotations may be performed on raw documents or on the results of automated concept identification and relation extraction tools. Users can inspect, correct or remove automatic text-mining results, manually add new annotations, and export the results to standard formats. Egas is compatible with the most recent versions of Google Chrome, Mozilla Firefox, Internet Explorer and Safari and is available for use at https://demo.bmd-software.com/egas/. Database URL: https://demo.bmd-software.com/egas/ PMID:27278817

  18. Banking biological collections: data warehousing, data mining, and data dilemmas in genomics and global health policy.

    PubMed

    Blatt, R J R

    2000-01-01

    While DNA databases may offer the opportunity to (1) assess population-based prevalence of specific genes and variants, (2) simplify the search for molecular markers, (3) improve targeted drug discovery and development for disease management, (4) refine strategies for disease prevention, and (5) provide the data necessary for evidence-based decision-making, serious scientific and social questions remain. Whether samples are identified, coded, or anonymous, biological banking raises profound ethical and legal issues pertaining to access, informed consent, privacy and confidentiality of genomic information, civil liberties, patenting, and proprietary rights. This paper provides an overview of key policy issues and questions pertaining to biological banking, with a focus on developments in specimen collection, transnational distribution, and public health and academic-industry research alliances. It highlights the challenges posed by the commercialization of genomics, and proposes the need for harmonization of biological banking policies. PMID:11878344

  19. Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

    PubMed

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  20. Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

    PubMed Central

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  1. Databank based mining on the track of antimicrobial weapons in plant genomes.

    PubMed

    Belarmino, Luis C; Benko-Iseppon, Ana M

    2010-05-01

    The expressive amount of nucleotide sequences from diverse plant species in databanks enables the use of computational approaches to discovery still unidentified genes and to infer about their function, structure and role in some biological processes. Of special interest are the antimicrobial peptides (AMP), whose functionalities have a very important role in defense against microbial infection in multicellular eukaryotes, being considered less susceptible to bacterial resistance than traditional antibiotics, with potential to develop a new class of therapeutic agents. Recent computational developments have provided various algorithms and resources to profit from the overwhelming information in data banks for biomining such peptides. This review focuses on the computational and bioinformatic approaches so far used for the identification of antimicrobial peptides in plant systems, highlighting alternative means of mining the entire plant peptide space that has recently become available. PMID:20088774

  2. Novel LanT Associated Lantibiotic Clusters Identified by Genome Database Mining

    PubMed Central

    Singh, Mangal; Sareen, Dipti

    2014-01-01

    Background Frequent use of antibiotics has led to the emergence of antibiotic resistance in bacteria. Lantibiotic compounds are ribosomally synthesized antimicrobial peptides against which bacteria are not able to produce resistance, hence making them a good alternative to antibiotics. Nisin is the oldest and the most widely used lantibiotic, in food preservation, without having developed any significant resistance against it. Having their antimicrobial potential and a limited number, there is a need to identify novel lantibiotics. Methodology/Findings Identification of novel lantibiotic biosynthetic clusters from an ever increasing database of bacterial genomes, can provide a major lead in this direction. In order to achieve this, a strategy was adopted to identify novel lantibiotic biosynthetic clusters by screening the sequenced genomes for LanT homolog, which is a conserved lantibiotic transporter specific to type IB clusters. This strategy resulted in identification of 54 bacterial strains containing the LanT homologs, which are not the known lantibiotic producers. Of these, 24 strains were subjected to a detailed bioinformatic analysis to identify genes encoding for precursor peptides, modification enzyme, immunity and quorum sensing proteins. Eight clusters having two LanM determinants, similar to haloduracin and lichenicidin were identified, along with 13 clusters having a single LanM determinant as in mersacidin biosynthetic cluster. Besides these, orphan LanT homologs were also identified which might be associated with novel bacteriocins, encoded somewhere else in the genome. Three identified gene clusters had a C39 domain containing LanT transporter, associated with the LanBC proteins and double glycine type precursor peptides, the only known example of such a cluster is that of salivaricin. Conclusion This study led to the identification of 8 novel putative two-component lantibiotic clusters along with 13 having a single LanM and 3 with LanBC genes

  3. Genome mining of mycosporine-like amino acid (MAA) synthesizing and non-synthesizing cyanobacteria: A bioinformatics study.

    PubMed

    Singh, Shailendra P; Klisch, Manfred; Sinha, Rajeshwar P; Häder, Donat-P

    2010-02-01

    Mycosporine-like amino acids (MAAs) are a family of more than 20 compounds having absorption maxima between 310 and 362 nm. These compounds are well known for their UV-absorbing/screening role in various organisms and seem to have evolutionary significance. In the present investigation we tested four cyanobacteria, e.g., Anabaena variabilis PCC 7937, Anabaena sp. PCC 7120, Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 6301, for their ability to synthesize MAA and conducted genomic and phylogenetic analysis to identify the possible set of genes that might be involved in the biosynthesis of these compounds. Out of the four investigated species, only A. variabilis PCC 7937 was able to synthesize MAA. Genome mining identified a combination of genes, YP_324358 (predicted DHQ synthase) and YP_324357 (O-methyltransferase), which were present only in A. variabilis PCC 7937 and missing in the other studied cyanobacteria. Phylogenetic analysis revealed that these two genes are transferred from a cyanobacterial donor to dinoflagellates and finally to metazoa by a lateral gene transfer event. All other cyanobacteria, which have these two genes, also had another copy of the DHQ synthase gene. The predicted protein structure for YP_324358 also suggested that this product is different from the chemically characterized DHQ synthase of Aspergillus nidulans contrary to the YP_324879, which was predicted to be similar to the DHQ synthase. The present study provides a first insight into the genes of cyanobacteria involved in MAA biosynthesis and thus widens the field of research for molecular, bioinformatics and phylogenetic analysis of these evolutionary and industrially important compounds. Based on the results we propose that YP_324358 and YP_324357 gene products are involved in the biosynthesis of the common core (deoxygadusol) of all MAAs. PMID:19879348

  4. The discovery of putative urine markers for the specific detection of prostate tumor by integrative mining of public genomic profiles.

    PubMed

    Chen, Min; Wang, Kai; Zhang, Liang; Li, Cheng; Yang, Yongliang

    2011-01-01

    Urine has emerged as an attractive biofluid for the noninvasive detection of prostate cancer (PCa). There is a strong imperative to discover candidate urinary markers for the clinical diagnosis and prognosis of PCa. The rising flood of various omics profiles presents immense opportunities for the identification of prospective biomarkers. Here we present a simple and efficient strategy to derive candidate urine markers for prostate tumor by mining cancer genomic profiles from public databases. Prostate, bladder and kidney are three major tissues from which cellular matters could be released into urine. To identify urinary markers specific for PCa, upregulated entities that might be shed in exosomes of bladder cancer and kidney cancer are first excluded. Through the ontology-based filtering and further assessment, a reduced list of 19 entities encoding urinary proteins was derived as putative PCa markers. Among them, we have found 10 entities closely associated with the process of tumor cell growth and development by pathway enrichment analysis. Further, using the 10 entities as seeds, we have constructed a protein-protein interaction (PPI) subnetwork and suggested a few urine markers as preferred prognostic markers to monitor the invasion and progression of PCa. Our approach is amenable to discover and prioritize potential markers present in a variety of body fluids for a spectrum of human diseases. PMID:22194848

  5. Fungal genomes mining to discover novel sterol esterases and lipases as catalysts

    PubMed Central

    2013-01-01

    Background Sterol esterases and lipases are enzymes able to efficiently catalyze synthesis and hydrolysis reactions of both sterol esters and triglycerides and due to their versatility could be widely used in different industrial applications. Lipases with this ability have been reported in the yeast Candida rugosa that secretes several extracellular enzymes with a high level of sequence identity, although different substrate specificity. This versatility has also been found in the sterol esterases from the ascomycetes Ophiostoma piceae and Melanocarpus albomyces. Results In this work we present an in silico search of new sterol esterase and lipase sequences from the genomes of environmental fungi. The strategy followed included identification and search of conserved domains from these versatile enzymes, phylogenetic studies, sequence analysis and 3D modeling of the selected candidates. Conclusions Six potential putative enzymes were selected and their kinetic properties and substrate selectivity are discussed on the basis of their similarity with previously characterized sterol esterases/lipases with known structures. PMID:24138290

  6. Evaluating the microtubule cytoskeleton and its interacting proteins in monocots by mining the rice genome

    PubMed Central

    Guo, Longbiao; Ho, Chin-Min Kimmy; Kong, Zhaosheng; Lee, Yuh-Ru Julie; Qian, Qian; Liu, Bo

    2009-01-01

    Background Microtubules (MTs) are assembled by heterodimers of α- and β-tubulins, which provide tracks for directional transport and frameworks for the spindle apparatus and the phragmoplast. MT nucleation and dynamics are regulated by components such as the γ-tubulin complex which are conserved among eukaryotes, and other components which are unique to plants. Following remarkable progress made in the model plant Arabidopsis thaliana toward revealing key components regulating MT activities, the completed rice (Oryza sativa) genome has prompted a survey of the MT cytoskeleton in this important crop as a model for monocots. Scope The rice genome contains three α-tubulin genes, eight β-tubulin genes and a single γ-tubulin gene. A functional γ-tubulin ring complex is expected to form in rice as genes encoding all components of the complex are present. Among proteins that interact with MTs, compared with A. thaliana, rice has more genes encoding some members such as the MAP65/Ase1p/PRC1 family, but fewer for the motor kinesins, the end-binding protein EB1 and the mitotic kinase Aurora. Although most known MT-interacting factors have apparent orthologues in rice, no orthologues of arabidopsis RIC1 and MAP18 have been identified in rice. Among all proteins surveyed here, only a few have had their functions characterized by genetic means in rice. Elucidating functions of proteins of the rice MT cytoskeleton, aided by recent technical advances made in this model monocot, will greatly advance our knowledge of how monocots employ their MTs to regulate their growth and form. PMID:19106179

  7. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.

    PubMed

    Stelzer, Gil; Rosen, Naomi; Plaschkes, Inbar; Zimmerman, Shahar; Twik, Michal; Fishilevich, Simon; Stein, Tsippi Iny; Nudel, Ron; Lieder, Iris; Mazor, Yaron; Kaplan, Sergey; Dahary, Dvir; Warshawsky, David; Guan-Golan, Yaron; Kohn, Asher; Rappaport, Noa; Safran, Marilyn; Lancet, Doron

    2016-01-01

    GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It automatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. VarElect's capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. © 2016 by John Wiley & Sons, Inc. PMID:27322403

  8. Genomic mining for novel FADH₂-dependent halogenases in marine sponge-associated microbial consortia.

    PubMed

    Bayer, Kristina; Scheuermayer, Matthias; Fieseler, Lars; Hentschel, Ute

    2013-02-01

    Many marine sponges (Porifera) are known to contain large amounts of phylogenetically diverse microorganisms. Sponges are also known for their large arsenal of natural products, many of which are halogenated. In this study, 36 different FADH₂-dependent halogenase gene fragments were amplified from various Caribbean and Mediterranean sponges using newly designed degenerate PCR primers. Four unique halogenase-positive fosmid clones, all containing the highly conserved amino acid motif "GxGxxG", were identified in the microbial metagenome of Aplysina aerophoba. Sequence analysis of one halogenase-bearing fosmid revealed notably two open reading frames with high homologies to efflux and multidrug resistance proteins. Single cell genomic analysis allowed for a taxonomic assignment of the halogenase genes to specific symbiotic lineages. Specifically, the halogenase cluster S1 is predicted to be produced by a deltaproteobacterial symbiont and halogenase cluster S2 by a poribacterial sponge symbiont. An additional halogenase gene is possibly produced by an actinobacterial symbiont of marine sponges. The identification of three novel, phylogenetically, and possibly also functionally distinct halogenase gene clusters indicates that the microbial consortia of sponges are a valuable resource for novel enzymes involved in halogenation reactions. PMID:22562484

  9. Data-mining approaches reveal hidden families of proteases in the genome of malaria parasite.

    PubMed

    Wu, Yimin; Wang, Xiangyun; Liu, Xia; Wang, Yufeng

    2003-04-01

    The search for novel antimalarial drug targets is urgent due to the growing resistance of Plasmodium falciparum parasites to available drugs. Proteases are attractive antimalarial targets because of their indispensable roles in parasite infection and development, especially in the processes of host erythrocyte rupture/invasion and hemoglobin degradation. However, to date, only a small number of proteases have been identified and characterized in Plasmodium species. Using an extensive sequence similarity search, we have identified 92 putative proteases in the P. falciparum genome. A set of putative proteases including calpain, metacaspase, and signal peptidase I have been implicated to be central mediators for essential parasitic activity and distantly related to the vertebrate host. Moreover, of the 92, at least 88 have been demonstrated to code for gene products at the transcriptional levels, based upon the microarray and RT-PCR results, and the publicly available microarray and proteomics data. The present study represents an initial effort to identify a set of expressed, active, and essential proteases as targets for inhibitor-based drug design. PMID:12671001

  10. miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.

    PubMed

    Yu, Lan; Shao, Chaogang; Ye, Xinghuo; Meng, Yijun; Zhou, Yincong; Chen, Ming

    2016-01-01

    MicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs of Arabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA-target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html. PMID:26732371

  11. [Constitutional requirements of rationing].

    PubMed

    Kluth, Winfried

    2008-01-01

    Rationing is an emotive issue in the field of public health. This complicates the rational discourse, which is indispensable for analyzing the rationing conditions as set out by constitutional law and which requires manifold differentiation and consideration that shall briefly be outlined in the following short contribution. Of central significance is the distinction between indirect and direct rationing as well as the reference to the essential responsibility of legislators for rationing decisions. PMID:19004184

  12. Genomic analysis of head and neck squamous cell carcinoma cell lines and human tumors: a rational approach to preclinical model selection

    PubMed Central

    Li, Hua; Wawrose, John S.; Gooding, William E.; Garraway, Levi A.; Lui, Vivian Wai Yan; Peyser, Noah D.; Grandis, Jennifer R.

    2014-01-01

    Head and neck squamous cell carcinoma (HNSCC) is the sixth most common type of cancer worldwide. The increasing amount of genomic information on human tumors and cell lines provides more biological data to design preclinical studies. We and others previously reported whole exome sequencing data of 106 HNSCC primary tumors. In 2012, high throughput genomic data and pharmacological profiling of anticancer drugs of hundreds of cancer cell lines were reported. Here we compared the genomic data of 39 HNSCC cell lines with the genomic findings in 106 HNSCC tumors. Amplification of eight genes (PIK3CA, EGFR, CCND2, KDM5A, ERBB2, PMS1, FGFR1 and WHSCIL1) and deletion of five genes (CDKN2A, SMAD4, NOTCH2, NRAS and TRIM33) were found in both HNSCC cell lines and tumors. Seventeen genes were only mutated in HNSCC cell lines (>10%) suggesting that these mutations may arise through immortalization in tissue culture. Conversely, 11 genes were only mutated in >10% of human HNSCC tumors. Several mutant genes in the EGFR pathway are shared both in cell lines and in tumors. Pharmacological profiling of eight anticancer agents in six HNSCC cell lines suggested that PIK3CA mutation may serve as a predictive biomarker for the drugs targeting the EGFR/PI3K pathway. These findings suggest that a correlation of gene mutations between HNSCC cell lines and human tumors may be used to guide the selection of preclinical models for translational research. PMID:24425785

  13. Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis.

    PubMed

    Esmaeel, Qassim; Pupin, Maude; Kieu, Nam Phuong; Chataigné, Gabrielle; Béchet, Max; Deravel, Jovana; Krier, François; Höfte, Monica; Jacques, Philippe; Leclère, Valérie

    2016-06-01

    Burkholderia is an important genus encompassing a variety of species, including pathogenic strains as well as strains that promote plant growth. We have carried out a global strategy, which combined two complementary approaches. The first one is genome guided with deep analysis of genome sequences and the second one is assay guided with experiments to support the predictions obtained in silico. This efficient screening for new secondary metabolites, performed on 48 gapless genomes of Burkholderia species, revealed a total of 161 clusters containing nonribosomal peptide synthetases (NRPSs), with the potential to synthesize at least 11 novel products. Most of them are siderophores or lipopeptides, two classes of products with potential application in biocontrol. The strategy led to the identification, for the first time, of the cluster for cepaciachelin biosynthesis in the genome of Burkholderia ambifaria AMMD and a cluster corresponding to a new malleobactin-like siderophore, called phymabactin, was identified in Burkholderia phymatum STM815 genome. In both cases, the siderophore was produced when the strain was grown in iron-limited conditions. Elsewhere, the cluster for the antifungal burkholdin was detected in the genome of B. ambifaria AMMD and also Burkholderia sp. KJ006. Burkholderia pseudomallei strains harbor the genetic potential to produce a novel lipopeptide called burkhomycin, containing a peptidyl moiety of 12 monomers. A mixture of lipopeptides produced by Burkholderia rhizoxinica lowered the surface tension of the supernatant from 70 to 27 mN·m(-1) . The production of nonribosomal secondary metabolites seems related to the three phylogenetic groups obtained from 16S rRNA sequences. Moreover, the genome-mining approach gave new insights into the nonribosomal synthesis exemplified by the identification of dual C/E domains in lipopeptide NRPSs, up to now essentially found in Pseudomonas strains. PMID:27060604

  14. Characterization of the Alkaline Laccase Ssl1 from Streptomyces sviceus with Unusual Properties Discovered by Genome Mining

    PubMed Central

    Gunne, Matthias; Urlacher, Vlada B.

    2012-01-01

    Fungal laccases are well investigated enzymes with high potential in diverse applications like bleaching of waste waters and textiles, cellulose delignification, and organic synthesis. However, they are limited to acidic reaction conditions and require eukaryotic expression systems. This raises a demand for novel laccases without these constraints. We have taken advantage of the laccase engineering database LccED derived from genome mining to identify and clone the laccase Ssl1 from Streptomyces sviceus which can circumvent the limitations of fungal laccases. Ssl1 belongs to the family of small laccases that contains only few characterized enzymes. After removal of the twin-arginine signal peptide Ssl1 was readily expressed in E. coli. Ssl1 is a small laccase with 32.5 kDa, consists of only two cupredoxin-like domains, and forms trimers in solution. Ssl1 oxidizes 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) and phenolic substrates like 2,6-dimethoxy phenol, guaiacol, and syringaldazine. The kcat value for ABTS oxidation was at least 20 times higher than for other substrates. The optimal pH for oxidation reactions is substrate dependent: for phenolic substrates the highest activities were detected at alkaline conditions (pH 9.0 for 2,6-dimethoxy phenol and guaiacol and pH 8.0 for syringaldazine), while the highest reaction rates with ABTS were observed at pH 4.0. Though originating from a mesophilic organism, Ssl demonstrates remarkable stability at elevated temperatures (T1/2,60°C = 88 min) and in a wide pH range (pH 5.0 to 11.0). Notably, the enzyme retained 80% residual activity after 5 days of incubation at pH 11. Detergents and organic co-solvents do not affect Ssl1 stability. The described robustness makes Ssl1 a potential candidate for industrial applications, preferably in processes that require alkaline reaction conditions. PMID:23285009

  15. Rationing medical education.

    PubMed

    Walsh, Kieran

    2016-03-01

    The purpose of this paper is to discuss the role of rationing in medical education. Medical education is expensive and there is a limit to that which governments, funders or individuals can spend on it. Rationing involves the allocation of resources that are limited. This paper discussed the pros and cons of the application of rationing to medical education and the different forms of rationing that could be applied. Even though some stakeholders in medical education might be taken aback at the prospect of rationing, the truth is that rationing has always occurred in one form or another in medical education and in healthcare more broadly. Different types of rationing exist in healthcare professional education. For example rationing may be implicit or explicit or may be based on macro-allocation or micro-allocation decisions. Funding can be distributed equally among learners, or according to the needs of individual learners, or to ensure that overall usefulness is maximised. One final option is to allow the market to operate freely and to decide in that way. These principles of rationing can apply to individual learners or to institutions or departments or learning modes. Rationing is occurring in medical education, even though it might be implicit. It is worth giving consideration to methods of rationing and to make thinking about rationing more explicit. PMID:27358649

  16. Characterization of novel archaeal lineages associated with acid mine drainage in Iron Mountain, CA using anaerobic cultivation and cultivation-independent genomic analysis

    NASA Astrophysics Data System (ADS)

    Baker, B. J.; Tyson, G. W.; Hugenholtz, P.; Banfield, J. F.

    2003-12-01

    Iron Mountain in northern California, contains a pyritic orebody undergoing dissolution from mining creating extremely acidic (generally ~pH 0.8), warm (>40° C), and highly concentrated metal solutions, referred to as acid mine drainage (AMD). AMD communities are limited in the number of lineages that have been associated with them. The archaeal members of the mine community, in the past, have been restricted to the Thermoplasmatales order. The various clades within the Thermoplasmatales have been named the "alphabet plasma" (ie. Aplasma through Gplasma). The majority of them remain uncultured. Anaerobic media containing ferric sulfate and glucose has been successful in enriching and maintaining members of the "alphabet plasmas". Analysis of aqueous chemistry of these cultures shows a reduction of ferric iron, suggesting a subset of these archaea are capable of iron reduction. This may be a relevant part of iron cycling in the mine previously overlooked. Recently, another deeply branched archaeal group, named WTF1102, has been identified. Completely independent of all previously identified AMD lineages, its closest relative available in present databases is to that of the euryarchaeota group referred to as VAL1, which consists entirely of uncultured and poorly represented in sequences. Screening of the community genomic library constructed from the site revealed a contiguous fragment from two shotgun clones, totaling ~4.4kb in length. These clones have been fully sequenced and contain two genes, a phosphatase and 16S rRNA. The 16S rRNA gene has a 515 bp long intron at 1102 (E. coli numbering) that contains an open reading frame which encodes for a ubitiquitin-like protein modifier. Phylogenetic analysis of the phosphotase amino acid sequence revealed it branches with that of other acidophiles, Thermoplasma and Ferroplasma. We are developing FISH probes to target the individual "alphabet plasma" and WTF1102. This work extends what we know about the diversity and

  17. Draft Genome of Streptomyces zinciresistens K42, a Novel Metal-Resistant Species Isolated from Copper-Zinc Mine Tailings

    PubMed Central

    Lin, Yanbing; Hao, Xiuli; Johnstone, Laurel; Miller, Susan J.; Baltrus, David A.; Rensing, Christopher; Wei, Gehong

    2011-01-01

    A draft genome sequence of Streptomyces zinciresistens K42, a novel Streptomyces species displaying a high level of resistance to zinc and cadmium, is presented here. The genome contains a large number of genes encoding proteins predicted to be involved in conferring metal resistance. Many of these genes appear to have been acquired through horizontal gene transfer. PMID:22038968

  18. Draft genome sequence of extremely acidophilic bacterium Acidithiobacillus ferrooxidans DLC-5 isolated from acid mine drainage in Northeast China.

    PubMed

    Chen, Peng; Yan, Lei; Wu, Zhengrong; Xu, Ruixiang; Li, Suyue; Wang, Ningbo; Liang, Ning; Li, Hongyu

    2015-12-01

    Acidithiobacillus ferrooxidans type strain DLC-5, isolated from Wudalianchi in Heihe of Heilongjiang Province, China. Here, we present the draft genome of strain DLC-5 which contains 4,232,149 bp in 2745 contigs with 57.628% GC content and includes 32,719 protein-coding genes and 64 tRNA-encoding genes. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. JNNH00000000.1. PMID:26697393

  19. Draft genome sequence of extremely acidophilic bacterium Acidithiobacillus ferrooxidans DLC-5 isolated from acid mine drainage in Northeast China

    PubMed Central

    Chen, Peng; Yan, Lei; Wu, Zhengrong; Xu, Ruixiang; Li, Suyue; Wang, Ningbo; Liang, Ning; Li, Hongyu

    2015-01-01

    Acidithiobacillus ferrooxidans type strain DLC-5, isolated from Wudalianchi in Heihe of Heilongjiang Province, China. Here, we present the draft genome of strain DLC-5 which contains 4,232,149 bp in 2745 contigs with 57.628% GC content and includes 32,719 protein-coding genes and 64 tRNA-encoding genes. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. JNNH00000000.1. PMID:26697393

  20. Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining

    PubMed Central

    Danchin, Etienne G. J.; Perfus-Barbeoch, Laetitia; Magliano, Marc; Rosso, Marie-Noëlle; Da Rocha, Martine; Da Silva, Corinne; Nottet, Nicolas; Labadie, Karine; Guy, Julie; Artiguenave, François; Abad, Pierre

    2013-01-01

    Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute

  1. Community genomic and proteomic analysis of chemoautotrophic, iron-oxidizing "Leptospirillum rubarum" (Group II) and Leptospirillum ferrodiazotrophum (Group III) in acid mine drainage biofilms

    SciTech Connect

    Goltsman, Daniela; Denef, Vincent; Singer, Steven; Verberkmoes, Nathan C; Lefsrud, Mark G; Mueller, Ryan; Dick, Gregory J.; Sun, Christine; Wheeler, Korin; Zelma, Adam; Baker, Brett J.; Hauser, Loren John; Land, Miriam L; Shah, Manesh B; Thelen, Michael P.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2009-01-01

    We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum Groups II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, CA acid mine drainage (AMD) biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum Groups II and III, respectively and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and > 60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid encodes conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacteria have genes for community-essential functions, including carbon fixation, biosynthesis of vitamins, fatty acids and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum Group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum Group II uses a methyl-dependent and Leptospirillum Group III a methyl-independent response pathway. Although only Leptospirillum Group III can fix nitrogen, these proteins were not identified by proteomics. Abundances of core proteins are similar in all communities, but abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum Groups II and III.

  2. Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms

    SciTech Connect

    Goltsman, Daniela; Denef, Vincent; Singer, Steven; Verberkmoes, Nathan C; Lefsrud, Mark G; Mueller, Ryan; Dick, Gregory J.; Sun, Christine; Wheeler, Korin; Zelma, Adam; Baker, Brett J.; Hauser, Loren John; Land, Miriam L; Shah, Manesh B; Thelen, Michael P.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2009-01-01

    We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.

  3. A Rational Expectations Experiment.

    ERIC Educational Resources Information Center

    Peterson, Norris A.

    1990-01-01

    Presents a simple classroom simulation of the Lucas supply curve mechanism with rational expectations. Concludes that the exercise has proved very useful as an introduction to the concepts of rational and adaptive expectations, the Lucas supply curve, the natural rate hypothesis, and random supply shocks. (DB)

  4. Enculturated Chimpanzees Imitate Rationally

    ERIC Educational Resources Information Center

    Buttelmann, David; Carpenter, Malinda; Call, Josep; Tomasello, Michael

    2007-01-01

    Human infants imitate others' actions "rationally": they copy a demonstrator's action when that action is freely chosen, but less when it is forced by some constraint (Gergely, Bekkering & Kiraly, 2002). We investigated whether enculturated chimpanzees (Pan troglodytes) also imitate rationally. Using Gergely and colleagues' (2002) basic procedure,…

  5. Standby Gasoline Rationing Plan

    SciTech Connect

    1980-06-01

    The final rules adopted by the President for a Standby Gasoline Rationing Plan are presented. The plan provides that eligibility for ration allotments will be determined primarily on the basis of motor vehicle registrations, taking into account historical differences in the use of gasoline among states. The regulations also provide authority for supplemental allotments to firms so that their allotment will equal a specified percentage of gasoline use during a base period. Priority classifications, i.e., agriculture, defense, etc., are established to assure adequate gasoline supplies for designated essential services. Ration rights must be provided by end-users to their suppliers for each gallon sold. DOE will regulate the distribution of gasoline at the wholesale level according to the transfer by suppliers of redeemed ration rights and the gasoline allocation regulations. Ration rights are transferable. A ration banking system is created to facilitate transfers of ration rights. Each state will be provided with a reserve of ration rights to provide for hardship needs and to alleviate inequities. (DC)

  6. Commercial Data Mining Software

    NASA Astrophysics Data System (ADS)

    Zhang, Qingyu; Segall, Richard S.

    This chapter discusses selected commercial software for data mining, supercomputing data mining, text mining, and web mining. The selected software are compared with their features and also applied to available data sets. The software for data mining are SAS Enterprise Miner, Megaputer PolyAnalyst 5.0, PASW (formerly SPSS Clementine), IBM Intelligent Miner, and BioDiscovery GeneSight. The software for supercomputing are Avizo by Visualization Science Group and JMP Genomics from SAS Institute. The software for text mining are SAS Text Miner and Megaputer PolyAnalyst 5.0. The software for web mining are Megaputer PolyAnalyst and SPSS Clementine . Background on related literature and software are presented. Screen shots of each of the selected software are presented, as are conclusions and future directions.

  7. Genome mining of the sordarin biosynthetic gene cluster from Sordaria araneosa Cain ATCC 36386: characterization of cycloaraneosene synthase and GDP-6-deoxyaltrose transferase.

    PubMed

    Kudo, Fumitaka; Matsuura, Yasunori; Hayashi, Takaaki; Fukushima, Masayuki; Eguchi, Tadashi

    2016-07-01

    Sordarin is a glycoside antibiotic with a unique tetracyclic diterpene aglycone structure called sordaricin. To understand its intriguing biosynthetic pathway that may include a Diels-Alder-type [4+2]cycloaddition, genome mining of the gene cluster from the draft genome sequence of the producer strain, Sordaria araneosa Cain ATCC 36386, was carried out. A contiguous 67 kb gene cluster consisting of 20 open reading frames encoding a putative diterpene cyclase, a glycosyltransferase, a type I polyketide synthase, and six cytochrome P450 monooxygenases were identified. In vitro enzymatic analysis of the putative diterpene cyclase SdnA showed that it catalyzes the transformation of geranylgeranyl diphosphate to cycloaraneosene, a known biosynthetic intermediate of sordarin. Furthermore, a putative glycosyltransferase SdnJ was found to catalyze the glycosylation of sordaricin in the presence of GDP-6-deoxy-d-altrose to give 4'-O-demethylsordarin. These results suggest that the identified sdn gene cluster is responsible for the biosynthesis of sordarin. Based on the isolated potential biosynthetic intermediates and bioinformatics analysis, a plausible biosynthetic pathway for sordarin is proposed. PMID:27072286

  8. Mining the Brassica oleracea genome for Q-type C2H2 zinc finger transcription factor proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Q-type zinc finger proteins have been studied in several plant species and have been associated with response to stress. A whole genome analysis of Arabidopsis identified 176 putative C2H2 transcription factors (TF). Q-type C2H2 TFs containing the QALGGH motif and are a subset of these. In Arabidops...

  9. PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

    PubMed Central

    Lei, Runhua; Rowley, Thaine W.; Zhu, Lifeng; Bailey, Carolyn A.; Engberg, Shannon E.; Wood, Mindy L.; Christman, Mary C.; Perry, George H.; Louis, Edward E.; Lu, Guoqing

    2012-01-01

    Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/.

  10. High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine

    PubMed Central

    Castro, Daniel B.A.; Pereira, Letícia Bianca; Silva, Marcus Vinícius M. e; Silva, Bárbara P. da; Palermo, Bruna Rafaella Z.; Carlos, Camila; Belgini, Daiane R.B.; Limache, Elmer Erasmo G.; Lacerda, Gileno V. Jr; Nery, Mariana B.P.; Gomes, Milene B.; Souza, Salatiel S. de; Silva, Thiago M. da; Rodrigues, Viviane D.; Paulino, Luciana C.; Vicentini, Renato; Ferraz, Lúcio F.C.; Ottoboni, Laura M.M.

    2015-01-01

    An actinobacterial strain, designated SO9-6, was isolated from a copper iron sulfide mineral. The organism is Gram-positive, facultatively anaerobic, and coccoid. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Kocuria. Here, we report the first draft genome sequence of Kocuria marina SO9-6 under accession JROM00000000 (http://www.ncbi.nlm.nih.gov/nuccore/725823918), which provides insights for heavy metal bioremediation and production of compounds of biotechnological interest. PMID:26484219

  11. Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach.

    PubMed

    Bhatnagar, Sonika; Mishra, Shubhi; Pathak, Ravi

    2011-02-01

    The purinergic P2Y receptors are G-protein coupled receptors (GPCRs) that control many physiological processes by mediating cellular responses to purines, pyrimidines and their analogues. They can be used as potential therapeutic targets in a variety of disease conditions. Therefore, it is critical to identify new members of this family of receptors from the human genome and characterize them for their role in health and disease. In the present work, molecular modeling was carried out for the 21 known P2Y receptors. Binding site analysis was done on the basis of docking and site-directed mutagenesis data. Thus, conserved features of P2Y receptors could be formulated. These features can be used to determine the purinergic nature of potential P2Y receptors in the human genome. We applied this knowledge to human genome GPCR sequences found by sensitive sequence search techniques and identified two orphan receptors, namely GPR34 and GP171 that have all the necessary conserved features of P2Y receptors. PMID:21142848

  12. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

    PubMed Central

    2014-01-01

    Background Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. Results We have developed ngs.plot – a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. Conclusions We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data. PMID:24735413

  13. MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

    PubMed Central

    Abby, Sophie S.; Néron, Bertrand; Ménager, Hervé; Touchon, Marie; Rocha, Eduardo P. C.

    2014-01-01

    Motivation Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose. Results Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM) protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate “Cas-finder” using publicly available protein profiles. Availability and Implementation MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher). It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The “Cas-finder” (models and HMM profiles) is distributed as a compressed tarball archive as Supporting Information. PMID:25330359

  14. The Construction of Moral Rationality.

    ERIC Educational Resources Information Center

    Moshman, D.

    1995-01-01

    Offers a theoretical account of moral rationality within a rational constructivist paradigm examining the nature and relationship of rationality and reasoning. Suggests progressive changes through developmental levels of moral rationality. Proposes a developmental moral epistemology that accommodates moral pluralism to a greater degree than does…

  15. Draft Genome Sequence of Mesorhizobium sp. UFLA 01-765, a Multitolerant, Efficient Symbiont and Plant Growth-Promoting Strain Isolated from Zn-Mining Soil Using Leucaena leucocephala as a Trap Plant

    PubMed Central

    Thijs, Sofie; Weyens, Nele; Vangronsveld, Jaco; Van Hamme, Jonathan D.; Bottos, Eric M.; Rineau, Francois

    2016-01-01

    We report the 7.4-Mb draft genome sequence of Mesorhizobium sp. strain UFLA 01-765, a Gram-negative bacterium of the Phyllobacteriaceae isolated from Zn-mining soil in Minas Gerais, Brazil. This strain promotes plant growth, efficiently fixes N2 in symbiosis with Leucaena leucocephala on multicontaminated soil, and has potential for application in bioremediation of marginal lands. PMID:26966214

  16. Mining the genome for susceptibility to diabetic nephropathy: the role of large-scale studies and consortia.

    PubMed

    Iyengar, Sudha K; Freedman, Barry I; Sedor, John R

    2007-03-01

    Approximately 30% of individuals with type 1 and type 2 diabetes develop persistent albuminuria, lose renal function, and are at increased risk for cardiovascular and other microvascular complications. Diabetes and kidney diseases rank within the top 10 causes of death in Westernized countries and cause significant morbidity. Given these observations, genetic, genomic, and proteomic investigations have been initiated to better define basic mechanisms for disease initiation and progression, to identify individuals at risk for diabetic complications, and to develop more efficacious therapies. In this review we have focused on linkage analyses of candidate genes or chromosomal regions, or coarse genome-wide scans, which have mapped either categorical (chronic kidney disease or end-stage renal disease) or quantitative kidney traits (albuminuria/proteinuria or glomerular filtration rate). Most loci identified to date have not been replicated, however, several linked chromosomal regions are concordant between independent samples, suggesting the presence of a diabetic nephropathy gene. Two genes, carnosinase (CNDP1) on 18q, and engulfment and cell motility 1 (ELMO1) on 7p14, have been identified as diabetic nephropathy susceptibility genes, but these results require authentication. The availability of patient data sets with large sample sizes, improvements in informatics, genotyping technology, and statistical methodologies should accelerate the discovery of valid diabetic nephropathy susceptibility genes. PMID:17418689

  17. [Rational use of antibiotics].

