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Sample records for rational genome mining

  1. Genome mining of Streptomyces ambofaciens.

    PubMed

    Aigle, Bertrand; Lautru, Sylvie; Spiteller, Dieter; Dickschat, Jeroen S; Challis, Gregory L; Leblond, Pierre; Pernodet, Jean-Luc

    2014-02-01

    Since the discovery of the streptomycin produced by Streptomyces griseus in the middle of the last century, members of this bacterial genus have been largely exploited for the production of secondary metabolites with wide uses in medicine and in agriculture. They have even been recognized as one of the most prolific producers of natural products among microorganisms. With the onset of the genomic era, it became evident that these microorganisms still represent a major source for the discovery of novel secondary metabolites. This was highlighted with the complete genome sequencing of Streptomyces coelicolor A3(2) which revealed an unexpected potential of this organism to synthesize natural products undetected until then by classical screening methods. Since then, analysis of sequenced genomes from numerous Streptomyces species has shown that a single species can carry more than 30 secondary metabolite gene clusters, reinforcing the idea that the biosynthetic potential of this bacterial genus is far from being fully exploited. This review highlights our knowledge on the potential of Streptomyces ambofaciens ATCC 23877 to synthesize natural products. This industrial strain was known for decades to only produce the drug spiramycin and another antibacterial compound, congocidine. Mining of its genome allowed the identification of 23 clusters potentially involved in the production of other secondary metabolites. Studies of some of these clusters resulted in the characterization of novel compounds and of previously known compounds but never characterized in this Streptomyces species. In addition, genome mining revealed that secondary metabolite gene clusters of phylogenetically closely related Streptomyces are mainly species-specific.

  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

    2016-01-04

    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.

  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. 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

  6. 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

  7. Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes.

    PubMed

    Kang, Zhen; Zhang, Junli; Jin, Peng; Yang, Sen

    2015-01-01

    Owing to our limited understanding of the relationship between sequence and function and the interaction between intracellular pathways and regulatory systems, the rational design of enzyme-coding genes and de novo assembly of a brand-new artificial genome for a desired functionality or phenotype are difficult to achieve. As an alternative approach, directed evolution has been widely used to engineer genomes and enzyme-coding genes. In particular, significant developments toward DNA synthesis, DNA assembly (in vitro or in vivo), recombination-mediated genetic engineering, and high-throughput screening techniques in the field of synthetic biology have been matured and widely adopted, enabling rapid semi-rational genome engineering to generate variants with desired properties. In this commentary, these novel tools and their corresponding applications in the directed evolution of genomes and enzymes are discussed. Moreover, the strategies for genome engineering and rapid in vitro enzyme evolution are also proposed.

  8. 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 ...

  9. Mining nematode genome data for novel drug targets.

    PubMed

    Foster, Jeremy M; Zhang, Yinhua; Kumar, Sanjay; Carlow, Clotilde K S

    2005-03-01

    Expressed sequence tag projects have currently produced over 400 000 partial gene sequences from more than 30 nematode species and the full genomic sequences of selected nematodes are being determined. In addition, functional analyses in the model nematode Caenorhabditis elegans have addressed the role of almost all genes predicted by the genome sequence. This recent explosion in the amount of available nematode DNA sequences, coupled with new gene function data, provides an unprecedented opportunity to identify pre-validated drug targets through efficient mining of nematode genomic databases. This article describes the various information sources available and strategies that can expedite this process.

  10. 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).

  11. 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.

  12. 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

  13. Data mining parasite genomes: haystack searching with a computer.

    PubMed

    Lawson, D

    1999-01-01

    A number of genomes of parasitic organisms are presently being sequenced in the public domain, including Plasmodium falciparum, Leishmania major and Trypanosoma brucei with the likelihood of at least expressed sequence tag (EST) projects for several filarial and apicomplexan species. The early and timely release of sequence data to the community via the World Wide Web (www), and the public databases, (EMBL and GENBANK), forms an invaluable resource. Data mining, or 'haystack searching' this resource is becoming more fruitful to all members of the scientific community as the volume of data, diversity of genomes sampled, and accessibility increase.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Mining Bacterial Genomes for Secondary Metabolite Gene Clusters.

    PubMed

    Adamek, Martina; Spohn, Marius; Stegmann, Evi; Ziemert, Nadine

    2017-01-01

    With the emergence of bacterial resistance against frequently used antibiotics, novel antibacterial compounds are urgently needed. Traditional bioactivity-guided drug discovery strategies involve laborious screening efforts and display high rediscovery rates. With the progress in next generation sequencing methods and the knowledge that the majority of antibiotics in clinical use are produced as secondary metabolites by bacteria, mining bacterial genomes for secondary metabolites with antimicrobial activity is a promising approach, which can guide a more time and cost-effective identification of novel compounds. However, what sounds easy to accomplish, comes with several challenges. To date, several tools for the prediction of secondary metabolite gene clusters are available, some of which are based on the detection of signature genes, while others are searching for specific patterns in gene content or regulation.Apart from the mere identification of gene clusters, several other factors such as determining cluster boundaries and assessing the novelty of the detected cluster are important. For this purpose, comparison of the predicted secondary metabolite genes with different cluster and compound databases is necessary. Furthermore, it is advisable to classify detected clusters into gene cluster families. So far, there is no standardized procedure for genome mining; however, different approaches to overcome all of these challenges exist and are addressed in this chapter. We give practical guidance on the workflow for secondary metabolite gene cluster identification, which includes the determination of gene cluster boundaries, addresses problems occurring with the use of draft genomes, and gives an outlook on the different methods for gene cluster classification. Based on comprehensible examples a protocol is set, which should enable the readers to mine their own genome data for interesting secondary metabolites.

  19. 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.

  20. 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.

  1. Rational Use of Land Resource During the Implementation of Transportless System of Coal Strata Surface Mining

    NASA Astrophysics Data System (ADS)

    Gvozdkova, T.; Tyulenev, M.; Zhironkin, S.; Trifonov, V. A.; Osipov, Yu M.

    2017-01-01

    Surface mining and open pits engineering affect the environment in a very negative way. Among other pollutions that open pits make during mineral deposits exploiting, particular problem is the landscape changing. Along with converting the land into pits, surface mining is connected with pilling dumps that occupy large ground. The article describes an analysis of transportless methods of several coal seams strata surface mining, applied for open pits of South Kuzbass coal enterprises (Western Siberia, Russia). To improve land-use management of open pit mining enterprises, the characteristics of transportless technological schemes for several coal seams strata surface mining are highlighted and observed. These characteristics help to systematize transportless open mining technologies using common criteria that characterize structure of the bottom part of a strata and internal dumping schemes. The schemes of transportless systems of coal strata surface mining implemented in South Kuzbass are given.

  2. 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

  3. Discovery of secondary metabolites from Bacillus spp. biocontrol strains using genome mining and mass spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome sequencing, data mining and mass spectrometry were used to identify secondary metabolites produced by several Bacillus spp. biocontrol strains. These biocontrol strains have shown promise in managing Fusarium head blight in wheat. Draft genomes were produced and screened in silico using genom...

  4. Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli.

    PubMed

    Santos, Christine Nicole S; Xiao, Wenhai; Stephanopoulos, Gregory

    2012-08-21

    Although microbial metabolic engineering has traditionally relied on rational and knowledge-driven techniques, significant improvements in strain performance can be further obtained through the use of combinatorial approaches exploiting phenotypic diversification and screening. Here, we demonstrate the combined use of global transcriptional machinery engineering and a high-throughput L-tyrosine screen towards improving L-tyrosine production in Escherichia coli. This methodology succeeded in generating three strains from two separate mutagenesis libraries (rpoA and rpoD) exhibiting up to a 114% increase in L-tyrosine titer over a rationally engineered parental strain with an already high capacity for production. Subsequent strain characterization through transcriptional analysis and whole genome sequencing allowed complete phenotype reconstruction from well-defined mutations and point to important roles for both the acid stress resistance pathway and the stringent response of E. coli in imparting this phenotype. As such, this study presents one of the first examples in which cell-wide measurements have helped to elucidate the genetic and biochemical underpinnings of an engineered cellular property, leading to the total restoration of metabolite overproduction from specific chromosomal mutations.

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

    PubMed

    Cherry, J Michael

    2015-12-02

    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.

  6. Community Genomic Analysis of Strain Variation of a Novel Archaeon in an Acid Mine Drainage Environment

    NASA Astrophysics Data System (ADS)

    Yelton, P.; Banfield, J.; Wilmes, P.

    2006-12-01

    Microorganisms play a significant role in acid mine drainage (AMD) generation within the Richmond Mine, Iron Mountain, California. To better understand the contributions of individual microbial species to this process, the assemblies of community genomic data from AMD biofilms were manually curated. Not reported previously is detailed analysis of genomic sequence from G-plasma, an archaeal population from a sample collected from the 5-way location in 2002. The G-plasma population exhibits a small number of differing nucleotide sequences at most genomic locations and comprises multiple genome types. Linkage between these sequence types indicates frequent homologous recombination. As the near complete genome is still in many fragments, the current investigation focused on the 25% of the genome in large, confidently linked pieces. Many predicted proteins from this organism were detected via proteomic analysis. In combination, information about genome heterogeneity and protein expression is providing clues to the role of this population in the biofilm community.

  7. Clinic-genomic association mining for colorectal cancer using publicly available datasets.

    PubMed

    Liu, Fang; Feng, Yaning; Li, Zhenye; Pan, Chao; Su, Yuncong; Yang, Rui; Song, Liying; Duan, Huilong; Deng, Ning

    2014-01-01

    In recent years, a growing number of researchers began to focus on how to establish associations between clinical and genomic data. However, up to now, there is lack of research mining clinic-genomic associations by comprehensively analysing available gene expression data for a single disease. Colorectal cancer is one of the malignant tumours. A number of genetic syndromes have been proven to be associated with colorectal cancer. This paper presents our research on mining clinic-genomic associations for colorectal cancer under biomedical big data environment. The proposed method is engineered with multiple technologies, including extracting clinical concepts using the unified medical language system (UMLS), extracting genes through the literature mining, and mining clinic-genomic associations through statistical analysis. We applied this method to datasets extracted from both gene expression omnibus (GEO) and genetic association database (GAD). A total of 23,517 clinic-genomic associations between 139 clinical concepts and 7914 genes were obtained, of which 3474 associations between 31 clinical concepts and 1689 genes were identified as highly reliable ones. Evaluation and interpretation were performed using UMLS, KEGG, and Gephi, and potential new discoveries were explored. The proposed method is effective in mining valuable knowledge from available biomedical big data and achieves a good performance in bridging clinical data with genomic data for colorectal cancer.

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

    PubMed Central

    Ghandchi, Frederick P.; Caetano-Anolles, Gustavo; Clough, Steven J.

    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

  9. Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.

    PubMed

    Eppig, Janan T; Smith, Cynthia L; Blake, Judith A; Ringwald, Martin; Kadin, James A; Richardson, Joel E; Bult, Carol J

    2017-01-01

    The Mouse Genome Informatics (MGI), resource ( www.informatics.jax.org ) has existed for over 25 years, and over this time its data content, informatics infrastructure, and user interfaces and tools have undergone dramatic changes (Eppig et al., Mamm Genome 26:272-284, 2015). Change has been driven by scientific methodological advances, rapid improvements in computational software, growth in computer hardware capacity, and the ongoing collaborative nature of the mouse genomics community in building resources and sharing data. Here we present an overview of the current data content of MGI, describe its general organization, and provide examples using simple and complex searches, and tools for mining and retrieving sets of data.

  10. 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

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

    PubMed

    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.

  12. 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...

  13. 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

  14. Genome sequence of Desulfosporosinus sp. OT, an acidophilic sulfate-reducing bacterium from copper mining waste in Norilsk, Northern Siberia.

    PubMed

    Abicht, Helge K; Mancini, Stefano; Karnachuk, Olga V; Solioz, Marc

    2011-11-01

    We have sequenced the genome of Desulfosporosinus sp. OT, a Gram-positive, acidophilic sulfate-reducing Firmicute isolated from copper tailing sediment in the Norilsk mining-smelting area in Northern Siberia, Russia. This represents the first sequenced genome of a Desulfosporosinus species. The genome has a size of 5.7 Mb and encodes 6,222 putative proteins.

  15. Expanding the computational toolbox for mining cancer genomes.

    PubMed

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

    2014-08-01

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

  16. Strain Prioritization and Genome Mining for Enediyne Natural Products

    PubMed Central

    Yan, Xiaohui; Ge, Huiming; Huang, Tingting; Hindra; Yang, Dong; Teng, Qihui; Crnovčić, Ivana; Li, Xiuling; Rudolf, Jeffrey D.; Lohman, Jeremy R.; Gansemans, Yannick; Zhu, Xiangcheng; Huang, Yong; Zhao, Li-Xing; Jiang, Yi; Van Nieuwerburgh, Filip; Rader, Christoph

    2016-01-01

    ABSTRACT The enediyne family of natural products has had a profound impact on modern chemistry, biology, and medicine, and yet only 11 enediynes have been structurally characterized to date. Here we report a genome survey of 3,400 actinomycetes, identifying 81 strains that harbor genes encoding the enediyne polyketide synthase cassettes that could be grouped into 28 distinct clades based on phylogenetic analysis. Genome sequencing of 31 representative strains confirmed that each clade harbors a distinct enediyne biosynthetic gene cluster. A genome neighborhood network allows prediction of new structural features and biosynthetic insights that could be exploited for enediyne discovery. We confirmed one clade as new C-1027 producers, with a significantly higher C-1027 titer than the original producer, and discovered a new family of enediyne natural products, the tiancimycins (TNMs), that exhibit potent cytotoxicity against a broad spectrum of cancer cell lines. Our results demonstrate the feasibility of rapid discovery of new enediynes from a large strain collection. PMID:27999165

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

    PubMed Central

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

    2016-01-01

    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 co-localized 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 auto-resistance. 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

  18. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.

    PubMed

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.