    PubMed

    Walger, P

    2016-06-01

    International and national campaigns draw attention worldwide to the rational use of the available antibiotics. This has been stimulated by the high prevalence rates of drug-resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE), a threatening spread of development of resistance in Gram-negative rod-shaped bacteria and the selection of Clostridium difficile with a simultaneous clear reduction in the development of new antibiotics. The implementation of antibiotic stewardship programs aims to maintain their effectiveness by a rational use of the available antibiotics. The essential target of therapy with antibiotics is successful treatment of individual patients with bacterial infections. The optimal clinical treatment results can only be achieved when the toxicity, selection of pathogens and development of resistance are minimized. This article presents the principles of a rational antibiotic therapy. PMID:27246321

  18. The ethics of rationing.

    PubMed

    Weale, A

    1995-10-01

    Rationing can occur at three levels of health care choice: the individual, the institutional and the social, with each level posing its own ethical problems. The institutional level is the focus of this paper. The principle of effectiveness may seem attractive, since it promises to ease the institutional dilemmas of rationing, but it is not straightforward to implement in the face of uncertainty. Greater efficiency also promises much, but concepts of benefit are contested and improving contractual performance has complications. Fairness can be a powerful criterion, but there are contested cases, for example age, where its meaning is unclear. Democratic responsiveness, for all its difficulties, is important to maintain in whatever process of rationing is chosen and this can be done by adopting some procedural devices. PMID:8556292

  19. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement.

    PubMed

    Kim, Tae-Sung; Raveendar, Sebastin; Suresh, Sundan; Lee, Gi-An; Lee, Jung-Ro; Cho, Joon-Hyeong; Lee, Sok-Young; Ma, Kyung-Ho; Cho, Gyu-Taek; Chung, Jong-Wook

    2015-01-01

    The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program. PMID:26540077

  20. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement

    PubMed Central

    Kim, Tae-Sung; Raveendar, Sebastin; Suresh, Sundan; Lee, Gi-An; Lee, Jung-Ro; Cho, Joon-Hyeong; Lee, Sok-Young; Ma, Kyung-Ho; Cho, Gyu-Taek; Chung, Jong-Wook

    2015-01-01

    The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program. PMID:26540077

  1. Biosynthesis of Antibiotic Leucinostatins in Bio-control Fungus Purpureocillium lilacinum and Their Inhibition on Phytophthora Revealed by Genome Mining.

    PubMed

    Wang, Gang; Liu, Zhiguo; Lin, Runmao; Li, Erfeng; Mao, Zhenchuan; Ling, Jian; Yang, Yuhong; Yin, Wen-Bing; Xie, Bingyan

    2016-07-01

    Purpureocillium lilacinum of Ophiocordycipitaceae is one of the most promising and commercialized agents for controlling plant parasitic nematodes, as well as other insects and plant pathogens. However, how the fungus functions at the molecular level remains unknown. Here, we sequenced two isolates (PLBJ-1 and PLFJ-1) of P. lilacinum from different places Beijing and Fujian. Genomic analysis showed high synteny of the two isolates, and the phylogenetic analysis indicated they were most related to the insect pathogen Tolypocladium inflatum. A comparison with other species revealed that this fungus was enriched in carbohydrate-active enzymes (CAZymes), proteases and pathogenesis related genes. Whole genome search revealed a rich repertoire of secondary metabolites (SMs) encoding genes. The non-ribosomal peptide synthetase LcsA, which is comprised of ten C-A-PCP modules, was identified as the core biosynthetic gene of lipopeptide leucinostatins, which was specific to P. lilacinum and T. ophioglossoides, as confirmed by phylogenetic analysis. Furthermore, gene expression level was analyzed when PLBJ-1 was grown in leucinostatin-inducing and non-inducing medium, and 20 genes involved in the biosynthesis of leucionostatins were identified. Disruption mutants allowed us to propose a putative biosynthetic pathway of leucinostatin A. Moreover, overexpression of the transcription factor lcsF increased the production (1.5-fold) of leucinostatins A and B compared to wild type. Bioassays explored a new bioactivity of leucinostatins and P. lilacinum: inhibiting the growth of Phytophthora infestans and P. capsici. These results contribute to our understanding of the biosynthetic mechanism of leucinostatins and may allow us to utilize P. lilacinum better as bio-control agent. PMID:27416025

  2. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds.

    PubMed

    Van Der Voort, Menno; Meijer, Harold J G; Schmidt, Yvonne; Watrous, Jeramie; Dekkers, Ester; Mendes, Rodrigo; Dorrestein, Pieter C; Gross, Harald; Raaijmakers, Jos M

    2015-01-01

    The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum. PMID:26217324

  3. Biosynthesis of Antibiotic Leucinostatins in Bio-control Fungus Purpureocillium lilacinum and Their Inhibition on Phytophthora Revealed by Genome Mining

    PubMed Central

    Li, Erfeng; Mao, Zhenchuan; Ling, Jian; Yang, Yuhong; Yin, Wen-Bing; Xie, Bingyan

    2016-01-01

    Purpureocillium lilacinum of Ophiocordycipitaceae is one of the most promising and commercialized agents for controlling plant parasitic nematodes, as well as other insects and plant pathogens. However, how the fungus functions at the molecular level remains unknown. Here, we sequenced two isolates (PLBJ-1 and PLFJ-1) of P. lilacinum from different places Beijing and Fujian. Genomic analysis showed high synteny of the two isolates, and the phylogenetic analysis indicated they were most related to the insect pathogen Tolypocladium inflatum. A comparison with other species revealed that this fungus was enriched in carbohydrate-active enzymes (CAZymes), proteases and pathogenesis related genes. Whole genome search revealed a rich repertoire of secondary metabolites (SMs) encoding genes. The non-ribosomal peptide synthetase LcsA, which is comprised of ten C-A-PCP modules, was identified as the core biosynthetic gene of lipopeptide leucinostatins, which was specific to P. lilacinum and T. ophioglossoides, as confirmed by phylogenetic analysis. Furthermore, gene expression level was analyzed when PLBJ-1 was grown in leucinostatin-inducing and non-inducing medium, and 20 genes involved in the biosynthesis of leucionostatins were identified. Disruption mutants allowed us to propose a putative biosynthetic pathway of leucinostatin A. Moreover, overexpression of the transcription factor lcsF increased the production (1.5-fold) of leucinostatins A and B compared to wild type. Bioassays explored a new bioactivity of leucinostatins and P. lilacinum: inhibiting the growth of Phytophthora infestans and P. capsici. These results contribute to our understanding of the biosynthetic mechanism of leucinostatins and may allow us to utilize P. lilacinum better as bio-control agent. PMID:27416025

  4. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds

    PubMed Central

    Van Der Voort, Menno; Meijer, Harold J. G.; Schmidt, Yvonne; Watrous, Jeramie; Dekkers, Ester; Mendes, Rodrigo; Dorrestein, Pieter C.; Gross, Harald; Raaijmakers, Jos M.

    2015-01-01

    The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum. PMID:26217324

  5. Recursive rational choice

    SciTech Connect

    Lewis, A.A.

    1981-11-01

    It is the purpose of the present study to indicate the means by which Kramer's results may be generalized to considerations of stronger computing devices than the finite state automata considered in Kramer's approach, and to domains of alternatives having the cardinality of the continuum. The means we employ in the approach makes use of the theory of recursive functions in the context of Church's Thesis. The result, which we consider as a preliminary result to a more general research program, shows that a choice function that is rational in the sense of Richter (not necessarily regular) when defined on a restricted family of subsets of a continuum of alternatives, when recursively represented by a partial predicate on equivalence classes of approximations by rational numbers, is recursively unsolvable. By way of Church's Thesis, therefore, such a function cannot be realized by means of a very general class of effectively computable procedures. An additional consequence that can be derived from the result of recursive unsolvability of rational choice in this setting is the placement of a minimal bound on the amount of computational complexity entailed by effective realizations of rational choice.

  6. Rational Emotive Education

    ERIC Educational Resources Information Center

    Knaus, William

    1977-01-01

    Rational Emotive Education--an outgrowth of theories developed by Albert Ellis--is a teaching design of mental health concepts and problem-solving activities designed to help students to approach and cope with their problems through experiential learning, via a structured, thematic sequence of emotive education lessons. (MJB)

  7. Rationality and social behavior.

    PubMed

    Tullberg, Jan

    2003-10-21

    This article penetrates the relationship between social behavior and rationality. A critical analysis is made of efforts to classify some behaviors as altruistic, as they simultaneously meet criteria of rationality by not truly being self-destructive. Newcomb's paradox is one attempt to create a hybrid behavior that is both irrational and still meets some criterion of rationality. Such dubious rationality is often seen as a source of altruistic behavior. Group selection is a controversial topic. Sober and Wilson (Unto Others--The Evolution and Psychology of Unselfish Behavior, Harvard University Press, Cambridge, MA, 1998) suggest that a very wide concept of group selection might be used to explain altruism. This concept also includes kin selection and reciprocity, which blurs its focus. The latter mechanisms hardly need further arguments to prove their existence. This article suggests that it is group selection in a strict sense that should be investigated to limit semantic neologism and confusion. In evaluation, the effort to muster a mechanism for altruism out of group selection has not been successful. However, this is not the end to group selection, but rather a good reason to investigate more promising possibilities. There is little reason to burden group selection with the instability of altruism caused by altruistic members of a group having lower fitness than egoistic members. Group selection is much more likely to develop in combination with group egoism. A common project is supported by incitement against free riding, where conformist members joined in solidarity achieve a higher fitness than members pursuing more individualistic options. Group egoism is in no conflict with rationality, and the effects of group selection will be supported rather than threatened by individual selection. Empirical evidence indicates a high level of traits such as conformism and out-group antagonism in line with group egoism. These traits are also likely candidates for

  8. Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli.

    PubMed

    Ma, Tian; Zhou, Yuanjie; Li, Xiaowei; Zhu, Fayin; Cheng, Yongbo; Liu, Yi; Deng, Zixin; Liu, Tiangang

    2016-02-01

    As a highly valued keto-carotenoid, astaxanthin is widely used in nutritional supplements and pharmaceuticals. Therefore, the demand for biosynthetic astaxanthin and improved efficiency of astaxanthin biosynthesis has driven the investigation of metabolic engineering of native astaxanthin producers and heterologous hosts. However, microbial resources for astaxanthin are limited. In this study, we found that the α-Proteobacterium Sphingomonas sp. ATCC 55669 could produce astaxanthin naturally. We used whole-genome sequencing to identify the astaxanthin biosynthetic pathway using a combined PacBio-Illumina approach. The putative astaxanthin biosynthetic pathway in Sphingomonas sp. ATCC 55669 was predicted. For further confirmation, a high-efficiency targeted engineering carotenoid synthesis platform was constructed in E. coli for identifying the functional roles of candidate genes. All genes involved in astaxanthin biosynthesis showed discrete distributions on the chromosome. Moreover, the overexpression of exogenous E. coli idi in Sphingomonas sp. ATCC 55669 increased astaxanthin production by 5.4-fold. This study described a new astaxanthin producer and provided more biosynthesis components for bioengineering of astaxanthin in the future. PMID:26580858

  9. Rational enzyme redesign

    SciTech Connect

    Ornstein, R.L.

    1994-05-01

    Protein engineering is first a means of elucidating structure-function relations in an enzyme, and second, a means of changing a protein to make it serve a different, but generally related, purpose. In principle, one may change the functional characteristics of an enzyme by altering its substrate specificity, kinetics, optimum range of activity, and chemical mechanism. Obviously one cannot make all possible combinations of amino acid changes for even the smallest enzyme, so the essential question is which changes to make. The intent of rational protein/enzyme redesign is to alter a protein/enzyme in a timely and premeditated fashion. This article provides an outline of the process of rational enzyme redesign.

  10. RATIONAL SPLINE SUBROUTINES

    NASA Technical Reports Server (NTRS)

    Schiess, J. R.

    1994-01-01

    Scientific data often contains random errors that make plotting and curve-fitting difficult. The Rational-Spline Approximation with Automatic Tension Adjustment algorithm lead to a flexible, smooth representation of experimental data. The user sets the conditions for each consecutive pair of knots:(knots are user-defined divisions in the data set) to apply no tension; to apply fixed tension; or to determine tension with a tension adjustment algorithm. The user also selects the number of knots, the knot abscissas, and the allowed maximum deviations from line segments. The selection of these quantities depends on the actual data and on the requirements of a particular application. This program differs from the usual spline under tension in that it allows the user to specify different tension values between each adjacent pair of knots rather than a constant tension over the entire data range. The subroutines use an automatic adjustment scheme that varies the tension parameter for each interval until the maximum deviation of the spline from the line joining the knots is less than or equal to a user-specified amount. This procedure frees the user from the drudgery of adjusting individual tension parameters while still giving control over the local behavior of the spline The Rational Spline program was written completely in FORTRAN for implementation on a CYBER 850 operating under NOS. It has a central memory requirement of approximately 1500 words. The program was released in 1988.

  11. Rational management of epilepsy.

    PubMed

    Viswanathan, Venkataraman

    2014-09-01

    Management of epilepsies in children has improved considerably over the last decade, all over the world due to the advances seen in the understanding of the patho-physiology of epileptogenesis, availability of both structural and functional imaging studies along with better quality EEG/video-EEG recordings and the availability of a plethora of newer anti-epileptic drugs which are tailormade to act on specific pathways. In spite of this, there is still a long way to go before one is able to be absolutely rational about which drug to use for which type of epilepsy. There have been a lot of advances in the area of epilepsy surgery and is certainly gaining ground for specific cases. Better understanding of the genetic basis of epilepsies will hopefully lead to a more rational treatment plan in the future. Also, a lot of work needs to be done to dispel various misunderstandings and myths about epilepsy which still exists in our country. PMID:24871077

  12. Genome mining for new α-amylase and glucoamylase encoding sequences and high level expression of a glucoamylase from Talaromyces stipitatus for potential raw starch hydrolysis.

    PubMed

    Xiao, Zhizhuang; Wu, Meiqun; Grosse, Stephan; Beauchemin, Manon; Lévesque, Michelle; Lau, Peter C K

    2014-01-01

    Mining fungal genomes for glucoamylase and α-amylase encoding sequences led to the selection of 23 candidates, two of which (designated TSgam-2 and NFamy-2) were advanced to testing for cooked or raw starch hydrolysis. TSgam-2 is a 66-kDa glucoamylase recombinantly produced in Pichia pastoris and originally derived for Talaromyces stipitatus. When harvested in a 20-L bioreactor at high cell density (OD600 > 200), the secreted TSgam-2 enzyme activity from P. pastoris strain GS115 reached 800 U/mL. In a 6-L working volume of a 10-L fermentation, the TSgam-2 protein yield was estimated to be ∼8 g with a specific activity of 360 U/mg. In contrast, the highest activity of NFamy-2, a 70-kDa α-amylase originally derived from Neosartorya fischeri, and expressed in P. pastoris KM71 only reached 8 U/mL. Both proteins were purified and characterized in terms of pH and temperature optima, kinetic parameters, and thermostability. TSgam-2 was more thermostable than NFamy-2 with a respective half-life (t1/2) of >300 min at 55 °C and >200 min at 40 °C. The kinetic parameters for raw starch adsorption of TSgam-2 and NFamy-2 were also determined. A combination of NFamy-2 and TSgam-2 hydrolyzed cooked potato and triticale starch into glucose with yields, 71-87 %, that are competitive with commercially available α-amylases. In the hydrolysis of raw starch, the best hydrolysis condition was seen with a sequential addition of 40 U of a thermostable Bacillus globigii amylase (BgAmy)/g starch at 80 °C for 16 h, and 40 U TSgam-2/g starch at 45 °C for 24 h. The glucose released was 8.7 g/10 g of triticale starch and 7.9 g/10 g of potato starch, representing 95 and 86 % of starch degradation rate, respectively. PMID:24046254

  13. Rational Approximations to Rational Models: Alternative Algorithms for Category Learning

    ERIC Educational Resources Information Center

    Sanborn, Adam N.; Griffiths, Thomas L.; Navarro, Daniel J.

    2010-01-01

    Rational models of cognition typically consider the abstract computational problems posed by the environment, assuming that people are capable of optimally solving those problems. This differs from more traditional formal models of cognition, which focus on the psychological processes responsible for behavior. A basic challenge for rational models…

  14. Longwall mining

    SciTech Connect

    1995-03-14

    As part of EIA`s program to provide information on coal, this report, Longwall-Mining, describes longwall mining and compares it with other underground mining methods. Using data from EIA and private sector surveys, the report describes major changes in the geologic, technological, and operating characteristics of longwall mining over the past decade. Most important, the report shows how these changes led to dramatic improvements in longwall mining productivity. For readers interested in the history of longwall mining and greater detail on recent developments affecting longwall mining, the report includes a bibliography.

  15. Genome Informatics

    PubMed Central

    Winslow, Raimond L.; Boguski, Mark S.

    2005-01-01

    This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape. PMID:12750305

  16. Mining with microbes

    SciTech Connect

    Rawlings., D.E.; Silver, S.

    1995-08-01

    Microbes are playing increasingly important roles in commercial mining operations, where they are being used in the {open_quotes}bioleaching{close_quotes} of copper, uranium, and gold ores. Direct leaching is when microbial metabolism changes the redox state of the metal being harvested, rendering it more soluble. Indirect leaching includes redox chemistry of other metal cations that are then coupled in chemical oxidation or reduction of the harvested metal ion and microbial attack upon and solubilization of the mineral matrix in which the metal is physically embedded. In addition, bacterial cells are used to detoxify the waste cyanide solution from gold-mining operations and as {open_quotes}absorbants{close_quotes} of the mineral cations. Bacterial cells may replace activated carbon or alternative biomass. With an increasing understanding of microbial physiology, biochemistry and molecular genetics, rational approaches to improving these microbial activities become possible. 40 refs., 3 figs.

  17. The Necessity of Public Relations for Sustainable Mining Activities

    NASA Astrophysics Data System (ADS)

    Lee, Hyunbock; Ji, Sangwoo

    2015-04-01

    other hand, in the survey to determine what the greatest difficulties of the current mining activities, 54% of mining companies chose environmental regulations, 26% of mining companies chose conflicts between mine area residents and mining companies. Environmental regulations are may defined as the greatest difficulty of current mining activities. But most of environmental regulation's problems are caused by frictions with residents, because all of South Korean mines are very close to villages. So, the biggest difficulty of mining activities can be defined conflicts between residents and mining companies. Moreover, general people in South Korea including some mining engineers recognize the mining industry as a declined and pollution industry. Without clear understanding of mining activities, any mine developments and policies related to mining activities cannot be made by rational discussions. And, if their recognition is not formed in a rational way, it will be turned to extreme fear or blind hatred. Therefore, to understand mining activities correctly, the effective public relations strategy is necessary such as corporate advertisements or public advertisements.

  18. Reasoning, decision making and rationality.

    PubMed

    Evans, J S; Over, D E; Manktelow, K I

    1993-01-01

    It is argued that reasoning in the real world supports decision making and is aimed at the achievement of goals. A distinction is developed between two notions of rationality: rationality which is reasoning in such a way as to achieve one's goals--within cognitive constraints--and rationality which is reasoning by a process of logic. This dichotomy is related to the philosophical distinction between practical and theoretical reasoning. It is argued that logicality (rationality) does not provide a good basis for rationality and some psychological research on deductive reasoning is re-examined in this light. First, we review belief bias effects in syllogistic reasoning, and argue that the phenomena do not support the interpretations of irrationality that are often placed upon them. Second, we review and discuss recent studies of deontic reasoning in the Wason selection task, which demonstrate the decision making, and rational nature of reasoning in realistic contexts. The final section of the paper examines contemporary decision theory and shows how it fails, in comparable manner to formal logic, to provide an adequate model for assessing the rationality of human reasoning and decision making. PMID:8287673

  19. Detoxifying the concept of rationing.

    PubMed

    Sabin, James

    2014-01-01

    Andrew Hantel's proposal for dealing with cancer drug shortages exemplifies the kind of clinician-led discussion of rationing the U.S. political process requires. I argue that the U.S. will not get a grip on healthcare cost escalation until we set true budgets for healthcare. We will not be able to do that until the public accepts that rationing, done right, is an ethical necessity, not an ethical abomination. Because endorsing rationing is a third rail for politicians, "top down" leadership is currently impossible. As a result, health professionals must lead a "bottom up" educational process. Hantel shows how this can be done. PMID:24972061

  20. Web Mining

    NASA Astrophysics Data System (ADS)

    Fürnkranz, Johannes

    The World-Wide Web provides every internet citizen with access to an abundance of information, but it becomes increasingly difficult to identify the relevant pieces of information. Research in web mining tries to address this problem by applying techniques from data mining and machine learning to Web data and documents. This chapter provides a brief overview of web mining techniques and research areas, most notably hypertext classification, wrapper induction, recommender systems and web usage mining.

  1. Text Mining.

    ERIC Educational Resources Information Center

    Trybula, Walter J.

    1999-01-01

    Reviews the state of research in text mining, focusing on newer developments. The intent is to describe the disparate investigations currently included under the term text mining and provide a cohesive structure for these efforts. A summary of research identifies key organizations responsible for pushing the development of text mining. A section…

  2. Data Mining.

    ERIC Educational Resources Information Center

    Benoit, Gerald

    2002-01-01

    Discusses data mining (DM) and knowledge discovery in databases (KDD), taking the view that KDD is the larger view of the entire process, with DM emphasizing the cleaning, warehousing, mining, and visualization of knowledge discovery in databases. Highlights include algorithms; users; the Internet; text mining; and information extraction.…

  3. Managed care and efficient rationing.

    PubMed

    Rosenthal, Meredith B; Newhouse, Joseph P

    2002-01-01

    Widespread dissatisfaction with managed care has led to calls for major reform and consumer protection. Although some have concluded that managed care backlash is simply a result of too much rationing, we propose an alternative view that focuses on the nature of services eliminated by managed care. In particular, we point out that managed care rations services largely without regard to consumer preferences. We question whether managed care's emphasis on supply-side control of moral hazard is consistent with the principles of efficient rationing. Further research on the nature of provider and consumer rationing decisions is needed to inform the design of supply-side and demand-side incentives that will lead to an efficient allocation of services. PMID:12148660

  4. The rationing agenda in the NHS. Rationing Agenda Group.

    PubMed Central

    New, B.

    1996-01-01

    The Rationing Agenda Group has been founded to deepen the British debate on rationing health care. It believes that rationing in health care is inevitable and that the public must be involved in the debate about issues relating to rationing. The group comprises people from all parts of health care, none of whom represent either their group or their institutions. RAG has begun by producing this document, which attempts to set an agenda of all the issues that need to be considered when debating the rationing of health care. We hope for responses to the document. The next stage will be to incorporate the responses into the agenda. Then RAG will divide the agenda into manageable chunks and commission expert, detailed commentaries. From this material a final paper will be published and used to prompt public debate. This stage should be reached early in 1997. While these papers are being prepared RAG is developing ways to involve the public in the debate and evaluate the whole process. We present as neutrally as possible all the issues related to rationing and priority setting in the NHS. We focus on the NHS for two reasons. Firstly, for those of us resident in the United Kingdom the NHS is the health care system with which we are most familiar and most concerned. Secondly, focusing on one system alone allows more coherent analysis than would be possible if issues in other systems were included as well. Our concern is with the delivery of health care, not its finance, though we discuss the possible effects of changing the financing system of the NHS. Finally, though our position is neutral, we hold two substantive views--namely, that rationing is unavoidable and that there should be more explicit debate about the principles and issues concerned. We consider the issues under four headings: preliminaries, ethics, democracy, and empirical questions. Preliminaries deal with the semantics of rationing, whether rationing is necessary, and with the range of services to which

  5. The rationing agenda in the NHS. Rationing Agenda Group.

    PubMed

    New, B

    1996-06-22

    The Rationing Agenda Group has been founded to deepen the British debate on rationing health care. It believes that rationing in health care is inevitable and that the public must be involved in the debate about issues relating to rationing. The group comprises people from all parts of health care, none of whom represent either their group or their institutions. RAG has begun by producing this document, which attempts to set an agenda of all the issues that need to be considered when debating the rationing of health care. We hope for responses to the document. The next stage will be to incorporate the responses into the agenda. Then RAG will divide the agenda into manageable chunks and commission expert, detailed commentaries. From this material a final paper will be published and used to prompt public debate. This stage should be reached early in 1997. While these papers are being prepared RAG is developing ways to involve the public in the debate and evaluate the whole process. We present as neutrally as possible all the issues related to rationing and priority setting in the NHS. We focus on the NHS for two reasons. Firstly, for those of us resident in the United Kingdom the NHS is the health care system with which we are most familiar and most concerned. Secondly, focusing on one system alone allows more coherent analysis than would be possible if issues in other systems were included as well. Our concern is with the delivery of health care, not its finance, though we discuss the possible effects of changing the financing system of the NHS. Finally, though our position is neutral, we hold two substantive views--namely, that rationing is unavoidable and that there should be more explicit debate about the principles and issues concerned. We consider the issues under four headings: preliminaries, ethics, democracy, and empirical questions. Preliminaries deal with the semantics of rationing, whether rationing is necessary, and with the range of services to which

  6. Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Next-generation sequencing (NGS) technologies are revolutionizing both medical and biological research through generation of massive SNP data sets for identifying heritable genome variation underlying key traits, from rare human diseases to important agronomic phenotypes in crop species. We evaluate...

  7. Mine system

    SciTech Connect

    Stoppani, B.R.

    1983-10-04

    A mine system comprises at least one mining machine adapted to haul itself, in a reciprocating manner, along a mineral face, and a control box housing means to control the various electrical elements of the machine(s), the box being located in a mine roadway at one end of the mineral face along which the machine(s) is reciprocating, and the box being electrically connected to a terminal box housed in a body of the machine(s).

  8. Rationalizing the Promotion of Non-Rational Behaviors in Organizations.

    ERIC Educational Resources Information Center

    Smith, Peter A. C.; Sharma, Meenakshi

    2002-01-01

    Organizations must balance rational/technical efficiency and emotions. Action learning has been proven to be effective for developing emotional openness in the workplace. Facilitators of action learning should draw upon the disciplines of counseling, Gestalt, psychodynamics, and Eastern philosophies. (Contains 23 references.) (SK)

  9. Mining a database of single amplified genomes from Red Sea brine pool extremophiles—improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA)

    PubMed Central

    Grötzinger, Stefan W.; Alam, Intikhab; Ba Alawi, Wail; Bajic, Vladimir B.; Stingl, Ulrich; Eppinger, Jörg

    2014-01-01

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  10. Rational Exponentials and Continued Fractions

    ERIC Educational Resources Information Center

    Denny, J. K.

    2012-01-01

    Using continued fraction expansions, we can approximate constants, such as pi and e, using an appropriate integer n raised to the power x[superscript 1/x], x a suitable rational. We review continued fractions and give an algorithm for producing these approximations.

  11. On Counting the Rational Numbers

    ERIC Educational Resources Information Center

    Almada, Carlos

    2010-01-01

    In this study, we show how to construct a function from the set N of natural numbers that explicitly counts the set Q[superscript +] of all positive rational numbers using a very intuitive approach. The function has the appeal of Cantor's function and it has the advantage that any high school student can understand the main idea at a glance…

  12. Teaching Rational Decision-Making.

    ERIC Educational Resources Information Center

    Woolever, Roberts

    1978-01-01

    Presented is an outline of a college course, "Education in American Society," that focused on teaching students rational decision-making skills while examining current issues in American Education. The outline is followed by student comments, reactions, and evaluations of the course. (JMD)

  13. Rational Suicide among the Elderly.

    ERIC Educational Resources Information Center

    Humphry, Derek

    1992-01-01

    Contends that old age, in and of itself, should never need to be a cause for self-destruction. Further argues that suicide and assisted suicide carried out in the face of terminal illness causing unbearable suffering should be ethically and legally acceptable. Outlines a perspective on rational suicide among the elderly. (Author/NB)

  14. Life in an Arsenic-Containing Gold Mine: Genome and Physiology of the Autotrophic Arsenite-Oxidizing Bacterium Rhizobium sp. NT-26

    PubMed Central

    Andres, Jérémy; Arsène-Ploetze, Florence; Barbe, Valérie; Brochier-Armanet, Céline; Cleiss-Arnold, Jessica; Coppée, Jean-Yves; Dillies, Marie-Agnès; Geist, Lucie; Joublin, Aurélie; Koechler, Sandrine; Lassalle, Florent; Marchal, Marie; Médigue, Claudine; Muller, Daniel; Nesme, Xavier; Plewniak, Frédéric; Proux, Caroline; Ramírez-Bahena, Martha Helena; Schenowitz, Chantal; Sismeiro, Odile; Vallenet, David; Santini, Joanne M.; Bertin, Philippe N.

    2013-01-01

    Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions. PMID:23589360

  15. African mining

    SciTech Connect

    Not Available

    1987-01-01

    This book contains papers presented at a conference addressing the development of the minerals industry in Africa. Topics covered include: A review - past, present and future - of Zimbabwe's mining industry; Geomorphological processes and related mineralization in Tanzania; and Rock mechanics investigations at Mufulira mine, Zambia.

  16. Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus.

    PubMed

    Wordley, Claire; Slate, Jon; Stapley, Jessica

    2011-01-01

    Online sequence databases can provide valuable resources for the development of cross-species genetic markers. In particular, mining expressed tag sequences (EST) for microsatellites and developing conserved cross-species microsatellite markers can provide a rapid and relatively inexpensive method to develop new markers for a range of species. Here, we adopt this approach to develop cross-species microsatellite markers in Anolis lizards, which is a model genus in evolutionary biology and ecology. Using EST sequences from Anolis carolinensis, we identified 127 microsatellites that satisfied our criteria, and tested 49 of these in five species of Anolis (carolinensis, distichus, apletophallus, porcatus and sagrei). We identified between 8 and 25 new variable genetic markers for five Anolis species. These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage. PMID:21429109

  17. Mining new crystal protein genes from Bacillus thuringiensis on the basis of mixed plasmid-enriched genome sequencing and a computational pipeline.

    PubMed

    Ye, Weixing; Zhu, Lei; Liu, Yingying; Crickmore, Neil; Peng, Donghai; Ruan, Lifang; Sun, Ming

    2012-07-01

    We have designed a high-throughput system for the identification of novel crystal protein genes (cry) from Bacillus thuringiensis strains. The system was developed with two goals: (i) to acquire the mixed plasmid-enriched genomic sequence of B. thuringiensis using next-generation sequencing biotechnology, and (ii) to identify cry genes with a computational pipeline (using BtToxin_scanner). In our pipeline method, we employed three different kinds of well-developed prediction methods, BLAST, hidden Markov model (HMM), and support vector machine (SVM), to predict the presence of Cry toxin genes. The pipeline proved to be fast (average speed, 1.02 Mb/min for proteins and open reading frames [ORFs] and 1.80 Mb/min for nucleotide sequences), sensitive (it detected 40% more protein toxin genes than a keyword extraction method using genomic sequences downloaded from GenBank), and highly specific. Twenty-one strains from our laboratory's collection were selected based on their plasmid pattern and/or crystal morphology. The plasmid-enriched genomic DNA was extracted from these strains and mixed for Illumina sequencing. The sequencing data were de novo assembled, and a total of 113 candidate cry sequences were identified using the computational pipeline. Twenty-seven candidate sequences were selected on the basis of their low level of sequence identity to known cry genes, and eight full-length genes were obtained with PCR. Finally, three new cry-type genes (primary ranks) and five cry holotypes, which were designated cry8Ac1, cry7Ha1, cry21Ca1, cry32Fa1, and cry21Da1 by the B. thuringiensis Toxin Nomenclature Committee, were identified. The system described here is both efficient and cost-effective and can greatly accelerate the discovery of novel cry genes. PMID:22544259

  18. Characterization of novel wheat NBS domain-containing sequences and their utilization, in silico, for genome-scale R-gene mining.

    PubMed

    Bouktila, Dhia; Habachi-Houimli, Yosra; Khalfallah, Yosra; Mezghani-Khemakhem, Maha; Makni, Mohamed; Makni, Hanem

    2014-08-01

    In crop improvement, the isolation, cloning and transfer of disease resistance genes (R-genes) is an ultimate goal usually starting from tentative R-gene analogs (RGAs) that are identified on the basis of their structure. For bread wheat, recent advances in genome sequencing are supporting the efforts of wheat geneticists worldwide. Among wheat R-genes, nucleotide-binding site (NBS)-encoding ones represent a major class. In this study, we have used a polymerase chain reaction-based approach to amplify and clone NBS-type RGAs from a bread wheat cultivar, 'Salambo 80.' Four novel complete ORF sequences showing similarities to previously reported R-genes/RGAs were used for in silico analyses. In a first step, where analyses were focused on the NBS domain, these sequences were phylogenetically assigned to two distinct groups: a first group close to leaf rust Lr21 resistance proteins; and a second one similar to cyst nematode resistance proteins. In a second step, sequences were used as initial seeds to walk up and downstream the NBS domain. This procedure enabled identifying 8 loci ranging in size between 2,115 and 7,653 bp. Ab initio gene prediction identified 8 gene models, among which two had complete ORFs. While GenBank survey confirmed the belonging of sequences to two groups, subsequent characterization using IWGSC genomic and proteomic data showed that the 8 gene models, reported in this study, were unique and their loci matched scaffolds on chromosome arms 1AS, 1BS, 4BS and 1DS. The gene model located on 1DS is a pseudo-Lr21 that was shown to have an NBS-LRR domain structure, while the potential association of the RGAs, here reported, is discussed. This study has produced novel R-gene-like loci and models in the wheat genome and provides the first steps toward further elucidation of their role in wheat disease resistance. PMID:24638930

  19. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome.

    PubMed

    Elsik, Christine G; Unni, Deepak R; Diesh, Colin M; Tayal, Aditi; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Bovine Genome Database (BGD) (http://BovineGenome.org). The goal of BGD is to support bovine genomics research by providing genome annotation and data mining tools. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies. PMID:26481361

  20. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome

    PubMed Central

    Elsik, Christine G.; Unni, Deepak R.; Diesh, Colin M.; Tayal, Aditi; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

    2016-01-01

    We report an update of the Bovine Genome Database (BGD) (http://BovineGenome.org). The goal of BGD is to support bovine genomics research by providing genome annotation and data mining tools. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies. PMID:26481361

  1. Genome Data Mining and Soil Survey for the Novel Group 5 [NiFe]-Hydrogenase To Explore the Diversity and Ecological Importance of Presumptive High-Affinity H2-Oxidizing Bacteria ▿†

    PubMed Central

    Constant, Philippe; Chowdhury, Soumitra Paul; Hesse, Laura; Pratscher, Jennifer; Conrad, Ralf

    2011-01-01

    Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H2 possess genes specifying a putative high-affinity [NiFe]-hydrogenase. This study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. We propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhyS and hhyL, respectively. Genome data mining revealed that the hhyL gene is unevenly distributed in the phyla Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The hhyL gene sequences comprised a phylogenetically distinct group, namely, the group 5 [NiFe]-hydrogenase genes. The presumptive high-affinity H2-oxidizing bacteria constituting group 5 were shown to possess a hydrogenase gene cluster, including the genes encoding auxiliary and structural components of the enzyme and four additional open reading frames (ORFs) of unknown function. A soil survey confirmed that both high-affinity H2 oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 106 to 108 hhyL gene copies g (dry weight)−1. Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H2-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H2 oxidation activity measured in soil. Our data indicate that the abundance of the hhyL gene should not be taken as a reliable proxy for the uptake of atmospheric H2 by soil, because high-affinity H2 oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur. PMID:21742924

  2. Draft Genome Sequences of Fungus Aspergillus calidoustus.

    PubMed

    Horn, Fabian; Linde, Jörg; Mattern, Derek J; Walther, Grit; Guthke, Reinhard; Scherlach, Kirstin; Martin, Karin; Brakhage, Axel A; Petzke, Lutz; Valiante, Vito

    2016-01-01

    Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504). The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining. PMID:26966204

  3. Draft Genome Sequences of Fungus Aspergillus calidoustus

    PubMed Central

    Horn, Fabian; Linde, Jörg; Mattern, Derek J.; Walther, Grit; Guthke, Reinhard; Scherlach, Kirstin; Martin, Karin; Brakhage, Axel A.; Petzke, Lutz

    2016-01-01

    Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504). The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining. PMID:26966204

  4. Mining apparatus

    SciTech Connect

    Ingle, J.E.; Lane, A.J.; Mcgee, D.A.

    1981-03-10

    An improved mining apparatus for excavating material, such as coal, for example, from an earth formation, such as a coal seam, for example, wherein a miner, having a forward and a rearward cutter, is guided through the coal seam and excavates a borehole therein, the borehole being filled with a working fluid during the operation of the miner, the working fluid facilitating the operation of the miner and providing a vehicle for removing the mined material. Substantially all of the operations of the miner are controlled from the earth's surface thereby eliminating the necessity and accompanying hazards and costs involved in utilizing personnel underground during the mining operations.

  5. Mining whole genomes and transcriptomes of Jatropha (Jatropha curcas) and Castor bean (Ricinus communis) for NBS-LRR genes and defense response associated transcription factors.

    PubMed

    Sood, Archit; Jaiswal, Varun; Chanumolu, Sree Krishna; Malhotra, Nikhil; Pal, Tarun; Chauhan, Rajinder Singh

    2014-11-01

    Jatropha (Jatropha curcas L.) and Castor bean (Ricinus communis) are oilseed crops of family Euphorbiaceae with the potential of producing high quality biodiesel and having industrial value. Both the bioenergy plants are becoming susceptible to various biotic stresses directly affecting the oil quality and content. No report exists as of today on analysis of Nucleotide Binding Site-Leucine Rich Repeat (NBS-LRR) gene repertoire and defense response transcription factors in both the plant species. In silico analysis of whole genomes and transcriptomes identified 47 new NBS-LRR genes in both the species and 122 and 318 defense response related transcription factors in Jatropha and Castor bean, respectively. The identified NBS-LRR genes and defense response transcription factors were mapped onto the respective genomes. Common and unique NBS-LRR genes and defense related transcription factors were identified in both the plant species. All NBS-LRR genes in both the species were characterized into Toll/interleukin-1 receptor NBS-LRRs (TNLs) and coiled-coil NBS-LRRs (CNLs), position on contigs, gene clusters and motifs and domains distribution. Transcript abundance or expression values were measured for all NBS-LRR genes and defense response transcription factors, suggesting their functional role. The current study provides a repertoire of NBS-LRR genes and transcription factors which can be used in not only dissecting the molecular basis of disease resistance phenotype but also in developing disease resistant genotypes in Jatropha and Castor bean through transgenic or molecular breeding approaches. PMID:25106526

  6. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species.

    PubMed

    Dettori, Maria Teresa; Micali, Sabrina; Giovinazzi, Jessica; Scalabrin, Simone; Verde, Ignazio; Cipriani, Guido

    2015-01-01

    A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10(-7) in peach to 9.48 × 10(-10) in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species. PMID:26185739

  7. Psychology and the Rationality of Emotion*

    PubMed Central

    Clore, Gerald L.

    2014-01-01

    Questions addressed by recent psychological research on emotion include questions about how thought shapes emotion and how emotion, in turn, shapes thought. Research on emotion and cognition paints a somewhat different picture than that seen in traditional discussions of passion and reason. This article reviews several aspects of this research, concentrating specifically on three views of rationality: Rationality as Process, Rationality as Product, and Rationality as Outcome. PMID:25125770

  8. Rational Thinking in School-Based Practice

    ERIC Educational Resources Information Center

    Clark, Mary Kristen; Flynn, Perry

    2011-01-01

    Purpose: We reflect on Alan Kamhi's (2011) prologue on balancing certainty and uncertainty as it pertains to school-based practice. Method: In schools, rational thinking depends on effective team processes, much like professional learning communities. We consider the conditions that are required for rational thinking and how rational team dialogue…

  9. Rationality and the Logic of Good Reasons.

    ERIC Educational Resources Information Center

    Fisher, Walter R.

    This paper contends that the rationality of the logic of good reasons is constituted in its use. To support this claim, the paper presents an analysis of the relationship between being reasonable and being rational. It then considers how following the logic of good reasons leads to rationality in the behavior of individuals and groups; the latter…

  10. Book Selection, Collection Development, and Bounded Rationality.

    ERIC Educational Resources Information Center

    Schwartz, Charles A.

    1989-01-01

    Reviews previously proposed schemes of classical rationality in book selection, describes new approaches to rational choice behavior, and presents a model of book selection based on bounded rationality in a garbage can decision process. The role of tacit knowledge and symbolic content in the selection process are also discussed. (102 references)…

  11. Databases and data mining for computational vaccinology.

    PubMed

    Flower, Darren R

    2003-05-01

    Drugs and vaccines are keys to the effective fight against disease. While the pharmaceutical industry has developed an awesome array of real and virtual approaches to rational drug discovery, the complexity of the immune system hampers attempts to design and develop vaccines in a rational manner. The goal of immunoinformatics (the application of informatics techniques to immunological macromolecules), an emergent sub-discipline of bioinformatics, is to develop computational vaccinology as a potent tool in the quest for new vaccines. Databases and data mining, the two principal weapons at the disposal of the in silico vaccinologist, will be presented in the light of current developments. PMID:12833673

  12. RELATIONSHIP BETWEEN PHYLOGENETIC DISTRIBUTION AND GENOMIC FEATURES IN NEUROSPORA CRASSA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the post-genome era, insufficient functional annotation of predicted genes greatly restricts the potential of mining genome data. We demonstrate that an evolutionary approach, which is independent of functional annotation, has great potential as a tool for genome analysis. We chose the genome o...

  13. Resistance Gene-Guided Genome Mining: Serial Promoter Exchanges in Aspergillus nidulans Reveal the Biosynthetic Pathway for Fellutamide B, a Proteasome Inhibitor.

    PubMed

    Yeh, Hsu-Hua; Ahuja, Manmeet; Chiang, Yi-Ming; Oakley, C Elizabeth; Moore, Shauna; Yoon, Olivia; Hajovsky, Heather; Bok, Jin-Woo; Keller, Nancy P; Wang, Clay C C; Oakley, Berl R

    2016-08-19

    Fungal genome projects are revealing thousands of cryptic secondary metabolism (SM) biosynthetic gene clusters that encode pathways that potentially produce valuable compounds. Heterologous expression systems should allow these clusters to be expressed and their products obtained, but approaches are needed to identify the most valuable target clusters. The inp cluster of Aspergillus nidulans contains a gene, inpE, that encodes a proteasome subunit, leading us to hypothesize that the inp cluster produces a proteasome inhibitor and inpE confers resistance to this compound. Previous efforts to express this cluster have failed, but by sequentially replacing the promoters of the genes of the cluster with a regulatable promotor, we have expressed them successfully. Expression reveals that the product of the inp cluster is the proteasome inhibitor fellutamide B, and our data allow us to propose a biosynthetic pathway for the compound. By deleting inpE and activating expression of the inp cluster, we demonstrate that inpE is required for resistance to internally produced fellutamide B. These data provide experimental validation for the hypothesis that some fungal SM clusters contain genes that encode resistant forms of the enzymes targeted by the compound produced by the cluster. PMID:27294372

  14. Genome mining in Sorangium cellulosum So ce56: identification and characterization of the homologous electron transfer proteins of a myxobacterial cytochrome P450.

    PubMed

    Ewen, Kerstin Maria; Hannemann, Frank; Khatri, Yogan; Perlova, Olena; Kappl, Reinhard; Krug, Daniel; Hüttermann, Jürgen; Müller, Rolf; Bernhardt, Rita

    2009-10-16

    Myxobacteria, especially members of the genus Sorangium, are known for their biotechnological potential as producers of pharmaceutically valuable secondary metabolites. The biosynthesis of several of those myxobacterial compounds includes cytochrome P450 activity. Although class I cytochrome P450 enzymes occur wide-spread in bacteria and rely on ferredoxins and ferredoxin reductases as essential electron mediators, the study of these proteins is often neglected. Therefore, we decided to search in the Sorangium cellulosum So ce56 genome for putative interaction partners of cytochromes P450. In this work we report the investigation of eight myxobacterial ferredoxins and two ferredoxin reductases with respect to their activity in cytochrome P450 systems. Intriguingly, we found not only one, but two ferredoxins whose ability to sustain an endogenous So ce56 cytochrome P450 was demonstrated by CYP260A1-dependent conversion of nootkatone. Moreover, we could demonstrate that the two ferredoxins were able to receive electrons from both ferredoxin reductases. These findings indicate that S. cellulosum can alternate between different electron transport pathways to sustain cytochrome P450 activity. PMID:19696019

  15. Coastal mining

    NASA Astrophysics Data System (ADS)

    Bell, Peter M.

    The Exclusive Economic Zone (EEZ) declared by President Reagan in March 1983 has met with a mixed response from those who would benefit from a guaranteed, 200-nautical-mile (370-km) protected underwater mining zone off the coasts of the United States and its possessions. On the one hand, the U.S. Department of the Interior is looking ahead and has been very successful in safeguarding important natural resources that will be needed in the coming decades. On the other hand, the mining industry is faced with a depressed metals and mining market.A report of the Exclusive Economic Zone Symposium held in November 1983 by the U.S. Geological Survey, the Mineral Management Service, and the Bureau of Mines described the mixed response as: “ … The Department of Interior … raring to go into promotion of deep-seal mining but industrial consortia being very pessimistic about the program, at least for the next 30 or so years.” (Chemical & Engineering News, February 5, 1983).

  16. Rational Prescription for a Dermatologist

    PubMed Central

    Prakash, Bhanu; Nadig, Prathiba; Nayak, Amitha

    2016-01-01

    The ultimate goal in dermatological therapy is to use the safest and least number of drugs in order to obtain the best possible effect in the shortest period and at reasonable cost. Rational drug use (RDU) is conventionally defined as the use of an appropriate, efficacious, safe and cost-effective drug given for the right indications in the right dose and formulation, at right time intervals. WHO estimates that more than half of all medicines are prescribed, dispensed or sold inappropriately, and that half of all patients fail to take them correctly as prescribed by the doctor. The process of Rational prescription for a Dermatologist (RPD) involves a series of steps such as defining the patient's illness, specifying the treatment objectives, using the principle of P-treatment, starting the treatment, providing appropriate information and monitoring the treatment. Reasons for irrational prescription could be physician related, patient related, industry related, regulations related. Practicing medicine irrationally can lead to disastrous events like increased morbidity and mortality, drain of resources, drug resistance etc. Principles to enhance the RDU in our practice and minimize errors of prescription are discussed in detail in this article. PMID:26955092

  17. In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data.

    PubMed

    Agarwal, Suyash; Nagpure, Naresh Sahebrao; Srivastava, Prachi; Kushwaha, Basdeo; Kumar, Ravindra; Pandey, Manmohan; Srivastava, Shreya

    2016-03-01

    MicroRNAs (miRNAs) are small, non-coding RNA molecules that bind to the mRNA of the target genes and regulate the expression of the gene at the post-transcriptional level. Zebrafish is an economically important freshwater fish species globally considered as a good predictive model for studying human diseases and development. The present study focused on uncovering known as well as novel miRNAs, target prediction of the novel miRNAs and the differential expression of the known miRNA using the small RNA sequencing data of the brain and pineal gland (dark and light treatments) obtained from NCBI SRA. A total of 165, 151 and 145 known zebrafish miRNAs were found in the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. Chromosomes 4 and 5 of zebrafish reference assembly GRCz10 were found to contain maximum number of miR genes. The miR-181a and miR-182 were found to be highly expressed in terms of number of reads in the brain and pineal gland, respectively. Other ncRNAs, such as tRNA, rRNA and snoRNA, were curated against Rfam. Using GRCz10 as reference, the subsequent bioinformatic analyses identified 25, 19 and 9 novel miRNAs from the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. Targets of the novel miRNAs were identified, based on sequence complementarity between miRNAs and mRNA, by searching for antisense hits in the 3'-UTR of reference RNA sequences of the zebrafish. The discovery of novel miRNAs and their targets in the zebrafish genome can be a valuable scientific resource for further functional studies not only in zebrafish but also in other economically important fishes. PMID:26981358

  18. In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data

    PubMed Central

    Agarwal, Suyash; Nagpure, Naresh Sahebrao; Srivastava, Prachi; Kushwaha, Basdeo; Kumar, Ravindra; Pandey, Manmohan; Srivastava, Shreya

    2015-01-01

    MicroRNAs (miRNAs) are small, non-coding RNA molecules that bind to the mRNA of the target genes and regulate the expression of the gene at the post-transcriptional level. Zebrafish is an economically important freshwater fish species globally considered as a good predictive model for studying human diseases and development. The present study focused on uncovering known as well as novel miRNAs, target prediction of the novel miRNAs and the differential expression of the known miRNA using the small RNA sequencing data of the brain and pineal gland (dark and light treatments) obtained from NCBI SRA. A total of 165, 151 and 145 known zebrafish miRNAs were found in the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. Chromosomes 4 and 5 of zebrafish reference assembly GRCz10 were found to contain maximum number of miR genes. The miR-181a and miR-182 were found to be highly expressed in terms of number of reads in the brain and pineal gland, respectively. Other ncRNAs, such as tRNA, rRNA and snoRNA, were curated against Rfam. Using GRCz10 as reference, the subsequent bioinformatic analyses identified 25, 19 and 9 novel miRNAs from the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. Targets of the novel miRNAs were identified, based on sequence complementarity between miRNAs and mRNA, by searching for antisense hits in the 3′-UTR of reference RNA sequences of the zebrafish. The discovery of novel miRNAs and their targets in the zebrafish genome can be a valuable scientific resource for further functional studies not only in zebrafish but also in other economically important fishes. PMID:26981358

  19. Mining machine

    SciTech Connect

    Parrott, G.A.

    1985-05-07

    A haulage system for a mining machine comprises a mining machine mounted on and/or guided by a conveyor and reciprocable with respect thereto, the conveyor being provided with a rack having plural rows of teeth of identical pitch, with the teeth of one row staggered with respect to an adjacent row(s), and the machine being provided with at least one power driven haulage sprocket comprising plural sets of peripherally arranged teeth of identical pitch, one set being angularly staggered with respect to an adjacent set(s), whereby one set is engageable with each row of teeth of the rack. The invention also includes a mining machine provided with such a power driven haulage sprocket, and a rack as above described and provided with end fittings for securing in articulated manner to an adjacent rack.

  20. Asteroid mining

    NASA Technical Reports Server (NTRS)

    Gertsch, Richard E.

    1992-01-01

    The earliest studies of asteroid mining proposed retrieving a main belt asteroid. Because of the very long travel times to the main asteroid belt, attention has shifted to the asteroids whose orbits bring them fairly close to the Earth. In these schemes, the asteroids would be bagged and then processed during the return trip, with the asteroid itself providing the reaction mass to propel the mission homeward. A mission to one of these near-Earth asteroids would be shorter, involve less weight, and require a somewhat lower change in velocity. Since these asteroids apparently contain a wide range of potentially useful materials, our study group considered only them. The topics covered include asteroid materials and properties, asteroid mission selection, manned versus automated missions, mining in zero gravity, and a conceptual mining method.

  1. Mining equipment

    SciTech Connect

    Goff, J.R.; Spence, A.M.

    1981-06-23

    In a system for the supply of fluid under pressure to machinery of an underground mine working, lengths of fixed conduit are secured to parts of the conveyor assembly, prior to the assembly of said parts at the underground mine working. When the conveyor assembly has been assembled, the length of fixed conduits are interconnected, either by straight lengths of flexible conduit, or by branched lengths of flexible conduit, where take off for fluid under pressure is required for the machinery, for example a roof support unit.

  2. The Implicitome: A Resource for Rationalizing Gene-Disease Associations.

    PubMed

    Hettne, Kristina M; Thompson, Mark; van Haagen, Herman H H B M; van der Horst, Eelke; Kaliyaperumal, Rajaram; Mina, Eleni; Tatum, Zuotian; Laros, Jeroen F J; van Mulligen, Erik M; Schuemie, Martijn; Aten, Emmelien; Li, Tong Shu; Bruskiewich, Richard; Good, Benjamin M; Su, Andrew I; Kors, Jan A; den Dunnen, Johan; van Ommen, Gert-Jan B; Roos, Marco; 't Hoen, Peter A C; Mons, Barend; Schultes, Erik A

    2016-01-01

    High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing biomedical knowledge for identification and interpretation of gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate the usefulness of the implicitome by rationalizing known and novel gene-disease associations, including those from GWAS. To facilitate the re-use of implicit gene-disease associations, we publish our data in compliance with FAIR Data Publishing recommendations [https://www.force11.org/group/fairgroup] using nanopublications. An online tool (http://knowledge.bio) is available to explore established and potential gene-disease associations in the context of other biomedical relations. PMID:26919047

  3. The Implicitome: A Resource for Rationalizing Gene-Disease Associations

    PubMed Central

    van der Horst, Eelke; Kaliyaperumal, Rajaram; Mina, Eleni; Tatum, Zuotian; Laros, Jeroen F. J.; van Mulligen, Erik M.; Schuemie, Martijn; Aten, Emmelien; Li, Tong Shu; Bruskiewich, Richard; Good, Benjamin M.; Su, Andrew I.; Kors, Jan A.; den Dunnen, Johan; van Ommen, Gert-Jan B.; Roos, Marco; ‘t Hoen, Peter A.C.; Mons, Barend; Schultes, Erik A.

    2016-01-01

    High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing biomedical knowledge for identification and interpretation of gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate the usefulness of the implicitome by rationalizing known and novel gene-disease associations, including those from GWAS. To facilitate the re-use of implicit gene-disease associations, we publish our data in compliance with FAIR Data Publishing recommendations [https://www.force11.org/group/fairgroup] using nanopublications. An online tool (http://knowledge.bio) is available to explore established and potential gene-disease associations in the context of other biomedical relations. PMID:26919047

  4. Refolding of proteins from inclusion bodies: rational design and recipes.

    PubMed

    Basu, Anindya; Li, Xiang; Leong, Susanna Su Jan

    2011-10-01

    The need to develop protein biomanufacturing platforms that can deliver proteins quickly and cost-effectively is ever more pressing. The rapid rate at which genomes can now be sequenced demands efficient protein production platforms for gene function identification. There is a continued need for the biotech industry to deliver new and more effective protein-based drugs to address new diseases. Bacterial production platforms have the advantage of high expression yields, but insoluble expression of many proteins necessitates the development of diverse and optimised refolding-based processes. Strategies employed to eliminate insoluble expression are reviewed, where it is concluded that inclusion bodies are difficult to eliminate for various reasons. Rational design of refolding systems and recipes are therefore needed to expedite production of recombinant proteins. This review article discusses efforts towards rational design of refolding systems and recipes, which can be guided by the development of refolding screening platforms that yield both qualitative and quantitative information on the progression of a given refolding process. The new opportunities presented by light scattering technologies for developing rational protein refolding buffer systems which in turn can be used to develop new process designs armed with better monitoring and controlling functionalities are discussed. The coupling of dynamic and static light scattering methodologies for incorporation into future bioprocess designs to ensure delivery of high-quality refolded proteins at faster rates is also discussed. PMID:21822901

  5. Decision making: rational or hedonic?

    PubMed Central

    Cabanac, Michel; Bonniot-Cabanac, Marie-Claude

    2007-01-01

    Three experiments studied the hedonicity of decision making. Participants rated their pleasure/displeasure while reading item-sentences describing political and social problems followed by different decisions (Questionnaire 1). Questionnaire 2 was multiple-choice, grouping the items from Questionnaire 1. In Experiment 1, participants answered Questionnaire 2 rapidly or slowly. Both groups selected what they had rated as pleasant, but the 'leisurely' group maximized pleasure less. In Experiment 2, participants selected the most rational responses. The selected behaviors were pleasant but less than spontaneous behaviors. In Experiment 3, Questionnaire 2 was presented once with items grouped by theme, and once with items shuffled. Participants maximized the pleasure of their decisions, but the items selected on Questionnaires 2 were different when presented in different order. All groups maximized pleasure equally in their decisions. These results support that decisions are made predominantly in the hedonic dimension of consciousness. PMID:17848195

  6. Rational design of helical architectures

    PubMed Central

    Chakrabarti, Dwaipayan; Fejer, Szilard N.; Wales, David J.

    2009-01-01

    Nature has mastered the art of creating complex structures through self-assembly of simpler building blocks. Adapting such a bottom-up view provides a potential route to the fabrication of novel materials. However, this approach suffers from the lack of a sufficiently detailed understanding of the noncovalent forces that hold the self-assembled structures together. Here we demonstrate that nature can indeed guide us, as we explore routes to helicity with achiral building blocks driven by the interplay between two competing length scales for the interactions, as in DNA. By characterizing global minima for clusters, we illustrate several realizations of helical architecture, the simplest one involving ellipsoids of revolution as building blocks. In particular, we show that axially symmetric soft discoids can self-assemble into helical columnar arrangements. Understanding the molecular origin of such spatial organisation has important implications for the rational design of materials with useful optoelectronic applications.

  7. Max Weber's Types of Rationality: Cornerstones for the Analysis of Rationalization Processes in History.

    ERIC Educational Resources Information Center

    Kalberg, Stephen

    1980-01-01

    Explores rationality in Max Weber's works and identifies four types of rationality which play major roles in his writing--practical, theoretical, substantive, and formal. Implications for society and education are discussed. (DB)

  8. Underground mining methods handbook

    SciTech Connect

    Hustrulid, W.A.

    1982-01-01

    Sections discuss: mine design considerations; stopes requiring minimum support (includes room-and-pillar mining and sublevel stoping); stopes requiring some additional support other than pillars (includes shrinkage stoping, cut-and-fill stoping, undercut-and-fill mining, timber-supported system, top-slice mining, longwall mining and shortwall mining); caving methods (sublevel and block caving); underground equipment; financial considerations; design; and mine ventilation.

  9. Using Fitness Landscapes for Rational Hepatitis C Immunogen Design

    NASA Astrophysics Data System (ADS)

    Hart, Gregory; Ferguson, Andrew

    2015-03-01

    Hepatitis C virus afflicts 170 million people worldwide, 2-3% of the global population. Prophylactic vaccination offers the most realistic and cost effective hope of controlling this epidemic, particularly in the developing world where expensive drug therapies are unavailable. Despite 20 years of research, the high mutability of the virus, and lack of knowledge of what constitutes effective immune responses, have impeded development of an effective vaccine. Coupling data mining of sequence databases with the Potts model, we have developed a computational approach to systematically identify viral vulnerabilities and perform rational design of vaccine immunogens. We applied our approach to the nonstructural proteins NS3, NSA, NSA, and NSB which are crucial for viral replication.The predictions of our model are in good accord with experimental measurements and clinical observations, and we have used our model to design immunogen candidates to elicit T-cell responses against vulnerable regions of theseviral proteins.

  10. The Rationality of Alcoholics Anonymous and the Spirituality of Rational Emotive Behavior Therapy.

    ERIC Educational Resources Information Center

    Velten, Emmett

    1996-01-01

    Argues that Alcoholics Anonymous (AA) and Rational Emotive Behavior Therapy (REBT) share important rational objectives and numerous cognitive-behavioral methods. Both emphasize a philosophical shift as a principal ingredient for change. Provides definitions of rationality and spirituality and explains how REBT and smart recovery are spiritual…

  11. Data mining

    SciTech Connect

    Lee, K.; Kargupta, H.; Stafford, B.G.; Buescher, K.L.; Ravindran, B.

    1998-12-31

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The objective of this project was to develop and implement data mining technology suited to the analysis of large collections of unstructured data. This has taken the form of a software tool, PADMA (Parallel Data Mining Agents), which incorporates parallel data accessing, parallel scalable hierarchical clustering algorithms, and a web-based user interface for submitting Structured Query Language (SQL) queries and interactive data visualization. The authors have demonstrated the viability and scalability of PADMA by applying it to an unstructured text database of 25,000 documents running on an IBM SP2 at Argonne National Laboratory. The utility of PADMA for discovering patterns in data has also been demonstrated by applying it to laboratory test data for Hepatitis C patients and autopsy reports in collaboration with the University of New Mexico School of Medicine.

  12. Developing Critical Rationality as a Pedagogical Aim

    ERIC Educational Resources Information Center

    Winch, Christopher

    2004-01-01

    The development of a conception of critical pedagogy is itself an aspect of the development of critical rationality within late modern societies, closely connected with the role of education in developing critical rationality. The role of critique pervades all aspects of life: for people as citizens, workers and self-determining private…

  13. Decision Making: Rational, Nonrational, and Irrational.

    ERIC Educational Resources Information Center

    Simon, Herbert A.

    1993-01-01

    Describes the current state of knowledge about human decision-making and problem-solving processes, explaining recent developments and their implications for management and management training. Rational goal-setting is the key to effective decision making and accomplishment. Bounded rationality is a realistic orientation, because the world is too…

  14. Rationality and Belief in Learning Mathematics

    ERIC Educational Resources Information Center

    Brown, Tony

    2016-01-01

    This paper argues that rationality and belief are mutually formative dimensions of school mathematics, where each term is more politically embedded than often depicted in the field of mathematics education research. School mathematics then presents not so much rational mathematical thought distorted by irrational beliefs but rather a particular…

  15. The Emotional and Moral Basis of Rationality

    ERIC Educational Resources Information Center

    Boostrom, Robert

    2013-01-01

    This chapter explores the basis of rationality, arguing that critical thinking tends to be taught in schools as a set of skills because of the failure to recognize that choosing to think critically depends on the prior development of stable sentiments or moral habits that nourish a rational self. Primary among these stable sentiments are the…

  16. Neurophysiology and Rationality in Political Thinking.

    ERIC Educational Resources Information Center

    Peterson, Steven A.

    Research both in cognitive psychology and psychobiology suggests that political behavior is often less rational than individuals believe it to be. Information processing, memory, and decision making are interlinked processes. Studies in cognitive psychology reveal that even though decision making requires rationality, individuals often adopt…

  17. On rational integrals of geodesic flows

    NASA Astrophysics Data System (ADS)

    Kozlov, Valery V.

    2014-11-01

    This paper is concerned with the problem of first integrals of the equations of geodesics on two-dimensional surfaces that are rational in the velocities (or momenta). The existence of nontrivial rational integrals with given values of the degrees of the numerator and the denominator is proved using the Cauchy-Kovalevskaya theorem.

  18. Fiber sources for complete calf starter rations.

    PubMed

    Murdock, F R; Wallenius, R W

    1980-11-01

    Complete calf starter rations containing either 1) alfalfa hay, 2) cottonseed hulls, or 3) alfalfa-beet pulp as sources of fiber were fed to Holstein heifer calves at two locations on a limited milk program from 3 days to 12 wk of age. Rations were isonitrogenous and similar in content of crude fiber and acid detergent fiber. Although growth and development were normal on all rations, calves fed the cottonseed hull ration consumed more starter and gained more body weight than calves fed the other sources of fiber. The similarity of feed efficiencies, rumen pH, and molar ratios of volatile fatty acids between rations indicated no appreciable differences in rumen development or function. The growth response of calves fed the cottonseed hull ration appeared to be a result of better ration acceptability for which no reason was evident. Calves raised at Puyallup gained more body weight than calves at Pullman, and these gains were made more efficiently. These location effects may be related to seasonal differences and greater demands for production of body heat. Although the incidence of scours was less for calves fed alfalfa hay starter, the incidence and severity of bloat were higher for that ration. PMID:6255021

  19. Professionalization in a Rationally Managed Corporate Organization.

    ERIC Educational Resources Information Center

    Alie, Raymond E.

    1982-01-01

    Explored the relationship of professionalization and rational corporate management. Subjects were 320 engineers in a merged manufacturing firm. Results indicated a relationship between graduate degree activity and organization membership, and confirmed that engineers exhibit greater professionalization in a rationally managed organization. (WAS)

  20. Are Grade Expectations Rational? A Classroom Experiment

    ERIC Educational Resources Information Center

    Hossain, Belayet; Tsigaris, Panagiotis

    2015-01-01

    This study examines students' expectations about their final grade. An attempt is made to determine whether students form expectations rationally. Expectations in economics, rational or otherwise, carry valuable information and have important implications in terms of both teaching effectiveness and the role of grades as an incentive structure…

  1. Approaches towards rational antiviral chemotherapy.

    PubMed Central

    Oxford, J. S.

    1979-01-01

    Present epidemic influenza is uncontrolled by immuno- or chemoprophylaxis. Mutants of varying antigenic composition arise with relatively high frequency in nature and are able to circumvent herd, or induced, immunity. Also, drug-resistant viruses can be selected in vitro and this resistance can be exchanged to other viruses by gene reassortment. Combined immuno- and chemoprophylaxis may provide a more effective approach to the ultimate control of the disease. Most antiviral compounds have been selected by random screening in the laboratory. Application of more specific enzyme assays such as the virion-associated RNA transcriptase assays may produce other compounds with a defined mode of action - semi-rational chemotherapy. RNA and polypeptide sequence studies are in progress elsewhere to define transcription and translation initiation sites or virus adsorption sites. Such knowledge could lead to a new generation of antiviral compounds. Specific delivery of virus inhibitory compounds is an interesting problem. Liposomes are lipid spheres, and these have been used for the delivery of antiviral compounds. Images Fig. 3a. Fig. 3b. Fig. 4 Fig. 5 PMID:461275

  2. The Mechanization of Mining.

    ERIC Educational Resources Information Center

    Marovelli, Robert L.; Karhnak, John M.

    1982-01-01

    Mechanization of mining is explained in terms of its effect on the mining of coal, focusing on, among others, types of mining, productivity, machinery, benefits to retired miners, fatality rate in underground coal mines, and output of U.S. mining industry. (Author/JN)

  3. Being 'rational' and being 'human': How National Health Service rationing decisions are constructed as rational by resource allocation panels.

    PubMed

    Russell, Jill; Greenhalgh, Trisha

    2014-09-01

    The English National Health Service Constitution states that patients have the right to expect all decisions about access to medicines and treatments to be made 'rationally'. Rationality in health care can be framed as instrumental, institutional or practical. In this article, we present a case example from an ethnographic study of the work of 'Individual Funding Request' panels to explore how rationality is enacted and accounted for in deliberations about the rationing of health care in the National Health Service. Our rhetorical analysis highlights how an embodied, practical rationality emerges as a significant aspect of rationality in practice, but at the same time has a problematic status in formal accounts of decision-making. We suggest that being both 'human' and 'rational' is a 'delicate balance' and creates a dilemma for Individual Funding Request panels. Aristotle's notion of phronesis provides a useful lens for theorising our observation of panel deliberations, and we argue for greater attention to the value of narrative ethics in helping us understand the challenges faced by resource allocators. PMID:24287296

  4. MouseMine: a new data warehouse for MGI.

    PubMed

    Motenko, H; Neuhauser, S B; O'Keefe, M; Richardson, J E

    2015-08-01

    MouseMine (www.mousemine.org) is a new data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Based on the InterMine software framework, MouseMine supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. Through MouseMine, users can access a significant portion of MGI data in new and useful ways. Importantly, MouseMine is also a member of a growing community of online data resources based on InterMine, including those established by other model organism databases. Adopting common interfaces and collaborating on data representation standards are critical to fostering cross-species data analysis. This paper presents a general introduction to MouseMine, presents examples of its use, and discusses the potential for further integration into the MGI interface. PMID:26092688

  5. Uses of antimicrobial genes from microbial genome

    DOEpatents

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20

    We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.

  6. Exploration and Mining Roadmap

    SciTech Connect

    none,

    2002-09-01

    This Exploration and Mining Technology Roadmap represents the third roadmap for the Mining Industry of the Future. It is based upon the results of the Exploration and Mining Roadmap Workshop held May 10 ñ 11, 2001.

  7. [The rational diagnostic of cholangiocarcinoma].

    PubMed

    Rydlo, Martin; Dvořáčková, Jana; Kupka, Tomáš; Klvaňa, Pavel; Havelka, Jaroslav; Uvírová, Magdalena; Geryk, Edvard; Czerný, Daniel; Jonszta, Tomáš; Bojková, Martina; Hrabovský, Vladimír; Jelínková, Veronika; Martínek, Arnošt; Dítě, Petr

    2016-02-01

    Cholangiocarcinoma (CC) is a rare malignant tumour arising from cholangiocytes, and its prognosis is usually unfavourable, mostly as a result of late diagnosis of the tumour. The current incidence of cholangiocarcinoma in the Czech Republic is 1.4/100,000 inhabitants per year; in less than 30 % of patients with CC, one of the known risk factors can be identified, most frequently, primary sclerosing cholangitis. Only patients with early diagnosed and surgically amenable cholangiocarcinoma are likely to have a longer survival time; in their case, survival for more than five years has been achieved in 20 % to 40 %. From the perspective of the need for early diagnosis of CC, a significant part is played by imaging and histopathologic evaluation; the early diagnostic significance of oncomarkers is limited. The rational early diagnosis of CC consists in effective use of differentiated advantages of different imaging modalities - MRI with DSA appears to be the optimal method, endosonography is a sensitive method for the identification of malignancy in the hepatic hilum or distal common bile duct, MRCP (magnetic resonance cholangiopancreatography) is used to display pathological changes in the biliary tree, ERCP (endoscopic retrograde cholangiopancreatography) allows material removal for histopathological examination. Other new approaches are also beneficial, such as IDUS - intraductal ultrasonography of biliary tract or SPY-GLASS, enabling examination of the bile ducts by direct view with the possibility of taking targeted biopsies. Sensitivity and specificity of histology and cytology can be increased by using the molecular cytogenetic FISH method, i.e. fluorescence in situ by hybridization, with a specificity of 97 %. PMID:27172439

  8. Mining review

    USGS Publications Warehouse

    McCartan, L.; Morse, D.E.; Plunkert, P.A.; Sibley, S.F.