  19. Precursor-centric genome-mining approach for lasso peptide discovery

    PubMed Central

    Maksimov, Mikhail O.; Pelczer, István; Link, A. James

    2012-01-01

    Lasso peptides are a class of ribosomally synthesized posttranslationally modified natural products found in bacteria. Currently known lasso peptides have a diverse set of pharmacologically relevant activities, including inhibition of bacterial growth, receptor antagonism, and enzyme inhibition. The biosynthesis of lasso peptides is specified by a cluster of three genes encoding a precursor protein and two enzymes. Here we develop a unique genome-mining algorithm to identify lasso peptide gene clusters in prokaryotes. Our approach involves pattern matching to a small number of conserved amino acids in precursor proteins, and thus allows for a more global survey of lasso peptide gene clusters than does homology-based genome mining. Of more than 3,000 currently sequenced prokaryotic genomes, we found 76 organisms that are putative lasso peptide producers. These organisms span nine bacterial phyla and an archaeal phylum. To provide validation of the genome-mining method, we focused on a single lasso peptide predicted to be produced by the freshwater bacterium Asticcacaulis excentricus. Heterologous expression of an engineered, minimal gene cluster in Escherichia coli led to the production of a unique lasso peptide, astexin-1. At 23 aa, astexin-1 is the largest lasso peptide isolated to date. It is also highly polar, in contrast to many lasso peptides that are primarily hydrophobic. Astexin-1 has modest antimicrobial activity against its phylogenetic relative Caulobacter crescentus. The solution structure of astexin-1 was determined revealing a unique topology that is stabilized by hydrogen bonding between segments of the peptide. PMID:22949633

  20. Precursor-centric genome-mining approach for lasso peptide discovery.

    PubMed

    Maksimov, Mikhail O; Pelczer, István; Link, A James

    2012-09-18

    Lasso peptides are a class of ribosomally synthesized posttranslationally modified natural products found in bacteria. Currently known lasso peptides have a diverse set of pharmacologically relevant activities, including inhibition of bacterial growth, receptor antagonism, and enzyme inhibition. The biosynthesis of lasso peptides is specified by a cluster of three genes encoding a precursor protein and two enzymes. Here we develop a unique genome-mining algorithm to identify lasso peptide gene clusters in prokaryotes. Our approach involves pattern matching to a small number of conserved amino acids in precursor proteins, and thus allows for a more global survey of lasso peptide gene clusters than does homology-based genome mining. Of more than 3,000 currently sequenced prokaryotic genomes, we found 76 organisms that are putative lasso peptide producers. These organisms span nine bacterial phyla and an archaeal phylum. To provide validation of the genome-mining method, we focused on a single lasso peptide predicted to be produced by the freshwater bacterium Asticcacaulis excentricus. Heterologous expression of an engineered, minimal gene cluster in Escherichia coli led to the production of a unique lasso peptide, astexin-1. At 23 aa, astexin-1 is the largest lasso peptide isolated to date. It is also highly polar, in contrast to many lasso peptides that are primarily hydrophobic. Astexin-1 has modest antimicrobial activity against its phylogenetic relative Caulobacter crescentus. The solution structure of astexin-1 was determined revealing a unique topology that is stabilized by hydrogen bonding between segments of the peptide.

  1. Genomic research and data-mining technology: implications for personal privacy and informed consent.

    PubMed

    Tavani, Herman T

    2004-01-01

    This essay examines issues involving personal privacy and informed consent that arise at the intersection of information and communication technology (ICT) and population genomics research. I begin by briefly examining the ethical, legal, and social implications (ELSI) program requirements that were established to guide researchers working on the Human Genome Project (HGP). Next I consider a case illustration involving deCODE Genetics, a privately owned genetic company in Iceland, which raises some ethical concerns that are not clearly addressed in the current ELSI guidelines. The deCODE case also illustrates some ways in which an ICT technique known as data mining has both aided and posed special challenges for researchers working in the field of population genomics. On the one hand, data-mining tools have greatly assisted researchers in mapping the human genome and in identifying certain "disease genes" common in specific populations (which, in turn, has accelerated the process of finding cures for diseases tha affect those populations). On the other hand, this technology has significantly threatened the privacy of research subjects participating in population genomics studies, who may, unwittingly, contribute to the construction of new groups (based on arbitrary and non-obvious patterns and statistical correlations) that put those subjects at risk for discrimination and stigmatization. In the final section of this paper I examine some ways in which the use of data mining in the context of population genomics research poses a critical challenge for the principle of informed consent, which traditionally has played a central role in protecting the privacy interests of research subjects participating in epidemiological studies.

  2. 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

  3. What the papers say: Text mining for genomics and systems biology

    PubMed Central

    2010-01-01

    Keeping up with the rapidly growing literature has become virtually impossible for most scientists. This can have dire consequences. First, we may waste research time and resources on reinventing the wheel simply because we can no longer maintain a reliable grasp on the published literature. Second, and perhaps more detrimental, judicious (or serendipitous) combination of knowledge from different scientific disciplines, which would require following disparate and distinct research literatures, is rapidly becoming impossible for even the most ardent readers of research publications. Text mining -- the automated extraction of information from (electronically) published sources -- could potentially fulfil an important role -- but only if we know how to harness its strengths and overcome its weaknesses. As we do not expect that the rate at which scientific results are published will decrease, text mining tools are now becoming essential in order to cope with, and derive maximum benefit from, this information explosion. In genomics, this is particularly pressing as more and more rare disease-causing variants are found and need to be understood. Not being conversant with this technology may put scientists and biomedical regulators at a severe disadvantage. In this review, we introduce the basic concepts underlying modern text mining and its applications in genomics and systems biology. We hope that this review will serve three purposes: (i) to provide a timely and useful overview of the current status of this field, including a survey of present challenges; (ii) to enable researchers to decide how and when to apply text mining tools in their own research; and (iii) to highlight how the research communities in genomics and systems biology can help to make text mining from biomedical abstracts and texts more straightforward. PMID:21106487

  4. 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

  5. Mining genomic databases to identify novel hydrogen producers.

    PubMed

    Kalia, Vipin C; Lal, Sadhana; Ghai, Rohit; Mandal, Manabendra; Chauhan, Ashwini

    2003-04-01

    The realization that fossil fuel reserves are limited and their adverse effect on the environment has forced us to look into alternative sources of energy. Hydrogen is a strong contender as a future fuel. Biological hydrogen production ranges from 0.37 to 3.3 moles H(2) per mole of glucose and, considering the high theoretical values of production (4.0 moles H(2) per mole of glucose), it is worth exploring approaches to increase hydrogen yields. Screening the untapped microbial population is a promising possibility. Sequence analysis and pathway alignment of hydrogen metabolism in complete and incomplete genomes has led to the identification of potential hydrogen producers.

  6. 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.

  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. A new genome-mining tool redefines the lasso peptide biosynthetic landscape.

    PubMed

    Tietz, Jonathan I; Schwalen, Christopher J; Patel, Parth S; Maxson, Tucker; Blair, Patricia M; Tai, Hua-Chia; Zakai, Uzma I; Mitchell, Douglas A

    2017-02-28

    Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis, heuristic scoring, and machine learning to identify biosynthetic gene clusters and predict RiPP precursor peptides. We initially focused on lasso peptides, which display intriguing physicochemical properties and bioactivities, but their hypervariability renders them challenging prospects for automated mining. Our approach yielded the most comprehensive mapping to date of lasso peptide space, revealing >1,300 compounds. We characterized the structures and bioactivities of six lasso peptides, prioritized based on predicted structural novelty, including one with an unprecedented handcuff-like topology and another with a citrulline modification exceptionally rare among bacteria. These combined insights significantly expand the knowledge of lasso peptides and, more broadly, provide a framework for future genome-mining efforts.

  9. Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp.

    PubMed Central

    Xu, Min; Wang, Yemin; Zhao, Zhilong; Gao, Guixi; Huang, Sheng-Xiong; Kang, Qianjin; He, Xinyi; Lin, Shuangjun; Pang, Xiuhua; Deng, Zixin

    2016-01-01

    ABSTRACT Genome sequencing projects in the last decade revealed numerous cryptic biosynthetic pathways for unknown secondary metabolites in microbes, revitalizing drug discovery from microbial metabolites by approaches called genome mining. In this work, we developed a heterologous expression and functional screening approach for genome mining from genomic bacterial artificial chromosome (BAC) libraries in Streptomyces spp. We demonstrate mining from a strain of Streptomyces rochei, which is known to produce streptothricins and borrelidin, by expressing its BAC library in the surrogate host Streptomyces lividans SBT5, and screening for antimicrobial activity. In addition to the successful capture of the streptothricin and borrelidin biosynthetic gene clusters, we discovered two novel linear lipopeptides and their corresponding biosynthetic gene cluster, as well as a novel cryptic gene cluster for an unknown antibiotic from S. rochei. This high-throughput functional genome mining approach can be easily applied to other streptomycetes, and it is very suitable for the large-scale screening of genomic BAC libraries for bioactive natural products and the corresponding biosynthetic pathways. IMPORTANCE Microbial genomes encode numerous cryptic biosynthetic gene clusters for unknown small metabolites with potential biological activities. Several genome mining approaches have been developed to activate and bring these cryptic metabolites to biological tests for future drug discovery. Previous sequence-guided procedures relied on bioinformatic analysis to predict potentially interesting biosynthetic gene clusters. In this study, we describe an efficient approach based on heterologous expression and functional screening of a whole-genome library for the mining of bioactive metabolites from Streptomyces. The usefulness of this function-driven approach was demonstrated by the capture of four large biosynthetic gene clusters for metabolites of various chemical types, including

  10. TFM-Explorer: mining cis-regulatory regions in genomes

    PubMed Central

    Tonon, Laurie; Varré, Jean-Stéphane

    2010-01-01

    DNA-binding transcription factors (TFs) play a central role in transcription regulation, and computational approaches that help in elucidating complex mechanisms governing this basic biological process are of great use. In this perspective, we present the TFM-Explorer web server that is a toolbox to identify putative TF binding sites within a set of upstream regulatory sequences of genes sharing some regulatory mechanisms. TFM-Explorer finds local regions showing overrepresentation of binding sites. Accepted organisms are human, mouse, rat, chicken and drosophila. The server employs a number of features to help users to analyze their data: visualization of selected binding sites on genomic sequences, and selection of cis-regulatory modules. TFM-Explorer is available at http://bioinfo.lifl.fr/TFM. PMID:20522509

  11. Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors

    PubMed Central

    Furlong, Michael; Seong, Jae Young

    2017-01-01

    Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples. PMID:28035082

  12. 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

  13. 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

  14. 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

  15. Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa.

    PubMed

    de Vries, Jantina; Pepper, Michael

    2012-08-01

    Scientific interest in genomics in Africa is on the rise with a number of funding initiatives aimed specifically at supporting research in this area. Genomics research on material of African origin raises a number of important ethical issues. A prominent concern relates to sample export, which is increasingly seen by researchers and ethics committees across the continent as being problematic. The concept of genomic sovereignty proposes that unique patterns of genomic variation can be found in human populations, and that these are commercially, scientifically or symbolically valuable and in need of protection against exploitation. Although it is appealing as a response to increasing concerns regarding sample export, there are a number of important conceptual problems relating to the term. It is not clear, for instance, whether it is appropriate that ownership over human genomic samples should rest with national governments. Furthermore, ethnic groups in Africa are frequently spread across multiple nation states, and protection offered in one state may not prevent researchers from accessing the same group elsewhere. Lastly, scientific evidence suggests that the assumption that genomic data is unique for population groups is false. Although the frequency with which particular variants are found can differ between groups, such genes or variants per se are not unique to any population group. In this paper, the authors describe these concerns in detail and argue that the concept of genomic sovereignty alone may not be adequate to protect the genetic resources of people of African descent.

  16. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing

    PubMed Central

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar. PMID:27679641

  17. 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 ).

  18. Phylogeny-guided (meta)genome mining approach for the targeted discovery of new microbial natural products.

    PubMed

    Kang, Hahk-Soo

    2017-02-01

    Genomics-based methods are now commonplace in natural products research. A phylogeny-guided mining approach provides a means to quickly screen a large number of microbial genomes or metagenomes in search of new biosynthetic gene clusters of interest. In this approach, biosynthetic genes serve as molecular markers, and phylogenetic trees built with known and unknown marker gene sequences are used to quickly prioritize biosynthetic gene clusters for their metabolites characterization. An increase in the use of this approach has been observed for the last couple of years along with the emergence of low cost sequencing technologies. The aim of this review is to discuss the basic concept of a phylogeny-guided mining approach, and also to provide examples in which this approach was successfully applied to discover new natural products from microbial genomes and metagenomes. I believe that the phylogeny-guided mining approach will continue to play an important role in genomics-based natural products research.

  19. BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics

    SciTech Connect

    Wu, Cathy H.; Hirschman, Lynette

    2016-10-29

    The objective of this project was to host BioCreative workshops to define and develop text mining tasks to meet the needs of the Genome Sciences community, focusing on metadata information extraction in metagenomics. Following the successful introduction of metagenomics at the BioCreative IV workshop, members of the metagenomics community and BioCreative communities continued discussion to identify candidate topics for a BioCreative metagenomics track for BioCreative V. Of particular interest was the capture of environmental and isolation source information from text. The outcome was to form a “community of interest” around work on the interactive EXTRACT system, which supported interactive tagging of environmental and species data. This experiment is included in the BioCreative V virtual issue of Database. In addition, there was broad participation by members of the metagenomics community in the panels held at BioCreative V, leading to valuable exchanges between the text mining developers and members of the metagenomics research community. These exchanges are reflected in a number of the overview and perspective pieces also being captured in the BioCreative V virtual issue. Overall, this conversation has exposed the metagenomics researchers to the possibilities of text mining, and educated the text mining developers to the specific needs of the metagenomics community.

  20. Strategies for the discovery of new natural products by genome mining.

    PubMed

    Zerikly, Malek; Challis, Gregory L

    2009-03-02

    Natural products have a very broad spectrum of applications. Many natural products are used clinically as antibacterial, antifungal, antiparasitic, anticancer and immunosuppressive agents and are therefore of utmost importance for our society. When in the 1940s the golden age of antibiotics was ushered in, a "gold rush fever" of natural product discovery in the pharmaceutical industry ensued for many decades. However, the traditional process of discovering new bioactive natural products is generally long and laborious, and known natural products are frequently rediscovered. A mass-withdrawal of pharmaceutical companies from new natural product discovery and natural products research has thus occurred in recent years. In this article, the concept of genome mining for novel natural product discovery, which promises to provide a myriad of new bioactive natural compounds, is summarized and discussed. Genome mining for new natural product discovery exploits the huge and constantly increasing quantity of DNA sequence data from a wide variety of organisms that is accumulating in publicly accessible databases. Genes encoding enzymes likely to be involved in natural product biosynthesis can be readily located in sequenced genomes by use of computational sequence comparison tools. This information can be exploited in a variety of ways in the search for new bioactive natural products.

  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. 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

  3. 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.

  4. Rational optimization of tolC as a powerful dual selectable marker for genome engineering

    PubMed Central

    Gregg, Christopher J.; Lajoie, Marc J.; Napolitano, Michael G.; Mosberg, Joshua A.; Goodman, Daniel B.; Aach, John; Isaacs, Farren J.; Church, George M.

    2014-01-01

    Selection has been invaluable for genetic manipulation, although counter-selection has historically exhibited limited robustness and convenience. TolC, an outer membrane pore involved in transmembrane transport in E. coli, has been implemented as a selectable/counter-selectable marker, but counter-selection escape frequency using colicin E1 precludes using tolC for inefficient genetic manipulations and/or with large libraries. Here, we leveraged unbiased deep sequencing of 96 independent lineages exhibiting counter-selection escape to identify loss-of-function mutations, which offered mechanistic insight and guided strain engineering to reduce counter-selection escape frequency by ∼40-fold. We fundamentally improved the tolC counter-selection by supplementing a second agent, vancomycin, which reduces counter-selection escape by 425-fold, compared colicin E1 alone. Combining these improvements in a mismatch repair proficient strain reduced counter-selection escape frequency by 1.3E6-fold in total, making tolC counter-selection as effective as most selectable markers, and adding a valuable tool to the genome editing toolbox. These improvements permitted us to perform stable and continuous rounds of selection/counter-selection using tolC, enabling replacement of 10 alleles without requiring genotypic screening for the first time. Finally, we combined these advances to create an optimized E. coli strain for genome engineering that is ∼10-fold more efficient at achieving allelic diversity than previous best practices. PMID:24452804

  5. Genome mining of the Streptomyces avermitilis genome and development of genome-minimized hosts for heterologous expression of biosynthetic gene clusters.