    2004-01-01

    The average annual growth rate of real gross domestic product (GDP) from the third quarter of 2001 through the second quarter of 2003 in the United States was about 2.6 percent. GDP growth rates in the third and fourth quarters of 2003 were about 8 percent and 4 percent, respectively. The upward trends in many sectors of the U.S. economy in 2003, however, were shared by few of the mineral materials industries. Annual output declined in most nonfuel mining and mineral processing industries, although there was an upward turn toward yearend as prices began to increase.

  9. Determination of Abutment Pressure in Coal Mines with Extremely Thick Alluvium Stratum: A Typical Kind of Rockburst Mines in China

    NASA Astrophysics Data System (ADS)

    Zhu, Sitao; Feng, Yu; Jiang, Fuxing

    2016-05-01

    This paper investigates the abutment pressure distribution in coal mines with extremely thick alluvium stratum (ETAS), which is a typical kind of mines encountering frequent intense rockbursts in China. This occurs due to poor understanding to abutment pressure distribution pattern and the consequent inappropriate mine design. In this study, a theoretical computational model of abutment pressure for ETAS longwall panels is proposed based on the analysis of load transfer mechanisms of key stratum (KS) and ETAS. The model was applied to determine the abutment pressure distribution of LW2302S in Xinjulong Coal Mine; the results of stress and microseismic monitoring verified the rationality of this model. The calculated abutment pressure of LW2302S was also used in the terminal mining line design of LW2301N for rockburst prevention, successfully protecting the main roadway from the adverse influence of the abutment pressure.

  10. Rationing of health care: is there an economic rationality to it?

    PubMed

    Zweifel, Peter

    2015-11-01

    The point of departure of this Editorial is the fact that we all are engaged in self-rationing in our everyday lives. We would like to spend more money on all sorts of nice things and devote more time to our cherished activities. Imposed rationing is characteristic of wartime governments, who seek to prevent the rich from gobbling up the resources left by the army. Since the publication in 1987 of David Callahan's Setting Limits: Medical Goals in an Aging Society (Callahan, Setting limits: medical goals in an aging society, Simon & Schuster, New York, 1987), rationing of health care has become a widely debated issue (the Internet is full of pertinent entries). While rationing has also been addressed by health economists, there are three puzzling observations. First, Callahan (Callahan, Setting limits: medical goals in an aging society, Simon & Schuster, New York, 1987) wrote for an American audience whereas rationing was introduced by the British National Health Service (NHS) well before 1987, with little debate. Second, the economic theory of rationing had been laid out by James Tobin [Ectrica 20(4): 521-533, 1952] as early as 1952--but health economists seem to have neglected his groundwork when writing about rationing. Third, they accept government-imposed rationing as inevitable in the case of health care, as though the self-rationing alternative was unavailable. An attempt is made here to provide rational explanations for these puzzles. PMID:25847329

  11. Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum

    PubMed Central

    Graupner, Katharina; Lackner, Gerald

    2015-01-01

    Janthinobacterium agaricidamnosum causes soft-rot disease of the cultured button mushroom Agaricus bisporus and is thus responsible for agricultural losses. Here, we present the genome sequence of J. agaricidamnosum DSM 9628. The 5.9-Mb genome harbors several secondary metabolite biosynthesis gene clusters, which renders this neglected bacterium a promising source for genome mining approaches. PMID:25883287

  12. Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum.

    PubMed

    Graupner, Katharina; Lackner, Gerald; Hertweck, Christian

    2015-01-01

    Janthinobacterium agaricidamnosum causes soft-rot disease of the cultured button mushroom Agaricus bisporus and is thus responsible for agricultural losses. Here, we present the genome sequence of J. agaricidamnosum DSM 9628. The 5.9-Mb genome harbors several secondary metabolite biosynthesis gene clusters, which renders this neglected bacterium a promising source for genome mining approaches. PMID:25883287

  13. Draft Genome Sequence of Fungus Clonostachys rosea Strain YKD0085

    PubMed Central

    Liu, Shuai; Chang, Yaowen; Hu, Xujia; Gong, Xuanyun; Hao, Xiaojiang

    2016-01-01

    Here, we report the draft genome sequence of Clonostachys rosea (strain YKD0085). The functional annotation of C. rosea provides important information related to its ability to produce secondary metabolites. The genome sequence presented here builds the basis for further genome mining. PMID:27340057

  14. Draft Genome Sequence of Fungus Clonostachys rosea Strain YKD0085.

    PubMed

    Liu, Shuai; Chang, Yaowen; Hu, Xujia; Gong, Xuanyun; Di, Yingtong; Dong, Jinyan; Hao, Xiaojiang

    2016-01-01

    Here, we report the draft genome sequence of Clonostachys rosea (strain YKD0085). The functional annotation of C. rosea provides important information related to its ability to produce secondary metabolites. The genome sequence presented here builds the basis for further genome mining. PMID:27340057

  15. Draft Genome Sequence of Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556.

    PubMed

    Komaki, Hisayuki; Ichikawa, Natsuko; Oguchi, Akio; Hamada, Moriyuki; Tamura, Tomohiko; Suzuki, Ken-Ichiro; Fujita, Nobuyuki

    2016-01-01

    Here, we report the draft genome sequence of strain NBRC 16556, deposited as Streptomyces hygroscopicus subsp. hygroscopicus into the NBRC culture collection. An average nucleotide identity analysis confirmed that the taxonomic identification is correct. The genome sequence will serve as a valuable reference for genome mining to search new secondary metabolites. PMID:27198007

  16. Frontiers of biomedical text mining: current progress.

    PubMed

    Zweigenbaum, Pierre; Demner-Fushman, Dina; Yu, Hong; Cohen, Kevin B

    2007-09-01

    It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain. Enormous progress has been made in the areas of information retrieval, evaluation methodologies and resource construction. Some problems, such as abbreviation-handling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon. However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research. In this article we review the current state of the art in biomedical text mining or 'BioNLP' in general, focusing primarily on papers published within the past year. PMID:17977867

  17. Frontiers of biomedical text mining: current progress

    PubMed Central

    Zweigenbaum, Pierre; Demner-Fushman, Dina; Yu, Hong; Cohen, Kevin B.

    2008-01-01

    It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain. Enormous progress has been made in the areas of information retrieval, evaluation methodologies and resource construction. Some problems, such as abbreviation-handling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon. However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research. In this article we review the current state of the art in biomedical text mining or ‘BioNLP’ in general, focusing primarily on papers published within the past year. PMID:17977867

  18. Pandemic Ventilator Rationing and Appeals Processes

    PubMed Central

    Patrone, Daniel; Resnik, David

    2014-01-01

    In a severe influenza pandemic, hospitals will likely experience serious and widespread shortages of patient pulmonary ventilators and of staff qualified to operate them. Deciding who will receive access to mechanical ventilation will often determine who lives and who dies. This prospect raises an important question whether pandemic preparedness plans should include some process by which individuals affected by ventilator rationing would have the opportunity to appeal adverse decisions. However, the issue of appeals processes to ventilator rationing decisions has been largely neglected in state pandemic planning efforts. If we are to devise just and effective plans for coping with a severe influenza pandemic, more attention to the issue of appeals processes for pandemic ventilator rationing decisions is needed. Arguments for and against appeals processes are considered, and some suggestions are offered to help efforts at devising more rational pandemic preparedness plans. PMID:20354793

  19. Orthogonal rational functions and tridiagonal matrices

    NASA Astrophysics Data System (ADS)

    Bultheel, A.; González-Vera, P.; Hendriksen, E.; Njåstad, O.

    2003-04-01

    We study the recurrence relation for rational functions whose poles are in a prescribed sequence of numbers that are real or infinite and that are orthogonal with respect to an Hermitian positive linear functional. We especially discuss the interplay between finite and infinite poles. The recurrence relation will also be described in terms of a tridiagonal matrix which is a generalization of the Jacobi. matrix of the polynomial situation which corresponds to placing all the poles at infinity. This matrix not only describes the recurrence relation, but it can be used to give a determinant expression for the orthogonal rational functions and it also allows for the formulation of a generalized eigenvalue problem whose eigenvalues are the zeros of an orthogonal rational function. These nodes can be used in rational Gauss-type quadrature formulas and the corresponding weights can be obtained from the first components of the corresponding eigenvectors.

  20. Rationality and allocating scarce medical resources.

    PubMed

    Forsberg, R P

    1995-02-01

    In an article titled, "Who Shall Live When Not All Can?", James Childress proposes a system for allocating scarce lifesaving medical resources based on random selection procedures. Childress writes of random selection procedures, [They] "cannot be dismissed as a 'non-rational' and 'non-human' ...without an inquiry into the reasons, including human values which might justify it." My thesis is that once we concentrate on determining the rationality of random selection procedures, we will see that Childress's claim that we cannot dismiss such procedures as 'non-rational' is open to question. My claim will be that while both random selection and social worth procedures are rationally defensible systems, random selection procedures easily lead to specific choices that are objectively irrational, apart from the limited perspective of the random selection process itself. PMID:7738457

  1. Skyrmions, rational maps, and scaling identities

    SciTech Connect

    Charalampidis, E. G.; Ioannidou, T. A.; Manton, N. S.

    2011-03-15

    Starting from approximate Skyrmion solutions obtained using the rational map ansatz, improved approximate Skyrmions are constructed using scaling arguments. Although the energy improvement is small, the change of shape clarifies whether the true Skyrmions are more oblate or prolate.

  2. Validation Testing of the Rational Behavior Inventory.

    ERIC Educational Resources Information Center

    Whiteman, Victor L.; Shorkey, Clayton T.

    1978-01-01

    The validity of the Rational Behavior Inventory was investigated by examining its relationship with four other measures of personality in addition to class standing and age. Results supported the validity of the measure. (JKS)

  3. A framework for rationing by clinical judgment.

    PubMed

    Hurst, Samia A; Danis, Marion

    2007-09-01

    Although rationing by clinical judgment is controversial, its acceptability partly depends on how it is practiced. In this paper, rationing by clinical judgment is defined in three different circumstances that represent increasingly wider circles of resource pools in which the rationing decision takes place: triage during acute shortage, comparison to other potential patients in a context of limited but not immediately strained resources, and determination of whether expected benefit of an intervention is deemed sufficient to warrant its cost by reference to published population based thresholds. Notions of procedural justice are applied along with an analytical framework of six minimal requisites in order to facilitate fair bedside rationing: (1) a closed system that offers reciprocity, (2) attention to general concerns of justice, (3) respect for individual variations, (4) application of a consistent process, (5) explicitness, and (6) review of decisions. The process could be monitored for its applicability and appropriateness. PMID:18210983

  4. Mine seepage problems in drift mine operations

    SciTech Connect

    DeRossett, C.; Johnson, D.E.; Bradshaw, D.B.

    1996-12-31

    Extensive mining in the Eastern Kentucky Coal Region has occurred in coal deposits located above valley floors. Underground mines present unique stability problems resulting from the creation of mine pools in abandoned works. {open_quotes}Blowouts{close_quotes} occur when hydrostatic pressures result in the cataclysmic failure of an outcrop-barrier. Additionally, seepage from flooded works results in saturation of colluvium, which may ultimately mobilize as landslides. Several case studies of both landslides and blowouts illustrate that considerations should be taken into account to control or prevent these problems. Underground mine maps and seepage conditions at the individual sites were examined to determine the mine layouts, outcrop-barrier widths, and structure of the mine floors. Discharge monitoring points were established in and near the landslides. These studies depict how mine layout, operation, and geology influence drainage conditions. The authors suggest that mine designs should incorporate drainage control to insure long-term stability and limit liability. The goal of the post-mining drainage plan is control of the mine drainage, which will reduce the size of mine pools and lower the hydrostatic pressure. Recommendations are made as to several methods that may be useful in controlling mine drainage.

  5. Proceedings: Fourth Workshop on Mining Scientific Datasets

    SciTech Connect

    Kamath, C

    2001-07-24

    Commercial applications of data mining in areas such as e-commerce, market-basket analysis, text-mining, and web-mining have taken on a central focus in the JCDD community. However, there is a significant amount of innovative data mining work taking place in the context of scientific and engineering applications that is not well represented in the mainstream KDD conferences. For example, scientific data mining techniques are being developed and applied to diverse fields such as remote sensing, physics, chemistry, biology, astronomy, structural mechanics, computational fluid dynamics etc. In these areas, data mining frequently complements and enhances existing analysis methods based on statistics, exploratory data analysis, and domain-specific approaches. On the surface, it may appear that data from one scientific field, say genomics, is very different from another field, such as physics. However, despite their diversity, there is much that is common across the mining of scientific and engineering data. For example, techniques used to identify objects in images are very similar, regardless of whether the images came from a remote sensing application, a physics experiment, an astronomy observation, or a medical study. Further, with data mining being applied to new types of data, such as mesh data from scientific simulations, there is the opportunity to apply and extend data mining to new scientific domains. This one-day workshop brings together data miners analyzing science data and scientists from diverse fields to share their experiences, learn how techniques developed in one field can be applied in another, and better understand some of the newer techniques being developed in the KDD community. This is the fourth workshop on the topic of Mining Scientific Data sets; for information on earlier workshops, see http://www.ahpcrc.org/conferences/. This workshop continues the tradition of addressing challenging problems in a field where the diversity of applications is

  6. Intergroup Conflict and Rational Decision Making

    PubMed Central

    Martínez-Tur, Vicente; Peñarroja, Vicente; Serrano, Miguel A.; Hidalgo, Vanesa; Moliner, Carolina; Salvador, Alicia; Alacreu-Crespo, Adrián; Gracia, Esther; Molina, Agustín

    2014-01-01

    The literature has been relatively silent about post-conflict processes. However, understanding the way humans deal with post-conflict situations is a challenge in our societies. With this in mind, we focus the present study on the rationality of cooperative decision making after an intergroup conflict, i.e., the extent to which groups take advantage of post-conflict situations to obtain benefits from collaborating with the other group involved in the conflict. Based on dual-process theories of thinking and affect heuristic, we propose that intergroup conflict hinders the rationality of cooperative decision making. We also hypothesize that this rationality improves when groups are involved in an in-group deliberative discussion. Results of a laboratory experiment support the idea that intergroup conflict –associated with indicators of the activation of negative feelings (negative affect state and heart rate)– has a negative effect on the aforementioned rationality over time and on both group and individual decision making. Although intergroup conflict leads to sub-optimal decision making, rationality improves when groups and individuals subjected to intergroup conflict make decisions after an in-group deliberative discussion. Additionally, the increased rationality of the group decision making after the deliberative discussion is transferred to subsequent individual decision making. PMID:25461384

  7. Mining biological databases for candidate disease genes

    NASA Astrophysics Data System (ADS)

    Braun, Terry A.; Scheetz, Todd; Webster, Gregg L.; Casavant, Thomas L.

    2001-07-01

    The publicly-funded effort to sequence the complete nucleotide sequence of the human genome, the Human Genome Project (HGP), has currently produced more than 93% of the 3 billion nucleotides of the human genome into a preliminary `draft' format. In addition, several valuable sources of information have been developed as direct and indirect results of the HGP. These include the sequencing of model organisms (rat, mouse, fly, and others), gene discovery projects (ESTs and full-length), and new technologies such as expression analysis and resources (micro-arrays or gene chips). These resources are invaluable for the researchers identifying the functional genes of the genome that transcribe and translate into the transcriptome and proteome, both of which potentially contain orders of magnitude more complexity than the genome itself. Preliminary analyses of this data identified approximately 30,000 - 40,000 human `genes.' However, the bulk of the effort still remains -- to identify the functional and structural elements contained within the transcriptome and proteome, and to associate function in the transcriptome and proteome to genes. A fortuitous consequence of the HGP is the existence of hundreds of databases containing biological information that may contain relevant data pertaining to the identification of disease-causing genes. The task of mining these databases for information on candidate genes is a commercial application of enormous potential. We are developing a system to acquire and mine data from specific databases to aid our efforts to identify disease genes. A high speed cluster of Linux of workstations is used to analyze sequence and perform distributed sequence alignments as part of our data mining and processing. This system has been used to mine GeneMap99 sequences within specific genomic intervals to identify potential candidate disease genes associated with Bardet-Biedle Syndrome (BBS).

  8. Data mining for ontology development.

    SciTech Connect

    Davidson, George S.; Strasburg, Jana; Stampf, David; Neymotin,Lev; Czajkowski, Carl; Shine, Eugene; Bollinger, James; Ghosh, Vinita; Sorokine, Alexandre; Ferrell, Regina; Ward, Richard; Schoenwald, David Alan

    2010-06-01

    A multi-laboratory ontology construction effort during the summer and fall of 2009 prototyped an ontology for counterfeit semiconductor manufacturing. This effort included an ontology development team and an ontology validation methods team. Here the third team of the Ontology Project, the Data Analysis (DA) team reports on their approaches, the tools they used, and results for mining literature for terminology pertinent to counterfeit semiconductor manufacturing. A discussion of the value of ontology-based analysis is presented, with insights drawn from other ontology-based methods regularly used in the analysis of genomic experiments. Finally, suggestions for future work are offered.

  9. Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tomato Functional Genomics Database (TFGD; http://ted.bti.cornell.edu) provides a comprehensive systems biology resource to store, mine, analyze, visualize and integrate large-scale tomato functional genomics datasets. The database is expanded from the previously described Tomato Expression Database...

  10. Waste disposal in underground mines -- A technology partnership to protect the environment

    SciTech Connect

    1995-12-31

    Environmentally compatible disposal sites must be found despite all efforts to avoid and reduce the generation of dangerous waste. Deep geologic disposal provides the logical solution as ever more categories of waste are barred from long-term disposal in near-surface sites through regulation and litigation. Past mining in the US has left in its wake large volumes of suitable underground space. EPA studies and foreign practice have demonstrated deep geologic disposal in mines to be rational and viable. In the US, where much of the mined underground space is located on public lands, disposal in mines would also serve the goal of multiple use. It is only logical to return the residues of materials mined from the underground to their origin. Therefore, disposal of dangerous wastes in mined underground openings constitutes a perfect match between mining and the protection and enhancement of the environment.

  11. The fungal genome initiative and lessons learned from genome sequencing.

    PubMed

    Cuomo, Christina A; Birren, Bruce W

    2010-01-01

    The sequence of Saccharomyces cerevisiae enabled systematic genome-wide experimental approaches, demonstrating the power of having the complete genome of an organism. The rapid impact of these methods on research in yeast mobilized an effort to expand genomic resources for other fungi. The "fungal genome initiative" represents an organized genome sequencing effort to promote comparative and evolutionary studies across the fungal kingdom. Through such an approach, scientists can not only better understand specific organisms but also illuminate the shared and unique aspects of fungal biology that underlie the importance of fungi in biomedical research, health, food production, and industry. To date, assembled genomes for over 100 fungi are available in public databases, and many more sequencing projects are underway. Here, we discuss both examples of findings from comparative analysis of fungal sequences, with a specific emphasis on yeast genomes, and on the analytical approaches taken to mine fungal genomes. New sequencing methods are accelerating comparative studies of fungi by reducing the cost and difficulty of sequencing. This has driven more common use of sequencing applications, such as to study genome-wide variation in populations or to deeply profile RNA transcripts. These and further technological innovations will continue to be piloted in yeasts and other fungi, and will expand the applications of sequencing to study fungal biology. PMID:20946837

  12. Dilemmas in rationing health care services: the case for implicit rationing.

    PubMed Central

    Mechanic, D.

    1995-01-01

    With tension between the demand for health services and the cost of providing them, rationing is increasingly evident in all medical systems. Until recently, rationing was primarily through the ability to pay or achieved implicitly by doctors working within fixed budgets. Such forms of rationing are commonly alleged to be inequitable and inefficient and explicit rationing is advocated as more appropriate. Utilisation management in the United States and quasi-markets separating purchasing from provision in the United Kingdom are seen as ways of using resources more efficiently and are increasingly explicit. There is also advocacy to ration explicitly at the point of service. Mechanic reviews the implications of these developments and explains why explicit approaches are likely to focus conflict and dissatisfaction and be politically unstable. Explicit rationing is unlikely to be as equitable as its proponents argue and is likely to make dissatisfaction and perceived deprivation more salient. Despite its limitations, implicit rationing at the point of service is more sensitive to the complexity of medical decisions and the needs and personal and cultural preferences of patients. All systems use a mix of rationing devices, but the clinical allocation of services should substantially depend on the discretion of professionals informed by practice guidelines, outcomes research, and other informational aids. Images p1657-a p1659-a PMID:7795458

  13. Application and Exploration of Big Data Mining in Clinical Medicine

    PubMed Central

    Zhang, Yue; Guo, Shu-Li; Han, Li-Na; Li, Tie-Ling

    2016-01-01

    Objective: To review theories and technologies of big data mining and their application in clinical medicine. Data Sources: Literatures published in English or Chinese regarding theories and technologies of big data mining and the concrete applications of data mining technology in clinical medicine were obtained from PubMed and Chinese Hospital Knowledge Database from 1975 to 2015. Study Selection: Original articles regarding big data mining theory/technology and big data mining's application in the medical field were selected. Results: This review characterized the basic theories and technologies of big data mining including fuzzy theory, rough set theory, cloud theory, Dempster–Shafer theory, artificial neural network, genetic algorithm, inductive learning theory, Bayesian network, decision tree, pattern recognition, high-performance computing, and statistical analysis. The application of big data mining in clinical medicine was analyzed in the fields of disease risk assessment, clinical decision support, prediction of disease development, guidance of rational use of drugs, medical management, and evidence-based medicine. Conclusion: Big data mining has the potential to play an important role in clinical medicine. PMID:26960378

  14. Structured eigenvalue problems for rational gauss quadrature

    NASA Astrophysics Data System (ADS)

    Fasino, Dario; Gemignani, Luca

    2007-08-01

    The connection between Gauss quadrature rules and the algebraic eigenvalue problem for a Jacobi matrix was first exploited in the now classical paper by Golub and Welsch (Math. Comput. 23(106), 221?230, 1969). From then on many computational problems arising in the construction of (polynomial) Gauss quadrature formulas have been reduced to solving direct and inverse eigenvalue problems for symmetric tridiagonals. Over the last few years (rational) generalizations of the classical Gauss quadrature formulas have been studied, i.e., formulas integrating exactly in spaces of rational functions. This paper wants to illustrate that stable and efficient procedures based on structured numerical linear algebra techniques can also be devised for the solution of the eigenvalue problems arising in the field of rational Gauss quadrature.

  15. German mining equipment

    SciTech Connect

    Not Available

    1993-10-01

    The German mining equipment industry developed to supply machines and services to the local mining industry, i.e., coal, lignite, salt, potash, ore mining, industrial minerals, and quarrying. The sophistication and reliability of its technology also won it worldwide export markets -- which is just as well since former major domestic mining sectors such as coal and potash have declined precipitously, and others such as ore mining have all but disappeared. Today, German mining equipment suppliers focus strongly on export sales, and formerly unique German mining technologies such as continuous mining with bucket wheel excavators and conveyors for open pits, or plowing of underground coal longwalls are widely used abroad. The status of the German mining equipment industry is reviewed.

  16. Rationality: a social-epistemology perspective

    PubMed Central

    Vanpoucke, Danny E. P.; Douven, Igor

    2014-01-01

    Both in philosophy and in psychology, human rationality has traditionally been studied from an “individualistic” perspective. Recently, social epistemologists have drawn attention to the fact that epistemic interactions among agents also give rise to important questions concerning rationality. In previous work, we have used a formal model to assess the risk that a particular type of social-epistemic interactions lead agents with initially consistent belief states into inconsistent belief states. Here, we continue this work by investigating the dynamics to which these interactions may give rise in the population as a whole. PMID:24994987

  17. 4. OVERALL VIEW OF MINE SITE, SHOWING MINE CAR TRACKS, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. OVERALL VIEW OF MINE SITE, SHOWING MINE CAR TRACKS, SNOWSHEDS AND TIPPLE (LEFT BACKGROUND). VIEW TO EAST. - Park Utah Mining Company: Keetley Mine Complex, 1 mile East of U.S. 40 at Keetley, Heber City, Wasatch County, UT

  18. 1. OVERALL VIEW OF MINE SITE FROM KEETLEY MINE ROAD, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. OVERALL VIEW OF MINE SITE FROM KEETLEY MINE ROAD, SHOWING TAILING DUMP. VIEW TO WEST. - Park Utah Mining Company: Keetley Mine Complex, 1 mile East of U.S. 40 at Keetley, Heber City, Wasatch County, UT

  19. Mining lease handbook

    SciTech Connect

    Not Available

    1992-01-01

    Mining leases and similar agreements are some of the most common documents encountered by mining attorneys. The mining Lease Handbook contains a collection of mining lease clauses which have been organized and assembled for over 25 years. The clauses in this book have been coordinated and cross-referenced to enable the Handbook user to create a mining lease having a logical structure with consistent terminology throughout. In many cases, alternative clauses are included. The accompanying commentary provides insight into the use of the various clauses while pointing our pitfalls to be avoided. This Handbook is devoted primarily to mining leases, several chapters cover the subjects of options, subleases, and ancillary documents.

  20. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies

    PubMed Central

    Karamitros, Timokratis; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from <1% to 53% of amino acids in each gene exhibiting at least one substitution within the pool of samples. The UL23 gene had one of the highest genetic variabilities at 35.2% in keeping with its role in development of drug resistance. The assembly of accurate, full-length HHV-1 genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal. PMID:27309375

  1. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

    PubMed

    Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from <1% to 53% of amino acids in each gene exhibiting at least one substitution within the pool of samples. The UL23 gene had one of the highest genetic variabilities at 35.2% in keeping with its role in development of drug resistance. The assembly of accurate, full-length HHV-1 genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal. PMID:27309375

  2. Biobanks for Genomics and Genomics for Biobanks

    PubMed Central

    Ducournau, Pascal; Gourraud, Pierre-Antoine; Pontille, David

    2003-01-01

    Biobanks include biological samples and attached databases. Human biobanks occur in research, technological development and medical activities. Population genomics is highly dependent on the availability of large biobanks. Ethical issues must be considered: protecting the rights of those people whose samples or data are in biobanks (information, autonomy, confidentiality, protection of private life), assuring the non-commercial use of human body elements and the optimal use of samples and data. They balance other issues, such as protecting the rights of researchers and companies, allowing long-term use of biobanks while detailed information on future uses is not available. At the level of populations, the traditional form of informed consent is challenged. Other dimensions relate to the rights of a group as such, in addition to individual rights. Conditions of return of results and/or benefit to a population need to be defined. With ‘large-scale biobanking’ a marked trend in genomics, new societal dimensions appear, regarding communication, debate, regulation, societal control and valorization of such large biobanks. Exploring how genomics can help health sector biobanks to become more rationally constituted and exploited is an interesting perspective. For example, evaluating how genomic approaches can help in optimizing haematopoietic stem cell donor registries using new markers and high-throughput techniques to increase immunogenetic variability in such registries is a challenge currently being addressed. Ethical issues in such contexts are important, as not only individual decisions or projects are concerned, but also national policies in the international arena and organization of democratic debate about science, medicine and society. PMID:18629026

  3. Expressive Thought and Non-Rational Inquiry.

    ERIC Educational Resources Information Center

    Newton, Richard F.

    A significant problem with inquiry teaching is that too much emphasis is placed on inquiry as a logical, scientific, and rational way of knowing. Feelings and mood are rarely dealt with except in rather off-handed remarks about intuitive leaps and creative encounters. Few consider what a model of inquiry based on mood and feeling might look like.…

  4. Rational Landen transformations on mathbb{R}

    NASA Astrophysics Data System (ADS)

    Manna, Dante; Moll, Victor H.

    2007-12-01

    The Landen transformation (a,b) mapsto ( (a+b)/2,sqrt{ab} ) preserves the value of an elliptic integral, and its iteration produces the classical arithmetic-geometric mean AGM (a,b) . We present analogous transformations for rational functions integrated over the whole real line.

  5. The Assessment of Rational Thinking: IQ ? RQ

    ERIC Educational Resources Information Center

    Stanovich, Keith E.; West, Richard F.

    2014-01-01

    In this article the authors argue that distinguishing between rationality and intelligence helps explain how people can be, at the same time, intelligent and irrational (Stanovich, 2009). As such, researchers need to study separately the individual differences in cognitive skills that underlie intelligence and the individual differences in…

  6. Solving Rational Expectations Models Using Excel

    ERIC Educational Resources Information Center

    Strulik, Holger

    2004-01-01

    Simple problems of discrete-time optimal control can be solved using a standard spreadsheet software. The employed-solution method of backward iteration is intuitively understandable, does not require any programming skills, and is easy to implement so that it is suitable for classroom exercises with rational-expectations models. The author…

  7. RATIONALIZATION OF THE RURAL-URBAN MIGRATION.

    ERIC Educational Resources Information Center

    MIRENGOFF, WILLIAM

    ALTHOUGH THE PATTERN OF RURAL TO URBAN MIGRATION IS BEGINNING TO SUBSIDE, THE PROBLEMS OF EMPLOYMENT FACED BY THESE RURAL MIGRANTS ARE CONTINUING. PROGRAMS TO DEAL EFFECTIVELY WITH THEIR RELOCATION AND EMPLOYMENT HAVE NOT BEEN DEVISED, AND EFFORTS TO DATE HAVE BEEN CURATIVE RATHER THAN PREVENTIVE. A PRACTICAL WAY TO RATIONALIZE THE RURAL-URBAN…

  8. Opinion Expression as a Rational Behavior.

    ERIC Educational Resources Information Center

    Kim, Sei-Hill

    This study looks at individuals' opinion expressions as a rational behavior based on a conscious calculus of expected benefits and costs (economic analysis). The influences of "issue benefit,""opinion congruence," and "issue knowledge," as sources of benefits and costs on opinion expression were hypothesized and tested. The study also examined the…

  9. Imitation in Infancy: Rational or Motor Resonance?

    ERIC Educational Resources Information Center

    Paulus, Markus; Hunnius, Sabine; Vissers, Marlies; Bekkering, Harold

    2011-01-01

    The present study investigates the contribution of 2 mechanisms to imitation in infancy. The principle of rational action suggests that infants normatively evaluate the efficiency of observed actions. In contrast, it has been proposed that motor resonance (i.e., the mapping of others' actions onto one's own motor repertoire) plays a central role…

  10. Rational Suggestions for Pre-Marital Counseling.

    ERIC Educational Resources Information Center

    Ball, J.D.; Henning, Lawrence H.

    1981-01-01

    To demonstrate the utility of Rational Emotive Therapy in pre-marital counseling, examples of specific irrational beliefs which clinicians can use to help couples are presented. Mental health practitioners are encouraged to apply these principles to other specific irrationalities they may discover in their own work experience. (Author)

  11. Some Contemporary Rational Emotive Behavior Therapy Songs.

    ERIC Educational Resources Information Center

    Watts, Richard E.

    1996-01-01

    Presents several new rational emotive behavior therapy (REBT) songs. Claims that the songs may be used in both academic and therapeutic settings as a humorous way to address cognitive distortions or irrational beliefs. Reports that students and clients have responded favorably to these songs. (RJM)

  12. Reflections on Rational-Emotive Therapy.

    ERIC Educational Resources Information Center

    Ellis, Albert

    1993-01-01

    Reflects rational-emotive therapy (RET) in 1955 and discusses some of its recent constructivist and humanist theories and practice. Distinguishes between general RET, called synonymous with general cognitive-behavioral therapy, from preferential RET, called unique kind of cognitive therapy that partially overlaps with general cognitive-behavioral…

  13. Rational Emotive Behavior Therapy with Troubled Students.

    ERIC Educational Resources Information Center

    Zionts, Paul; Zionts, Laura

    1997-01-01

    Based on the early work of Albert Ellis, seeks to identify and challenge irrational beliefs that underlie behavior problems. Outlines concepts and methods of Rational Emotive Behavior Theory and describes the application both in counseling and as a mental health curriculum for troubled children and youth. Offers classroom techniques. (RJM)

  14. Macroeconomics after Two Decades of Rational Expectations.

    ERIC Educational Resources Information Center

    McCallum, Bennett T.

    1994-01-01

    Discusses real business cycle analysis, growth theory, and other economic concepts in the context of the rational expectations revolution in macroeconomics. Focuses on post-1982 research. Concludes that the rejuvenation of growth analysis is an encouraging development because it could lead to changes in welfare policy. (CFR)

  15. Rational Rhymes for Addressing Common Childhood Issues

    ERIC Educational Resources Information Center

    Warren, Jeffrey M.

    2011-01-01

    Music-based interventions are valuable tools counselors can use when working with children. Specific types of music-based interventions, such as songs or rhymes, can be especially pertinent in addressing the thoughts, feelings, and behaviors of children. Rational-emotive behavior therapy (REBT) provides a therapeutic framework that encourages…

  16. Rational and Mechanistic Perspectives on Reinforcement Learning

    ERIC Educational Resources Information Center

    Chater, Nick

    2009-01-01

    This special issue describes important recent developments in applying reinforcement learning models to capture neural and cognitive function. But reinforcement learning, as a theoretical framework, can apply at two very different levels of description: "mechanistic" and "rational." Reinforcement learning is often viewed in mechanistic terms--as…

  17. Mine drainage and surface mine reclamation. Volume I. Mine water and mine waste

    SciTech Connect

    Not Available

    1988-01-01

    Mine waste and mine reclamation are topics of major interest to the mining industry, the government and the general public. This publication and its companion volume are the proceedings of a conference held in Pittsburgh, April 19-21, 1988. There were nine sessions (50 papers) that dealt with the geochemistry, hydrology and problems of mine waste and mine water, especially acid mine drainage. These comprise Volume 1. The nine sessions (43 papers) that dealt with reclamation and restoration of disturbed lands, as well as related policy issues, are included in volume 2. Volume 2 also contains the ten papers that pertained to control of subsidence and mine fires at abandoned mines. Poster session presentations are, in general, represented by abstracts; these have been placed in the back of both volumes.

  18. Mine drainage and surface mine reclamation. Volume II. Mine reclamation, abandoned mine lands and policy issues

    SciTech Connect

    Not Available

    1988-01-01

    Mine waste and mine reclamation are topics of major interest to the mining industry, the government and the general public. This publication and its companion volume are the proceedings of a conference held in Pittsburgh, April 19-21, 1988. There were nine sessions (50 papers) that dealt with the geochemistry, hydrology and problems of mine waste and mine water, especially acid mine drainage. These comprise Volume 1. The nine sessions (43 papers) that dealt with reclamation and restoration of disturbed lands, as well as related policy issues, are included in volume 2. Volume 2 also contains the ten papers that pertained to control of subsidence and mine fires at abandoned mines. Poster session presentations are, in general, represented by abstracts; these have been placed in the back of both volumes.