    PubMed

    Ikeda, Haruo; Kazuo, Shin-ya; Omura, Satoshi

    2014-02-01

    To date, several actinomycete genomes have been completed and annotated. Among them, Streptomyces microorganisms are of major pharmaceutical interest because they are a rich source of numerous secondary metabolites. S. avermitilis is an industrial microorganism used for the production of an anthelmintic agent, avermectin, which is a commercially important antiparasitic agent in human and veterinary medicine, and agricultural pesticides. Genome analysis of S. avermitilis provides significant information for not only industrial applications but also understanding the features of this genus. On genome mining of S. avermitilis, the microorganism has been found to harbor at least 38 secondary metabolic gene clusters and 46 insertion sequence (IS)-like sequences on the genome, which have not been searched so far. A significant use of the genome data of Streptomyces microorganisms is the construction of a versatile host for heterologous expression of exogenous biosynthetic gene clusters by genetic engineering. Since S. avermitilis is used as an industrial microorganism, the microorganism is already optimized for the efficient supply of primary metabolic precursors and biochemical energy to support multistep biosynthesis. The feasibility of large-deletion mutants of S. avermitilis has been confirmed by heterologous expression of more than 20 exogenous biosynthetic gene clusters.

  6. Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks.

    PubMed

    Mohimani, Hosein; Pevzner, Pavel A

    2016-01-01

    Covering: 2000 to 2015. While recent breakthroughs in the discovery of peptide antibiotics and other Peptidic Natural Products (PNPs) raise a challenge for developing new algorithms for their analyses, the computational technologies for high-throughput PNP discovery are still lacking. We discuss the computational bottlenecks in analyzing PNPs and review recent advances in genome mining, peptidogenomics, and spectral networks that are now enabling the discovery of new PNPs via mass spectrometry. We further describe the connections between these advances and the new generation of software tools for PNP dereplication, de novo sequencing, and identification.

  7. Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides.

    PubMed

    Leikoski, Niina; Liu, Liwei; Jokela, Jouni; Wahlsten, Matti; Gugger, Muriel; Calteau, Alexandra; Permi, Perttu; Kerfeld, Cheryl A; Sivonen, Kaarina; Fewer, David P

    2013-08-22

    Ribosomal peptides are produced through the posttranslational modification of short precursor peptides. Cyanobactins are a growing family of cyclic ribosomal peptides produced by cyanobacteria. However, a broad systematic survey of the genetic capacity to produce cyanobactins is lacking. Here we report the identification of 31 cyanobactin gene clusters from 126 genomes of cyanobacteria. Genome mining suggested a complex evolutionary history defined by horizontal gene transfer and rapid diversification of precursor genes. Extensive chemical analyses demonstrated that some cyanobacteria produce short linear cyanobactins with a chain length ranging from three to five amino acids. The linear peptides were N-prenylated and O-methylated on the N and C termini, respectively, and named aeruginosamide and viridisamide. These findings broaden the structural diversity of the cyanobactin family to include highly modified linear peptides with rare posttranslational modifications.

  8. Mining Plant Genomic and Genetic Data Using the GnpIS Information System.

    PubMed

    Adam-Blondon, A-F; Alaux, M; Durand, S; Letellier, T; Merceron, G; Mohellibi, N; Pommier, C; Steinbach, D; Alfama, F; Amselem, J; Charruaud, D; Choisne, N; Flores, R; Guerche, C; Jamilloux, V; Kimmel, E; Lapalu, N; Loaec, M; Michotey, C; Quesneville, H

    2017-01-01

    GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.

  9. Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server.

    PubMed

    Proietti, Carla; Zakrzewski, Martha; Watkins, Thomas S; Berger, Bernard; Hasan, Shihab; Ratnatunga, Champa N; Brion, Marie-Jo; Crompton, Peter D; Miles, John J; Doolan, Denise L; Krause, Lutz

    2016-12-06

    Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression. The software has a focus on multivariate techniques, which can attribute variance in the measurements to multiple explanatory variables and confounders. Various normalization methods are provided. Extensive help pages and a tutorial are available via a wiki server. Using GMine we reanalyzed proteome microarray data of host antibody response against Plasmodium falciparum. Our results support the hypothesis that immunity to malaria is a higher-order phenomenon related to a pattern of responses and not attributable to any single antigen. We also analyzed gene expression across resting and activated T cells, identifying many immune-related genes with differential expression. This highlights both the plasticity of T cells and the operation of a hardwired activation program. These application examples demonstrate that GMine facilitates an accurate and in-depth analysis of complex molecular datasets, including genomics, transcriptomics and proteomics data.

  10. Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server

    PubMed Central

    Proietti, Carla; Zakrzewski, Martha; Watkins, Thomas S.; Berger, Bernard; Hasan, Shihab; Ratnatunga, Champa N.; Brion, Marie-Jo; Crompton, Peter D.; Miles, John J.; Doolan, Denise L.; Krause, Lutz

    2016-01-01

    Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression. The software has a focus on multivariate techniques, which can attribute variance in the measurements to multiple explanatory variables and confounders. Various normalization methods are provided. Extensive help pages and a tutorial are available via a wiki server. Using GMine we reanalyzed proteome microarray data of host antibody response against Plasmodium falciparum. Our results support the hypothesis that immunity to malaria is a higher-order phenomenon related to a pattern of responses and not attributable to any single antigen. We also analyzed gene expression across resting and activated T cells, identifying many immune-related genes with differential expression. This highlights both the plasticity of T cells and the operation of a hardwired activation program. These application examples demonstrate that GMine facilitates an accurate and in-depth analysis of complex molecular datasets, including genomics, transcriptomics and proteomics data. PMID:27922118

  11. Mining genomic patterns in Mycobacterium tuberculosis H37Rv using a web server Tuber-Gene.

    PubMed

    Rishishwar, Lavanya; Pant, Bhasker; Pant, Kumud; Pardasani, Kamal R

    2011-10-01

    Mycobacterium tuberculosis (MTB), causative agent of tuberculosis, is one of the most dreaded diseases of the century. It has long been studied by researchers throughout the world using various wet-lab and dry-lab techniques. In this study, we focus on mining useful patterns at genomic level that can be applied for in silico functional characterization of genes from the MTB complex. The model developed on the basis of the patterns found in this study can correctly identify 99.77% of the input genes from the genome of MTB strain H37Rv. The model was tested against four other MTB strains and the homologue M. bovis to further evaluate its generalization capability. The mean prediction accuracy was 85.76%. It was also observed that the GC content remained fairly constant throughout the genome, implicating the absence of any pathogenicity island transferred from other organisms. This study reveals that dinucleotide composition is an efficient functional class discriminator for MTB complex. To facilitate the application of this model, a web server Tuber-Gene has been developed, which can be freely accessed at http://www.bifmanit.org/tb2/.

  12. 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

  13. Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks.

    PubMed

    Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

    2016-10-20

    The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO2)-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO3) as the sole carbon source. Here, we report the genome sequence of 5.07 Mb Serratia sp. ISTD04.

  14. Genome mining and functional genomics for siderophore production in Aspergillus niger.

    PubMed

    Franken, Angelique C W; Lechner, Beatrix E; Werner, Ernst R; Haas, Hubertus; Lokman, B Christien; Ram, Arthur F J; van den Hondel, Cees A M J J; de Weert, Sandra; Punt, Peter J

    2014-11-01

    Iron is an essential metal for many organisms, but the biologically relevant form of iron is scarce because of rapid oxidation resulting in low solubility. Simultaneously, excessive accumulation of iron is toxic. Consequently, iron uptake is a highly controlled process. In most fungal species, siderophores play a central role in iron handling. Siderophores are small iron-specific chelators that can be secreted to scavenge environmental iron or bind intracellular iron with high affinity. A second high-affinity iron uptake mechanism is reductive iron assimilation (RIA). As shown in Aspergillus fumigatus and Aspergillus nidulans, synthesis of siderophores in Aspergilli is predominantly under control of the transcription factors SreA and HapX, which are connected by a negative transcriptional feedback loop. Abolishing this fine-tuned regulation corroborates iron homeostasis, including heme biosynthesis, which could be biotechnologically of interest, e.g. the heterologous production of heme-dependent peroxidases. Aspergillus niger genome inspection identified orthologues of several genes relevant for RIA and siderophore metabolism, as well as sreA and hapX. Interestingly, genes related to synthesis of the common fungal extracellular siderophore triacetylfusarinine C were absent. Reverse-phase high-performance liquid chromatography (HPLC) confirmed the absence of triacetylfusarinine C, and demonstrated that the major secreted siderophores of A. niger are coprogen B and ferrichrome, which is also the dominant intracellular siderophore. In A. niger wild type grown under iron-replete conditions, the expression of genes involved in coprogen biosynthesis and RIA was low in the exponential growth phase but significantly induced during ascospore germination. Deletion of sreA in A. niger resulted in elevated iron uptake and increased cellular ferrichrome accumulation. Increased sensitivity toward phleomycin and high iron concentration reflected the toxic effects of excessive

  15. An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria.

    PubMed

    Maansson, Maria; Vynne, Nikolaj G; Klitgaard, Andreas; Nybo, Jane L; Melchiorsen, Jette; Nguyen, Don D; Sanchez, Laura M; Ziemert, Nadine; Dorrestein, Pieter C; Andersen, Mikael R; Gram, Lone

    2016-01-01

    Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds, including the thiomarinols that were reported from P. luteoviolacea here for the first time. By comparative genomics, we identified the biosynthetic cluster responsible for the production of the antibiotic indolmycin, which could not be predicted with standard methods. In conclusion, we present an efficient, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes. IMPORTANCE We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a species known

  16. From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules.

    PubMed

    Jeske, Olga; Jogler, Mareike; Petersen, Jörn; Sikorski, Johannes; Jogler, Christian

    2013-10-01

    Most members of the phylum Planctomycetes share many unusual traits that are unique for bacteria, since they divide independent of FtsZ through asymmetric budding, possess a complex life cycle and comprise a compartmentalized cell plan. Besides their complex cell biological features Planctomycetes are environmentally important and play major roles in global matter fluxes. Such features have been successfully employed in biotechnological applications such as the anaerobic oxidation of ammonium in wastewater treatment plants or the utilization of enzymes for biotechnological processes. However, little is known about planctomycetal secondary metabolites. This is surprising as Planctomycetes have several key features in common with known producers of small bioactive molecules such as Streptomycetes or Myxobacteria: a complex life style and large genome sizes. Planctomycetal genomes with an average size of 6.9 MB appear as tempting targets for drug discovery approaches. To enable the hunt for bioactive molecules from Planctomycetes, we performed a comprehensive genome mining approach employing the antiSMASH secondary metabolite identification pipeline and found 102 candidate genes or clusters within the analyzed 13 genomes. However, as most genes and operons related to secondary metabolite production are exclusively expressed under certain environmental conditions, we optimized Phenotype MicroArray protocols for Rhodopirellula baltica and Planctomyces limnophilus to allow high throughput screening of putative stimulating carbon sources. Our results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomycetes. Thus, this study provides the necessary starting point to explore planctomycetal small molecules for drug development.

  17. Merging Chemical Ecology with Bacterial Genome Mining for Secondary Metabolite Discovery

    PubMed Central

    Vizcaino, Maria I.; Guo, Xun; Crawford, Jason M.

    2013-01-01

    The integration of chemical ecology and bacterial genome mining can enhance the discovery of structurally diverse natural products in functional contexts. By examining bacterial secondary metabolism in the framework of its ecological niche, insights can be drawn for the upregulation of orphan biosynthetic pathways and the enhancement of enzyme substrate supply to illuminate new secondary metabolic pathways that would otherwise be silent or undetected under typical laboratory cultivation conditions. Access to these new natural products (i.e., the chemotypes) facilitates experimental genotype-to-phenotype linkages. Here, we describe select functional natural products produced by Xenorhabdus and Photorhabdus bacteria, with experimentally linked biosynthetic gene clusters, as illustrative examples of synergy between chemical ecology and bacterial genome mining in connecting genotypes to phenotypes through chemotype characterization. These Gammaproteobacteria share a mutualistic relationship with nematodes and a pathogenic relationship with insects, and in select cases, humans. The natural products encoded by these bacteria distinguish their interactions with animal hosts and other microorganisms in their multipartite symbiotic lifestyles. Though both genera have similar lifestyles, their genetic, chemical, and physiological attributes are distinct. Both undergo phenotypic variation and produce a profuse number of bioactive secondary metabolites. We provide further detail in the context of regulation, production, processing, and function of these genetically encoded small molecules with respect to their roles in mutualism and pathogenicity. These collective insights more widely promote the discovery of atypical orphan biosynthetic pathways encoding novel small molecules in symbiotic systems, which could open new avenues for investigating and exploiting microbial chemical signaling in host-bacteria interactions. PMID:24127069

  18. Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria.

    PubMed

    Wang, Hao; Fewer, David P; Sivonen, Kaarina

    2011-01-01

    Cyanobacteria are a rich source of natural products with interesting biological activities. Many of these are peptides and the end products of a non-ribosomal pathway. However, several cyanobacterial peptide classes were recently shown to be produced through the proteolytic cleavage and post-translational modification of short precursor peptides. A new class of bacteriocins produced through the proteolytic cleavage and heterocyclization of precursor proteins was recently identified from marine cyanobacteria. Here we show the widespread occurrence of bacteriocin gene clusters in cyanobacteria through comparative analysis of 58 cyanobacterial genomes. A total of 145 bacteriocin gene clusters were discovered through genome mining. These clusters encoded 290 putative bacteriocin precursors. They ranged in length from 28 to 164 amino acids with very little sequence conservation of the core peptide. The gene clusters could be classified into seven groups according to their gene organization and domain composition. This classification is supported by phylogenetic analysis, which further indicated independent evolutionary trajectories of gene clusters in different groups. Our data suggests that cyanobacteria are a prolific source of low-molecular weight post-translationally modified peptides.

  19. 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.

  20. 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.

  1. An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria

    PubMed Central

    Maansson, Maria; Vynne, Nikolaj G.; Klitgaard, Andreas; Nybo, Jane L.; Melchiorsen, Jette; Nguyen, Don D.; Sanchez, Laura M.; Ziemert, Nadine; Dorrestein, Pieter C.

    2016-01-01

    ABSTRACT Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds, including the thiomarinols that were reported from P. luteoviolacea here for the first time. By comparative genomics, we identified the biosynthetic cluster responsible for the production of the antibiotic indolmycin, which could not be predicted with standard methods. In conclusion, we present an efficient, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes. IMPORTANCE We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a

  2. 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

  3. 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.

  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. 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.

  6. Discovery a novel organic solvent tolerant esterase from Salinispora arenicola CNP193 through genome mining.

    PubMed

    Fang, Yaowei; Wang, Shujun; Liu, Shu; Jiao, Yuliang

    2015-09-01

    An esterase gene, encoding a 325-amino-acid protein (SAestA), was mined form obligate marine actinomycete strain Salinispora arenicola CNP193 genome sequence. Phylogenetic analysis of the deduced amino acid sequence showed that the enzyme belonged to the family IV of lipolytic enzymes. The gene was cloned, expressed in Escherichia coli as a His-tagged protein, purified and characterized. The molecular weight of His-tagged SAestA is ∼38 kDa. SAestA-His6 was active in a temperature (5-40 °C) and pH range (7.0-11.0), and maximal activity was determined at pH 9.0 and 30 °C. The activity was severely inhibited by Hg(2+), Cu(2+), and Zn(2+). In particular, this enzyme showed remarkable stability in presence of organic solvents (25%, v/v) with log P>2.0 even after incubation for 7 days. All these characteristics suggested that SAestA may be a potential candidate for application in industrial processes in aqueous/organic media.

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

    PubMed

    Evans, Barbara J

    2014-07-01

    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.

  8. Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

    SciTech Connect

    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.

    2015-04-09

    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. In this paper, 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. Finally, 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.

  9. Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Causal Genes and Mutations on Pig Chromosome 17

    PubMed Central

    Hu, Zhi-Liang; Ramos, Antonio M.; Humphray, Sean J.; Rogers, Jane; Reecy, James M.; Rothschild, Max F.

    2011-01-01

    The newly available pig genome sequence has provided new information to fine map quantitative trait loci (QTL) in order to eventually identify causal variants. With targeted genomic sequencing efforts, we were able to obtain high quality BAC sequences that cover a region on pig chromosome 17 where a number of meat quality QTL have been previously discovered. Sequences from 70 BAC clones were assembled to form an 8-Mbp contig. Subsequently, we successfully mapped five previously identified QTL, three for meat color and two for lactate related traits, to the contig. With an additional 25 genetic markers that were identified by sequence comparison, we were able to carry out further linkage disequilibrium analysis to narrow down the genomic locations of these QTL, which allowed identification of the chromosomal regions that likely contain the causative variants. This research has provided one practical approach to combine genetic and molecular information for QTL mining. PMID:22303339

  10. 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

  11. Draft genome sequence of Sinorhizobium meliloti CCNWSX0020, a nitrogen-fixing symbiont with copper tolerance capability isolated from lead-zinc mine tailings.

    PubMed

    Li, Zhefei; Ma, Zhanqiang; Hao, Xiuli; Wei, Gehong

    2012-03-01

    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.

  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

    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.

  13. 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...

  14. 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

    2017-01-01

    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 identified, 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 amplified with specific products and 24 (80.0%) were polymorphic. For the amplified 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 significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly 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.

  15. 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

  16. 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

  17. 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...

  18. Identification and activation of novel biosynthetic gene clusters by genome mining in the kirromycin producer Streptomyces collinus Tü 365.

    PubMed

    Iftime, Dumitrita; Kulik, Andreas; Härtner, Thomas; Rohrer, Sabrina; Niedermeyer, Timo Horst Johannes; Stegmann, Evi; Weber, Tilmann; Wohlleben, Wolfgang

    2016-03-01

    Streptomycetes are prolific sources of novel biologically active secondary metabolites with pharmaceutical potential. S. collinus Tü 365 is a Streptomyces strain, isolated 1972 from Kouroussa (Guinea). It is best known as producer of the antibiotic kirromycin, an inhibitor of the protein biosynthesis interacting with elongation factor EF-Tu. Genome Mining revealed 32 gene clusters encoding the biosynthesis of diverse secondary metabolites in the genome of Streptomyces collinus Tü 365, indicating an enormous biosynthetic potential of this strain. The structural diversity of secondary metabolisms predicted for S. collinus Tü 365 includes PKS, NRPS, PKS-NRPS hybrids, a lanthipeptide, terpenes and siderophores. While some of these gene clusters were found to contain genes related to known secondary metabolites, which also could be detected in HPLC-MS analyses, most of the uncharacterized gene clusters are not expressed under standard laboratory conditions. With this study we aimed to characterize the genome information of S. collinus Tü 365 to make use of gene clusters, which previously have not been described for this strain. We were able to connect the gene clusters of a lanthipeptide, a carotenoid, five terpenoid compounds, an ectoine, a siderophore and a spore pigment-associated gene cluster to their respective biosynthesis products.

  19. Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

    DOE PAGES

    Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; ...

    2015-04-09

    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. In this paper, 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 themore » identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. Finally, 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.« less

  20. The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining.

    PubMed

    Ellis, Lynda B M; Hou, Bo Kyeng; Kang, Wenjun; Wackett, Lawrence P

    2003-01-01

    The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants. Currently, it contains information on over 130 metabolic pathways, 800 reactions, 750 compounds and 500 enzymes. In the past two years, it has increased its breath to include more examples of microbial metabolism of metals and metalloids; and expanded the types of information it includes to contain microbial biotransformations of, and binding interactions with many chemical elements. It has also increased the ways in which this data can be accessed (mined). Structure-based searching was added, for exact matches, similarity, or substructures. Analysis of UM-BBD reactions has lead to a prototype, guided, pathway prediction system. Guided prediction means that the user is shown all possible biotransformations at each step and guides the process to its conclusion. Mining the UM-BBD's data provides a unique view into how the microbial world recycles organic functional groups. UM-BBD users are encouraged to comment on all aspects of the database, including the information it contains and the tools by which it can be mined. The database and prediction system develop under the direction of the scientific community.

  1. 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

  2. InCoB2014: mining biological data from genomics for transforming industry and health.

    PubMed

    Schönbach, Christian; Tan, Tin; Ranganathan, Shoba

    2014-01-01

    The 13th International Conference on Bioinformatics (InCoB2014) was held for the first time in Australia, at Sydney, July 31-2 August, 2014. InCoB is the annual scientific gathering of the Asia-Pacific Bioinformatics Network (APBioNet), hosted since 2002 in the Asia-Pacific region. Of 106 full papers submitted to the BMC track of InCoB2014, 50 (47.2%) were accepted in BMC Bioinformatics, BMC Genomics and BMC Systems Biology supplements, with three papers in a new BMC Medical Genomics supplement. While the majority of presenters and authors were from Asia and Australia, the increasing number of US and European conference attendees augurs well for the international flavour of InCoB. Next year's InCoB will be held jointly with the Genome Informatics Workshop (GIW), September 9-11, 2015 in Tokyo, Japan, with a view to integrate bioinformatics communities in the region.

  3. Sequencing pools of individuals - mining genome-wide polymorphism data without big funding.

    PubMed

    Schlötterer, Christian; Tobler, Raymond; Kofler, Robert; Nolte, Viola

    2014-11-01

    The analysis of polymorphism data is becoming increasingly important as a complementary tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs, genomic sequencing of individuals at the population scale is still restricted to a few model species. Whole-genome sequencing of pools of individuals (Pool-seq) provides a cost-effective alternative to sequencing individuals separately. With the availability of custom-tailored software tools, Pool-seq is being increasingly used for population genomic research on both model and non-model organisms. In this Review, we not only demonstrate the breadth of questions that are being addressed by Pool-seq but also discuss its limitations and provide guidelines for users.

  4. 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.

  5. 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

  6. Accurate Prediction of Protein Functional Class From Sequence in the Mycobacterium Tuberculosis and Escherichia Coli Genomes Using Data Mining

    PubMed Central

    Karwath, Andreas; Clare, Amanda; Dehaspe, Luc

    2000-01-01

    The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history of M. tuberculosis and E. coli. PMID:11119305

  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.

  8. 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

    2016-02-03

    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.

  9. Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set

    PubMed Central

    Wren, Jonathan D; Johnson, David; Gruenwald, Le

    2005-01-01

    There is an enormous amount of information encoded in each genome – enough to create living, responsive and adaptive organisms. Raw sequence data alone is not enough to understand function, mechanisms or interactions. Changes in a single base pair can lead to disease, such as sickle-cell anemia, while some large megabase deletions have no apparent phenotypic effect. Genomic features are varied in their data types and annotation of these features is spread across multiple databases. Herein, we develop a method to automate exploration of genomes by iteratively exploring sequence data for correlations and building upon them. First, to integrate and compare different annotation sources, a sequence matrix (SM) is developed to contain position-dependant information. Second, a classification tree is developed for matrix row types, specifying how each data type is to be treated with respect to other data types for analysis purposes. Third, correlative analyses are developed to analyze features of each matrix row in terms of the other rows, guided by the classification tree as to which analyses are appropriate. A prototype was developed and successful in detecting coinciding genomic features among genes, exons, repetitive elements and CpG islands. PMID:16026599

  10. Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

    PubMed Central

    Johnston, Chad W.; Edgar, Robyn E.; Dejong, Chris A.; Merwin, Nishanth J.; Rees, Philip N.; Magarvey, Nathan A.

    2016-01-01

    Microbial natural products are an evolved resource of bioactive small molecules, which form the foundation of many modern therapeutic regimes. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) represent a class of natural products which have attracted extensive interest for their diverse chemical structures and potent biological activities. Genome sequencing has revealed that the vast majority of genetically encoded natural products remain unknown. Many bioinformatic resources have therefore been developed to predict the chemical structures of natural products, particularly nonribosomal peptides and polyketides, from sequence data. However, the diversity and complexity of RiPPs have challenged systematic investigation of RiPP diversity, and consequently the vast majority of genetically encoded RiPPs remain chemical “dark matter.” Here, we introduce an algorithm to catalog RiPP biosynthetic gene clusters and chart genetically encoded RiPP chemical space. A global analysis of 65,421 prokaryotic genomes revealed 30,261 RiPP clusters, encoding 2,231 unique products. We further leverage the structure predictions generated by our algorithm to facilitate the genome-guided discovery of a molecule from a rare family of RiPPs. Our results provide the systematic investigation of RiPP genetic and chemical space, revealing the widespread distribution of RiPP biosynthesis throughout the prokaryotic tree of life, and provide a platform for the targeted discovery of RiPPs based on genome sequencing. PMID:27698135

  11. Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining.

    PubMed

    Skinnider, Michael A; Johnston, Chad W; Edgar, Robyn E; Dejong, Chris A; Merwin, Nishanth J; Rees, Philip N; Magarvey, Nathan A

    2016-10-18

    Microbial natural products are an evolved resource of bioactive small molecules, which form the foundation of many modern therapeutic regimes. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) represent a class of natural products which have attracted extensive interest for their diverse chemical structures and potent biological activities. Genome sequencing has revealed that the vast majority of genetically encoded natural products remain unknown. Many bioinformatic resources have therefore been developed to predict the chemical structures of natural products, particularly nonribosomal peptides and polyketides, from sequence data. However, the diversity and complexity of RiPPs have challenged systematic investigation of RiPP diversity, and consequently the vast majority of genetically encoded RiPPs remain chemical "dark matter." Here, we introduce an algorithm to catalog RiPP biosynthetic gene clusters and chart genetically encoded RiPP chemical space. A global analysis of 65,421 prokaryotic genomes revealed 30,261 RiPP clusters, encoding 2,231 unique products. We further leverage the structure predictions generated by our algorithm to facilitate the genome-guided discovery of a molecule from a rare family of RiPPs. Our results provide the systematic investigation of RiPP genetic and chemical space, revealing the widespread distribution of RiPP biosynthesis throughout the prokaryotic tree of life, and provide a platform for the targeted discovery of RiPPs based on genome sequencing.

  12. 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

  13. 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

  14. 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

  15. 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/.

  16. 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

  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. Rational Teaching.

    ERIC Educational Resources Information Center

    Macmillan, C. J. B.

    1985-01-01

    The recognition of teaching as a special relationship among individuals is currently being overlooked in much contemporary educational research and policymaking. The author examines the philosophy of rationality in teaching and relates it to the educational vision presented in George Orwell's novel, "Nineteen Eighty-Four." (CB)

  19. 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.

  20. Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans

    PubMed Central

    Liu, Liwei; Hao, Tingting; Xie, Zhoujie; Horsman, Geoff P.; Chen, Yihua

    2016-01-01

    Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as “poor” sources of natural products. PMID:27869143

  1. InCoB2014: mining biological data from genomics for transforming industry and health

    PubMed Central

    2014-01-01

    The 13th International Conference on Bioinformatics (InCoB2014) was held for the first time in Australia, at Sydney, July 31-2 August, 2014. InCoB is the annual scientific gathering of the Asia-Pacific Bioinformatics Network (APBioNet), hosted since 2002 in the Asia-Pacific region. Of 106 full papers submitted to the BMC track of InCoB2014, 50 (47.2%) were accepted in BMC Bioinformatics, BMC Genomics and BMC Systems Biology supplements, with three papers in a new BMC Medical Genomics supplement. While the majority of presenters and authors were from Asia and Australia, the increasing number of US and European conference attendees augurs well for the international flavour of InCoB. Next year's InCoB will be held jointly with the Genome Informatics Workshop (GIW), September 9-11, 2015 in Tokyo, Japan, with a view to integrate bioinformatics communities in the region. PMID:25521539

  2. Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans.

    PubMed

    Liu, Liwei; Hao, Tingting; Xie, Zhoujie; Horsman, Geoff P; Chen, Yihua

    2016-11-21

    Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as "poor" sources of natural products.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. Applied genomics: data mining reveals species-specific malaria diagnostic targets more sensitive than 18S rRNA.

    PubMed

    Demas, Allison; Oberstaller, Jenna; DeBarry, Jeremy; Lucchi, Naomi W; Srinivasamoorthy, Ganesh; Sumari, Deborah; Kabanywanyi, Abdunoor M; Villegas, Leopoldo; Escalante, Ananias A; Kachur, S Patrick; Barnwell, John W; Peterson, David S; Udhayakumar, Venkatachalam; Kissinger, Jessica C

    2011-07-01

    Accurate and rapid diagnosis of malaria infections is crucial for implementing species-appropriate treatment and saving lives. Molecular diagnostic tools are the most accurate and sensitive method of detecting Plasmodium, differentiating between Plasmodium species, and detecting subclinical infections. Despite available whole-genome sequence data for Plasmodium falciparum and P. vivax, the majority of PCR-based methods still rely on the 18S rRNA gene targets. Historically, this gene has served as the best target for diagnostic assays. However, it is limited in its ability to detect mixed infections in multiplex assay platforms without the use of nested PCR. New diagnostic targets are needed. Ideal targets will be species specific, highly sensitive, and amenable to both single-step and multiplex PCRs. We have mined the genomes of P. falciparum and P. vivax to identify species-specific, repetitive sequences that serve as new PCR targets for the detection of malaria. We show that these targets (Pvr47 and Pfr364) exist in 14 to 41 copies and are more sensitive than 18S rRNA when utilized in a single-step PCR. Parasites are routinely detected at levels of 1 to 10 parasites/μl. The reaction can be multiplexed to detect both species in a single reaction. We have examined 7 P. falciparum strains and 91 P. falciparum clinical isolates from Tanzania and 10 P. vivax strains and 96 P. vivax clinical isolates from Venezuela, and we have verified a sensitivity and specificity of ∼100% for both targets compared with a nested 18S rRNA approach. We show that bioinformatics approaches can be successfully applied to identify novel diagnostic targets and improve molecular methods for pathogen detection. These novel targets provide a powerful alternative molecular diagnostic method for the detection of P. falciparum and P. vivax in conventional or multiplex PCR platforms.