  19. Mine waste management

    SciTech Connect

    Hutchinson, I.P.G.; Ellison, R.D.

    1992-01-01

    This book reports on mine waste management. Topics covered include: Performance review of modern mine waste management units; Mine waste management requirements; Prediction of acid generation potential; Attenuation of chemical constituents; Climatic considerations; Liner system design; Closure requirements; Heap leaching; Ground water monitoring; and Economic impact evaluation.

  20. Mountaintop mining update

    SciTech Connect

    Buchsbaum, L.

    2006-07-15

    In a bad year for the US mining industry's safety record and public image, Morehead State University hosted a public meeting titled 'Mountaintop mining, health and safety forum'. This was a balanced event, with representatives from the mining industry as well as activists from the environmental community. A full account is given of the presentations and debate at the forum. 6 photos.

  1. Data Mining for CRM

    NASA Astrophysics Data System (ADS)

    Thearling, Kurt

    Data Mining technology allows marketing organizations to better understand their customers and respond to their needs. This chapter describes how Data Mining can be combined with customer relationship management to help drive improved interactions with customers. An example showing how to use Data Mining to drive customer acquisition activities is presented.

  2. Genome size evolution: sizing mammalian genomes.

    PubMed

    Redi, C A; Capanna, E

    2012-01-01

    The study of genome size (GS) and its variation is so fascinating to the scientific community because it constitutes the link between the present-day analytical and molecular studies of the genome and the old trunk of the holistic and synthetic view of the genome. The GS of several taxa vary over a broad range and do not correlate with the complexity of the organisms (the C-value paradox). However, the biology of transposable elements has let us reach a satisfactory view of the molecular mechanisms that give rise to GS variation and novelties, providing a less perplexing view of the significance of the GS (C-enigma). The knowledge of the composition and structure of a genome is a pre-requisite for trying to understand the evolution of the main genome signature: its size. The radiation of mammals provides an approximately 180-million-year test case for theories of how GS evolves. It has been found from data-mining GS databases that GS is a useful cyto-taxonomical instrument at the level of orders/superorders, providing genomic signatures characterizing Monotremata, Marsupialia, Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. A hypothetical ancestral mammalian-like GS of 2.9-3.7 pg has been suggested. This value appears compatible with the average values calculated for the high systematic levels of the extant Monotremata (∼2.97 pg) and Marsupialia (∼4.07 pg), suggesting invasion of mobile DNA elements concurrently with the separation of the older clades of Afrotheria (∼5.5 pg) and Xenarthra (∼4.5 pg) with larger GS, leaving the Euarchontoglires (∼3.4 pg) and Laurasiatheria (∼2.8 pg) genomes with fewer transposable elements. However, the paucity of GS data (546 mammalian species sized from 5,488 living species) for species, genera, and families calls for caution. Considering that mammalian species may be vanished even before they are known, GS data are sorely needed to phenotype the effects brought about by their variation and to validate any

  3. Genome Sequence of Paenibacillus sp. Strain FJAT-28004 for the Genome Sequencing Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria

    PubMed Central

    Liu, Guo-hong; Wang, Jie-ping; Che, Jian-Mei; Zhu, Yu-Jing; Chen, Qian-Qian; Ruan, Chuan-Qing

    2015-01-01

    Paenibacillus sp. strain FJAT-28004 is a spore forming and strictly aerobic bacterium. Here, we report the draft 7,479,858-bp genome sequence of Paenibacillus sp. FJAT-28004, which will provide useful information for genomic taxonomy and phylogenomics of the genus Paenibacillus, as well as for the functional gene mining and application of Paenibacillus sp. FJAT-28004. PMID:26494657

  4. Data Mining Model Comparison

    NASA Astrophysics Data System (ADS)

    Giudici, Paolo

    The aim of this contribution is to illustrate the role of statistical models and, more generally, of statistics, in choosing a Data Mining model. After a preliminary introduction on the distinction between Data Mining and statistics, we will focus on the issue of how to choose a Data Mining methodology. This well illustrates how statistical thinking can bring real added value to a Data Mining analysis, as otherwise it becomes rather difficult to make a reasoned choice. In the third part of the paper we will present, by means of a case study in credit risk management, how Data Mining and statistics can profitably interact.

  5. Mined area detection overview

    NASA Astrophysics Data System (ADS)

    Burch, Ian A.; Deas, Robert M.; Port, Daniel M.

    2002-08-01

    An overview of the progress on the UK MOD Applied Research Program for Land Mine Detection. The Defense Science and Technology Laboratory (Dstl) carries out and manages the whole of the UK MOD's Mined Area Detection Applied Research Program both within its own laboratories and in partnership with industrial and academic research organizations. This paper will address two specific areas of Applied Research: hand held mine detection and vehicle mounted mine detection in support of the Mine Detection Neutralization and Route Marking System which started in April 1997. Both are multi-sensor systems, incorporating between them metal detection, ground penetrating radar, nuclear quadrupole resonance, ultra-wideband radar, and polarized thermal imaging.

  6. Cognitive Distance, Absorptive Capacity and Group Rationality: A Simulation Study

    PubMed Central

    Curşeu, Petru Lucian; Krehel, Oleh; Evers, Joep H. M.; Muntean, Adrian

    2014-01-01

    We report the results of a simulation study in which we explore the joint effect of group absorptive capacity (as the average individual rationality of the group members) and cognitive distance (as the distance between the most rational group member and the rest of the group) on the emergence of collective rationality in groups. We start from empirical results reported in the literature on group rationality as collective group level competence and use data on real-life groups of four and five to validate a mathematical model. We then use this mathematical model to predict group level scores from a variety of possible group configurations (varying both in cognitive distance and average individual rationality). Our results show that both group competence and cognitive distance are necessary conditions for emergent group rationality. Group configurations, in which the groups become more rational than the most rational group member, are groups scoring low on cognitive distance and scoring high on absorptive capacity. PMID:25314132

  7. Development of the Rational Behavior Inventory: Initial Validity and Reliability

    ERIC Educational Resources Information Center

    Shorkey, Clayton T.; Whiteman, Victor L.

    1977-01-01

    The results of initial validity and reliability studies on the Rational Behavior Inventory are presented. The instrument was developed to be used for assessment, treatment planning, and evaluation of clients by counselors who use Rational Emotive Therapy. (Author/JKS)

  8. Rationally Irrational: The Case of Sexual Burglary.

    PubMed

    Pedneault, Amelie; Beauregard, Eric; Harris, Danielle A; Knight, Raymond A

    2015-08-01

    The present study investigated rationality in sexually motivated burglaries. Specifically, we analyzed the situational cues identified by sexual burglars in their target selection. The research project investigated 224 individual incidents of residential burglary with apparent sexual motivations. Situational characteristics of the incidents were recorded and analyzed using forward sequential regressions. Results indicated that most sexually motivated burglaries occurred in occupied residences with deficient physical guardianship, when the victim was alone. Violence, theft, penetration, and fetishism were found to be committed in circumstances that increased the benefits and lowered the risks. Results showed that sexual burglary is rational in nature-sexual burglars chose residences that were easy to break into. We found little support for the premise that such opportunities arose while carrying out regular burglaries. Instead, the data indicated that sexual burglars acted opportunistically on situational cues that are markedly dissimilar to those of regular burglars. PMID:24469848

  9. Rational orbits around charged black holes

    SciTech Connect

    Misra, Vedant; Levin, Janna

    2010-10-15

    We show that all eccentric timelike orbits in Reissner-Nordstroem spacetime can be classified using a taxonomy that draws upon an isomorphism between periodic orbits and the set of rational numbers. By virtue of the fact that the rationals are dense, the taxonomy can be used to approximate aperiodic orbits with periodic orbits. This may help reduce computational overhead for calculations in gravitational wave astronomy. Our dynamical systems approach enables us to study orbits for both charged and uncharged particles in spite of the fact that charged particle orbits around a charged black hole do not admit a simple one-dimensional effective potential description. Finally, we show that comparing periodic orbits in the Reissner-Nordstroem and Schwarzschild geometries enables us to distinguish charged and uncharged spacetimes by looking only at the orbital dynamics.

  10. Moral Credentialing and the Rationalization of Misconduct

    PubMed Central

    Brown, Ryan P.; Tamborski, Michael; Wang, Xiaoqian; Barnes, Collin D.; Mumford, Michael D.; Connelly, Shane; Devenport, Lynn D.

    2010-01-01

    Recent studies lead to the paradoxical conclusion that the act of affirming one’s egalitarian or pro-social values and virtues might subsequently facilitate prejudiced or self-serving behavior, an effect previously referred to as “moral credentialing.” The present study extends this paradox to the domain of academic misconduct and investigates the hypothesis that such an effect might be limited by the extent to which misbehavior is rationalizable. Using a paradigm designed to investigate deliberative and rationalized forms of cheating (von Hippel, Lakin, & Shakarchi, 2005), we found that when participants had credentialed themselves (versus a non-close acquaintance) via a set of hypothetical moral dilemmas, they were more likely to cheat on a subsequent math task, but only if cheating was highly rationalizable. When cheating was difficult to rationalize, moral credentialing had almost no impact on cheating. PMID:21503267

  11. Data mining in radiology

    PubMed Central

    Kharat, Amit T; Singh, Amarjit; Kulkarni, Vilas M; Shah, Digish

    2014-01-01

    Data mining facilitates the study of radiology data in various dimensions. It converts large patient image and text datasets into useful information that helps in improving patient care and provides informative reports. Data mining technology analyzes data within the Radiology Information System and Hospital Information System using specialized software which assesses relationships and agreement in available information. By using similar data analysis tools, radiologists can make informed decisions and predict the future outcome of a particular imaging finding. Data, information and knowledge are the components of data mining. Classes, Clusters, Associations, Sequential patterns, Classification, Prediction and Decision tree are the various types of data mining. Data mining has the potential to make delivery of health care affordable and ensure that the best imaging practices are followed. It is a tool for academic research. Data mining is considered to be ethically neutral, however concerns regarding privacy and legality exists which need to be addressed to ensure success of data mining. PMID:25024513

  12. Data mining in radiology.

    PubMed

    Kharat, Amit T; Singh, Amarjit; Kulkarni, Vilas M; Shah, Digish

    2014-04-01

    Data mining facilitates the study of radiology data in various dimensions. It converts large patient image and text datasets into useful information that helps in improving patient care and provides informative reports. Data mining technology analyzes data within the Radiology Information System and Hospital Information System using specialized software which assesses relationships and agreement in available information. By using similar data analysis tools, radiologists can make informed decisions and predict the future outcome of a particular imaging finding. Data, information and knowledge are the components of data mining. Classes, Clusters, Associations, Sequential patterns, Classification, Prediction and Decision tree are the various types of data mining. Data mining has the potential to make delivery of health care affordable and ensure that the best imaging practices are followed. It is a tool for academic research. Data mining is considered to be ethically neutral, however concerns regarding privacy and legality exists which need to be addressed to ensure success of data mining. PMID:25024513

  13. [What did bachelard mean by "applied rationalism" ?].

    PubMed

    Tiles, Mary

    2013-01-01

    Bachelard was concerned with the processes whereby scientific knowledge is acquired, including the activity of knowing subjects. He did not equate reasoning with logic but rather argued that reasoning resulted from the use of mathematics in organizing both thought and experimental practices, which is why he conceived science as applied mathematics. This had material and technical implications, for Bachelard was concerned with the element of reason inherent in technical materialism as well as the concrete reality inherent in applied rationalism. PMID:24091650

  14. Suicide: Rationality and Responsibility for Life

    PubMed Central

    Ho, Angela Onkay

    2014-01-01

    Objectives: Death by suicide is widely held as an undesirable outcome. Most Western countries place emphasis on patient autonomy, a concept of controversy in relation to suicide. This paper explores the tensions between patients’ rights and many societies’ overarching desire to prevent suicide, while clarifying the relations between mental disorders, mental capacity, and rational suicide. Methods: A literature search was conducted using search terms of suicide and ethics in the PubMed and LexisNexis Academic databases. Article titles and abstracts were reviewed and deemed relevant if the paper addressed topics of rational suicide, patient autonomy or rights, or responsibility for life. Further articles were found from reference lists and by suggestion from preliminary reviewers of this paper. Results: Suicidal behaviour in a person cannot be reliably predicted, yet various associations and organizations have developed standards of care for managing patients exhibiting suicidal behaviour. The responsibility for preventing suicide tends to be placed on the treating clinician. In cases where a person is capable of making treatment decisions—uninfluenced by any mental disorder—there is growing interest in the concept of rational suicide. Conclusions: There is much debate about whether suicide can ever be rational. Designating suicide as an undesirable event that should never occur raises the debate of who is responsible for one’s life and runs the risk of erroneously attributing blame for suicide. While upholding patient rights of autonomy in psychiatric care is laudable, cases of suicidality warrant a delicate consideration of clinical judgment, duty of care, and legal obligations. PMID:24881162

  15. Rational design of nanomaterials for water treatment

    NASA Astrophysics Data System (ADS)

    Li, Renyuan; Zhang, Lianbin; Wang, Peng

    2015-10-01

    The ever-increasing human demand for safe and clean water is gradually pushing conventional water treatment technologies to their limits. It is now a popular perception that the solutions to the existing and future water challenges will hinge upon further developments in nanomaterial sciences. The concept of rational design emphasizes on `design-for-purpose' and it necessitates a scientifically clear problem definition to initiate the nanomaterial design. The field of rational design of nanomaterials for water treatment has experienced a significant growth in the past decade and is poised to make its contribution in creating advanced next-generation water treatment technologies in the years to come. Within the water treatment context, this review offers a comprehensive and in-depth overview of the latest progress in rational design, synthesis and applications of nanomaterials in adsorption, chemical oxidation and reduction reactions, membrane-based separation, oil-water separation, and synergistic multifunctional all-in-one nanomaterials/nanodevices. Special attention is paid to the chemical concepts related to nanomaterial design throughout the review.

  16. Rational design of nanomaterials for water treatment.

    PubMed

    Li, Renyuan; Zhang, Lianbin; Wang, Peng

    2015-11-01

    The ever-increasing human demand for safe and clean water is gradually pushing conventional water treatment technologies to their limits. It is now a popular perception that the solutions to the existing and future water challenges will hinge upon further developments in nanomaterial sciences. The concept of rational design emphasizes on 'design-for-purpose' and it necessitates a scientifically clear problem definition to initiate the nanomaterial design. The field of rational design of nanomaterials for water treatment has experienced a significant growth in the past decade and is poised to make its contribution in creating advanced next-generation water treatment technologies in the years to come. Within the water treatment context, this review offers a comprehensive and in-depth overview of the latest progress in rational design, synthesis and applications of nanomaterials in adsorption, chemical oxidation and reduction reactions, membrane-based separation, oil-water separation, and synergistic multifunctional all-in-one nanomaterials/nanodevices. Special attention is paid to the chemical concepts related to nanomaterial design throughout the review. PMID:26437738

  17. Promoting rational prescribing: an international perspective.

    PubMed Central

    Hogerzeil, H V

    1995-01-01

    Irrational prescribing is a global problem. Rational prescribing cannot be defined without a method of measurement and a reference standard. The former is now available but the latter needs further development. Proven effective interventions to promote rational prescribing in developed countries are treatment protocols based on wide consultation and consensus, properly introduced and with a possibility of feedback; face-to-face education focussed on a particular prescribing problem in selected individuals; structured order forms; and focussed educational campaigns. Essential drugs lists are probably effective when based on consensus and used within a comprehensive educational programme. Printed materials alone are not effective. In most cases the usefulness of such strategies in developing countries has not been proven and should be studied. Medical education in clinical pharmacology and pharmacotherapy should be based on the practical needs of future prescribes, should include the principles of rational therapeutics and problem solving, and should immunize the students against the influences they are likely to encounter in their professional life, such as patient pressure, drug promotion and irrational prescribing by peers. Within the scope of a national formulary, specialist departments in teaching hospitals should define prescribing policies as the basis for prescribing, teaching, examinations and medical audit. PMID:7756093

  18. Linear parameter estimation of rational biokinetic functions.

    PubMed

    Doeswijk, T G; Keesman, K J

    2009-01-01

    For rational biokinetic functions such as the Michaelis-Menten equation, in general, a nonlinear least-squares method is a good estimator. However, a major drawback of a nonlinear least-squares estimator is that it can end up in a local minimum. Rearranging and linearizing rational biokinetic functions for parameter estimation is common practice (e.g. Lineweaver-Burk linearization). By rearranging, however, the error is distorted. In addition, the rearranged model frequently leads to a so-called 'errors-in-variables' estimation problem. Applying the ordinary least squares (OLS) method to the linearly reparameterized function ensures a global minimum, but its estimates become biased if the regression variables contain errors and thus bias compensation is needed. Therefore, in this paper, a bias compensated total least squares (CTLS) method, which as OLS is a direct method, is proposed to solve the estimation problem. The applicability of a general linear reparameterization procedure and the advances of CTLS over ordinary least squares and nonlinear least squares approaches are shown by two simulation examples. The examples contain Michaelis-Menten kinetics and enzyme kinetics with substrate inhibition. Furthermore, CTLS is demonstrated with real data of an activated sludge experiment. It is concluded that for rational biokinetic models CTLS is a powerful alternative to the existing least-squares methods. PMID:19004464

  19. The Use of Drug Discovery Tools in Rational Organometallic Catalyst Design

    SciTech Connect

    Sumpter, Bobby G; Drummond, Michael L

    2007-01-01

    A computational procedure is detailed where techniques common in the drug discovery process - 2D- and 3D-Quantitative Structure-Activity Relationships (QSAR) - are applied to rationalize the catalytic activity of a synthetically flexible, Ti-N=P ethylene polymerization catalyst system. Once models relating molecular properties to catalyst activity are built with the two QSAR approaches, two database mining approaches are used to select a small number of ligands from a larger database that are likely to produce catalysts with high activity when grafted onto the Ti-N=P framework.. The software employed throughout this work is freely available, easy to use, and was applied in a "black box" approach, to highlight areas where the drug discovery tools, designed to address organic molecules, have difficulty in addressing issues arising from the presence of a metal atom. In general, 3D-QSAR offers an efficient way to screen new potential ligands and separate those likely to lead to poor catalysts from those that are likely to contribute to highly active catalysts. The results for 2D-QSAR appear to be quantitatively unreliable, likely due to the presence of a metal atom; nonetheless, there is evidence that qualitative predictions from different models may be reliable. Pitfalls in the database mining techniques are identified, none of which are insurmountable. The lessons learned about the potential uses and drawbacks of the techniques described herein are readily applicable to other catalyst frameworks, thereby enabling a rational approach to catalyst improvement and design.

  20. Farm animal genomics and informatics: an update

    PubMed Central

    Fadiel, Ahmed; Anidi, Ifeanyi; Eichenbaum, Kenneth D.

    2005-01-01

    Farm animal genomics is of interest to a wide audience of researchers because of the utility derived from understanding how genomics and proteomics function in various organisms. Applications such as xenotransplantation, increased livestock productivity, bioengineering new materials, products and even fabrics are several reasons for thriving farm animal genome activity. Currently mined in rapidly growing data warehouses, completed genomes of chicken, fish and cows are available but are largely stored in decentralized data repositories. In this paper, we provide an informatics primer on farm animal bioinformatics and genome project resources which drive attention to the most recent advances in the field. We hope to provide individuals in biotechnology and in the farming industry with information on resources and updates concerning farm animal genome projects. PMID:16275782

  1. Logical and Psychological Aspects of Rational Number Pedagogical Reasoning.

    ERIC Educational Resources Information Center

    Orton, Robert E.; And Others

    1995-01-01

    Synthesizes research on content knowledge of rational numbers, the learning of rational number order and equivalence concepts, and teachers' pedagogical reasoning about these concepts. Uses teachers' descriptions of how a hypothetical student would understand rational numbers to sketch a formative model of pedagogical reasoning. (16 references)…

  2. Cognitive Rationality and Its Logic-Mathematical Language

    ERIC Educational Resources Information Center

    Masalova, Svetlana

    2012-01-01

    The article deals with the cognitive (flexible) rationality, combining rational and irrational moments of the scientific search of the cognizing subject. Linguo-cognitive model of the concept as the flexible regulative rationality reveals the activity of the cognitive processes and the mentality of the epistemological-ontic subject, its leading…

  3. Rational Analyses of Information Foraging on the Web

    ERIC Educational Resources Information Center

    Pirolli, Peter

    2005-01-01

    This article describes rational analyses and cognitive models of Web users developed within information foraging theory. This is done by following the rational analysis methodology of (a) characterizing the problems posed by the environment, (b) developing rational analyses of behavioral solutions to those problems, and (c) developing cognitive…

  4. Design and implementation of the cacao genome database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Cacao Genome Database (CGD, www.cacaogenomedb.org) is being developed to provide a comprehensive data mining resource of genomic, genetic and breeding data for Theobroma cacao. Designed using Chado and a collection of Drupal modules, known as Tripal, CGD currently contains the genetically anchor...

  5. F-theory and all things rational: surveying U(1) symmetries with rational sections

    NASA Astrophysics Data System (ADS)

    Lawrie, Craig; Schäfer-Nameki, Sakura; Wong, Jin-Mann

    2015-09-01

    We study elliptic fibrations for F-theory compactifications realizing 4d and 6d supersymmetric gauge theories with abelian gauge factors. In the fibration these U(1) symmetries are realized in terms of additional rational section. We obtain a universal characterization of all the possible U(1) charges of matter fields by determining the corresponding codimension two fibers with rational sections. In view of modelling supersymmetric Grand Unified Theories, one of the main examples that we analyze are U(1) symmetries for SU(5) gauge theories with overline{5} and 10 matter. We use a combination of constraints on the normal bundle of rational curves in Calabi-Yau three- and four-folds, as well as the splitting of rational curves in the fibers in codimension two, to determine the possible configurations of smooth rational sections. This analysis straightforwardly generalizes to multiple U(1)s. We study the flops of such fibers, as well as some of the Yukawa couplings in codimension three. Furthermore, we carry out a universal study of the U(1)-charged GUT singlets, including their KK-charges, and determine all realizations of singlet fibers. By giving vacuum expectation values to these singlets, we propose a systematic way to analyze the Higgsing of U(1)s to discrete gauge symmetries in F-theory.

  6. Allele mining and enhanced genetic recombination for rice breeding.

    PubMed

    Leung, Hei; Raghavan, Chitra; Zhou, Bo; Oliva, Ricardo; Choi, Il Ryong; Lacorte, Vanica; Jubay, Mona Liza; Cruz, Casiana Vera; Gregorio, Glenn; Singh, Rakesh Kumar; Ulat, Victor Jun; Borja, Frances Nikki; Mauleon, Ramil; Alexandrov, Nickolai N; McNally, Kenneth L; Sackville Hamilton, Ruaraidh

    2015-12-01

    Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources. PMID:26606925

  7. What Information Theory Says about Bounded Rational Best Response

    NASA Technical Reports Server (NTRS)

    Wolpert, David H.

    2005-01-01

    Probability Collectives (PC) provides the information-theoretic extension of conventional full-rationality game theory to bounded rational games. Here an explicit solution to the equations giving the bounded rationality equilibrium of a game is presented. Then PC is used to investigate games in which the players use bounded rational best-response strategies. Next it is shown that in the continuum-time limit, bounded rational best response games result in a variant of the replicator dynamics of evolutionary game theory. It is then shown that for team (shared-payoff) games, this variant of replicator dynamics is identical to Newton-Raphson iterative optimization of the shared utility function.

  8. Planning of the reforestation at abandoned coal mines using GIS

    NASA Astrophysics Data System (ADS)

    Choi, Y.; Oh, S.; Park, H.; Kwon, H.

    2009-12-01

    This study presents a prototype of decision support system for planning the reforestation at abandoned coal mines. The characteristics of deforested zone due to mine development were analyzed and categorized to define the schema of GIS database. Multiple criteria (i.e. forest-climate zone, mining method, visibility, managerial condition, slope gradient, reforestation purpose) were considered to classify the deforested zone and to assign unique IDs to the key index fields in tables. ArcMap, ArcObjects and Visual Basic.NET were used to implement the system. The application to the Samcheok coal block in Korea shows that the system could present a rational solution to select suitable trees for the reforestation and can also provide cost evaluation tools to support the environmental planning work.

  9. Collaborative Data Mining

    NASA Astrophysics Data System (ADS)

    Moyle, Steve

    Collaborative Data Mining is a setting where the Data Mining effort is distributed to multiple collaborating agents - human or software. The objective of the collaborative Data Mining effort is to produce solutions to the tackled Data Mining problem which are considered better by some metric, with respect to those solutions that would have been achieved by individual, non-collaborating agents. The solutions require evaluation, comparison, and approaches for combination. Collaboration requires communication, and implies some form of community. The human form of collaboration is a social task. Organizing communities in an effective manner is non-trivial and often requires well defined roles and processes. Data Mining, too, benefits from a standard process. This chapter explores the standard Data Mining process CRISP-DM utilized in a collaborative setting.

  10. Research on bounded rationality of fuzzy choice functions.

    PubMed

    Wu, Xinlin; Zhao, Yong

    2014-01-01

    The rationality of a fuzzy choice function is a hot research topic in the study of fuzzy choice functions. In this paper, two common fuzzy sets are studied and analyzed in the framework of the Banerjee choice function. The complete rationality and bounded rationality of fuzzy choice functions are defined based on the two fuzzy sets. An assumption is presented to study the fuzzy choice function, and especially the fuzzy choice function with bounded rationality is studied combined with some rationality conditions. Results show that the fuzzy choice function with bounded rationality also satisfies some important rationality conditions, but not vice versa. The research gives supplements to the investigation in the framework of the Banerjee choice function. PMID:24782677

  11. Implementation of Paste Backfill Mining Technology in Chinese Coal Mines

    PubMed Central

    Chang, Qingliang; Zhou, Huaqiang; Bai, Jianbiao

    2014-01-01

    Implementation of clean mining technology at coal mines is crucial to protect the environment and maintain balance among energy resources, consumption, and ecology. After reviewing present coal clean mining technology, we introduce the technology principles and technological process of paste backfill mining in coal mines and discuss the components and features of backfill materials, the constitution of the backfill system, and the backfill process. Specific implementation of this technology and its application are analyzed for paste backfill mining in Daizhuang Coal Mine; a practical implementation shows that paste backfill mining can improve the safety and excavation rate of coal mining, which can effectively resolve surface subsidence problems caused by underground mining activities, by utilizing solid waste such as coal gangues as a resource. Therefore, paste backfill mining is an effective clean coal mining technology, which has widespread application. PMID:25258737

  12. Implementation of paste backfill mining technology in Chinese coal mines.

    PubMed

    Chang, Qingliang; Chen, Jianhang; Zhou, Huaqiang; Bai, Jianbiao

    2014-01-01

    Implementation of clean mining technology at coal mines is crucial to protect the environment and maintain balance among energy resources, consumption, and ecology. After reviewing present coal clean mining technology, we introduce the technology principles and technological process of paste backfill mining in coal mines and discuss the components and features of backfill materials, the constitution of the backfill system, and the backfill process. Specific implementation of this technology and its application are analyzed for paste backfill mining in Daizhuang Coal Mine; a practical implementation shows that paste backfill mining can improve the safety and excavation rate of coal mining, which can effectively resolve surface subsidence problems caused by underground mining activities, by utilizing solid waste such as coal gangues as a resource. Therefore, paste backfill mining is an effective clean coal mining technology, which has widespread application. PMID:25258737

  13. Mining agreements III

    SciTech Connect

    Not Available

    1991-01-01

    This book cover the following: Forms of mining agreements; Preliminary letter agreements; Acquisition of mineral interests involving securities; Partnership tax treatment in mining agreements; Non-tax consequences of partnerships under state law; Protection against joint venturers' liabilities; Joint venture decision making; Mining royalties; Commingling and unitization provisions; Indemnification and insurance provisions; Area of interest provision; Dispute resolution; and Non-participation and default provisions.

  14. Genome walking.

    PubMed

    Shapter, Frances M; Waters, Daniel L E

    2014-01-01

    Genome walking is a method for determining the DNA sequence of unknown genomic regions flanking a region of known DNA sequence. The Genome walking has the potential to capture 6-7 kb of sequence in a single round. Ideal for identifying gene promoter regions where only the coding region. Genome walking also has significant utility for capturing homologous genes in new species when there are areas in the target gene with strong sequence conservation to the characterized species. The increasing use of next-generation sequencing technologies will see the principles of genome walking adapted to in silico methods. However, for smaller projects, PCR-based genome walking will remain an efficient method of characterizing unknown flanking sequence. PMID:24243201

  15. [The impact of ethical and moral competence in decision making on rationalism and rationing nursing interventions].

    PubMed

    Schwerdt, R

    2005-08-01

    The intraprofessional discourse about economical aspects in nursing from an ethical point of view has not taken place yet. To cope with the increasing restriction of resources, some preconditions have to be met: It is necessary to communicate issues in rationalizing and rationing in nursing openly. Person-oriented criteria in the nursing process indicate a high level of competence and user-oriented quality in nursing care. But nursing professionals do not decide in favor or against resources to perform this task on a high or poor quality level. Democratic decision-making on providing nursing services depends on a continuous societal discourse about allocation criteria. PMID:16133753

  16. A baseline lunar mine

    NASA Technical Reports Server (NTRS)

    Gertsch, Richard E.

    1992-01-01

    A models lunar mining method is proposed that illustrates the problems to be expected in lunar mining and how they might be solved. While the method is quite feasible, it is, more importantly, a useful baseline system against which to test other, possible better, methods. Our study group proposed the slusher to stimulate discussion of how a lunar mining operation might be successfully accomplished. Critics of the slusher system were invited to propose better methods. The group noted that while nonterrestrial mining has been a vital part of past space manufacturing proposals, no one has proposed a lunar mining system in any real detail. The group considered it essential that the design of actual, workable, and specific lunar mining methods begin immediately. Based on an earlier proposal, the method is a three-drum slusher, also known as a cable-operated drag scraper. Its terrestrial application is quite limited, as it is relatively inefficient and inflexible. The method usually finds use in underwater mining from the shore and in moving small amounts of ore underground. When lunar mining scales up, the lunarized slusher will be replaced by more efficient, high-volume methods. Other aspects of lunar mining are discussed.

  17. Canada's largest mining scheme

    SciTech Connect

    Not Available

    1984-05-01

    A large coal mining development in Canada's British Columbia, is opening up the wilderness in the northeastern part of that province. North East Coal Development, two open-pit mines operated by Quintette Coal Ltd., and Teck Corporation, both Vancouver-based mining companies, has started to ship to a group of Japanese steel companies 6,500,000 tons annually of metallurgical and additional quantities of thermal coal. To open this wilderness, some 80 miles southwest of Dawson Creek, and to develop the two surface mines, processing plants, and associated facilities involved several massive multimillion-dollar projects. These projects are discussed.

  18. Craniofacial reconstruction using rational cubic ball curves.

    PubMed

    Majeed, Abdul; Mt Piah, Abd Rahni; Gobithaasan, R U; Yahya, Zainor Ridzuan

    2015-01-01

    This paper proposes the reconstruction of craniofacial fracture using rational cubic Ball curve. The idea of choosing Ball curve is based on its robustness of computing efficiency over Bezier curve. The main steps are conversion of Digital Imaging and Communications in Medicine (Dicom) images to binary images, boundary extraction and corner point detection, Ball curve fitting with genetic algorithm and final solution conversion to Dicom format. The last section illustrates a real case of craniofacial reconstruction using the proposed method which clearly indicates the applicability of this method. A Graphical User Interface (GUI) has also been developed for practical application. PMID:25880632

  19. Rational instability in the natural coalition forming

    NASA Astrophysics Data System (ADS)

    Vinogradova, Galina; Galam, Serge

    2013-12-01

    The work aims to investigate a paradigm of instability in coalition forming among countries, using a model inspired from Statistical Physics. The instability is a consequence of decentralized maximization of the individual benefits where contradictory associations into coalitions occur due to independent evolution of pairwise propensity bonds. In contrast to the existing literature we analyze the phenomena within a long horizon rationality of actors. This allows to explore the complex behaviors and phenomena such as instability, infinite cycling and non-optimal stability. Along with the formal implementation, we illustrate the phenomena in a multi-thread simulation created for this aim, and provide analysis of several real cases including the Eurozone.

  20. Craniofacial Reconstruction Using Rational Cubic Ball Curves

    PubMed Central

    Majeed, Abdul; Mt Piah, Abd Rahni; Gobithaasan, R. U.; Yahya, Zainor Ridzuan

    2015-01-01

    This paper proposes the reconstruction of craniofacial fracture using rational cubic Ball curve. The idea of choosing Ball curve is based on its robustness of computing efficiency over Bezier curve. The main steps are conversion of Digital Imaging and Communications in Medicine (Dicom) images to binary images, boundary extraction and corner point detection, Ball curve fitting with genetic algorithm and final solution conversion to Dicom format. The last section illustrates a real case of craniofacial reconstruction using the proposed method which clearly indicates the applicability of this method. A Graphical User Interface (GUI) has also been developed for practical application. PMID:25880632

  1. Improving Learning Performance Through Rational Resource Allocation

    NASA Technical Reports Server (NTRS)

    Gratch, J.; Chien, S.; DeJong, G.

    1994-01-01

    This article shows how rational analysis can be used to minimize learning cost for a general class of statistical learning problems. We discuss the factors that influence learning cost and show that the problem of efficient learning can be cast as a resource optimization problem. Solutions found in this way can be significantly more efficient than the best solutions that do not account for these factors. We introduce a heuristic learning algorithm that approximately solves this optimization problem and document its performance improvements on synthetic and real-world problems.

  2. Bioinformatics and genomic medicine.

    PubMed

    Kim, Ju Han

    2002-01-01

    Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational science. Clinical informatics has long developed methodologies to improve biomedical research and clinical care by integrating experimental and clinical information systems. The informatics revolution in both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics. Postgenome informatics, powered by high-throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever, in much the same way that biochemistry did a generation ago. This paper describes how these technologies will impact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics and proteomics. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine-learning algorithms are discussed. Use of integrative biochip informatics technologies, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and the integrated management of biomolecular databases, are also discussed. PMID:12544491

  3. Prophage Genomics

    PubMed Central

    Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brüssow, Harald

    2003-01-01

    The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria. PMID:12794192

  4. Implementation of a Flexible Tool for Automated Literature-Mining and Knowledgebase Development (DevToxMine)

    EPA Science Inventory

    Deriving novel relationships from the scientific literature is an important adjunct to datamining activities for complex datasets in genomics and high-throughput screening activities. Automated text-mining algorithms can be used to extract relevant content from the literature and...