  8. Rational Belief.

    DTIC Science & Technology

    1983-05-01

    numbers; may include program from the Standard Distribution for element number(s), project number(s), task Unclassified Scientific and Technical number...Grant TA - Task Block 13. A.trac.t Include a brief (Maximum PE - Program WU- Work Unit 200 words) factual summary of the most Element Accession No...rational constraints for nondeductive argument and inference. Such a notion would also provide a framework for decision theory. The program of finding

  9. Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): mining and characterization of new genomic and molecular markers.

    PubMed

    Cárdenas, Leyla; Sánchez, Roland; Gomez, Daniela; Fuenzalida, Gonzalo; Gallardo-Escárate, Cristián; Tanguy, Arnaud

    2011-09-01

    The marine gastropod Concholepas concholepas, locally known as the "loco", is the main target species of the benthonic Chilean fisheries. Genetic and genomic tools are necessary to study the genome of this species in order to understand the molecular basis of its development, growth, and other key traits to improve the management strategies and to identify local adaptation to prevent loss of biodiversity. Here, we use pyrosequencing technologies to generate the first transcriptomic database from adult specimens of the loco. After trimming, a total of 140,756 Expressed Sequence Tag sequences were achieved. Clustering and assembly analysis identified 19,219 contigs and 105,435 singleton sequences. BlastN analysis showed a significant identity with Expressed Sequence Tags of different gastropod species available in public databases. Similarly, BlastX results showed that only 895 out of the total 124,654 had significant hits and may represent novel genes for marine gastropods. From this database, simple sequence repeat motifs were also identified and a total of 38 primer pairs were designed and tested to assess their potential as informative markers and to investigate their cross-species amplification in different related gastropod species. This dataset represents the first publicly available 454 data for a marine gastropod endemic to the southeastern Pacific coast, providing a valuable transcriptomic resource for future efforts of gene discovery and development of functional markers in other marine gastropods.

  10. Discovery of the rhizopodin biosynthetic gene cluster in Stigmatella aurantiaca Sg a15 by genome mining.

    PubMed

    Pistorius, Dominik; Müller, Rolf

    2012-02-13

    The field of bacterial natural product research is currently undergoing a paradigm change concerning the discovery of natural products. Previously most efforts were based on isolation of the most abundant compound in an extract, or on tracking bioactivity. However, traditional activity-guided approaches are limited by the available test panels and frequently lead to the rediscovery of already known compounds. The constantly increasing availability of bacterial genome sequences provides the potential for the discovery of a huge number of new natural compounds by in silico identification of biosynthetic gene clusters. Examination of the information on the biosynthetic machinery can further prevent rediscovery of known compounds, and can help identify so far unknown biosynthetic pathways of known compounds. By in silico screening of the genome of the myxobacterium Stigmatella aurantiaca Sg a15, a trans-AT polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) gene cluster was identified that could not be correlated to any secondary metabolite known to be produced by this strain. Targeted gene inactivation and analysis of extracts from the resulting mutants by high performance liquid chromatography coupled to high resolution mass spectrometry (HPLC-HRMS), in combination with the use of statistical tools resulted in the identification of a compound that was absent in the mutants extracts. By matching with our in-house database of myxobacterial secondary metabolites, this compound was identified as rhizopodin. A detailed analysis of the rhizopodin biosynthetic machinery is presented in this manuscript.

  11. Target recognition, resistance, immunity and genome mining of class II bacteriocins from Gram-positive bacteria.

    PubMed

    Kjos, Morten; Borrero, Juan; Opsata, Mona; Birri, Dagim J; Holo, Helge; Cintas, Luis M; Snipen, Lars; Hernández, Pablo E; Nes, Ingolf F; Diep, Dzung B

    2011-12-01

    Due to their very potent antimicrobial activity against diverse food-spoiling bacteria and pathogens and their favourable biochemical properties, peptide bacteriocins from Gram-positive bacteria have long been considered promising for applications in food preservation or medical treatment. To take advantage of bacteriocins in different applications, it is crucial to have detailed knowledge on the molecular mechanisms by which these peptides recognize and kill target cells, how producer cells protect themselves from their own bacteriocin (self-immunity) and how target cells may develop resistance. In this review we discuss some important recent progress in these areas for the non-lantibiotic (class II) bacteriocins. We also discuss some examples of how the current wealth of genome sequences provides an invaluable source in the search for novel class II bacteriocins.

  12. Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes.

    PubMed

    Adu-Oppong, Boahemaa; Gasparrini, Andrew J; Dantas, Gautam

    2017-01-01

    Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance. Here, we review genomic and functional methods that have been developed for accessing the antimicrobial biosynthesis and resistance capacity of microbiomes and highlight outstanding examples of their applications.

  13. 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

  14. Genome mining unearths a hybrid nonribosomal peptide synthetase-like-pteridine synthase biosynthetic gene cluster

    PubMed Central

    Park, Hyun Bong; Perez, Corey E; Barber, Karl W; Rinehart, Jesse; Crawford, Jason M

    2017-01-01

    Nonribosomal peptides represent a large class of metabolites with pharmaceutical relevance. Pteridines, such as pterins, folates, and flavins, are heterocyclic metabolites that often serve as redox-active cofactors. The biosynthetic machineries for construction of these distinct classes of small molecules operate independently in the cell. Here, we discovered an unprecedented nonribosomal peptide synthetase-like-pteridine synthase hybrid biosynthetic gene cluster in Photorhabdus luminescens using genome synteny analysis. P. luminescens is a Gammaproteobacterium that undergoes phenotypic variation and can have both pathogenic and mutualistic roles. Through extensive gene deletion, pathway-targeted molecular networking, quantitative proteomic analysis, and NMR, we show that the genetic locus affects the regulation of quorum sensing and secondary metabolic enzymes and encodes new pteridine metabolites functionalized with cis-amide acyl-side chains, termed pepteridine A (1) and B (2). The pepteridines are produced in the pathogenic phenotypic variant and represent the first reported metabolites to be synthesized by a hybrid NRPS-pteridine pathway. These studies expand our view of the combinatorial biosynthetic potential available in bacteria. DOI: http://dx.doi.org/10.7554/eLife.25229.001

  15. 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

    2016-06-20

    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.

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

    PubMed

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

    2016-01-06

    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.

  17. Genome mining of fungal lipid-degrading enzymes for industrial applications.

    PubMed

    Vorapreeda, Tayvich; Thammarongtham, Chinae; Cheevadhanarak, Supapon; Laoteng, Kobkul

    2015-08-01

    Lipases are interesting enzymes, which contribute important roles in maintaining lipid homeostasis and cellular metabolisms. Using available genome data, seven lipase families of oleaginous and non-oleaginous yeast and fungi were categorized based on the similarity of their amino acid sequences and conserved structural domains. Of them, triacylglycerol lipase (patatin-domain-containing protein) and steryl ester hydrolase (abhydro_lipase-domain-containing protein) families were ubiquitous enzymes found in all species studied. The two essential lipases rendered signature characteristics of integral membrane proteins that might be targeted to lipid monolayer particles. At least one of the extracellular lipase families existed in each species of yeast and fungi. We found that the diversity of lipase families and the number of genes in individual families of oleaginous strains were greater than those identified in non-oleaginous species, which might play a role in nutrient acquisition from surrounding hydrophobic substrates and attribute to their obese phenotype. The gene/enzyme catalogue and relevant informative data of the lipases provided by this study are not only valuable toolboxes for investigation of the biological role of these lipases, but also convey potential in various industrial applications.

  18. 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…

  19. Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences.

    PubMed

    Ganapathiraju, Madhavi K; Mitchell, Asia D; Thahir, Mohamed; Motwani, Kamiya; Ananthasubramanian, Seshan

    2012-12-01

    Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

  20. 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

  1. Canaries in the coal mine: Personal and professional impact of undergoing whole genome sequencing on medical professionals.

    PubMed

    Zierhut, Heather; McCarthy Veach, Patricia; LeRoy, Bonnie

    2015-11-01

    Public interest in personal whole genome sequencing is increasing. The technology is publicly available and is being used as an educational tool in higher education. Empirical evidence regarding its utility is vital. The goals of this study were to characterize the process of whole genome sequencing in a population of medical and basic science professionals undergoing whole genome sequencing as a part of an educational symposium. Thirty-eight individuals completed one or more surveys from the time of informed consent for whole genome sequencing to 3 months post-symposium. The four surveys assessed demographics, decision-making, communication, decision regret, and personal and professional impact. The most prevalent motivation to participate was professional enhancement, followed by curiosity about the technology, and personal health benefits. The most important initial impact concerned medical implications. Over time, however, impact on professional development was greater than on personal health. Anticipated reactions to receiving whole genome sequencing results generally matched participants' actual reactions and decision regret remained low over time. Benefits and risks of whole genome sequencing included medically actionable results and misunderstanding by healthcare providers. Whole genome sequencing generally had a positive impact professionally and personally on participants. Further education of providers and the public about whole genome sequencing and psychosocial support is warranted.

  2. 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

    Rangel, Wesley Melo; Thijs, Sofie; Moreira, Fatima Maria de Souza; Weyens, Nele; Vangronsveld, Jaco; Van Hamme, Jonathan D; Bottos, Eric M; Rineau, Francois

    2016-03-10

    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.

  3. Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria.

    PubMed

    Tan, Gao-Yi; Liu, Tiangang

    2017-01-01

    Natural products (NPs) and their derivatives are widely used as frontline treatments for many diseases. Actinobacteria spp. are used to produce most of NP antibiotics and have also been intensively investigated for NP production, derivatization, and discovery. However, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in Actinobacteria, especially in the cases of genome mining and heterologous expression, it is often difficult to rationally and systematically engineer synthetic pathways to maximize biosynthetic efficiency. With the emergence of new tools and methods in metabolic engineering, the synthetic pathways of many chemicals, such as fatty acids and biofuels, in model organisms (e.g. Escherichia coli ), have been refactored to realize precise and flexible control of production. These studies also offer a promising approach for synthetic pathway refactoring in Actinobacteria. In this review, the great potential of Actinobacteria as a microbial cell factory for biosynthesis of NPs is discussed. To this end, recent progress in metabolic engineering of NP synthetic pathways in Actinobacteria are summarized and strategies and perspectives to rationally and systematically refactor synthetic pathways in Actinobacteria are highlighted.

  4. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.

    PubMed

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

    2013-10-01

    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

  5. Mining plant genome browsers as a means for efficient connection of physical, genetic and cytogenetic mapping: An example using soybean

    PubMed Central

    Belarmino, Luis C.; da S. Oliveira, Ana R.; Brasileiro-Vidal, Ana C.; de A. Bortoleti, Kyria C.; Bezerra-Neto, João Pacífico; Abdelnoor, Ricardo V.; Benko-Iseppon, Ana M.

    2012-01-01

    Physical maps are important tools to uncover general chromosome structure as well as to compare different plant lineages and species, helping to elucidate genome structure, evolution and possibilities regarding synteny and colinearity. The increasing production of sequence data has opened an opportunity to link information from mapping studies to the underlying sequences. Genome browsers are invaluable platforms that provide access to these sequences, including tools for genome analysis, allowing the integration of multivariate information, and thus aiding to explain the emergence of complex genomes. The present work presents a tutorial regarding the use of genome browsers to develop targeted physical mapping, providing also a general overview and examples about the possibilities regarding the use of Fluorescent In Situ Hybridization (FISH) using bacterial artificial chromosomes (BAC), simple sequence repeats (SSR) and rDNA probes, highlighting the potential of such studies for map integration and comparative genetics. As a case study, the available genome of soybean was accessed to show how the physical and in silico distribution of such sequences may be compared at different levels. Such evaluations may also be complemented by the identification of sequences beyond the detection level of cytological methods, here using members of the aquaporin gene family as an example. The proposed approach highlights the complementation power of the combination of molecular cytogenetics and computational approaches for the anchoring of coding or repetitive sequences in plant genomes using available genome browsers, helping in the determination of sequence location, arrangement and number of repeats, and also filling gaps found in computational pseudochromosome assemblies. PMID:22802719

  6. 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.

  7. 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.

  8. -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis.

    PubMed

    Undabarrena, Agustina; Ugalde, Juan A; Seeger, Michael; Cámara, Beatriz

    2017-01-01

    Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

  9. 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...

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

    PubMed

    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

    2015-09-01

    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.

  12. Mining Gold Dust under the Genome Wide Significance Level: A Two-Stage Approach to Analysis of GWAS

    PubMed Central

    Shi, Gang; Boerwinkle, Eric; Morrison, Alanna C.; Gu, C. Charles; Chakravarti, Aravinda; Rao, DC

    2013-01-01

    We propose a two-stage approach to analyze genome-wide association (GWA) data in order to identify a set of promising single-nucleotide polymorphisms (SNPs). In stage one, we select a list of top signals from single SNP analyses by controlling false discovery rate (FDR). In stage two, we use the least absolute shrinkage and selection operator (LASSO) regression to reduce false positives. The proposed approach was evaluated using simulated quantitative traits based on genome-wide SNP data on 8,861 Caucasian individuals from the Atherosclerosis Risk in Communities (ARIC) Study. Our first stage, targeted at controlling false negatives, yields better power than using Bonferroni corrected significance level. The LASSO regression reduces the number of significant SNPs in stage two: it reduces false positive SNPs and it reduces true positive SNPs also at simulated causal loci due to linkage disequilibrium. Interestingly, the LASSO regression preserves the power from stage one, i.e., the number of causal loci detected from the LASSO regression in stage two is almost the same as in stage one, while reducing false positives further. Real data on systolic blood pressure in the ARIC study was analyzed using our two-stage approach which identified two significant SNPs, one of which was reported to be genome-significant in a meta-analysis containing a much larger sample size. On the other hand, a single SNP association scan did not yield any significant results. PMID:21254218

  13. Mining gold dust under the genome wide significance level: a two-stage approach to analysis of GWAS.

    PubMed

    Shi, Gang; Boerwinkle, Eric; Morrison, Alanna C; Gu, C Charles; Chakravarti, Aravinda; Rao, D C

    2011-02-01

    We propose a two-stage approach to analyze genome-wide association data in order to identify a set of promising single-nucleotide polymorphisms (SNPs). In stage one, we select a list of top signals from single SNP analyses by controlling false discovery rate. In stage two, we use the least absolute shrinkage and selection operator (LASSO) regression to reduce false positives. The proposed approach was evaluated using simulated quantitative traits based on genome-wide SNP data on 8,861 Caucasian individuals from the Atherosclerosis Risk in Communities (ARIC) Study. Our first stage, targeted at controlling false negatives, yields better power than using Bonferroni-corrected significance level. The LASSO regression reduces the number of significant SNPs in stage two: it reduces false-positive SNPs and it reduces true-positive SNPs also at simulated causal loci due to linkage disequilibrium. Interestingly, the LASSO regression preserves the power from stage one, i.e., the number of causal loci detected from the LASSO regression in stage two is almost the same as in stage one, while reducing false positives further. Real data on systolic blood pressure in the ARIC study was analyzed using our two-stage approach which identified two significant SNPs, one of which was reported to be genome-significant in a meta-analysis containing a much larger sample size. On the other hand, a single SNP association scan did not yield any significant results.