  5. Success stories in genomic medicine from resource-limited countries.

    PubMed

    Mitropoulos, Konstantinos; Al Jaibeji, Hayat; Forero, Diego A; Laissue, Paul; Wonkam, Ambroise; Lopez-Correa, Catalina; Mohamed, Zahurin; Chantratita, Wasun; Lee, Ming Ta Michael; Llerena, Adrian; Brand, Angela; Ali, Bassam R; Patrinos, George P

    2015-01-01

    In recent years, the translation of genomic discoveries into mainstream medical practice and public health has gained momentum, facilitated by the advent of new technologies. However, there are often major discrepancies in the pace of implementation of genomic medicine between developed and developing/resource-limited countries. The main reason does not only lie in the limitation of resources but also in the slow pace of adoption of the new findings and the poor understanding of the potential that this new discipline offers to rationalize medical diagnosis and treatment. Here, we present and critically discuss examples from the successful implementation of genomic medicine in resource-limited countries, focusing on pharmacogenomics, genome informatics, and public health genomics, emphasizing in the latter case genomic education, stakeholder analysis, and economics in pharmacogenomics. These examples can be considered as model cases and be readily replicated for the wide implementation of pharmacogenomics and genomic medicine in other resource-limited environments. PMID:26081768

  6. Rational development of radiopharmaceuticals for HIV-1.

    PubMed

    Lau, Chuen-Yen; Maldarelli, Frank; Eckelman, William C; Neumann, Ronald D

    2014-04-01

    The global battle against HIV-1 would benefit from a sensitive and specific radiopharmaceutical to localize HIV-infected cells. Ideally, this probe would be able to identify latently infected host cells containing replication competent HIV sequences. Clinical and research applications would include assessment of reservoirs, informing clinical management by facilitating assessment of burden of infection in different compartments, monitoring disease progression and monitoring response to therapy. A "rational" development approach could facilitate efficient identification of an appropriate targeted radiopharmaceutical. Rational development starts with understanding characteristics of the disease that can be effectively targeted and then engineering radiopharmaceuticals to hone in on an appropriate target, which in the case of HIV-1 (HIV) might be an HIV-specific product on or in the host cell, a differentially expressed gene product, an integrated DNA sequence specific enzymatic activity, part of the inflammatory response, or a combination of these. This is different from the current approach that starts with a radiopharmaceutical for a target associated with a disease, mostly from autopsy studies, without a strong rationale for the potential to impact patient care. At present, no targeted therapies are available for HIV latency, although a number of approaches are under study. Here we discuss requirements for a radiopharmaceutical useful in strategies targeting persistently infected cells. The radiopharmaceutical for HIV should be developed based on HIV biology, studied in an animal model and then in humans, and ultimately used in clinical and research settings. PMID:24607432

  7. Rational Combinations of Targeted Agents in AML

    PubMed Central

    Bose, Prithviraj; Grant, Steven

    2015-01-01

    Despite modest improvements in survival over the last several decades, the treatment of AML continues to present a formidable challenge. Most patients are elderly, and these individuals, as well as those with secondary, therapy-related, or relapsed/refractory AML, are particularly difficult to treat, owing to both aggressive disease biology and the high toxicity of current chemotherapeutic regimens. It has become increasingly apparent in recent years that coordinated interruption of cooperative survival signaling pathways in malignant cells is necessary for optimal therapeutic results. The modest efficacy of monotherapy with both cytotoxic and targeted agents in AML testifies to this. As the complex biology of AML continues to be elucidated, many “synthetic lethal” strategies involving rational combinations of targeted agents have been developed. Unfortunately, relatively few of these have been tested clinically, although there is growing interest in this area. In this article, the preclinical and, where available, clinical data on some of the most promising rational combinations of targeted agents in AML are summarized. While new molecules should continue to be combined with conventional genotoxic drugs of proven efficacy, there is perhaps a need to rethink traditional philosophies of clinical trial development and regulatory approval with a focus on mechanism-based, synergistic strategies. PMID:26113989

  8. Strategies in the rational drug design.

    PubMed

    Mavromoustakos, T; Durdagi, S; Koukoulitsa, C; Simcic, M; Papadopoulos, M G; Hodoscek, M; Grdadolnik, S Golic

    2011-01-01

    Rational design is applied in the discovery of novel lead drugs. Its rapid development is mainly attributed to the tremendous advancements in the computer science, statistics, molecular biology, biophysics, biochemistry, medicinal chemistry, pharmacokinetics and pharmacodynamics experienced in the last few decades. The promising feature that characterizes the application of rational drug design is that it uses for developing potential leads in drug discovery all known theoretical and experimental knowledge of the system under study. The utilization of the knowledge of the molecular basis of the system ultimately aims to reduce human power cost, time saving and laboratory expenses in the drug discovery. In this review paper various strategies applied for systems which include: (i) absence of knowledge of the receptor active site; (ii) the knowledge of a homology model of a receptor, (iii) the knowledge of the experimentally determined (i.e. X-ray crystallography, NMR spectroscopy) coordinates of the active site of the protein in absence and (iv) the presence of the ligand will be analyzed. PMID:21568895

  9. Of Models and Machines: Implementing Bounded Rationality.

    PubMed

    Dick, Stephanie

    2015-09-01

    This essay explores the early history of Herbert Simon's principle of bounded rationality in the context of his Artificial Intelligence research in the mid 1950s. It focuses in particular on how Simon and his colleagues at the RAND Corporation translated a model of human reasoning into a computer program, the Logic Theory Machine. They were motivated by a belief that computers and minds were the same kind of thing--namely, information-processing systems. The Logic Theory Machine program was a model of how people solved problems in elementary mathematical logic. However, in making this model actually run on their 1950s computer, the JOHNNIAC, Simon and his colleagues had to navigate many obstacles and material constraints quite foreign to the human experience of logic. They crafted new tools and engaged in new practices that accommodated the affordances of their machine, rather than reflecting the character of human cognition and its bounds. The essay argues that tracking this implementation effort shows that "internal" cognitive practices and "external" tools and materials are not so easily separated as they are in Simon's principle of bounded rationality--the latter often shaping the dynamics of the former. PMID:26685521

  10. Aquaculture Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genomics chapter covers the basics of genome mapping and sequencing and the current status of several relevant species. The chapter briefly describes the development and use of (cDNA, BAC, etc.) libraries for mapping and obtaining specific sequence information. Other topics include comparative ...

  11. Mining Glossary and Games.

    ERIC Educational Resources Information Center

    National Energy Foundation, Salt Lake City, UT.

    This booklet was produced in an effort to increase the awareness and appreciation of young people for the Earth's resources. The Mining Education Glossary is intended to provide easy reference to mining terms which are used in the minerals recovery industry and as a useful resource for teaching basic learning skills. Accompanying the glossary are…

  12. Underground Coal Mining

    NASA Technical Reports Server (NTRS)

    Hill, G. M.

    1980-01-01

    Computer program models coal-mining production, equipment failure and equipment repair. Underground mine is represented as collection of work stations requiring service by production and repair crews alternately. Model projects equipment availability and productivity, and indicates proper balance of labor and equipment. Program is in FORTRAN IV for batch execution; it has been implemented on UNIVAC 1108.

  13. Boosting association rule mining in large datasets via Gibbs sampling.

    PubMed

    Qian, Guoqi; Rao, Calyampudi Radhakrishna; Sun, Xiaoying; Wu, Yuehua

    2016-05-01

    Current algorithms for association rule mining from transaction data are mostly deterministic and enumerative. They can be computationally intractable even for mining a dataset containing just a few hundred transaction items, if no action is taken to constrain the search space. In this paper, we develop a Gibbs-sampling-induced stochastic search procedure to randomly sample association rules from the itemset space, and perform rule mining from the reduced transaction dataset generated by the sample. Also a general rule importance measure is proposed to direct the stochastic search so that, as a result of the randomly generated association rules constituting an ergodic Markov chain, the overall most important rules in the itemset space can be uncovered from the reduced dataset with probability 1 in the limit. In the simulation study and a real genomic data example, we show how to boost association rule mining by an integrated use of the stochastic search and the Apriori algorithm. PMID:27091963

  14. PRB mines mature

    SciTech Connect

    Buchsbaum, L.

    2007-08-15

    Already seeing the results of reclamation efforts, America's largest surface mines advance as engineers prepare for the future. 30 years after the signing of the Surface Mining Control and Reclamation Act by Jimmy Carter, western strip mines in the USA, especially in the Powder River Basin, are producing more coal than ever. The article describes the construction and installation of a $38.5 million near-pit crusher and overland belt conveyor system at Foundation Coal West's (FCW) Belle Ayr surface mine in Wyoming, one of the earliest PRB mines. It goes on to describe the development by Rio Tinto of an elk conservatory, the Rochelle Hill Conservation Easement, on reclaimed land at Jacobs Ranch, adjacent to the Rochelle Hills. 4 photos.

  15. Semantic text mining support for lignocellulose research

    PubMed Central

    2012-01-01

    Background Biofuels produced from biomass are considered to be promising sustainable alternatives to fossil fuels. The conversion of lignocellulose into fermentable sugars for biofuels production requires the use of enzyme cocktails that can efficiently and economically hydrolyze lignocellulosic biomass. As many fungi naturally break down lignocellulose, the identification and characterization of the enzymes involved is a key challenge in the research and development of biomass-derived products and fuels. One approach to meeting this challenge is to mine the rapidly-expanding repertoire of microbial genomes for enzymes with the appropriate catalytic properties. Results Semantic technologies, including natural language processing, ontologies, semantic Web services and Web-based collaboration tools, promise to support users in handling complex data, thereby facilitating knowledge-intensive tasks. An ongoing challenge is to select the appropriate technologies and combine them in a coherent system that brings measurable improvements to the users. We present our ongoing development of a semantic infrastructure in support of genomics-based lignocellulose research. Part of this effort is the automated curation of knowledge from information on fungal enzymes that is available in the literature and genome resources. Conclusions Working closely with fungal biology researchers who manually curate the existing literature, we developed ontological natural language processing pipelines integrated in a Web-based interface to assist them in two main tasks: mining the literature for relevant knowledge, and at the same time providing rich and semantically linked information. PMID:22595090

  16. Sinbase: an integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

    PubMed

    Wang, Linhai; Yu, Jingyin; Li, Donghua; Zhang, Xiurong

    2015-01-01

    Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/. PMID:25480115

  17. Time series prediction using a rational fraction neural networks

    SciTech Connect

    Lee, K.; Lee, Y.C.; Barnes, C.; Aldrich, C.H.; Kindel, J.

    1988-01-01

    An efficient neural network based on a rational fraction representation has been trained to perform time series prediction. The network is a generalization of the Volterra-Wiener network while still retaining the computational efficiency of the latter. Because of the second order convergent nature of the learning algorithm, the rational net is computationally far more efficient than multilayer networks. The rational fractional representation is, however, more restrictive than the multilayer networks.

  18. Positivity preserving using GC1 rational quartic spline

    NASA Astrophysics Data System (ADS)

    Abdul Karim, Samsul Ariffin; Pang, Kong Voon; Hashim, Ishak

    2013-04-01

    In this paper, we study the shape preserving interpolation for positive data using a rational quartic spline which has a quartic numerator and linear denominator. The rational quartic splines have GC1 continuity at join knots. Simple data dependent constraints are derived on the shape parameters in the description of the rational interpolant. Numerical comparison between the proposed scheme and the existing scheme is discussed. The results indicate that the proposed scheme works well for all tested data sets.

  19. Draft Genome Sequence of the Aureocin A53-Producing Strain Staphylococcus aureus A53.

    PubMed

    Santos, Olinda Cabral Silva; Duarte, Andreza Freitas Souza; Albano, Rodolpho Mattos; Bastos, Maria Carmo Freire

    2016-01-01

    Here, we present the 2,658,363-bp draft genome sequence of the aureocin A53-producing strain Staphylococcus aureus A53. This genome information may contribute to the optimal and rational exploitation of aureocin A53 as an antimicrobial agent and to its production in large scale. PMID:27563042

  20. Draft Genome Sequence of the Aureocin A53–Producing Strain Staphylococcus aureus A53

    PubMed Central

    Santos, Olinda Cabral Silva; Duarte, Andreza Freitas Souza; Albano, Rodolpho Mattos

    2016-01-01

    Here, we present the 2,658,363-bp draft genome sequence of the aureocin A53–producing strain Staphylococcus aureus A53. This genome information may contribute to the optimal and rational exploitation of aureocin A53 as an antimicrobial agent and to its production in large scale. PMID:27563042

  1. 1. VIEW OF PHILLIPS MINE. CAMERA POINTED SOUTHEAST. SULLIVAN MINE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. VIEW OF PHILLIPS MINE. CAMERA POINTED SOUTHEAST. SULLIVAN MINE IS LOCATED ROUGHLY 75 YARDS BEYOND AND ROUGHLY IN LINE WITH THE SNOW ON THE RIGHT SIDE OF THE IMAGE. - Florida Mountain Mining Sites, Phillips Mine, East side of Florida Mountain, Silver City, Owyhee County, ID

  2. 1. VIEW OF SULLIVAN MINE ON RIGHT WITH PHILLIPS MINE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. VIEW OF SULLIVAN MINE ON RIGHT WITH PHILLIPS MINE LOCATED APPROXIMATELY 200 YARDS THROUGH TREES IN THE DIRECTION OF THE MOUND ON THE LEFT SIDE OF ROAD. CAMERA POINTING NORTH-NORTHEAST. - Florida Mountain Mining Sites, Sullivan Mine, East side of Florida Mountain, Silver City, Owyhee County, ID

  3. 2. EMPIRE STATE MINE. VIEW OF COLLAPSED BUILDINGS AT MINE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. EMPIRE STATE MINE. VIEW OF COLLAPSED BUILDINGS AT MINE WITH TAILINGS ON RIGHT. CAMERA POINTED SOUTHWEST. COLLAPSED ADIT APPROXIMATELY 25 YARDS UPHILL TO THE LEFT OF FAR BUILDING. TIP TOP AND ONTARIO ARE LOCATED OUT OF THE PICTURE TO THE RIGHT. - Florida Mountain Mining Sites, Empire State Mine, West side of Florida Mountain, Silver City, Owyhee County, ID

  4. Rationally designed nanovehicles to overcome cancer chemoresistance.

    PubMed

    Livney, Yoav D; Assaraf, Yehuda G

    2013-11-01

    Drug resistance is a primary hindrance towards curative cancer chemotherapy. Nanotechnology holds great promise in establishing efficacious and innovative strategies to overcome chemoresistance, and markedly facilitate complementary treatments and cancer diagnostics. Various nanomedical devices are being introduced and evaluated, demonstrating encouraging results. While stealth liposomes serve as a benchmark, astonishing progress is witnessed in polymeric nanovehicles, sometimes combined with low molecular weight surfactants, some of which inhibit drug resistance in addition to solubilizing drugs. Cutting edge multifunctional or quadrugnostic nanoparticles currently developed offer simultaneous targeted delivery of chemotherapeutics and chemosensitizers or drug-resistance gene silencing cargo, along with diagnostic imaging agents, like metallic NPs. Viral and cellular components offer exciting new routes for cancer targeting and treatment. Targeting intracellular compartments is another challenging frontier spawning pioneering approaches and results. To further enhance rational design of nanomedicine for overcoming drug resistance, we review the latest thoughts and accomplishments in recent literature. PMID:23954781

  5. Update on rational targeted therapy in AML.

    PubMed

    Shafer, Danielle; Grant, Steven

    2016-07-01

    Acute myeloid leukemia (AML) remains a challenge to both patients and clinicians. Despite improvements in our understanding of the disease, treatment has changed minimally and outcomes remain poor for the majority of patients. Within the last decade, there have been an increasing number of potential targets and pathways identified for development in AML. The classes of agents described in this review include but are not limited to epigenetic modifiers such as IDH inhibitors, BET inhibitors, and HDAC inhibitors as well as cell cycle and signaling inhibitors such as Aurora kinase inhibitors and CDK inhibitors. While the developments are encouraging, it is unlikely that targeting a single pathway will result in long-term disease control. Accordingly, we will also highlight potential rational partners for the novel agents described herein. PMID:26972558

  6. Rationalizing radio medical advice for maritime emergencies.

    PubMed

    Aujla, K; Nag, R; Ferguson, J; Howell, M; Cahill, C

    2003-01-01

    The provision of radio medical advice by the National Health Service for British coastal waters has developed in an ad hoc fashion. In 1999, the closure of one of the two centres providing such advice led to unexpected problems. The demographic characteristics of the offshore population covered by each centre were markedly different and this resulted in a different spectrum of medical emergencies presenting to the sole remaining centre. Subsequent data collection of the details of medical emergencies presenting from offshore allowed an audit to inform the development of training packages for both base and remote practitioners. This has led to an ongoing national rationalization of ship-to-shore radio medical advice for the UK. PMID:12952706

  7. Rational elicitation of cold-sensitive phenotypes.

    PubMed

    Baliga, Chetana; Majhi, Sandipan; Mondal, Kajari; Bhattacharjee, Antara; VijayRaghavan, K; Varadarajan, Raghavan

    2016-05-01

    Cold-sensitive phenotypes have helped us understand macromolecular assembly and biological phenomena, yet few attempts have been made to understand the basis of cold sensitivity or to elicit it by design. We report a method for rational design of cold-sensitive phenotypes. The method involves generation of partial loss-of-function mutants, at either buried or functional sites, coupled with selective overexpression strategies. The only essential input is amino acid sequence, although available structural information can be used as well. The method has been used to elicit cold-sensitive mutants of a variety of proteins, both monomeric and dimeric, and in multiple organisms, namely Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster This simple, yet effective technique of inducing cold sensitivity eliminates the need for complex mutations and provides a plausible molecular mechanism for eliciting cold-sensitive phenotypes. PMID:27091994

  8. Rational Design of Biobetters with Enhanced Stability.

    PubMed

    Courtois, Fabienne; Schneider, Curtiss P; Agrawal, Neeraj J; Trout, Bernhardt L

    2015-08-01

    Biotherapeutics are the fastest growing class of pharmaceutical with a rapidly evolving market facing the rise of biosimilar and biobetter products. In contrast to a biosimilar, which is derived from the same gene sequence as the innovator product, a biobetter has enhanced properties, such as enhanced efficacy or reduced immunogenicity. Little work has been carried out so far to increase the intrinsic stability of biotherapeutics via sequence changes, even though, aggregation, the primary degradation pathway of proteins, leads to issues ranging from manufacturing failure to immunological response and to loss of therapeutic activity. Using our spatial aggregation propensity tool as a first step to a rational design approach to identify aggregation-prone regions, biobetters of rituximab have been produced with enhanced stability by introducing site-specific mutations. Significant stabilization against aggregation was achieved for rituximab with no decrease in its binding affinity to the antigen. PMID:26096711

  9. Rational design of class I MHC ligands

    NASA Astrophysics Data System (ADS)

    Rognan, D.; Scapozza, L.; Folkers, G.; Daser, Angelika

    1995-04-01

    From the knowledge of the three-dimensional structure of a class I MHC protein, several non natural peptides were designed in order to either optimize the interactions of one secondary anchor amino acid with its HLA binding pocket or to substitute the non interacting part with spacer residues. All peptides were synthesized and tested for binding to the class I MHC protein in an in vitro reconstitution assay. As predicted, the non natural peptides present an enhanced binding to the HLA-B27 molecule with respect to their natural parent peptides. This study constitutes the first step towards the rational design of non peptidic MHC ligands that should be very promising tools for the selective immunotherapy of autoimmune diseases.

  10. Rationalization of some genetic anticodonic assignments

    NASA Technical Reports Server (NTRS)

    Lacey, J. C., Jr.; Hall, L. M.; Mullins, D. W., Jr.

    1985-01-01

    The hydrophobicity of most amino acids correlates well with that of their anticodon nucleotides, with Trp, Tyr, Ile, and Ser being the exceptions to this rule. Using previous data on hydrophobicity and binding constants, and new data on rates of esterification of polyadenylic acid with several N-acetylaminoacyl imidazolides, several of the anticodon assignments are rationalized. Chemical reasons are shown supporting the idea of the inclusion of the Ile in the catalog of biological amino acids late in the evolution, through a mutation of the existing tRNA and its aminoacyl-tRNA-synthetase. It was found that an addition of hexane increases the incorporation of hydrophobic Ac-Phe into poly-A, in support of the Fox (1965) and Oparin (1965) emphasis on the biogenetic importance of phase-separated systems.

  11. Update on rational targeted therapy in AML

    PubMed Central

    Shafer, Danielle; Grant, Steven

    2016-01-01

    Acute myeloid leukemia (AML) remains a challenge to both patients and clinicians. Despite improvements in our understanding of the disease, treatment has changed minimally and outcomes remain poor for the majority of patients. Within the last decade, there have been an increasing number of potential targets and pathways identified for development in AML. The classes of agents described in this review include but are not limited to epigenetic modifiers such as IDH inhibitors, BET inhibitors, and HDAC inhibitors as well as cell cycle and signaling inhibitors such as Aurora kinase inhibitors and CDK inhibitors. While the developments are encouraging, it is unlikely that targeting a single pathway will result in long-term disease control. Accordingly, we will also highlight potential rational partners for the novel agents described herein. PMID:26972558

  12. Allowable rotation numbers for Siegel disks of rational maps

    NASA Astrophysics Data System (ADS)

    Manlove, Joseph Michael

    The results presented here answers in part a conjecture of Douady about sharpness of the Brjuno condition. Douady hypothesized that a Siegel disk exists for a rational function if and only if the Brjuno condition is satisfied by the rotation number. It is known that the Brjuno condition is sharp for quadratic polynomials and many special families. This thesis focuses on a class of rational functions, many of which have not been considered previously. Specific examples of maps for which these results apply include quadratic rational maps with an attracting cycle. Also included are those rational functions arising of Newton's method on cubic polynomials with distinct roots.

  13. Cyborg pantocrator: international relations theory from decisionism to rational choice.

    PubMed

    Guilhot, Nicolas

    2011-01-01

    International relations theory took shape in the 1950s in reaction to the behavioral social science movement, emphasizing the limits of rationality in a context of high uncertainty, weak rules, and the possibility of lethal conflict. Yet the same discipline rapidly developed "rational choice" models applied to foreign policy decision making or nuclear strategy. This paper argues that this transformation took place almost seamlessly around the concept of "decision." Initially associated with an antirationalist or "decisionist" approach to politics, the sovereign decision became the epitome of political rationality when it was redescribed as "rational choice," thus easing the cultural acceptance of political realism in the postwar years. PMID:21732376

  14. The rational use of drugs and WHO.

    PubMed

    1985-01-01

    On November 25-29, 1985, the World Health Organization held a Conference in Nairobi of Experts on the Rational Use of Drugs. In the early 1980s, both the International Federation of Pharmaceutical Manufacturers Association (IFPMA) and Health Action International (HAI) had developed codes of pharmaceutical marketing practices in order to come to terms with the malpractices in this field. A more comprehensive approach was needed, however. Prime responsibility for rational drug use must rest with the member governments, operating through national regulatory authorities and assisted in their work by guidelines on minimum requirements for national drug regulation prepared by WHO. The Dag Hammarskjold Foundation organized a seminar on Another Development in Pharmaceuticals as an independent contribution to the international debate on this global issue. The seminar emphasized that development should be need-oriented, self-reliant, and based on structural transformations. Governments view the pharmaceutical crisis as 1 facet of the more general problem of spiralling health costs which put an intolerable burden on already overstretched welfare services. The pharmaceutical industry sees the crisis largely in terms of excessively restrictive regulations which stifle innovation of products. Some doctors and pharmacists feel that increased regulatory measures will erode their rights to prescribe and to control the supply and information to patients. On the other hand, some clinical pharmacologists and administrators express concern about excessive, irrational and uneconomic prescribing and its effects on public health. Consumer groups define the problem in terms of an overbearing and greedy business community. The general public fail to understand the effects of pharmaceuticals. PMID:12341043

  15. Antarctic Genomics

    PubMed Central

    Clarke, Andrew; Cockell, Charles S.; Convey, Peter; Detrich III, H. William; Fraser, Keiron P. P.; Johnston, Ian A.; Methe, Barbara A.; Murray, Alison E.; Peck, Lloyd S.; Römisch, Karin; Rogers, Alex D.

    2004-01-01

    With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies. PMID:18629155

  16. The UCSC Genome Browser database: 2015 update.

    PubMed

    Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T; Li, Chin H; Miga, Karen H; Nguyen, Ngan; Paten, Benedict; Raney, Brian J; Smit, Arian F A; Speir, Matthew L; Zweig, Ann S; Haussler, David; Kuhn, Robert M; Kent, W James

    2015-01-01

    Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

  17. The UCSC Genome Browser database: 2015 update

    PubMed Central

    Rosenbloom, Kate R.; Armstrong, Joel; Barber, Galt P.; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R.; Fujita, Pauline A.; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A.; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S.; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T.; Li, Chin H.; Miga, Karen H.; Nguyen, Ngan; Paten, Benedict; Raney, Brian J.; Smit, Arian F. A.; Speir, Matthew L.; Zweig, Ann S.; Haussler, David; Kuhn, Robert M.; Kent, W. James

    2015-01-01

    Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), ‘mined the web’ for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

  18. Recent developments of genomic research in soybean.

    PubMed

    Chan, Ching; Qi, Xinpeng; Li, Man-Wah; Wong, Fuk-Ling; Lam, Hon-Ming

    2012-07-20

    Soybean is an important cash crop with unique and important traits such as the high seed protein and oil contents, and the ability to perform symbiotic nitrogen fixation. A reference genome of cultivated soybeans was established in 2010, followed by whole-genome re-sequencing of wild and cultivated soybean accessions. These efforts revealed unique features of the soybean genome and helped to understand its evolution. Mapping of variations between wild and cultivated soybean genomes were performed. These genomic variations may be related to the process of domestication and human selection. Wild soybean germplasms exhibited high genomic diversity and hence may be an important source of novel genes/alleles. Accumulation of genomic data will help to refine genetic maps and expedite the identification of functional genes. In this review, we summarize the major findings from the whole-genome sequencing projects and discuss the possible impacts on soybean researches and breeding programs. Some emerging areas such as transcriptomic and epigenomic studies will be introduced. In addition, we also tabulated some useful bioinformatics tools that will help the mining of the soybean genomic data. PMID:22835978

  19. Land Mines Removal

    NASA Technical Reports Server (NTRS)

    1999-01-01

    The same rocket fuel that helps power the Space Shuttle as it thunders into orbit will now be taking on a new role, with the potential to benefit millions of people worldwide. Leftover rocket fuel from NASA is being used to make a flare that destroys land mines where they were buried, without using explosives. The flare is safe to handle and easy to use. People working to deactivate the mines simply place the flare next to the uncovered land mine and ignite it from a safe distance using a battery-triggered electric match. The flare burns a hole in the land mine's case and ignites its explosive contents. The explosive burns away, disabling the mine and rendering it harmless. Using leftover rocket fuel to help destroy land mines incurs no additional costs to taxpayers. To ensure enough propellant is available for each Shuttle mission, NASA allows for a small percentage of extra propellant in each batch. Once mixed, surplus fuel solidifies and carnot be saved for use in another launch. In its solid form, it is an ideal ingredient for the new flare. The flare was developed by Thiokol Propulsion in Brigham City, Utah, the NASA contractor that designs and builds rocket motors for the Solid Rocket Booster Space Shuttle. An estimated 80 million or more active land mines are scattered around the world in at least 70 countries, and kill or maim 26,000 people a year. Worldwide, there is one casualty every 22 minutes

  20. Land Mines Removal

    NASA Technical Reports Server (NTRS)

    1999-01-01

    The same rocket fuel that helps power the Space Shuttle as it thunders into orbit will now be taking on a new role, with the potential to benefit millions of people worldwide. Leftover rocket fuel from NASA is being used to make a flare that destroys land mines where they were buried, without using explosives. The flare is safe to handle and easy to use. People working to deactivate the mines simply place the flare next to the uncovered land mine and ignite it from a safe distance using a battery-triggered electric match. The flare burns a hole in the land mine's case and ignites its explosive contents. The explosive burns away, disabling the mine and rendering it harmless. Using leftover rocket fuel to help destroy land mines incurs no additional costs to taxpayers. To ensure enough propellant is available for each Shuttle mission, NASA allows for a small percentage of extra propellant in each batch. Once mixed, surplus fuel solidifies and carnot be saved for use in another launch. In its solid form, it is an ideal ingredient for new the flare. The flare was developed by Thiokol Propulsion in Brigham City, Utah, the NASA contractor that designs and builds rocket motors for the Solid Rocket Booster Space Shuttle. An estimated 80 million or more active land mines are scattered around the world in at least 70 countries, and kill or maim 26,000 people a year. Worldwide, there is one casualty every 22 minutes.

  1. Lactobacillus mixtipabuli sp. nov. isolated from total mixed ration silage.

    PubMed

    Tohno, Masanori; Kitahara, Maki; Irisawa, Tomohiro; Ohmori, Hideyuki; Masuda, Takaharu; Ohkuma, Moriya; Tajima, Kiyoshi

    2015-06-01

    Using a polyphasic taxonomic approach, we investigated three bacterial strains - IWT30T, IWT8 and IWT75 - isolated from total mixed ration silage prepared in Hachimantai, Iwate, Japan. The isolates comprised Gram-stain positive, non-motile, non-spore-forming, catalase-negative, rod-shaped bacteria. Good growth occurred at 15-45 °C and at pH 4.0-7.5. Their major cellular fatty acids were C18:1ω9c and C19:1 cyclo 9,10.The G+C content of genomic DNA of strain IWT30T was 44.6 mol%. Comparative 16S rRNA gene sequence analysis showed that these novel strains belonged to the genus Lactobacillus. These strains shared 100 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Lactobacillus silagei, Lactobacillus odoratitofui, Lactobacillus similis, Lactobacillus collinoides, Lactobacillus paracollinoides and Lactobacillus kimchicus, with sequence similarity values of 99.5, 98.8, 98.7, 97.8, 97.8 and 96.8 %, respectively. The level of DNA-DNA relatedness between these strains and their closest phylogenetic neighbours was less than 30 %. On the basis of additional phylogenetic analysis of pheS and rpoA gene sequences and phenotypic and chemotaxonomic characteristics, we conclude that these three strains represent a novel species of the genus Lactobacillus, for which we propose the name Lactobacillus mixtipabuli sp. nov. The type strain is IWT30T ( = JCM 19805T = DSM 28580T). PMID:25807979

  2. Strata mechanics in coal mining

    SciTech Connect

    Jeremic, M.L.

    1985-01-01

    This book considers the following topics: coal measure; coal seam feature; roof and floor strata; virgin strata pressure; deformation and failure of structure; room and pillar mining; longwall mining; slice mining; open slope mining; sub-level caving; and coal pillar structure.

  3. Data Mining in Child Welfare.

    ERIC Educational Resources Information Center

    Schoech, Dick; Quinn, Andrew; Rycraft, Joan R.

    2000-01-01

    Examines the historical and larger context of data mining and describes data mining processes, techniques, and tools. Illustrates these using a child welfare dataset concerning the employee turnover that is mined, using logistic regression and a Bayesian neural network. Discusses the data mining process, the resulting models, their predictive…

  4. Land reclamation beautifies coal mines

    SciTech Connect

    Coblentz, B.

    2009-07-15

    The article explains how the Mississippi Agricultural and Forestry Experiments station, MAFES, has helped prepare land exploited by strip mining at North American Coal Corporation's Red Hills Mine. The 5,800 acre lignite mine is over 200 ft deep and uncovers six layers of coal. About 100 acres of land a year is mined and reclaimed, mostly as pine plantations. 5 photos.

  5. Draft Genome Sequence of Halomonas smyrnensis AAD6T

    PubMed Central

    Sogutcu, Elif; Emrence, Zeliha; Arikan, Muzzaffer; Cakiris, Aris; Abaci, Neslihan; Öner, Ebru Toksoy; Üstek, Duran

    2012-01-01

    Halomonas smyrnensis AAD6T is a Gram-negative, aerobic, exopolysaccharide-producing, and moderately halophilic bacterium that produces levan, a fructose homopolymer with many potential uses in various industries. We report the draft genome sequence of H. smyrnensis AAD6T, which will accelerate research on the rational design and optimization of microbial levan production. PMID:23012275

  6. Genomic Testing

    MedlinePlus

    ... Working Group Independent Web site Informing the effective integration of genomics into health practice—Lynch syndrome ACCE Model for Evaluating Genetic Tests Recommendations by the EGAPP Working Group Top of ... ...

  7. Closedure - Mine Closure Technologies Resource

    NASA Astrophysics Data System (ADS)

    Kauppila, Päivi; Kauppila, Tommi; Pasanen, Antti; Backnäs, Soile; Liisa Räisänen, Marja; Turunen, Kaisa; Karlsson, Teemu; Solismaa, Lauri; Hentinen, Kimmo

    2015-04-01

    Closure of mining operations is an essential part of the development of eco-efficient mining and the Green Mining concept in Finland to reduce the environmental footprint of mining. Closedure is a 2-year joint research project between Geological Survey of Finland and Technical Research Centre of Finland that aims at developing accessible tools and resources for planning, executing and monitoring mine closure. The main outcome of the Closedure project is an updatable wiki technology-based internet platform (http://mineclosure.gtk.fi) in which comprehensive guidance on the mine closure is provided and main methods and technologies related to mine closure are evaluated. Closedure also provides new data on the key issues of mine closure, such as performance of passive water treatment in Finland, applicability of test methods for evaluating cover structures for mining wastes, prediction of water effluents from mine wastes, and isotopic and geophysical methods to recognize contaminant transport paths in crystalline bedrock.

  8. Agents and Data Mining in Bioinformatics: Joining Data Gathering and Automatic Annotation with Classification and Distributed Clustering

    NASA Astrophysics Data System (ADS)

    Bazzan, Ana L. C.

    Multiagent systems and data mining techniques are being frequently used in genome projects, especially regarding the annotation process (annotation pipeline). This paper discusses annotation-related problems where agent-based and/or distributed data mining has been successfully employed.

  9. Rationing health protection: a proposal to exempt nuisance dust from US Clean Air Act regulations.

    PubMed

    Centner, Terence J; Colson, Gregory

    2013-03-15

    The US House of Representative has passed a bill called the "Farm Dust Regulation Prevention Act" (Dust Act) that would exempt most types of particulate matter (PM) in rural areas from the air quality controls of the US Clean Air Act. The Dust Act would markedly change the country's air quality standards. An examination of the proposed provisions shows that they would exempt non-combustion PM pollutants from mining, smelting, petroleum production, and power generation from existing air quality standards. Persons downwind from pollutants generated in rural areas could be exposed to concentrations of carcinogenic heavy metals, asbestos, and benzene known to adversely affect their health and ecological resources. Existing federal air quality standards based on science would be replaced by a flexible standard that rations health protection. PMID:23376304

  10. Towards the Rational Design of Nanoparticle Catalysts

    NASA Astrophysics Data System (ADS)

    Dash, Priyabrat

    This research is focused on development of routes towards the rational design of nanoparticle catalysts. Primarily, it is focused on two main projects; (1) the use of imidazolium-based ionic liquids (ILs) as greener media for the design of quasi-homogeneous nanoparticle catalysts and (2) the rational design of heterogeneous-supported nanoparticle catalysts from structured nanoparticle precursors. Each project has different studies associated with the main objective of the design of nanoparticle catalysts. In the first project, imidazolium-based ionic liquids have been used for the synthesis of nanoparticle catalysts. In particular, studies on recyclability, reuse, mode-of-stability, and long-term stability of these ionic-liquid supported nanoparticle catalysts have been done; all of which are important factors in determining the overall "greenness" of such synthetic routes. Three papers have been published/submitted for this project. In the first publication, highly stable polymer-stabilized Au, Pd and bimetallic Au-Pd nanoparticle catalysts have been synthesized in imidazolium-based 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM]PF6) ionic liquid (Journal of Molecular Catalysis A: Chemical, 2008, 286, 114). The resulting nanoparticles were found to be effective and selective quasi-homogeneous catalysts towards a wide-range of hydrogenation reactions and the catalyst solution was reused for further catalytic reactions with minimal loss in activity. The synthesis of very pure and clean ILs has allowed a platform to study the effects of impurities in the imidazolium ILs on nanoparticle stability. In a later study, a new mode of stabilization was postulated where the presence of low amounts of 1-methylimidazole has substantial effects on the resulting stability of Au and Pd-Au nanoparticles in these ILs (Chemical Communications, 2009, 812). In further continuation of this study, a comparative study involving four stabilization protocols for nanoparticle

  11. 78 FR 39531 - Mine Rescue Teams

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-01

    ... July 1, 2013 Part V Department of Labor Mine Safety and Health Administration 30 CFR Part 49 Mine... and Regulations#0;#0; ] DEPARTMENT OF LABOR Mine Safety and Health Administration 30 CFR Part 49 Mine... Miner Act Requirements for Underground Coal Mine Operators and Mine Rescue Teams Type of mine...