  14. Mining of novel species-specific primers for PCR detection of Listeria monocytogenes based on genomic approach.

    PubMed

    Tao, Tingting; Chen, Qiming; Bie, Xiaomei; Lu, Fengxia; Lu, Zhaoxin

    2015-12-01

    Listeria monocytogenes in contaminated food is considered as a serious health threat for consumers due to its high mortality rate. The objective of this study was to obtain novel species-specific target-genes and primers for the molecular detection of L. monocytogenes using a comparative genomic approach. By comparative analysis of L. monocytogenes and non-L. monocytogenes genome sequences in the GenBank database with BLAST program, 26 specific target sequences were used as candidates and the primers were designed for L. monocytogenes species-specificity verification by using PCR assay. Finally, the three genes LMOf2365_0970, LMOf2365_2721 and mpl were identified to have L. monocytogenes species-specificity and be unique as detection targets for diagnostic application. The species-specific primer Lm8 of gene LMOf2365_0970, Lm13 of gene LMOf2365_2721 and Lm20 of gene mpl showed better specificity and sensitivity than the primers described previously. The PCR detection limits of the three specific primer sets were 430, 43, 4.3 fg/μL for genomic DNA, and 5 × 10(3), 50, 5 cfu/mL for pure culture of L. monocytogenes. There was no interference in specificity of detecting L. monocytogenes by co-culture with other foodborne pathogens in high concentration. Moreover, after 6-8 h of enrichment, L. monocytogenes in the artificially contaminated milk samples at an inoculum dose of 38 cfu/10 mL milk could be detected successfully with the studied three primers. Therefore, the three specific genes and primers can be applied to establish a novel rapid and accurate method for detecting L. monocytogenes in food materials.

  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. 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

    2015-11-02

    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.

  17. 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

  18. SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining.

    PubMed

    Zhang, Yuanwei; Zhong, Liangwen; Xu, Bo; Yang, Yifan; Ban, Rongjun; Zhu, Jun; Cooke, Howard J; Hao, Qiaomei; Shi, Qinghua

    2013-01-01

    Human infertility affects 10-15% of couples, half of which is attributed to the male partner. Abnormal spermatogenesis is a major cause of male infertility. Characterizing the genes involved in spermatogenesis is fundamental to understand the mechanisms underlying this biological process and in developing treatments for male infertility. Although many genes have been implicated in spermatogenesis, no dedicated bioinformatic resource for spermatogenesis is available. We have developed such a database, SpermatogenesisOnline 1.0 (http://mcg.ustc.edu.cn/sdap1/spermgenes/), using manual curation from 30 233 articles published before 1 May 2012. It provides detailed information for 1666 genes reported to participate in spermatogenesis in 37 organisms. Based on the analysis of these genes, we developed an algorithm, Greed AUC Stepwise (GAS) model, which predicted 762 genes to participate in spermatogenesis (GAS probability >0.5) based on genome-wide transcriptional data in Mus musculus testis from the ArrayExpress database. These predicted and experimentally verified genes were annotated, with several identical spermatogenesis-related GO terms being enriched for both classes. Furthermore, protein-protein interaction analysis indicates direct interactions of predicted genes with the experimentally verified ones, which supports the reliability of GAS. The strategy (manual curation and data mining) used to develop SpermatogenesisOnline 1.0 can be easily extended to other biological processes.

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

    PubMed

    Yang, Xiaohan; Ye, Chu-Yu; Bisaria, Anjali; Tuskan, Gerald A; Kalluri, Udaya C

    2011-12-01

    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 biofuels 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 evidence 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 characterization in relation to cell wall biosynthesis.

  20. 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

  1. 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

  2. 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)

  3. Alternative Disaster Feeding Ration

    DTIC Science & Technology

    2012-06-08

    or relations with each ration type: MREs are not vegetarian ; HDRs are religiously sensitive; and high calorie bars appear minimalistic implying lack...each ration type: MREs are not vegetarian ; HDRs are religiously sensitive; and high calorie bars appear minimalistic implying lack of compassion

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

    PubMed Central

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

    2015-01-01

    Abstract 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

  6. Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia.

    PubMed

    Mojib, Nazia; Amad, Maan; Thimma, Manjula; Aldanondo, Naroa; Kumaran, Mande; Irigoien, Xabier

    2014-06-01

    The tropical oligotrophic oceanic areas are characterized by high water transparency and annual solar radiation. Under these conditions, a large number of phylogenetically diverse mesozooplankton species living in the surface waters (neuston) are found to be blue pigmented. In the present study, we focused on understanding the metabolic and genetic basis of the observed blue phenotype functional equivalence between the blue-pigmented organisms from the phylum Arthropoda, subclass Copepoda (Acartia fossae) and the phylum Chordata, class Appendicularia (Oikopleura dioica) in the Red Sea. Previous studies have shown that carotenoid-protein complexes are responsible for blue coloration in crustaceans. Therefore, we performed carotenoid metabolic profiling using both targeted and nontargeted (high-resolution mass spectrometry) approaches in four different blue-pigmented genera of copepods and one blue-pigmented species of appendicularia. Astaxanthin was found to be the principal carotenoid in all the species. The pathway analysis showed that all the species can synthesize astaxanthin from β-carotene, ingested from dietary sources, via 3-hydroxyechinenone, canthaxanthin, zeaxanthin, adonirubin or adonixanthin. Further, using de novo assembled transcriptome of blue A. fossae (subclass Copepoda), we identified highly expressed homologous β-carotene hydroxylase enzymes and putative carotenoid-binding proteins responsible for astaxanthin formation and the blue phenotype. In blue O. dioica (class Appendicularia), corresponding putative genes were identified from the reference genome. Collectively, our data provide molecular evidences for the bioconversion and accumulation of blue astaxanthin-protein complexes underpinning the observed ecological functional equivalence and adaptive convergence among neustonic mesozooplankton.

  7. Genome mining in Amycolatopsis balhimycina for ferredoxins capable of supporting cytochrome P450 enzymes involved in glycopeptide antibiotic biosynthesis.

    PubMed

    Geib, Nina; Weber, Tilmann; Wörtz, Tanja; Zerbe, Katja; Wohlleben, Wolfgang; Robinson, John A

    2010-05-01

    Ferredoxins are required to supply electrons to the cytochrome P450 enzymes involved in cross-linking reactions during the biosynthesis of the glycopeptide antibiotics balhimycin and vancomycin. However, the biosynthetic gene clusters for these antibiotics contain no ferredoxin- or ferredoxin reductase-like genes. In a search for potential ferredoxin partners for these P450s, here, we report an in silico analysis of the draft genome sequence of the balhimycin producer Amycolatopsis balhimycina, which revealed 11 putative Fe-S-containing ferredoxin genes. We show that two members (balFd-V and balFd-VII), produced as native-like holo-[3Fe-4S] ferredoxins in Escherichia coli, could supply electrons to the P450 OxyB (CYP165B) from both A. balhimycina and the vancomycin producer Amycolatopsis orientalis, and support in vitro turnover of peptidyl carrier protein-bound peptide substrates into monocyclic cross-linked products. These results show that ferredoxins encoded in the antibiotic-producing strain can act in a degenerate manner in supporting the catalytic functions of glycopeptide biosynthetic P450 enzymes from the same as well as heterologous gene clusters.

  8. Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings.

    PubMed

    Rahman, Sumayah F; Kantor, Rose S; Huddy, Robert; Thomas, Brian C; van Zyl, Andries W; Harrison, Susan T L; Banfield, Jillian F

    2017-02-19

    Thiocyanate (SCN(-) ) is a toxic compound that forms when cyanide (CN(-) ), used to recover gold, reacts with sulfur species. SCN(-) -degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory-based reactors operated without suspended solids. Despite minor upsets during the acclimation period, the SCN(-) degradation performance was largely unchanged under stable operating conditions. Here, we characterized the microbial community in the SCN(-) degrading bioreactor that included solid particulate tailings and determined how it differed from the biofilm-based communities in solids-free reactor systems inoculated from the same source. Genome-based analysis revealed that the presence of solids decreased microbial diversity, selected for different strains, suppressed growth of thiobacilli inferred to be primarily responsible for SCN(-) degradation, and promoted growth of Trupera, an organism not detected in the reactors without solids. In the solids reactor community, heterotrophy and aerobic respiration represent the dominant metabolisms. Many organisms have genes for denitrification and sulfur oxidation, but only one Thiobacillus sp. in the solids reactor has SCN(-) degradation genes. The presence of the solids prevented floc and biofilm formation, leading to the observed reduced microbial diversity. Collectively the presence of the solids and lack of biofilm community may result in a process with reduced resilience to process perturbations, including fluctuations in the influent composition and pH. The results from this investigation have provided novel insights into the community composition of this industrially relevant

  9. Identification by Genome Mining of a Type I Polyketide Gene Cluster from Streptomyces argillaceus Involved in the Biosynthesis of Pyridine and Piperidine Alkaloids Argimycins P

    PubMed Central

    Ye, Suhui; Molloy, Brian; Braña, Alfredo F.; Zabala, Daniel; Olano, Carlos; Cortés, Jesús; Morís, Francisco; Salas, José A.; Méndez, Carmen

    2017-01-01

    Genome mining of the mithramycin producer Streptomyces argillaceus ATCC 12956 revealed 31 gene clusters for the biosynthesis of secondary metabolites, and allowed to predict the encoded products for 11 of these clusters. Cluster 18 (renamed cluster arp) corresponded to a type I polyketide gene cluster related to the previously described coelimycin P1 and streptazone gene clusters. The arp cluster consists of fourteen genes, including genes coding for putative regulatory proteins (a SARP-like transcriptional activator and a TetR-like transcriptional repressor), genes coding for structural proteins (three PKSs, one aminotransferase, two dehydrogenases, two cyclases, one imine reductase, a type II thioesterase, and a flavin reductase), and one gene coding for a hypothetical protein. Identification of encoded compounds by this cluster was achieved by combining several strategies: (i) inactivation of the type I PKS gene arpPIII; (ii) inactivation of the putative TetR-transcriptional repressor arpRII; (iii) cultivation of strains in different production media; and (iv) using engineered strains with higher intracellular concentration of malonyl-CoA. This has allowed identifying six new alkaloid compounds named argimycins P, which were purified and structurally characterized by mass spectrometry and nuclear magnetic resonance spectroscopy. Some argimycins P showed a piperidine ring with a polyene side chain (argimycin PIX); others contain also a fused five-membered ring (argimycins PIV-PVI). Argimycins PI-PII showed a pyridine ring instead, and an additional N-acetylcysteinyl moiety. These compounds seem to play a negative role in growth and colony differentiation in S. argillaceus, and some of them show weak antibiotic activity. A pathway for the biosynthesis of argimycins P is proposed, based on the analysis of proposed enzyme functions and on the structure of compounds encoded by the arp cluster. PMID:28239372

  10. RGS2 expression predicts amyloid-β sensitivity, MCI and Alzheimer's disease: genome-wide transcriptomic profiling and bioinformatics data mining

    PubMed Central

    Hadar, A; Milanesi, E; Squassina, A; Niola, P; Chillotti, C; Pasmanik-Chor, M; Yaron, O; Martásek, P; Rehavi, M; Weissglas-Volkov, D; Shomron, N; Gozes, I; Gurwitz, D

    2016-01-01

    Alzheimer's disease (AD) is the most frequent cause of dementia. Misfolded protein pathological hallmarks of AD are brain deposits of amyloid-β (Aβ) plaques and phosphorylated tau neurofibrillary tangles. However, doubts about the role of Aβ in AD pathology have been raised as Aβ is a common component of extracellular brain deposits found, also by in vivo imaging, in non-demented aged individuals. It has been suggested that some individuals are more prone to Aβ neurotoxicity and hence more likely to develop AD when aging brains start accumulating Aβ plaques. Here, we applied genome-wide transcriptomic profiling of lymphoblastoid cells lines (LCLs) from healthy individuals and AD patients for identifying genes that predict sensitivity to Aβ. Real-time PCR validation identified 3.78-fold lower expression of RGS2 (regulator of G-protein signaling 2; P=0.0085) in LCLs from healthy individuals exhibiting high vs low Aβ sensitivity. Furthermore, RGS2 showed 3.3-fold lower expression (P=0.0008) in AD LCLs compared with controls. Notably, RGS2 expression in AD LCLs correlated with the patients' cognitive function. Lower RGS2 expression levels were also discovered in published expression data sets from postmortem AD brain tissues as well as in mild cognitive impairment and AD blood samples compared with controls. In conclusion, Aβ sensitivity phenotyping followed by transcriptomic profiling and published patient data mining identified reduced peripheral and brain expression levels of RGS2, a key regulator of G-protein-coupled receptor signaling and neuronal plasticity. RGS2 is suggested as a novel AD biomarker (alongside other genes) toward early AD detection and future disease modifying therapeutics. PMID:27701409

  11. Dragon Plant Biology Explorer. A Text-Mining Tool for Integrating Associations between Genetic and Biochemical Entities with Genome Annotation and Biochemical Terms Lists[w

    PubMed Central

    Bajic, Vladimir B.; Veronika, Merlin; Veladandi, Pardha Sarathi; Meka, Archana; Heng, Mok-Wei; Rajaraman, Kanagasabai; Pan, Hong; Swarup, Sanjay

    2005-01-01

    We introduce a tool for text mining, Dragon Plant Biology Explorer (DPBE) that integrates information on Arabidopsis (Arabidopsis thaliana) genes with their functions, based on gene ontologies and biochemical entity vocabularies, and presents the associations as interactive networks. The associations are based on (1) user-provided PubMed abstracts; (2) a list of Arabidopsis genes compiled by The Arabidopsis Information Resource; (3) user-defined combinations of four vocabulary lists based on the ones developed by the general, plant, and Arabidopsis GO consortia; and (4) three lists developed here based on metabolic pathways, enzymes, and metabolites derived from AraCyc, BRENDA, and other metabolism databases. We demonstrate how various combinations can be applied to fields of (1) gene function and gene interaction analyses, (2) plant development, (3) biochemistry and metabolism, and (4) pharmacology of bioactive compounds. Furthermore, we show the suitability of DPBE for systems approaches by integration with “omics” platform outputs. Using a list of abiotic stress-related genes identified by microarray experiments, we show how this tool can be used to rapidly build an information base on the previously reported relationships. This tool complements the existing biological resources for systems biology by identifying potentially novel associations using text analysis between cellular entities based on genome annotation terms. Thus, it allows researchers to efficiently summarize existing information for a group of genes or pathways, so as to make better informed choices for designing validation experiments. Last, DPBE can be helpful for beginning researchers and graduate students to summarize vast information in an unfamiliar area. DPBE is freely available for academic and nonprofit users at http://research.i2r.a-star.edu.sg/DRAGON/ME2/. PMID:16172098

  12. [Concepts of rational taxonomy].