  12. Coal mine subsidence

    SciTech Connect

    Rahall, N.J.

    1991-05-01

    This paper examines the efficacy of the Department of the Interior's Office of Surface Mining Reclamation and Enforcement's (OSMRE) efforts to implement the federally assisted coal mine subsidence insurance program. Coal mine subsidence, a gradual settling of the earth's surface above an underground mine, can damage nearby land and property. To help protect property owners from subsidence-related damage, the Congress passed legislation in 1984 authorizing OSMRE to make grants of up to $3 million to each state to help the states establish self-sustaining, state-administered insurance programs. Of the 21 eligible states, six Colorado, Indiana, Kentucky, Ohio, West Virginia, and Wyoming applied for grants. This paper reviews the efforts of these six states to develop self-sustaining insurance programs and assessed OSMRE's oversight of those efforts.

  13. Minerals and mine drainage

    SciTech Connect

    Thomson, B.M.; Turney, W.R.

    1996-11-01

    This paper provides a review of literature published in 1995 on the subject of wastewater related to minerals and mine drainage. Topics covered include: environmental regulations and impacts; and characterization, prevention, treatment and reclamation. 65 refs.

  14. Indonesian coal mining

    SciTech Connect

    2008-11-15

    The article examines the opportunities and challenges facing the Indonesian coal mining industry and how the coal producers, government and wider Indonesian society are working to overcome them. 2 figs., 1 tab.

  15. Rational Decisionmaking in Higher Education. An NCHEMS Executive Overview.

    ERIC Educational Resources Information Center

    Chaffee, Ellen Earle

    Five models of organizational decision-making are described, and a case study of the rational model as seen in the budget process at Stanford University during the 1970s is presented. Several issues are addressed to help administrators who are interested in increasing the organization's rational decision-making. The five models are as follows: the…

  16. Imagination and the Pursuit of a Rational Rhetoric.

    ERIC Educational Resources Information Center

    Foster, David E.

    The works of certain rhetorical thinkers contain strategies directed at achieving assent or cooperation. Such writings demonstrate means by which readers' rational responses can be deliberately challenged and disrupted. While people often cite Aristotle's maxim "Man is a rational animal," critics have asserted that the statement misrepresents both…

  17. Studying Quality beyond Technical Rationality: Political and Symbolic Perspectives

    ERIC Educational Resources Information Center

    Blanco Ramírez, Gerardo

    2013-01-01

    The underlying paradigms that influence research on quality have remained alarmingly under-researched; this article analyses the constraints that a technical-rational approach for the study of quality in higher education imposes. Technical rationality has been the dominant paradigm that shapes research on quality in higher education.…

  18. An Empirical Evaluation of Ellis' Rational Emotive Theory.

    ERIC Educational Resources Information Center

    Wright, Loyd S.; Couch, R. David

    Ellis' rational emotive theory is based on the assumption that people are born with a potential for both rational and irrational thinking. To analyze the relationship of irrational beliefs to sensitivity, depression, submission, anxiety, and neuroticism, an Irrationality Scale, containing eight irrational beliefs, was constructed from a review of…

  19. Counseling Children and Adolescents: Rational Emotive Behavior Therapy and Humanism.

    ERIC Educational Resources Information Center

    Vernon, Ann

    1996-01-01

    Describes specific parallels between rational emotive behavior therapy and humanism. Places specific emphasis on the application of these principles with children and adolescents. Concepts are illustrated with case studies and a description of the similarities between rational emotive and humanistic, or affective, education. Highlights emotional…

  20. Rational Emotive Behavior Therapy Has a Humanistic Orientation-Definitely.

    ERIC Educational Resources Information Center

    Woods, Paul J.

    1996-01-01

    Challenges criticisms that rational emotive behavior therapy (REBT) is not humanistic. Responds to misconceptions regarding the term "rational" and concludes that, although REBT is closely identified with secular humanism, REBT can also be seen as a set of analytical and therapeutic skills that religious humanists can use. (RJM)

  1. Bounded Rationality, Retaliation, and the Spread of Urban Violence

    ERIC Educational Resources Information Center

    Jacobs, Bruce A.; Wright, Richard

    2010-01-01

    Drawing from in-depth interviews with 52 active street criminals, this article examines the grounded theoretic implications of bounded rationality for retaliatory street violence. The bounds on rationality that this article explores are anger, uncertainty, and time pressure. These bounds create imperfections in the retaliatory decision-making…

  2. An Educational Interpretation of Jurgen Habermas's Communicative Rationality.

    ERIC Educational Resources Information Center

    Han, Gicheol

    2002-01-01

    Suggests taking Habermas's notion of communicative rationality as a reference point from which to organize educational activities and evaluate their "being educational" in the classroom. Communicative rationality in the classroom provides a perspective from which one can establish a normative standard for being educational. (Contains endnotes and…

  3. Rationality and Integration in a Family Childrearing Decision.

    ERIC Educational Resources Information Center

    Diana, Mark S.

    This paper illuminates how concepts of rationality developed by Diesing in l962 are reflected in parents' childrearing decisions. After examining technical (TR), economic (ER), social (SR), legal (LR), and political (PR) rationalities or decision-making styles, consideration is given to integrative effects and the influence of parents' friends and…

  4. Passionate Rationalism: The Role of Emotion in Decision Making

    ERIC Educational Resources Information Center

    Lakomski, Gabriele; Evers, Colin W.

    2010-01-01

    Purpose: The purpose of this paper is to argue that emotion has a central role to play in rational decision making based on recent research in the neuroanatomy of emotion. As a result, traditional rational decision-making theories, including Herbert Simon's modified model of satisficing that sharply demarcates emotions and values from rationality…

  5. Rational Emotive Behavior Therapy: Origins, Constructs, and Applications.

    ERIC Educational Resources Information Center

    Watson, Joshua C.

    In 1956, Dr. Albert Ellis presented his seminal work on Rational Therapy, subsequently renamed Rational Emotive Behavior Therapy (REBT) in 1993. This paper explores the origins, theoretical foundations, applications, and implications of REBT and provides a look at the empirical research available in support of the approach's efficacy. REBT is…

  6. The Rationality of Narrative Inquiry in Research and Professional Development.

    ERIC Educational Resources Information Center

    Conle, Carola

    2001-01-01

    Using Habermas' Theory of Communicative Action and concept of communicative rationality, the paper proposes that narrative inquiry can be a rational enterprise, presenting narrative inquiry as a narrative discourse which has the dual function of being a method of inquiry and a means of personal and professional development in teacher education.…

  7. Rational Experimental Design for Electrical Resistivity Imaging

    NASA Astrophysics Data System (ADS)

    Mitchell, V.; Pidlisecky, A.; Knight, R.

    2008-12-01

    Over the past several decades advances in the acquisition and processing of electrical resistivity data, through multi-channel acquisition systems and new inversion algorithms, have greatly increased the value of these data to near-surface environmental and hydrological problems. There has, however, been relatively little advancement in the design of actual surveys. Data acquisition still typically involves using a small number of traditional arrays (e.g. Wenner, Schlumberger) despite a demonstrated improvement in data quality from the use of non-standard arrays. While optimized experimental design has been widely studied in applied mathematics and the physical and biological sciences, it is rarely implemented for non-linear problems, such as electrical resistivity imaging (ERI). We focus specifically on using ERI in the field for monitoring changes in the subsurface electrical resistivity structure. For this application we seek an experimental design method that can be used in the field to modify the data acquisition scheme (spatial and temporal sampling) based on prior knowledge of the site and/or knowledge gained during the imaging experiment. Some recent studies have investigated optimized design of electrical resistivity surveys by linearizing the problem or with computationally-intensive search algorithms. We propose a method for rational experimental design based on the concept of informed imaging, the use of prior information regarding subsurface properties and processes to develop problem-specific data acquisition and inversion schemes. Specifically, we use realistic subsurface resistivity models to aid in choosing source configurations that maximize the information content of our data. Our approach is based on first assessing the current density within a region of interest, in order to provide sufficient energy to the region of interest to overcome a noise threshold, and then evaluating the direction of current vectors, in order to maximize the

  8. Data Stream Mining

    NASA Astrophysics Data System (ADS)

    Gaber, Mohamed Medhat; Zaslavsky, Arkady; Krishnaswamy, Shonali

    Data mining is concerned with the process of computationally extracting hidden knowledge structures represented in models and patterns from large data repositories. It is an interdisciplinary field of study that has its roots in databases, statistics, machine learning, and data visualization. Data mining has emerged as a direct outcome of the data explosion that resulted from the success in database and data warehousing technologies over the past two decades (Fayyad, 1997,Fayyad, 1998,Kantardzic, 2003).

  9. Mining Specifications: A Roadmap

    NASA Astrophysics Data System (ADS)

    Zeller, Andreas

    Recent advances in software validation and verification make it possible to widely automate whether a specification is satisfied. This progress is hampered, though, by the persistent difficulty of writing specifications. Are we facing a “specification crisis”? In this paper, I show how to alleviate the burden of writing specifications by reusing and extending specifications as mined from existing software and give an overview on the state of the art in specification mining, its origins, and its potential.

  10. QuadBase2: web server for multiplexed guanine quadruplex mining and visualization

    PubMed Central

    Dhapola, Parashar; Chowdhury, Shantanu

    2016-01-01

    DNA guanine quadruplexes or G4s are non-canonical DNA secondary structures which affect genomic processes like replication, transcription and recombination. G4s are computationally identified by specific nucleotide motifs which are also called putative G4 (PG4) motifs. Despite the general relevance of these structures, there is currently no tool available that can allow batch queries and genome-wide analysis of these motifs in a user-friendly interface. QuadBase2 (quadbase.igib.res.in) presents a completely reinvented web server version of previously published QuadBase database. QuadBase2 enables users to mine PG4 motifs in up to 178 eukaryotes through the EuQuad module. This module interfaces with Ensembl Compara database, to allow users mine PG4 motifs in the orthologues of genes of interest across eukaryotes. PG4 motifs can be mined across genes and their promoter sequences in 1719 prokaryotes through ProQuad module. This module includes a feature that allows genome-wide mining of PG4 motifs and their visualization as circular histograms. TetraplexFinder, the module for mining PG4 motifs in user-provided sequences is now capable of handling up to 20 MB of data. QuadBase2 is a comprehensive PG4 motif mining tool that further expands the configurations and algorithms for mining PG4 motifs in a user-friendly way. PMID:27185890

  11. QuadBase2: web server for multiplexed guanine quadruplex mining and visualization.

    PubMed

    Dhapola, Parashar; Chowdhury, Shantanu

    2016-07-01

    DNA guanine quadruplexes or G4s are non-canonical DNA secondary structures which affect genomic processes like replication, transcription and recombination. G4s are computationally identified by specific nucleotide motifs which are also called putative G4 (PG4) motifs. Despite the general relevance of these structures, there is currently no tool available that can allow batch queries and genome-wide analysis of these motifs in a user-friendly interface. QuadBase2 (quadbase.igib.res.in) presents a completely reinvented web server version of previously published QuadBase database. QuadBase2 enables users to mine PG4 motifs in up to 178 eukaryotes through the EuQuad module. This module interfaces with Ensembl Compara database, to allow users mine PG4 motifs in the orthologues of genes of interest across eukaryotes. PG4 motifs can be mined across genes and their promoter sequences in 1719 prokaryotes through ProQuad module. This module includes a feature that allows genome-wide mining of PG4 motifs and their visualization as circular histograms. TetraplexFinder, the module for mining PG4 motifs in user-provided sequences is now capable of handling up to 20 MB of data. QuadBase2 is a comprehensive PG4 motif mining tool that further expands the configurations and algorithms for mining PG4 motifs in a user-friendly way. PMID:27185890

  12. Fatal SIR diseases and rational exemption to vaccination.

    PubMed

    d'Onofrio, Alberto; Manfredi, Piero; Salinelli, Ernesto

    2008-12-01

    A challenge to disease control in modern societies is the spread of rational exemption to vaccination as a consequence of the rational comparison between the steadily declining risk of infection and the risk of side effects from the vaccine. Here, we consider rational exemption in an susceptible-infectious-removed (SIR) model with information-dependent vaccination where individuals use information on the disease's mortality as their information set. Using suitable assumptions on the dynamics of the population, we show the dynamic implications of the interaction between rational exemption, current and delayed information and the risk of death by the disease. In particular, we illustrate the onset of the long cycles caused by rational exemption when vaccination decisions are based on delayed informations. PMID:18840601

  13. Cognitive Rationalizations for Tanning-Bed Use: A Preliminary Exploration

    PubMed Central

    Banerjee, Smita C.; Hay, Jennifer L.; Greene, Kathryn

    2016-01-01

    Objectives To examine construct and predictive utility of an adapted cognitive rationalization scale for tanning-bed use. Methods Current/former tanning-bed-using undergraduate students (N = 216; 87.6% females; 78.4% white) at a large northeastern university participated in a survey. A cognitive rationalization for tanning-bed use scale was adapted. Standardized self-report measures of past tanning-bed use, advantages of tanning, perceived vulnerability to photoaging, tanning-bed use dependence, and tanning- bed use intention were also administered. Results The cognitive rationalization scale exhibited strong construct and predictive validity. Current tanners and tanning-bed-use-dependent participants endorsed rationalizations more strongly than did former tanners and not-tanning-bed-use-dependent participants respectively. Conclusions Findings indicate that cognitive rationalizations help explain discrepancy between inconsistent cognitions. PMID:23985280

  14. Morenci Mine, AZ

    NASA Technical Reports Server (NTRS)

    2007-01-01

    The Morenci open-pit copper mine in southeast Arizona is North America's leading producer of copper. In the 1860s, prospectors arrived looking for gold; instead they found copper. Underground mining began in the 1870s, and the first pit was opened in 1939. Phelps Dodge employs over 200 people in the mining and refining operations. Around-the-clock removal of 700,000 tons of rock per day results in production of 382 thousand tons of copper per year. Phelps Dodge is now developing the Safford Mine, about 12 km southwest of Morenci. It will be the first new copper mine in the US in more than 30 years. When production starts in 2008, the Safford Mine will produce 109 thousand tons of copper. This ASTER image uses shortwavelength infrared bands to highlight in bright pink the altered rocks in the Morenci pit associated with copper mineralization.

    The image covers an area of 21 x 16.9 km, was acquired on July 14, 2007, and is centered near 33.1 degrees north latitude, 109.5 degrees west longitude.

    The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

  15. "easyMine" - realistic and systematic mine detection simulation tooltion

    NASA Astrophysics Data System (ADS)

    Böttger, U.; Beier, K.; Biering, B.; Müller, C.; Peichl, M.; Spyra, W.

    2004-05-01

    Mine detection is to date mainly performed with metal detectors, although new methods for UXO detection are explored worldwide. The main problem for the mine detection to date is, that there exist some ideas of which sensor combinations could yield a high score, but until now there is no systematic analysis of mine detection methods together with realistic environmental conditions to conclude on a physically and technically optimized sensor combination. This gap will be removed by a project "easyMine" (Realistic and systematic Mine Detection Simulation Tool) which will result in a simulation tool for optimizing land mine detection in a realistic mine field. The project idea for this software tool is presented, that will simulate the closed chain of mine detection, including the mine in its natural environment, the sensor, the evaluation and application of the measurements by an user. The tool will be modularly designed. Each chain link will be an independent, exchangeable sub- module and will describe a stand alone part of the whole mine detection procedure. The advantage of the tool will be the evaluation of very different kinds of sensor combinations in relation of their real potential for mine detection. Three detection methods (metal detector, GPR and imaging IR-radiometry) will be explained to be introduced into the easyMine software tool in a first step. An actual example for land mine detection problem will be presented and approaches for solutions with easyMine will be shown.

  16. LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

    PubMed Central

    Sun, Cheng; Shepard, Donald B.; Chong, Rebecca A.; López Arriaza, José; Hall, Kathryn; Castoe, Todd A.; Feschotte, Cédric; Pollock, David D.; Mueller, Rachel Lockridge

    2012-01-01

    Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ∼14 to ∼120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders. PMID:22200636

  17. Rational choice, neuroeconomy and mixed emotions.

    PubMed

    Livet, Pierre

    2010-01-27

    Experimental psychology has shown differences between predictions of theory of decision and human choices. Emotions like regret can partly explain these differences. Neuroimagery used in combination with behavioural economics (neuroeconomics) has been used in order to try to disentangle the different emotional and rational factors (regret, rejoicing, reward, costs, uncertainty, trade-off between positive and negative aspects of different options). Emotions then appear as much more complex and mixed affective states than usually assumed. Not only might we feel a positive affect in punishing unfair partners, but mixed emotions can, for example, combine transmutation of previous anxiety into relief and elation by comparison with another less exciting option (elating relief). At the level of complexity of these mixed emotions--which we formally represent by comparisons between 'unexpected utilities' and expected ones--the main biases that Kahnemann and Tversky have shown can be explained. In spite of the complexity of these mixed emotions, some of these hypotheses might be partially tested by brain imagery. PMID:20026464

  18. Biodiversity, conservation biology, and rational choice.

    PubMed

    Frank, David

    2014-03-01

    This paper critically discusses two areas of Sahotra Sarkar's recent work in environmental philosophy: biodiversity and conservation biology and roles for decision theory in incorporating values explicitly in the environmental policy process. I argue that Sarkar's emphasis on the practices of conservation biologists, and especially the role of social and cultural values in the choice of biodiversity constituents, restricts his conception of biodiversity to particular practical conservation contexts. I argue that life scientists have many reasons to measure many types of diversity, and that biodiversity metrics could be value-free. I argue that Sarkar's emphasis on the limitations of normative decision theory is in tension with his statement that decision theory can "put science and ethics together." I also challenge his claim that multi-criteria decision tools lacking axiomatic foundations in preference and utility theory are "without a rational basis," by presenting a case of a simple "outranking" multi-criteria decision rule that can violate a basic normative requirement of preferences (transitivity) and ask whether there may nevertheless be contexts in which such a procedure might assist decision makers. PMID:24216191

  19. Rationalizing meat consumption. The 4Ns.

    PubMed

    Piazza, Jared; Ruby, Matthew B; Loughnan, Steve; Luong, Mischel; Kulik, Juliana; Watkins, Hanne M; Seigerman, Mirra

    2015-08-01

    Recent theorizing suggests that the 4Ns - that is, the belief that eating meat is natural, normal, necessary, and nice - are common rationalizations people use to defend their choice of eating meat. However, such theorizing has yet to be subjected to empirical testing. Six studies were conducted on the 4Ns. Studies 1a and 1b demonstrated that the 4N classification captures the vast majority (83%-91%) of justifications people naturally offer in defense of eating meat. In Study 2, individuals who endorsed the 4Ns tended also to objectify (dementalize) animals and included fewer animals in their circle of moral concern, and this was true independent of social dominance orientation. Subsequent studies (Studies 3-5) showed that individuals who endorsed the 4Ns tend not to be motivated by ethical concerns when making food choices, are less involved in animal-welfare advocacy, less driven to restrict animal products from their diet, less proud of their animal-product decisions, tend to endorse Speciesist attitudes, tend to consume meat and animal products more frequently, and are highly committed to eating meat. Furthermore, omnivores who strongly endorsed the 4Ns tended to experience less guilt about their animal-product decisions, highlighting the guilt-alleviating function of the 4Ns. PMID:25865663

  20. Learning rational temporal eye movement strategies.

    PubMed

    Hoppe, David; Rothkopf, Constantin A

    2016-07-19

    During active behavior humans redirect their gaze several times every second within the visual environment. Where we look within static images is highly efficient, as quantified by computational models of human gaze shifts in visual search and face recognition tasks. However, when we shift gaze is mostly unknown despite its fundamental importance for survival in a dynamic world. It has been suggested that during naturalistic visuomotor behavior gaze deployment is coordinated with task-relevant events, often predictive of future events, and studies in sportsmen suggest that timing of eye movements is learned. Here we establish that humans efficiently learn to adjust the timing of eye movements in response to environmental regularities when monitoring locations in the visual scene to detect probabilistically occurring events. To detect the events humans adopt strategies that can be understood through a computational model that includes perceptual and acting uncertainties, a minimal processing time, and, crucially, the intrinsic costs of gaze behavior. Thus, subjects traded off event detection rate with behavioral costs of carrying out eye movements. Remarkably, based on this rational bounded actor model the time course of learning the gaze strategies is fully explained by an optimal Bayesian learner with humans' characteristic uncertainty in time estimation, the well-known scalar law of biological timing. Taken together, these findings establish that the human visual system is highly efficient in learning temporal regularities in the environment and that it can use these regularities to control the timing of eye movements to detect behaviorally relevant events. PMID:27382164

  1. Digital Family Histories for Data Mining

    PubMed Central

    Hoyt, Robert; Linnville, Steven; Chung, Hui-Min; Hutfless, Brent; Rice, Courtney

    2013-01-01

    As we move closer to ubiquitous electronic health records (EHRs), genetic, familial, and clinical information will need to be incorporated into EHRs as structured data that can be used for data mining and clinical decision support. While the Human Genome Project has produced new and exciting genomic data, the cost to sequence the human personal genome is high, and significant controversies regarding how to interpret genomic data exist. Many experts feel that the family history is a surrogate marker for genetic information and should be part of any paper-based or electronic health record. A digital family history is now part of the Meaningful Use Stage 2 menu objectives for EHR reimbursement, projected for 2014. In this study, a secure online family history questionnaire was designed to collect data on a unique cohort of Vietnam-era repatriated male veterans and a comparison group in order to compare participant and family disease rates on common medical disorders with a genetic component. This article describes our approach to create the digital questionnaire and the results of analyzing family history data on 319 male participants. PMID:24159269

  2. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  3. Underground at Black Diamond Mines

    SciTech Connect

    Higgins, C.T.

    1989-10-01

    Although California is noted for its mining history and annually leads the nation in total monetary value of minerals produced, there a few opportunities for the public to tour underground mines. One reason is that nearly all mining in the state today is done above ground in open pits. Another reason is that active underground mines are not commonly favorable to public tours. There is one place, Black Diamond Mines Regional Preserve, where the public can safely tour a formerly active underground mine. Black Diamond Mines Regional Preserve is a 3,600-acre parkland about 5 miles southwest of Antioch in Contra Costa County. The Preserve was established in the early 1970s and is administered by the East Bay Regional Park District. Black Diamond Mines Preserve is noteworthy for its mining history as well as its natural history, both of which are briefly described here.

  4. Tribology of earthmoving, mining, and minerals processing

    SciTech Connect

    Hawk, Jeffrey A.; Wilson, Rick D.

    2001-01-01

    -service operating conditions. This knowledge has allowed the rational selection of wear-resistant materials for use as earthmoving, mining, and minerals processing components, and new wear-resistant materials can be designed using our knowledge of the impact and abrasion mechanisms encountered in the day-to-day operation of components used in these operations.

  5. Listeria Genomics

    NASA Astrophysics Data System (ADS)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  6. CAERs's mine mapping program and Kentucky's mine mapping initiative

    SciTech Connect

    Hiett, J.

    2007-07-01

    Since 1884 the Kentucky Department of Mines and Minerals (KDMM now OMSL) has had a mine mapping function as it relates to mine safety. The CAER's Mine Mapping Program has provided this service to that agency since 1972. The program has been in continuous operation under the current staff and management over that period. Functions include operating the Mine Map Repository/Mine Map Information Center of the OMSL; and receiving and processing all annual coal mine license maps, old maps, and related data. The Kentucky Mine Mapping Initiative's goal is to ensure that every underground and surface mine map in Kentucky is located, digitized and online. The Kentucky mine mapping website plays a vital role in the safety of Kentuckians. The purpose of the web service is to make available electronic maps of mined out areas and approximately 32,000 engineering drawings of operating or closed mines that are located in the state. Future phases of the project will include the archival scanning of all submitted mine maps; the recovery from outside sources of maps that were destroyed in a 1948 fire; and the development of further technology to process maps and related data. 7 photos.

  7. XML algebras for data mining

    NASA Astrophysics Data System (ADS)

    Zhang, Ming; Yao, JingTao

    2004-04-01

    The XML is a new standard for data representation and exchange on the Internet. There are studies on XML query languages as well as XML algebras in literature. However, attention has not been paid to research on XML algebras for data mining due to partially the fact that there is no widely accepted definition of XML mining tasks. This paper tries to examine the XML mining tasks and provide guidelines to design XML algebras for data mining. Some summarization and comparison have been done to existing XML algebras. We argue that by adding additional operators for mining tasks, XML algebras may work well for data mining with XML documents.

  8. Conveyorized applications to surface mining

    SciTech Connect

    Peterson, A.N.

    1983-06-01

    Worldwide, there are numerous conveyorized surface mines successfully operating today. Each surface mine is unique and requires a custom made system which ideally begins as part of the mine development plan. When properly applied, conveyorized systems can offer major cost savings in both capital costs and operating and maintenance costs. With modern technology, both required availability and flexibility have been satisfied on the many currently operating mines. Conveyorized systems offer a valuable ''tool'' which when combined with the other proven mining technology results in the most efficient surface mine operations which spells lower costs and higher profits.

  9. Underground mine communications: a survey

    SciTech Connect

    Yarkan, S.; Guzelgoz, S.; Arslan, H.; Murphy, R.R.

    2009-07-01

    After a recent series of unfortunate underground mining disasters, the vital importance of communications for underground mining is underlined one more time. Establishing reliable communication is a very difficult task for underground mining due to the extreme environmental conditions. Until now, no single communication system exists which can solve all of the problems and difficulties encountered in underground mine communications. However, combining research with previous experiences might help existing systems improve, if not completely solve all of the problems. In this survey, underground mine communication is investigated. Major issues which underground mine communication systems must take into account are discussed. Communication types, methods, and their significance are presented.

  10. Rational management of diarrhoea in children.

    PubMed

    1991-01-01

    Most health professionals in developing and developed countries consider oral rehydration therapy (ORT) to be the most effective treatment for diarrhea. An estimated 1,500 million episodes of diarrhea occur annually and 3 million of these results in death of children 5 years old. Caretakers must give increased amounts of fluids (rice water, tea, and gruel) to children with diarrhea to prevent dehydration. If they become dehydrated, caretakers must take them to a health workers so he/she can assess and treat them with oral rehydration solution (ORS) or, in the case of severe dehydration, rehydrate them intravenously. Drugs should not be used to treat diarrhea cases. Nevertheless, surveys in 4 Asian nations indicated that drug use ranged from 22-68% of diarrhea episodes and ORS use ranged only from 9-21%. Drug use is very expensive. In fact, Peru spent US$2 million on antidiarrheals in 1988- 1989. Further, drugs often make up 40% of health care costs in developing countries, so ORS use reduces these costs. Indeed drug us deflects from correct case management of diarrhea. In addition, drugs have no proven value for acute diarrhea. They do not decrease the fluid loss responsible for death and may even have serious side effects, such as central nerve depression and gastrointestinal toxicity. If health workers suspect cholera or dysentery, however, they can administer effective and relatively inexpensive antibiotics. Since the early 1980s, almost all developing countries had a national control of diarrheal disease program. In several countries, hospital admission rates for diarrhea fell 61% and the case fatality rate fell 71% after ORT introduction. Some hospitals have even saved as much as 60% in costs due to these declines. WHO has a book available which covers rational use of drugs in managing acute diarrhea in children. PMID:12284331

  11. Rationally designed substrates for SERS biosensing

    NASA Astrophysics Data System (ADS)

    Yan, Bo

    The large electromagnetic field enhancement provided by nanostructured noble metal surfaces forms the foundation for a series of enabling optical analytical techniques, such as surface enhanced Raman spectroscopy (SERS), surface enhanced IR absorption spectroscopy (SEIRA), surface enhanced fluorescent microscopy (SEF), to name only a few. Critical sensing applications have, however, other substrate requirements than mere peak signal enhancement. The substrate needs to be reliable, provide reproducible signal enhancements, and be amenable to a combination with microfluidic chips or other integrated sensor platforms. These needs motivate the development of engineerable SERS substrate "chips" with defined near- and far-field responses. In this dissertation, two types of rationally designed SERS substrates - nanoparticle cluster arrays (NCAs) and SERS stamp - will be introduced and characterized. NCAs were fabricated through a newly developed template guided self-assembly fabrication approach, in which chemically synthesized nanoparticles are integrated into predefined patterns using a hybrid top-down/bottom-up approach. Since this method relies on chemically defined building blocks, it can overcome the resolution limit of conventional lithographical methods and facilitates higher structural complexity. NCAs sustain near-field interactions within individual clusters as well as between entire neighboring clusters and create a multi-scale cascaded E-field enhancement throughout the entire array. SERS stamps were generated using an oblique angle metal deposition on a lithographically defined piston. When mounted on a nanopositioning stage, the SERS stamps were enabled to contact biological surfaces with pristine nanostructured metal surfaces for a label-free spectroscopic characterization. The developed engineered substrates were applied and tested in critical sensing applications, including the ultra-trace detection of explosive vapors, the rapid discrimination of

  12. Deep mine cooling system

    SciTech Connect

    Conan, J.

    1984-11-06

    A deep mine cooling system comprising a compressor supplied with air and rotatively driven by a motor and an expansion turbine supplied with compressed air from said compressor and driving an actuating unit, wherein the compressed air, after leaving the compressor but prior to reaching the expansion turbine, passes through a steam generator whose output provides the energy required to operate an absorption refrigeration machine used to cool utility water for mining, said compressed air on leaving the steam generator going to a first heat exchanger in which it yields calories to a water circuit comprising a second heat exchanger, said second heat exchanger giving off the calories absorbed by the water in the first heat exchanger to the air fed by the second heat exchanger to a drying cell that is regenerated by said air from the second heat exchanger, said drying cell being part of a set of two cells working in alternation, the other cell in the set receiving the compressed air from the first heat exchanger, such that the compressed air is fed to said expansion turbine after leaving said drying unit, and wherein the air exhausted from said expansion turbine is sent to a third heat exchanger after which it is distributed according to the needs of the mine, said third exchanger being traversed by the water collected in the mine, cooled in said exchanger and circulated upon leaving said exchanger to meet the cool water requirements of the mine.

  13. String Mining in Bioinformatics

    NASA Astrophysics Data System (ADS)

    Abouelhoda, Mohamed; Ghanem, Moustafa

    Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word "data-mining" is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

  14. Mining the earth

    SciTech Connect

    Young, J.E.

    1992-01-01

    Substances extracted from the earth - stone, iron, bronze - have been so critical to human development that historians name the ages of our past after them. But while scholars have carefully tracked human use of minerals, they have never accounted for the vast environmental damage incurred in mineral production. Few people would guess that a copper mining operation has removed a piece of Utah seven times the weight of all the material dug for the Panama Canal. Few would dream that mines and smelters take up to a tenth of all the energy used each year, or that the waste left by mining measures in the billions of tons - dwarfing the world's total accumulation of more familiar kinds of waste, such as municipal garbage. Indeed, more material is now stripped from the earth by mining than by all the natural erosion of the earth's rivers. The effects of mining operations on the environment are discussed under the following topics: minerals in the global economy, laying waste, at what cost cleaning up, and dipping out. It is concluded that in the long run, the most effective strategy for minimizing new damage is not merely to make mineral extraction cleaner, but to reduce the rich nations needs for virgin (non-recycled) minerals.

  15. Challenges and Triumphs to Genomics-Based Natural Product Discovery

    PubMed Central

    Jensen, Paul R.; Chavarria, Krystle L.; Fenical, William; Moore, Bradley S.; Ziemert, Nadine

    2013-01-01

    Genome sequencing is rapidly changing the field of natural products research by providing opportunities to assess the biosynthetic potential of strains prior to chemical analysis or biological testing. Ready access to sequence data is driving the development of new bioinformatic tools and methods to identify the products of silent or cryptic pathways. While genome mining has fast become a useful approach to natural product discovery, it has also become clear that identifying pathways of interest is much easier than finding the associated products. This has led to bottlenecks in the discovery process that must be overcome for the potential of genomics-based natural product discovery to be fully realized. In this perspective, we address some of these challenges in the context of our work with the marine actinomycete genus Salinispora, which is proving to be a useful model with which to apply genome mining as an approach to natural product discovery. PMID:24104399

  16. Rational eating: can it lead to overweightness or underweightness?

    PubMed

    Levy, Amnon

    2002-09-01

    Although a deviation from the physiologically optimal weight increases the probability of dying, the steady state for an expected lifetime-utility maximiser is a state of overweightness. However, even a small initial deviation from this rationally stationary weight is followed by explosive oscillations. These oscillations might lead to severe and chronic underweightness in a late stage of life. In the presence of socio-cultural norms of appearance, the rationally stationary weight of fat people is lower than otherwise and the rationally stationary weight of lean people is greater than otherwise. PMID:12349887

  17. Rational choices for the wavelengths of a two color interferometer

    SciTech Connect

    Jobes, F.C.

    1995-07-01

    If in a two color interferometer for plasma density measurements, the two wavelengths are chosen to have a ratio that is a rational number, and if the signals from each of the wavelengths are multiplied in frequency by the appropriate integer of the rational number and then heterodyned together, the resultant signal will have all effects of component motion nulled out. A phase measurement of this signal will have only plasma density information in it. With CO{sub 2} lasers, it is possible to find suitable wavelength pairs which are close enough to rational numbers to produce an improvement of about 100 in density resolution, compared to standard two color interferometers.

  18. Monotonicity preserving using GC1 rational quartic spline

    NASA Astrophysics Data System (ADS)

    Karim, Samsul Ariffin Abdul; Pang, Kong Voon

    2012-09-01

    This paper proposed GC1 rational quartic spline (quartic numerator and linear denominator) with two parameters to preserve the shape of the monotone data. Simple data dependent constraints will be derived on one of the parameters while the other is free to modify and refine the resultant shape of the data. Both parameters are independent to each other. The method under consideration here, avoid the modification of the derivative when the sufficient condition for the monotonicity are violated as can be noticed in the original construction of C1 rational quartic spline with linear denominator. Numerical comparison between the proposed scheme and C1 rational quartic spline will be given.