    PubMed

    Pavlinov, I Ia

    2011-01-01

    The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the

  13. 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.

  14. Fuzzy capital rationing model

    NASA Astrophysics Data System (ADS)

    Bas, E.; Kahraman, C.

    2009-02-01

    In this paper, we study the fuzzification of Weingartner's pure capital rationing model and its analysis. We develop a primal-dual pair based on t-norm/t-conorm relation for the constraints and objective function for a fully fuzzified pure capital rationing problem except project selection variables. We define the [alpha]-interval under which the weak duality is proved. We perform sensitivity analysis for a change in a budget level or in a cash flow level of a non-basic as well as a basic variable. We analyze the problem based on duality and complementary slackness results. We illustrate the proposed model by computational analysis, and interpret the results.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.…

  20. Genome- and proteome-wide screening strategies for antigen discovery and immunogen design.

    PubMed

    Schussek, Sophie; Trieu, Angela; Doolan, Denise L

    2014-01-01

    Infectious diseases remain a leading global cause of morbidity and mortality and there is an urgent need for effective approaches to develop vaccines, especially against complex pathogens. The availability of comprehensive genomic, proteomic and transcriptomic datasets has shifted the paradigm of vaccine development from microbiological to sequence-based approaches. However, how to effectively translate raw data into candidate vaccines is not yet obvious. Herein, we review cutting-edge technologies and screening strategies to mine genomic sequence information for state-of-the-art rational vaccine design, and highlight recent trends. Interdisciplinary approaches which cross the traditional boundaries of genomics, molecular biology, cell biology, immunology and computer science, and which prioritise antigens according to clinically relevant criteria, offer potential solutions to the widespread threat that complex pathogens pose to public health.

  1. 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.

  2. Rational drug design.

    PubMed

    Mandal, Soma; Moudgil, Mee'nal; Mandal, Sanat K

    2009-12-25

    In this article, current knowledge of drug design is reviewed and an approach of rational drug design is presented. The process of drug development is challenging, expensive, and time consuming, although this process has been accelerated due to the development of computational tools and methodologies. The current target based drug design approach is incomplete because most of the drugs developed by structure guided approaches have been shown to have serious toxic side effects. Otherwise these drugs would have been an ideal choice for the treatment of diseases. Hence, rational drug design would require a multidisciplinary approach. In this regard, incorporation of gene expression technology and bioinformatics tools would be indispensable in the structure based drug design. Global gene expression data and analysis of such data using bioinformatics tools will have numerous benefits such as efficiency, cost effectiveness, time saving, and will provide strategies for combination therapy in addition to overcoming toxic side effects. As a result of incorporation of gene expression data, partial benefit of the structure based drug design is slowly emerging and rapidly changing the approach of the drug development process. To achieve the full benefit of developing a successful drug, multidisciplinary approaches (approaches such as computational chemistry and gene expression analysis, as discussed in this article) would be necessary. In the future, there is adequate room for the development of more sophisticated methodologies.

  3. Bound Rationality and Organizational Learning.

    DTIC Science & Technology

    1989-09-23

    8217 . 90 0 8 0.. O 4 BOUNDED RATIONALITY AND ORGANIZATIONAL LEARNING Technical Report AlP - 107 Herbert A. Simon Department of Psychology Carnegie Mellon...ACCESSION No N/A N/A N/A N/A 1 1 TITLE (include Security Classificarnon) Bounded rationality and organizational learning 12 PERSONAL AUTHOR(S) HretA io 13a...organizations organizational psychology organizational learning bounded rationality cognitive psychology 𔄃 ABSTRACT (Continue on reverse if necessary

  4. Rational-Spline Subroutines

    NASA Technical Reports Server (NTRS)

    Schiess, James R.; Kerr, Patricia A.; Smith, Olivia C.

    1988-01-01

    Smooth curves drawn among plotted data easily. Rational-Spline Approximation with Automatic Tension Adjustment algorithm leads to flexible, smooth representation of experimental data. "Tension" denotes mathematical analog of mechanical tension in spline or other mechanical curve-fitting tool, and "spline" as denotes mathematical generalization of tool. Program differs from usual spline under tension, allows user to specify different values of tension between adjacent pairs of knots rather than constant tension over entire range of data. Subroutines use automatic adjustment scheme that varies tension parameter for each interval until maximum deviation of spline from line joining knots less than or equal to amount specified by user. Procedure frees user from drudgery of adjusting individual tension parameters while still giving control over local behavior of spline.

  5. Who Should Ration?

    PubMed

    Rosoff, Philip M

    2017-02-01

    A principal component of physician decision making is judging what interventions are clinically appropriate. Due to the inexorable and steady increase of health care costs in the US, physicians are constantly being urged to exercise judicious financial stewardship with due regard for the financial implications of what they prescribe. When applied on a case-by-case basis, this otherwise reasonable approach can lead to either inadvertent or overt and arbitrary restriction of interventions for some patients rather than others on the basis of clinically irrelevant characteristics such as ethnicity, gender, age, or skin color. In the absence of systemwide reform in which the resources saved from one patient or group of patients are reallocated for the benefit of others, prudence is urged in the application of "bedside rationing."

  6. Critical care rationing: international comparisons.

    PubMed

    Evans, Timothy W; Nava, Stefano; Mata, Guillermo Vazquez; Guidet, Bertrand; Estenssoro, Elisa; Fowler, Robert; Scheunemann, Leslie P; White, Douglas; Manthous, Constantine A

    2011-12-01

    Every country has finite resources that are expended to provide citizens with social "goods," including education, protection, infrastructure, and health care. Rationing-of any resource-refers to distribution of an allotted amount and may involve withholding some goods that would benefit some citizens. Health-care rationing is controversial because good health complements so many human endeavors. We explored (perceptions regarding) critical care rationing in seven industrialized countries. Academic physicians from England, Spain, Italy, France, Argentina, Canada, and the United States wrote essays that addressed specific questions including: (1) What historical, cultural, and medical institutional features inform my country's approach to rationing of health care? (2) What is known about formal rationing, especially in critical care, in my country? (3) How does rationing occur in my ICU? Responses suggest that critical care is rationed, by varying mechanisms, in all seven countries. We speculate that while no single "best" method of rationing is likely to be acceptable or optimal for all countries, professional societies could serve international health by developing evidence-based guidelines for just and effective rationing of critical care.

  7. 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…

  8. 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.

  9. Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology

    PubMed Central

    Tall, Ben D.; Gangiredla, Jayanthi; Grim, Christopher J.; Patel, Isha R.; Jackson, Scott A.; Mammel, Mark K.; Kothary, Mahendra H.; Sathyamoorthy, Venugopal; Carter, Laurenda; Fanning, Séamus; Iversen, Carol; Pagotto, Franco; Stephan, Roger; Lehner, Angelika; Farber, Jeffery; Yan, Qiong Q.; Gopinath, Gopal R.

    2017-01-01

    Cronobacter (previously known as Enterobacter sakazakii) is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae. These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the seven Cronobacter species from one another and from non-Cronobacter species. The microarray was also able to cluster strains within each species into well-defined subgroups. These results also support previous studies on the phylogenic separation of species members of the genus and clearly highlight the evolutionary sequence divergence among each species of the genus compared to phylogenetically-related species. This review extends these studies and illustrates how the microarray can also be used as an investigational tool to mine genomic data sets from strains. Three case studies describing the use of the microarray are shown and include: (1) the determination of allelic differences among Cronobacter sakazakii strains possessing the virulence plasmid pESA3; (2) mining of malonate and myo-inositol alleles among subspecies of Cronobacter dublinensis strains to determine subspecies identity; and (3) lastly using the microarray to demonstrate sequence divergence and phylogenetic relatedness trends for 13 outer-membrane protein alleles among 240 Cronobacter and phylogenetically-related strains. The goal of this review is to

  10. Evaluation of the Rational Environment

    DTIC Science & Technology

    1988-07-01

    three evaluations of the Delta release of the Rational Environments. John Devitofran- ceschi took care of the Rational machine at the SEI. Frost...Feiler, P. H., Smeaton , R. The Project Management Experiment: Evaluation of Ada Environments. Technical Report CMU/SEI-88-TR-7, Software Engineering

  11. Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing data.

    PubMed

    Li, Cheng-Wei; Chen, Bor-Sen

    2016-10-01

    Recent studies have demonstrated that cell cycle plays a central role in development and carcinogenesis. Thus, the use of big databases and genome-wide high-throughput data to unravel the genetic and epigenetic mechanisms underlying cell cycle progression in stem cells and cancer cells is a matter of considerable interest. Real genetic-and-epigenetic cell cycle networks (GECNs) of embryonic stem cells (ESCs) and HeLa cancer cells were constructed by applying system modeling, system identification, and big database mining to genome-wide next-generation sequencing data. Real GECNs were then reduced to core GECNs of HeLa cells and ESCs by applying principal genome-wide network projection. In this study, we investigated potential carcinogenic and stemness mechanisms for systems cancer drug design by identifying common core and specific GECNs between HeLa cells and ESCs. Integrating drug database information with the specific GECNs of HeLa cells could lead to identification of multiple drugs for cervical cancer treatment with minimal side-effects on the genes in the common core. We found that dysregulation of miR-29C, miR-34A, miR-98, and miR-215; and methylation of ANKRD1, ARID5B, CDCA2, PIF1, STAMBPL1, TROAP, ZNF165, and HIST1H2AJ in HeLa cells could result in cell proliferation and anti-apoptosis through NFκB, TGF-β, and PI3K pathways. We also identified 3 drugs, methotrexate, quercetin, and mimosine, which repressed the activated cell cycle genes, ARID5B, STK17B, and CCL2, in HeLa cells with minimal side-effects.

  12. 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...

  13. Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes.

    PubMed

    Rigoutsos, I; Gao, Y; Floratos, A; Parida, L

    1999-01-01

    We have used the Teiresias algorithm to carry out unsupervised pattern discovery in a database containing the unaligned ORFs from the 17 publicly available complete archaeal and bacterial genomes and build a 1D dictionary of motifs. These motifs which we refer to as seqlets account for and cover 97.88% of this genomic input at the level of amino acid positions. Each of the seqlets in this 1D dictionary was located among the sequences in Release 38.0 of the Protein Data Bank and the structural fragments corresponding to each seqlet's instances were identified and aligned in three dimensions: those of the seqlets that resulted in RMSD errors below a pre-selected threshold of 2.5 Angstroms were entered in a 3D dictionary of structurally conserved seqlets. These two dictionaries can be thought of as cross-indices that facilitate the tackling of tasks such as automated functional annotation of genomic sequences, local homology identification, local structure characterization, comparative genomics, etc.

  14. 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

    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

  15. 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

  16. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

    PubMed

    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.

  17. 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

  18. Rationalizing Hybrid Earthquake Probabilities

    NASA Astrophysics Data System (ADS)

    Gomberg, J.; Reasenberg, P.; Beeler, N.; Cocco, M.; Belardinelli, M.

    2003-12-01

    An approach to including stress transfer and frictional effects in estimates of the probability of failure of a single fault affected by a nearby earthquake has been suggested in Stein et al. (1997). This `hybrid' approach combines conditional probabilities, which depend on the time elapsed since the last earthquake on the affected fault, with Poissonian probabilities that account for friction and depend only on the time since the perturbing earthquake. The latter are based on the seismicity rate change model developed by Dieterich (1994) to explain the temporal behavior of aftershock sequences in terms of rate-state frictional processes. The model assumes an infinite population of nucleation sites that are near failure at the time of the perturbing earthquake. In the hybrid approach, assuming the Dieterich model can lead to significant transient increases in failure probability. We explore some of the implications of applying the Dieterich model to a single fault and its impact on the hybrid probabilities. We present two interpretations that we believe can rationalize the use of the hybrid approach. In the first, a statistical distribution representing uncertainties in elapsed and/or mean recurrence time on the fault serves as a proxy for Dieterich's population of nucleation sites. In the second, we imagine a population of nucleation patches distributed over the fault with a distribution of maturities. In both cases we find that the probability depends on the time since the last earthquake. In particular, the size of the transient probability increase may only be significant for faults already close to failure. Neglecting the maturity of a fault may lead to overestimated rate and probability increases.

  19. Dependent rational providers.

    PubMed

    Brothers, Kyle B

    2011-04-01

    Provider claims to conscientious objection have generated a great deal of heated debate in recent years. However, the conflicts that arise when providers make claims to the "conscience" are only a subset of the more fundamental challenges that arise in health care practice when patients and providers come into conflict. In this piece, the author provides an account of patient-provider conflict from within the moral tradition of St. Thomas Aquinas. He argues that the practice of health care providers should be understood as a form of practical reasoning and that this practical reasoning must necessarily incorporate both "moral" and "professional" commitments. In order to understand how the practical reasoning of provider should account for the needs and commitments of the patient and vice versa, he explores the account of dependence provided by Alasdair MacIntyre in his book Dependent Rational Animals. MacIntyre argues that St. Thomas' account of practical reasoning should be extended and adapted to account for the embodied vulnerability of all humans. In light of this insight, providers must view patients not only as the subjects of their moral reflection but also as fellow humans upon whom the provider depends for feedback on the effectiveness and relevance of her practical reasoning. The author argues that this account precludes responsive providers from adopting either moral or professional conclusions on the appropriateness of interventions outside the individual circumstances that arise in particular situations. The adoption of this orientation toward patients will neither eradicate provider-patient conflict nor compel providers to perform interventions to which they object. But this account does require that providers attend meaningfully to the suffering of patients and seek feedback on whether their intervention has effectively addressed that suffering.

  20. 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.

  1. The TB Structural Genomics Consortium: A decade of progress

    PubMed Central

    Chim, Nicholas; Habel, Jeff E.; Johnston, Jodie M.; Krieger, Inna; Miallau, Linda; Sankaranarayanan, Ramasamy; Morse, Robert P.; Bruning, John; Swanson, Stephanie; Kim, Haelee; Kim, Chang-Yub; Li, Hongye; Bulloch, Esther M.; Payne, Richard J.; Manos-Turvey, Alexandra; Hung, Li-Wei; Baker, Edward N.; Lott, J. Shaun; James, Michael N.G.; Terwilliger, Thomas C.; Eisenberg, David S.; Sacchettini, James C.; Goulding, Celia W.