  19. ChromClust: A semi-supervised chromatin clustering toolkit for mining histone modifications interplay.

    PubMed

    Noureen, Nighat; Touseef, Muhammad; Fazal, Sahar; Qadir, Muhammad Abdul

    2015-12-01

    Mining patterns of histone modifications interplay from epigenomic profiles are one of the leading research areas these days. Various methods based on clustering approaches and hidden Markov models have been presented so far with some limitations. Here we present ChromClust, a semi-supervised clustering tool for mining commonly occurring histone modifications at various locations of the genome. Applying our method to 11 chromatin marks in nine human cell types recovered 11 clusters based on distinct chromatin signatures mapping to various elements of the genome. Our approach is efficient in respect to time and space usage along with the added facility of maintaining database at the backend. It outperforms the existing methods with respect to mining patterns in a semi-supervised fashion mapping to various functional elements of the genome. It will aid in future by saving the resources of time and space along with efficiently retrieving the hidden interplay of histone combinations. PMID:26551295

  20. Whither genomics?

    PubMed Central

    Murray, Andrew W

    2000-01-01

    The flood of data from genome-wide analysis is transforming biology. We need to develop new, interdisciplinary approaches to convert these data into information about the components and structures of individual biological pathways and to use the resulting information to yield knowledge about general principles that explain the functions and evolution of life. PMID:11104516

  1. Linking Virus Genomes with Host Taxonomy.

    PubMed

    Mihara, Tomoko; Nishimura, Yosuke; Shimizu, Yugo; Nishiyama, Hiroki; Yoshikawa, Genki; Uehara, Hideya; Hingamp, Pascal; Goto, Susumu; Ogata, Hiroyuki

    2016-03-01

    Environmental genomics can describe all forms of organisms--cellular and viral--present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts. PMID:26938550

  2. Linking Virus Genomes with Host Taxonomy

    PubMed Central

    Mihara, Tomoko; Nishimura, Yosuke; Shimizu, Yugo; Nishiyama, Hiroki; Yoshikawa, Genki; Uehara, Hideya; Hingamp, Pascal; Goto, Susumu; Ogata, Hiroyuki

    2016-01-01

    Environmental genomics can describe all forms of organisms—cellular and viral—present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts. PMID:26938550

  3. Minerals and mine drainage

    SciTech Connect

    Liang, H.C.; Thomson, B.M.

    2009-09-15

    A review of literature published in 2008 and early 2009 on research related to the production of acid mine drainage and/or in the dissolution of minerals as a result of mining, with special emphasis on the effects of these phenomena on the water quality in the surrounding environment, is presented. This review is divided into six sections: 1) Site Characterization and Assessment, 2) Protection, Prevention, and Restoration, 3) Toxicity Assessment, 4) Environmental Fate and Transport, 5) Biological Characterization, and 6) Treatment Technologies. Because there is much overlap in research areas associated with minerals and mine drainage, many papers presented in this review can be classified into more than one category, and the six sections should not be regarded as being mutually-exclusive, nor should they be thought of as being all-inclusive.

  4. Mine drainage and surface-mine reclamation. Volume 2. Mine reclamation, abandoned mine lands, and policy issues. Information Circular/1988

    SciTech Connect

    Not Available

    1988-01-01

    Mine waste and mine reclamation are topics of major interest to the mining industry, the government and the general public. The publication and its companion volume are the proceedings of a conference held in Pittsburgh, April 19-21, 1988. There were nine sessions (50 papers) that dealt with the geochemistry, hydrology and problems of mine waste and mine water, especially acid mine drainage. The nine sessions (43 papers) that dealt with reclamation and restoration of disturbed lands, as well as related policy issues, are included in volume 2. Volume 2 also contains the ten papers that pertained to control of subsidence and mine fires at abandoned mines. Poster session presentations are, in general, represented by abstracts.

  5. Gravity in a Mine Shaft.

    ERIC Educational Resources Information Center

    Hall, Peter M.; Hall, David J.

    1995-01-01

    Discusses the effects of gravity, local density compared to the density of the earth, the mine shaft, centrifugal force, and air buoyancy on the weight of an object at the top and at the bottom of a mine shaft. (JRH)

  6. Pneumatic stowing seals mines

    SciTech Connect

    Brezovec, D.

    1983-11-01

    A mechanized technique to seal abandoned mines has been used successfully to close 13 openings at Duquesne Light Co.'s mined-out Warwick No. 2 mine, near Greensboro, Pa. The mechanized system, which uses a pneumatic stower and crushed limestone, closed the entries more economically and in less time than it would have taken to install traditional concrete block stopping and clay plug seals, according to John C. Draper. Draper, a mining engineer with Duquesne Light's coal department, was in charge of installing the Warwick seals in a Bureau of Mines-sponsored field test on the pneumatic sealing technique. The lowest estimated cost for installing conventional stopping and plug closures for the 13 Warwick openings was $225,000, says Draper, while the openings were closed using the mechanized system for $245,000. Draper says the newer stopping cost more in the instance because work was stopped often to gather information for the experiment. The experimental closures were installed in 38 days. The job would have taken at least 149 days if traditional closures were being installed, Draper say. To install a traditional concrete block/clay plug closure, the mine opening must be cleaned thoroughly and the roof must be supported for some 3 ft from the outside. Then a solid wall or stopping must be built 25 ft from the surface and the entry must be packed with clay to the surface. Much of this job requires workers to remain underground. In pneumatic stowing, 1 1/2-in. crushed limestone with fines is conveyed through a pipeline and into the mine opening under low air pressure. Watertight seals can be installed by blowing about 10 ft of rock into the opening against the top to act as roof support. Safety posts are installed and about 10 or 15 ft of mine entry is cleaned. About 2 in. of raw cement or bentonite is placed on the floor and limestone mixed with dry cement or bentonite is blown into the opening.

  7. Harvesting bioenergy with rationally designed complex functional materials

    NASA Astrophysics Data System (ADS)

    Kuang, Liangju

    A key challenge in renewable energy is to capture, convert and store solar power with earth-abundant materials and environmentally benign technologies. The goal of this thesis is to develop rationally designed complex functional materials for bio-renewable energy applications. On one hand, photoconversion membrane proteins (MPs) are nature's nanoengineering feats for renewable energy management. Harnessing their functions in synthetic systems could help understand, predict, and ultimately control matter and energy at the nanoscale. This is particularly enticing in the post-genome era as recombinant or cell-free expression of many MPs with high yields becomes possible. However, the labile nature of lipid bilayers renders them unsuitable for use in a broad range of engineered systems. A knowledge gap exists about how to design robust synthetic nanomembranes as lipid-bilayer-mimics to support MP functions and how to direct hierarchical MP reconstitution into those membranes to form 2-D or 3-D ordered proteomembrane arrays. Our studies on proteorhodopsin (PR) and bacterial reaction center (BRC), the two light-harvesting MPs, reveal that a charge-interaction-directed reconstitution (CIDR) mechanism induces spontaneous reconstitution of detergent-solubilized MPs into various amphiphilic block copolymer membranes, many of which have far superior stability than lipid bilayers. Our preliminary data also suggest MPs are not enslaved by the biological membranes they derive from; rather, the chemically nonspecific material properties of MP-supporting membranes may act as allosteric regulators. Versatile chemical designs are possible to modulate the conformational energetics of MPs, hence their transport performance in synthetic systems. On the other hand, microalgae are widely regarded as a sustainable feedstock for biofuel production. Microalgae-derived biofuels have not been commercialized yet because current technologies for microalgae dewatering add a huge cost to the

  8. 30 CFR 77.1200 - Mine map.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... SAFETY STANDARDS, SURFACE COAL MINES AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Maps § 77.1200 Mine...) The location of railroad tracks and public highways leading to the mine, and mine buildings of a permanent nature with identifying names shown; (k) Underground mine workings underlying and within...

  9. 30 CFR 77.1200 - Mine map.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... SAFETY STANDARDS, SURFACE COAL MINES AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Maps § 77.1200 Mine...) The location of railroad tracks and public highways leading to the mine, and mine buildings of a permanent nature with identifying names shown; (k) Underground mine workings underlying and within...

  10. 30 CFR 77.1200 - Mine map.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... SAFETY STANDARDS, SURFACE COAL MINES AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Maps § 77.1200 Mine...) The location of railroad tracks and public highways leading to the mine, and mine buildings of a permanent nature with identifying names shown; (k) Underground mine workings underlying and within...

  11. 30 CFR 77.1200 - Mine map.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... SAFETY STANDARDS, SURFACE COAL MINES AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Maps § 77.1200 Mine...) The location of railroad tracks and public highways leading to the mine, and mine buildings of a permanent nature with identifying names shown; (k) Underground mine workings underlying and within...

  12. 30 CFR 77.1200 - Mine map.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... SAFETY STANDARDS, SURFACE COAL MINES AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Maps § 77.1200 Mine...) The location of railroad tracks and public highways leading to the mine, and mine buildings of a permanent nature with identifying names shown; (k) Underground mine workings underlying and within...

  13. 30 CFR 75.373 - Reopening mines.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Reopening mines. 75.373 Section 75.373 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Ventilation § 75.373 Reopening mines. After a mine is...

  14. 30 CFR 75.1200 - Mine map.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Mine map. 75.1200 Section 75.1200 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Maps § 75.1200 Mine map. The operator of a coal mine shall...

  15. 30 CFR 75.1200 - Mine map.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Mine map. 75.1200 Section 75.1200 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Maps § 75.1200 Mine map. The operator of a coal mine shall...

  16. 30 CFR 75.373 - Reopening mines.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Reopening mines. 75.373 Section 75.373 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Ventilation § 75.373 Reopening mines. After a mine is...

  17. 30 CFR 75.1200 - Mine map.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Mine map. 75.1200 Section 75.1200 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Maps § 75.1200 Mine map. The operator of a coal mine shall...

  18. 30 CFR 75.1200 - Mine map.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Mine map. 75.1200 Section 75.1200 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Maps § 75.1200 Mine map. The operator of a coal mine shall...

  19. 30 CFR 75.373 - Reopening mines.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Reopening mines. 75.373 Section 75.373 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Ventilation § 75.373 Reopening mines. After a mine is...

  20. 30 CFR 75.373 - Reopening mines.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Reopening mines. 75.373 Section 75.373 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Ventilation § 75.373 Reopening mines. After a mine is...

  1. 30 CFR 75.1200 - Mine map.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Mine map. 75.1200 Section 75.1200 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Maps § 75.1200 Mine map. The operator of a coal mine shall...

  2. 30 CFR 75.373 - Reopening mines.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Reopening mines. 75.373 Section 75.373 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR COAL MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Ventilation § 75.373 Reopening mines. After a mine is...

  3. WIRELESS MINE WIDE TELECOMMUNICATIONS TECHNOLOGY

    SciTech Connect

    Zvi H. Meiksin

    2002-04-01

    Two industrial prototype units for through-the-earth wireless communication were constructed and tested. Preparation for a temporary installation in NIOSH's Lake Lynn mine for the through-the-earth and the in-mine system were completed. Progress was made in the programming of the in-mine system to provide data communication. Work has begun to implement a wireless interface between equipment controllers and our in-mine system.

  4. Towards Rational Decision-Making in Secondary Education.

    ERIC Educational Resources Information Center

    Cohn, Elchanan

    Without a conscious effort to achieve optimum resource allocation, there is a real danger that educational resources may be wasted. This document uses input-output analysis to develop a model for rational decision-making in secondary education. (LLR)

  5. Monotonicity preserving splines using rational Ball cubic interpolation

    NASA Astrophysics Data System (ADS)

    Zakaria, Wan Zafira Ezza Wan; Jamal, Ena; Ali, Jamaludin Md.

    2015-10-01

    In scientific application and Computer Aided Design (CAD), users usually need to generate a spline passing through a given set of data which preserves certain shape properties of the data such as positivity, monotonicity or convexity [1]. The required curves have to be a smooth shape-preserving interpolation. In this paper a rational cubic spline in Ball representation is developed to generate an interpolant that preserves monotonicity. In this paper to control the shape of the interpolant three shape parameters are introduced. The shape parameters in the description of the rational cubic interpolation are subjected to monotonicity constrained. The necessary and sufficient conditions of the rational cubic interpolation are derived and visually the proposed rational cubic interpolant gives a very pleasing result.

  6. Rationally designing the mechanical properties of protein hydrogels

    NASA Astrophysics Data System (ADS)

    Cao, Yi

    Naturally occurring biomaterials possess diverse mechanical properties, which are critical to their unique biological functions. However, it remains challenging to rationally control the mechanical properties of synthetic biomaterials. Here we provide a bottom-up approach to rationally design the mechanical properties of protein-based hydrogels. We first use atomic fore microscope (AFM) based single-molecule force spectroscopy to characterize the mechanical stability of individual protein building blocks. We then rationally design the mechanical properties of hydrogels by selecting different combination of protein building blocks of known mechanical properties. As a proof-of-principle, we demonstrate the engineering of hydrogels of distinct extensibility and toughness. This simple combinatorial approach allows direct translation of the mechanical properties of proteins from the single molecule level to the macroscopic level and represents an important step towards rationally designing the mechanical properties of biomaterials.

  7. Strange Bedfellows?: Rational-Emotive Therapy and Pastoral Counseling.

    ERIC Educational Resources Information Center

    Lawrence, Constance; Huber, Charles H.

    1982-01-01

    Discusses integrating Rational-Emotive Therapy with biblical precepts as a basis for pastoral counselors to bridge the gap between religion and psychotherapy. Illustrates the use of biblical quotations in disputing irrational beliefs. Presents a case example. (Author/RC)

  8. Finding Bounded Rational Equilibria. Part 1; Iterative Focusing

    NASA Technical Reports Server (NTRS)

    Wolpert, David H.

    2004-01-01

    A long-running difficulty with conventional game theory has been how to modify it to accommodate the bounded rationality characterizing all real-world players. A recurring issue in statistical physics is how best to approximate joint probability distributions with decoupled (and therefore far more tractable) distributions. It has recently been shown that the same information theoretic mathematical structure, known as Probability Collectives (PC) underlies both issues. This relationship between statistical physics and game theory allows techniques and insights from the one field to be applied to the other. In particular, PC provides a formal model-independent definition of the degree of rationality of a player and of bounded rationality equilibria. This pair of papers extends previous work on PC by introducing new computational approaches to effectively find bounded rationality equilibria of common-interest (team) games.

  9. Cubic Polynomials with Rational Roots and Critical Points

    ERIC Educational Resources Information Center

    Gupta, Shiv K.; Szymanski, Waclaw

    2010-01-01

    If you want your students to graph a cubic polynomial, it is best to give them one with rational roots and critical points. In this paper, we describe completely all such cubics and explain how to generate them.

  10. Innovation in energy systems: a case study of gasoline rationing

    SciTech Connect

    Sullivan, M.C.

    1981-01-01

    The purpose of the study is to develop a theoretical understanding of the implementation of new programs (innovations) by organizations, verify concepts with a case study of gasoline rationing, and apply knowledge gained to an analysis of the Standby Gasoline Rationing Plan. Major hypotheses of the study are: (1) Role specialization is required during the initial stage of implementation. (2) Decentralization is required during the initial stage of implementation. (3) Role specialization hinders implementation during the later stage. (4) Centralization is required during the later stage of implementation. The concept of technology delivery system is employed to demonstrate how organizational structure (degree of specialization centralization, etc.) is related to technological requirements and social need. The four major hypotheses were verified with the innovation theory as well as the case study of rationing. Application to the Standby Gasoline Rationing Plan leads to the conclusion that major problems would occur with plan implementation.

  11. What Rational-Emotive Therapy Is and Is Not

    ERIC Educational Resources Information Center

    Ellis, Albert

    1974-01-01

    Albert Ellis refutes a review of the functional characteristics of Rational-Emotive Therapy given by Dugald S. Arbuckle. Ellis concludes that Arbuckle only minimally understands RET theory or the behaviors consequent to it. (PC)

  12. The Rational Approach to Budget Cuts: One University's Experience.

    ERIC Educational Resources Information Center

    Hardy, Cynthia

    1988-01-01

    The University of Montreal's choice of the rational model of decision-making in managing budget cutbacks is explored and compared with other approaches, including the bureaucratic, garbage can, political, and collegial models. (MSE)

  13. Genetics and Genomics of the Genus Amycolatopsis.

    PubMed

    Kumari, Rashmi; Singh, Priya; Lal, Rup

    2016-09-01

    Actinobacteria are gram-positive filamentous bacteria which contains some of the most deadly human pathogens (Mycobacterium tuberculosis, M. leprae, Corynebacterium diphtheriae, Nocardia farcinica), plant pathogens (Streptomyces scabies, Leifsonia xyli) along with organisms that produces antibiotic (Streptomycetes, Amycolatopsis, Salinospora). Interestingly, these bacteria are equipped with an extraordinary capability of producing antibiotics and other metabolites which have medicinal properties. With the advent of inexpensive genome sequencing techniques and their clinical importance, many genomes of Actinobacteria have been successfully sequenced. These days, with the constant increasing number of drug-resistant bacteria, the urgent need for discovering new antibiotics has emerged as a major scientific challenge. And, unfortunately the traditional method of screening bacterial strains for the production of antibiotics has decreased leading to a paradigm shift in the planning and execution of discovery of novel biosynthetic gene clusters via genome mining process. The entire focus has shifted to the evaluation of genetic capacity of organisms for metabolite production and activation of cryptic gene clusters. This has been made possible only due to the availability of genome sequencing and has been augmented by genomic studies and new biotechnological approaches. Through this article, we present the analysis of the genomes of species belonging to the genus Amycolatopsis, sequenced till date with a focus on completely sequenced genomes and their application for further studies. PMID:27407288

  14. Orthogonal rational functions and quadrature on an interval

    NASA Astrophysics Data System (ADS)

    van Deun, J.; Bultheel, A.

    2003-04-01

    Rational functions with real poles and poles in the complex lower half-plane, orthogonal on the real line, are well known. Quadrature formulas similar to the Gauss formulas for orthogonal polynomials have been studied. We generalize to the case of arbitrary complex poles and study orthogonality on a finite interval. The zeros of the orthogonal rational functions are shown to satisfy a quadratic eigenvalue problem. In the case of real poles, these zeros are used as nodes in the quadrature formulas.

  15. Pharmacodynamics of nicotine: implications for rational treatment of nicotine addiction.

    PubMed

    Benowitz, N L

    1991-05-01

    Rational treatment of the pharmacologic aspects of tobacco addiction includes nicotine substitution therapy. Understanding the pharmacodynamics of nicotine and its role in the addiction process provides a basis for rational therapeutic intervention. Pharmacodynamic considerations are discussed in relation to the elements of smoking cessation therapy: setting objectives, selecting appropriate medication and dosing form, selecting the optimal doses and dosage regimens, assessing therapeutic outcome, and adjusting therapy to optimize benefits and minimize risks. PMID:1859911

  16. REMOTE SENSING AND MOUNTAINTOP MINING

    EPA Science Inventory

    Coal mining is Appalachia has undergone dramatic changes in the past decade. Modem mining practices know as Mountaintop Mining (MTM) and Valley Fills (VF) are at the center of an environmental and legal controversy that has spawned lawsuits and major environmental investigations....

  17. Review of South American mines

    SciTech Connect

    Not Available

    1984-07-01

    A general overview is presented of the mining activity and plans for South America. The countries which are presented are Columbia, Argentina, Brazil, Venezuela, Chile, Peru, and Bolivia. The products of the mines include coal, bauxite, gold, iron, uranium, copper and numerous other minor materials. A discussion of current production, support and processing facilities, and mining strategies is also given.

  18. Mine-Mouth Geyser Problem.

    ERIC Educational Resources Information Center

    de Nevers, Noel

    1982-01-01

    An oilwell drilling rig accidentally drilled into an underground salt mine, draining a lake and filling the mine, with water jetting out of the mine 400 feet into the air. An explanation of the jetting phenomenon is offered in terms of the laws of fluid dynamics, with supporting diagrams and calculations. (Author/JN)

  19. Effects of feeding rations with genetically modified whole cottonseed to lactating Holstein cows.

    PubMed

    Castillo, A R; Gallardo, M R; Maciel, M; Giordano, J M; Conti, G A; Gaggiotti, M C; Quaino, O; Gianni, C; Hartnell, G F

    2004-06-01

    Two experiments were conducted to evaluate dry matter intake (DMI), milk yield, and milk composition from feeding rations that contained different sources of genetically modified whole cottonseed to Argentinean Holstein dairy cows. Twenty-four lactating multiparous Argentinean Holstein dairy cows were used in 2 experiments with a replicated 4 x 4 Latin square design, with cows averaging 565 kg body weight and 53 d in milk at the beginning of the experiments. Treatments in Experiment 1 were: Bollgard cotton containing the cry1Ac gene, Bollgard II cotton containing cry1Ac and cry2Ab genes, Roundup Ready cotton containing the cp4 epsps gene, and a control nongenetically modified but genetically similar cottonseed. In Experiment 2, two commercial sources, a parental control line, and the transgenic cotton containing both cry1Ac and cp4 epsps genes were used as treatments. All cows received the same total mixed ration but with different whole cottonseed sources. Cottonseed was included to provide 2.50 kg per cow daily (dry matter [DM] basis) or about 10% of the total diet DM. The ingredient composition of the total mixed ration was 32% alfalfa hay, 28% corn silage, 22% corn grain, 17% soybean meal, and 2% minerals and vitamins. In addition, genomic DNA was extracted from a subset of milk samples and analyzed by polymerase chain reaction followed by Southern blot hybridization for small fragments of the cry1Ac transgene and an endogenous cotton gene, acp1. No sample was positive for transgenic or plant DNA fragments at the limits of detection for the assays following detailed data evaluation criteria. The DMI, milk yield, milk composition, body weight, and body condition score did not differ among treatments. Cottonseed from genetically modified varieties used in these studies yielded similar performance in lactating dairy cows when compared to non-transgenic control and reference cottonseed. PMID:15453492

  20. Rational-driver approximation in car-following theory.

    PubMed

    Lubashevsky, Ihor; Wagner, Peter; Mahnke, Reinhard

    2003-11-01

    The problem of a car following a lead car driven with constant velocity is considered. To derive the governing equations for the following car dynamics a cost functional is constructed. This functional ranks the outcomes of different driving strategies, which applies to fairly general properties of the driver behavior. Assuming rational-driver behavior, the existence of the Nash equilibrium is proved. Rational driving is defined by supposing that a driver corrects continuously the car motion to follow the optimal path minimizing the cost functional. The corresponding car-following dynamics is described quite generally by a boundary value problem based on the obtained extremal equations. Linearization of these equations around the stationary state results in a generalization of the widely used optimal velocity model. Under certain conditions (the "dense traffic" limit) the rational car dynamics comprises two stages, fast and slow. During the fast stage a driver eliminates the velocity difference between the cars, the subsequent slow stage optimizes the headway. In the dense traffic limit an effective Hamiltonian description is constructed. This allows a more detailed nonlinear analysis. Finally, the differences between rational and bounded rational driver behavior are discussed. The latter, in particular, justifies some basic assumptions used recently by the authors to construct a car-following model lying beyond the frameworks of rationality. PMID:14682848

  1. Putting the cacao genome to work: Development and utilization of Theobroma cacao SNP markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Next Generation Sequencing technology is driving the sequencing and assembly of whole genomes at an ever increasing rate. With the release of the Theobroma cacao genome sequence, vast amounts of data are currently available to researchers worldwide, however mining this data to provide cacao breeder...

  2. Draft Genome Sequence of Pedobacter sp. Strain NL19, a Producer of Potent Antibacterial Compounds

    PubMed Central

    2015-01-01

    Here, we report the draft genome sequence of Pedobacter sp. strain NL19. The genome has 5.99 Mbp and a G+C content of 39.0%. NL19 was isolated from sludge from an abandoned uranium mine in the north of Portugal, and it produces potent antibacterials against Gram-positive and Gram-negative bacteria. PMID:25814603

  3. Draft Genome Sequence of Pedobacter sp. Strain NL19, a Producer of Potent Antibacterial Compounds.

    PubMed

    Santos, Tiago; Cruz, Andreia; Caetano, Tânia; Covas, Cláudia; Mendo, Sónia

    2015-01-01

    Here, we report the draft genome sequence of Pedobacter sp. strain NL19. The genome has 5.99 Mbp and a G+C content of 39.0%. NL19 was isolated from sludge from an abandoned uranium mine in the north of Portugal, and it produces potent antibacterials against Gram-positive and Gram-negative bacteria. PMID:25814603

  4. Functional genomic approaches for understanding the mode of action of Bacillus sp biocontrol strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete genome sequencing of several Bacillus sp. strains has shed new light on the mode of action of these antagonists of plant pathogens. The use of genomic data mining tools provided the ability to quickly determine the potential of these strains to produce bioactive secondary metabolites. Our B...

  5. Genome Sequence of the Acidophilic Sulfate-Reducing Peptococcaceae Strain CEB3

    PubMed Central

    Petzsch, Patrick; Poehlein, Anja; Johnson, D. Barrie; Daniel, Rolf; Schlömann, Michael

    2015-01-01

    We report the draft genome of the Peptococcaceae strain CEB3 that originated from an acidic (pH 2.5) stream draining an abandoned copper mine. Strain CEB3 is one of the very few reported acidophilic sulfate-reducing isolates. The 5.04-Mb draft genome harbors 5,069 predicted protein-encoding and 66 RNA genes. PMID:26251503

  6. Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering.

    PubMed

    Voigt, Franka; Wiedemann, Lisa; Zuliani, Cecilia; Querques, Irma; Sebe, Attila; Mátés, Lajos; Izsvák, Zsuzsanna; Ivics, Zoltán; Barabas, Orsolya

    2016-01-01

    Sleeping Beauty (SB) is a prominent Tc1/mariner superfamily DNA transposon that provides a popular genome engineering tool in a broad range of organisms. It is mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends. To facilitate SB's applications, here we determine the crystal structure of the transposase catalytic domain and use it to model the SB transposase/transposon end/target DNA complex. Together with biochemical and cell-based transposition assays, our structure reveals mechanistic insights into SB transposition and rationalizes previous hyperactive transposase mutations. Moreover, our data enables us to design two additional hyperactive transposase variants. Our work provides a useful resource and proof-of-concept for structure-based engineering of tailored SB transposases. PMID:27025571

  7. Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering

    PubMed Central

    Voigt, Franka; Wiedemann, Lisa; Zuliani, Cecilia; Querques, Irma; Sebe, Attila; Mátés, Lajos; Izsvák, Zsuzsanna; Ivics, Zoltán; Barabas, Orsolya

    2016-01-01

    Sleeping Beauty (SB) is a prominent Tc1/mariner superfamily DNA transposon that provides a popular genome engineering tool in a broad range of organisms. It is mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends. To facilitate SB's applications, here we determine the crystal structure of the transposase catalytic domain and use it to model the SB transposase/transposon end/target DNA complex. Together with biochemical and cell-based transposition assays, our structure reveals mechanistic insights into SB transposition and rationalizes previous hyperactive transposase mutations. Moreover, our data enables us to design two additional hyperactive transposase variants. Our work provides a useful resource and proof-of-concept for structure-based engineering of tailored SB transposases. PMID:27025571

  8. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis.

    PubMed

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-01-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria. PMID:27615705

  9. Lunabotics Mining Competition

    NASA Technical Reports Server (NTRS)

    Mueller, Rob; Murphy, Gloria

    2010-01-01

    This slide presentation describes a competition to design a lunar robot (lunabot) that can be controlled either remotely or autonomously, isolated from the operator, and is designed to mine a lunar aggregate simulant. The competition is part of a systems engineering curriculum. The 2010 competition winners in five areas of the competition were acknowledged, and the 2011 competition was announced.

  10. Plutonium mining for cleanup.

    PubMed

    Bramlitt, E T

    1988-08-01

    Cleanup is the act of making a contaminated site relatively free of Pu so it may be used without radiological safety restrictions. Contaminated ground is the focus of major cleanups. Cleanup traditionally involves determining Pu content of soil, digging up soil in which radioactivity exceeds guidelines, and relocating excised soil to a waste-disposal site. Alternative technologies have been tested at Johnston Atoll (JA), where there is as much as 100,000 m3 of Pu-contaminated soil. A mining pilot plant operated for the first 6 mo of 1986 and made 98% of soil tested "clean", from more than 40 kBq kg-1 (1000 pCi g-1) to less than about 500 Bq kg-1 (15 pCi g-1) by concentrating Pu in 2% of the soil. The pilot plant is now installed at the U.S. Department of Energy Nevada Test Site for evaluating cleanup of other contaminated soils and refining cleanup effectiveness. A full-scale cleanup plant has been programmed for JA in 1988. In this paper, previous cleanups are reviewed, and the mining endeavor at JA is detailed. "True soil cleanup" is contrasted with the classical "soil relocation cleanup." The mining technology used for Pu cleanup has been in use for more than a century. Mining for cleanup, however, is unique. It is envisioned as being prominent for radiological and other cleanups in the future. PMID:3410718

  11. Mineral mining equipment

    SciTech Connect

    Monks, H.

    1980-11-25

    A mineral mining machine hauls itself along a working face by engaging a round link chain. The links of the chain are fed sequentially from link-retaining pockets in a track component arranged around the working face, around a driven sprocket assembly on the machine and returned to the pockets.

  12. Mining Your Own Data

    NASA Astrophysics Data System (ADS)

    Clark, Maurice

    2014-05-01

    Conducting asteroid photometry frequently requires imaging one area of the sky for many hours. Apart from the asteroid being studied, there may be many other objects of interest buried in the data. The value of mining your own asteroid data is discussed, using examples from observations made by the author, primarily at the Preston Gott Observatory at Texas Tech University.

  13. Mining Task Force Report.

    ERIC Educational Resources Information Center

    Saskatchewan Inst. of Applied Science and Technology, Saskatoon.

    In fall 1988, the Board of Directors of the Saskatchewan Institute of Applied Science and Technology (SIAST) created a task force to study the training needs of the mining industry in the province and evaluate SIAST's responsiveness to those needs. After assessing the technological changes taking place in the industry, surveying manpower needs,…

  14. String Mining in Bioinformatics

    NASA Astrophysics Data System (ADS)

    Abouelhoda, Mohamed; Ghanem, Moustafa

    Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word “data-mining” is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

  15. Contextual Text Mining

    ERIC Educational Resources Information Center

    Mei, Qiaozhu

    2009-01-01

    With the dramatic growth of text information, there is an increasing need for powerful text mining systems that can automatically discover useful knowledge from text. Text is generally associated with all kinds of contextual information. Those contexts can be explicit, such as the time and the location where a blog article is written, and the…

  16. Citrus Genomics

    PubMed Central

    Talon, Manuel; Gmitter Jr., Fred G.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop. PMID:18509486

  17. Ancient genomics

    PubMed Central

    Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  18. Genomic Imprinting

    PubMed Central

    Bajrami, Emirjeta; Spiroski, Mirko

    2016-01-01

    BACKGROUND: Genomic imprinting is the inheritance out of Mendelian borders. Many of inherited diseases and human development violates Mendelian law of inheritance, this way of inheriting is studied by epigenetics. AIM: The aim of this review is to analyze current opinions and options regarding to this way of inheriting. RESULTS: Epigenetics shows that gene expression undergoes changes more complex than modifications in the DNA sequence; it includes the environmental influence on the gametes before conception. Humans inherit two alleles from mother and father, both are functional for the majority of the genes, but sometimes one is turned off or “stamped” and doesn’t show in offspring, that gene is imprinted. Imprinting means that that gene is silenced, and gene from other parent is expressed. The mechanisms for imprinting are still incompletely defined, but they involve epigenetic modifications that are erased and then reset during the creation of eggs and sperm. Genomic imprinting is a process of silencing genes through DNA methylation. The repressed allele is methylated, while the active allele is unmethylated. The most well-known conditions include Prader-Willi syndrome, and Angelman syndrome. Both of these syndromes can be caused by imprinting or other errors involving genes on the long arm of chromosome 15. CONCLUSIONS: Genomic imprinting and other epigenetic mechanisms such as environment is shown that plays role in offspring neurodevelopment and autism spectrum disorder. PMID:27275355

  19. Rational polypharmacy in the bipolar affective disorders.

    PubMed

    Post, R M; Ketter, T A; Pazzaglia, P J; Denicoff, K; George, M S; Callahan, A; Leverich, G; Frye, M

    1996-01-01

    positive response in longer-term prophylaxis. Hypnotic benzodiazepines with anticonvulsant properties, such as clonazepam or lorazepam, are often used to help to induce sleep in escalating bipolar patients, and may be useful adjuncts as well. Patients who were inadequately responsive to either carbamazepine or valproate alone may be responsive to the anticonvulsant combination. In a similar fashion, one can also utilize several mood-stabilizing drugs (lithium and an anticonvulsant such as carbamazepine or valproate) in the treatment of depressive breakthroughs, and then augment this combination (if necessary) with a catecholamine-active antidepressant such as bupropion or a serotonin-selective reuptake inhibitor (SSRI) such as fluoxetine, paroxetine, sertraline or if necessary a monoamine oxidase inhibitor (MAOI). Once the patient has responded to a combination of drugs, it becomes problematic to decide whether the last agent added was the crucial ingredient in helping the patient achieve remission or that remission might have occurred with this agent alone. A conservative approach would have merit in patients who are finally stabilized on complex polypharmacy regimens only after many years of sequential trials; in this instance, the potential risk of re-exacerbating the illness with a taper of one of the drugs in the regimen. Rational polypharmacy should thus be implemented with careful delineation of the prior course of illness (typically using life chart methodology) and targeted treatment outcomes titrated against side effects, using sequential clinical trials in individual patients who have not adequately responded to monotherapy. In this fashion, it is hoped that pharmacodynamic differences among agents can be maximized and pharmacokinetic and side effects minimized. PMID:9294735

  20. Multisource causal data mining

    NASA Astrophysics Data System (ADS)

    Woodley, Robert; Gosnell, Michael; Shallenberger, Kevin

    2012-06-01

    Analysts are faced with mountains of data, and finding that relevant piece of information is the proverbial needle in a haystack, only with dozens of haystacks. Analysis tools that facilitate identifying causal relationships across multiple data sets are sorely needed. 21st Century Systems, Inc. (21CSi) has initiated research called Causal-View, a causal datamining visualization tool, to address this challenge. Causal-View is built on an agent-enabled framework. Much of the processing that Causal-View will do is in the background. When a user requests information, Data Extraction Agents launch to gather information. This initial search is a raw, Monte Carlo type search designed to gather everything available that may have relevance to an individual, location, associations, and more. This data is then processed by Data- Mining Agents. The Data-Mining Agents are driven by user supplied feature parameters. If the analyst is looking to see if the individual frequents a known haven for insurgents he may request information on his last known locations. Or, if the analyst is trying to see if there is a pattern in the individual's contacts, the mining agent can be instructed with the type and relevance of the information fields to look at. The same data is extracted from the database, but the Data Mining Agents customize the feature set to determine causal relationships the user is interested in. At this point, a Hypothesis Generation and Data Reasoning Agents take over to form conditional hypotheses about the data and pare the data, respectively. The newly formed information is then published to the agent communication backbone of Causal- View to be displayed. Causal-View provides causal analysis tools to fill the gaps in the causal chain. We present here the Causal-View concept, the initial research into data mining tools that assist in forming the causal relationships, and our initial findings.