    2012-01-01

    Summary The TB Structural Genomics Consortium is a worldwide organization of collaborators whose mission is the comprehensive structural determination and analyses of Mycobacterium tuberculosis proteins to ultimately aid in tuberculosis diagnosis and treatment. Congruent to the overall vision, Consortium members have additionally established an integrated facilities core to streamline M. tuberculosis structural biology and developed bioinformatics resources for data mining. This review aims to share the latest Consortium developments with the TB community, including recent structures of proteins that play significant roles within M. tuberculosis. Atomic resolution details may unravel mechanistic insights and reveal unique and novel protein features, as well as important protein-protein and protein-ligand interactions, which ultimately leads to a better understanding of M. tuberculosis biology and may be exploited for rational, structure-based therapeutics design. PMID:21247804

  2. McLuhan and Rationality.

    ERIC Educational Resources Information Center

    Levinson, Paul

    1981-01-01

    Looks at McLuhan's method of exploration. Considers why he dismisses logic and traditional rationality, how he supports his stance, and why his contribution to communications media theory is not diminished by his attempt to avoid logical accountability. (PD)

  3. Mining New Crystal Protein Genes from Bacillus thuringiensis on the Basis of Mixed Plasmid-Enriched Genome Sequencing and a Computational Pipeline

    PubMed Central

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

    2012-01-01

    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

  4. ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

    PubMed Central

    Undabarrena, Agustina; Ugalde, Juan A.; Seeger, Michael

    2017-01-01

    Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment. PMID:28229018

  5. Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H(2)-oxidizing bacteria.

    PubMed

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

    2011-09-01

    Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H(2) 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 H(2)-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 H(2) oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 10(6) to 10(8) hhyL gene copies g (dry weight)(-1). Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H(2)-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H(2) 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 H(2) by soil, because high-affinity H(2) oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur.

  6. 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.

  7. Genome mining of lipolytic exoenzymes from Bacillus safensis S9 and Pseudomonas alcaliphila ED1 isolated from a dairy wastewater lagoon.

    PubMed

    Ficarra, Florencia A; Santecchia, Ignacio; Lagorio, Sebastián H; Alarcón, Sergio; Magni, Christian; Espariz, Martín

    2016-11-01

    Dairy production plants produce highly polluted wastewaters rich in organic molecules such as lactose, proteins and fats. Fats generally lead to low overall performance of the treatment system. In this study, a wastewater dairy lagoon was used as microbial source and different screening strategies were conducted to select 58 lipolytic microorganisms. Exoenzymes and RAPD analyses revealed genetic and phenotypic diversity among isolates. Bacillus safensis, Pseudomonas alcaliphila and the potential pathogens, B. cereus, Aeromonas and Acinetobacter were identified by 16S-rRNA, gyrA, oprI and/or oprL sequence analyses. Five out of 10 selected isolates produced lipolytic enzymes and grew in dairy wastewater. Based on these abilities and their safety, B. safensis S9 and P. alcaliphila ED1 were selected and their genome sequences determined. The genome of strain S9 and ED1 consisted of 3,794,315 and 5,239,535 bp and encoded for 3990 and 4844 genes, respectively. Putative extracellular enzymes with lipolytic (12 and 16), proteolytic (20) or hydrolytic (10 and 15) activity were identified for S9 and ED1 strains, respectively. These bacteria also encoded other technological relevant proteins such as amylases, proteases, glucanases, xylanases and pectate lyases.

  8. Genome mining of the biosynthetic gene cluster of the polyene macrolide antibiotic tetramycin and characterization of a P450 monooxygenase involved in the hydroxylation of the tetramycin B polyol segment.

    PubMed

    Cao, Bo; Yao, Fen; Zheng, Xiaoqing; Cui, Dongbing; Shao, Yucheng; Zhu, Changxiong; Deng, Zixin; You, Delin

    2012-10-15

    A polyene macrolide antibiotic tetramycin biosynthetic gene cluster was identified by genome mining and isolated from Streptomyces hygrospinosus var. beijingensis. Genetic and in silico analyses gave insights into the mechanism of biosynthesis of tetramycin, and a model of the tetramycin biosynthetic pathway is proposed. Inactivation of a cytochrome P450 monooxygenase gene, tetrK, resulted in the production of a tetramycin B precursor: tetramycin A, which lacks a hydroxy group in its polyol region. TetrK was subsequently overexpressed heterologously in E. coli with a His(6) tag, and purified TetrK efficiently hydroxylated tetramycin A to afford tetramycin B. Kinetic studies revealed no inhibition of TetrK by substrate or product. Surprisingly, sequence-alignment analysis showed that TetrK, as a hydroxylase, has much higher homology with epoxidase PimD than with hydroxylases NysL and AmphL. The 3D structure of TetrK was then constructed by homology modeling with PimD as reference. Although TetrK and PimD catalyzed different chemical reactions, homology modeling indicated that they might share the same catalytic sites, despite also possessing some different sites correlated with substrate binding and substrate specificity. These findings offer good prospects for the production of improved antifungal polyene analogues.

  9. 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.

  10. 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

    2016-01-04

    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.

  11. Cloning, expression and characterization of a novel GH5 exo/endoglucanase of Thermobifida halotolerans YIM 90462(T) by genome mining.

    PubMed

    Zhang, Feng; Zhang, Xiao-Mei; Yin, Yi-Rui; Li, Wen-Jun

    2015-12-01

    The 1389-bp thcel5A gene, which encodes a family 5 of glycoside hydrolases (GH5), was screened from the draft genome of Thermobifida halotolerans YIM 90462(T). ThCel5A was most similar (77% identity) to a GH5 endoglucanase from Thermobifida fusca YX, followed by cellulases from Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111, Nocardiopsis alba ATCC BAA-2165, and Kribbella flavida DSM 17836. The deduced amino acid sequence of ThCel5A, which consisted of 462 amino acid residues, encompassed a family 2 cellulose-binding module and a GH5 catalytic domain. Notably, ThCel5A hydrolysed soluble as well as insoluble cellulose substrates. The enzymatic hydrolysis assay showed that the activity of recombinant ThCel5A was optimized at pH 8.0 and 50°C. Moreover, it retained hydrolytic activity in the presence of various metal ions and >90% activity within the range of pH 8.0-9.0 after 30 min at 50°C. These results suggested that this enzyme has considerable potential in industrial applications.

  12. 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)

  13. Planning the Mine and Mining the Plan

    NASA Astrophysics Data System (ADS)

    Boucher, D. S.; Chen, N.

    2016-11-01

    Overview of best practices used in the terrestrial mining industry when developing a mine site towards production. The intent is to guide planners towards an effective and well constructed roadmap for the development of ISRU mining activities. A strawman scenario is presented as an illustration for lunar mining of water ice.

  14. 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.

  15. 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)

  16. 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.

  17. 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...

  18. 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)

  19. MineWolf Tiller Test and Evaluation

    DTIC Science & Technology

    2007-11-01

    Croatie ont conduit ces essais en coopération. Le projet a été conduit conformément à la méthodologie spécifiée par « l’Accord du groupe de travail... projet était organisé par le Programme international d’essais et évaluations (PIEE) et employait les méthodes soulignées dans « l’Accord du groupe de...préparer le sol des opérations de suivi mais elle devrait être réduite pour les opérations de « déminage. » Le MineWolf est une machine efficace

  20. Mining and engineering natural-product biosynthetic pathways.

    PubMed

    Wilkinson, Barrie; Micklefield, Jason

    2007-07-01

    Natural products continue to fulfill an important role in the development of therapeutic agents. In addition, with the advent of chemical genetics and high-throughput screening platforms, these molecules have become increasingly valuable as tools for interrogating fundamental aspects of biological systems. To access the vast portion of natural-product structural diversity that remains unexploited for these and other applications, genome mining and microbial metagenomic approaches are proving particularly powerful. When these are coupled with recombineering and related genetic tools, large biosynthetic gene clusters that remain intractable or cryptic in the native host can be more efficiently cloned and expressed in a suitable heterologous system. For lead optimization and the further structural diversification of natural-product libraries, combinatorial biosynthetic engineering has also become indispensable. However, our ability to rationally redesign biosynthetic pathways is often limited by our lack of understanding of the structure, dynamics and interplay between the many enzymes involved in complex biosynthetic pathways. Despite this, recent structures of fatty acid synthases should allow a more accurate prediction of the likely architecture of related polyketide synthase and nonribosomal peptide synthetase multienzymes.

  1. Northern Trust Mines

    EPA Pesticide Factsheets

    The United States and the Navajo Nation entered into settlement agreements that provide funds to conduct investigations and any needed cleanup at 16 of the 46 priority mines, including six mines in the Northern Abandoned Uranium Mine Region.

  2. 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.

  3. 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.

  4. Rational approximations for tomographic reconstructions

    NASA Astrophysics Data System (ADS)

    Reynolds, Matthew; Beylkin, Gregory; Monzón, Lucas

    2013-06-01

    We use optimal rational approximations of projection data collected in x-ray tomography to improve image resolution. Under the assumption that the object of interest is described by functions with jump discontinuities, for each projection we construct its rational approximation with a small (near optimal) number of terms for a given accuracy threshold. This allows us to augment the measured data, i.e., double the number of available samples in each projection or, equivalently, extend (double) the domain of their Fourier transform. We also develop a new, fast, polar coordinate Fourier domain algorithm which uses our nonlinear approximation of projection data in a natural way. Using augmented projections of the Shepp-Logan phantom, we provide a comparison between the new algorithm and the standard filtered back-projection algorithm. We demonstrate that the reconstructed image has improved resolution without additional artifacts near sharp transitions in the image.

  5. Air-Activated Ration Heaters

    DTIC Science & Technology

    2008-12-01

    regulated. After use, the product of the heating reaction is zinc oxide, an inert chemical used in many different products such as sunscreen , creams...low cost, easy-to-use chemical heater called the Flameless Ration Heater (FRH). The FRH consists of a magnesium/iron mixture sealed in a waterproof...Prescribed by ANSI Std Z39-18 2 1. HEATER DESIGN There is a narrow operating temperature range for chemical heaters for this specific

  6. 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

  7. 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…

  8. A Semantical Approach to Equilibria and Rationality

    NASA Astrophysics Data System (ADS)

    Pavlovic, Dusko

    Game theoretic equilibria are mathematical expressions of rationality. Rational agents are used to model not only humans and their software representatives, but also organisms, populations, species and genes, interacting with each other and with the environment. Rational behaviors are achieved not only through conscious reasoning, but also through spontaneous stabilization at equilibrium points.

  9. 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.

  10. Surface mining

    SciTech Connect

    Not Available

    1989-06-01

    This paper reports on a GAO study of attorney and expert witness fees awarded as a result of litigation brought under the Surface Mining Control and Reclamation Act. As of March 24, 1989, a total of about $1.4 million had been awarded in attorney fees and expenses - about $1.3 subject to the provisions of the Employee Retirement Income Security Act, a comparison of its features with provisions of ERISA showed that the plan differed from ERISA provisions in areas such as eligibility, funding, and contribution limits.

  11. Biomimetic transport and rational drug delivery.

    PubMed

    Ranney, D F

    2000-01-15

    Medicine and pharmaceutics are encountering critical needs and opportunities for transvascular drug delivery that improves site targeting and tissue permeation by mimicking natural tissue addressing and transport mechanisms. This is driven by the accelerated development of genomic agents requiring targeted controlled release. Although rationally designed for in vitro activity, such agents are not highly effective in vivo, due to opsonization and degradation by plasma constituents, and failure to transport across the local vascular endothelium and tissue matrix. A growing knowledge of the addresses of the body can be applied to engineer "Bio-Logically" staged delivery systems with sequential bioaddressins complementary to the discontinuous compartments encountered--termed discontinuum pharmaceutics. Effective tissue targeting is accomplished by leukocytes, bacteria, and viruses. We are increasingly able to mimic their bioaddressins by genomic means. Approaches described in this commentary include: (a) endothelial-directed adhesion mediated by oligosaccharides and carbohydrates (e.g. dermatan sulfate as a mimic of sulfated CD44) and peptidomimetics interacting with adhesins, selectins, integrins, hyaluronans, and locally induced growth factors (e.g. vascular endothelial growth factor, VEGF) and coagulation factors (e.g. factor VIII antigen); (b) improved tissue permeation conferred by hydrophilically "cloaked" carrier systems; (c) "uncloaking" by matrix dilution or selective triggering near the target cells; and (d) target binding-internalization by terminally exposed hydrophobic moieties, cationic polymers, and receptor-binding lectins, peptides, or carbohydrates. This commentary also describes intermediate technology solutions (e.g. "hybrid drugs"), and highlights the high-resolution, dynamic magnetic resonance imaging and radiopharmaceutical imaging technologies plus the groups and organizations capable of accelerating these important initiatives.

  12. Wikipedia Mining

    NASA Astrophysics Data System (ADS)

    Nakayama, Kotaro; Ito, Masahiro; Erdmann, Maike; Shirakawa, Masumi; Michishita, Tomoyuki; Hara, Takahiro; Nishio, Shojiro

    Wikipedia, a collaborative Wiki-based encyclopedia, has become a huge phenomenon among Internet users. It covers a huge number of concepts of various fields such as arts, geography, history, science, sports and games. As a corpus for knowledge extraction, Wikipedia's impressive characteristics are not limited to the scale, but also include the dense link structure, URL based word sense disambiguation, and brief anchor texts. Because of these characteristics, Wikipedia has become a promising corpus and a new frontier for research. In the past few years, a considerable number of researches have been conducted in various areas such as semantic relatedness measurement, bilingual dictionary construction, and ontology construction. Extracting machine understandable knowledge from Wikipedia to enhance the intelligence on computational systems is the main goal of "Wikipedia Mining," a project on CREP (Challenge for Realizing Early Profits) in JSAI. In this paper, we take a comprehensive, panoramic view of Wikipedia Mining research and the current status of our challenge. After that, we will discuss about the future vision of this challenge.

  13. Chemogenomic approaches to rational drug design

    PubMed Central

    Rognan, D

    2007-01-01

    Paradigms in drug design and discovery are changing at a significant pace. Concomitant to the sequencing of over 180 several genomes, the high-throughput miniaturization of chemical synthesis and biological evaluation of a multiple compounds on gene/protein expression and function opens the way to global drug-discovery approaches, no more focused on a single target but on an entire family of related proteins or on a full metabolic pathway. Chemogenomics is this emerging research field aimed at systematically studying the biological effect of a wide array of small molecular-weight ligands on a wide array of macromolecular targets. Since the quantity of existing data (compounds, targets and assays) and of produced information (gene/protein expression levels and binding constants) are too large for manual manipulation, information technologies play a crucial role in planning, analysing and predicting chemogenomic data. The present review will focus on predictive in silico chemogenomic approaches to foster rational drug design and derive information from the simultaneous biological evaluation of multiple compounds on multiple targets. State-of-the-art methods for navigating in either ligand or target space will be presented and concrete drug design applications will be mentioned. PMID:17533416

  14. 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.

  15. 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

  16. 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

  17. Rational Design of Small Molecules Targeting Oncogenic Noncoding RNAs from Sequence.

    PubMed

    Disney, Matthew D; Angelbello, Alicia J

    2016-12-20

    The discovery of RNA catalysis in the 1980s and the dissemination of the human genome sequence at the start of this century inspired investigations of the regulatory roles of noncoding RNAs in biology. In fact, the Encyclopedia of DNA Elements (ENCODE) project has shown that only 1-2% of the human genome encodes protein, yet 75% is transcribed into RNA. Functional studies both preceding and following the ENCODE project have shown that these noncoding RNAs have important roles in regulating gene expression, developmental timing, and other critical functions. RNA's diverse roles are often a consequence of the various folds that it adopts. The single-stranded nature of the biopolymer enables it to adopt intramolecular folds with noncanonical pairings to lower its free energy. These folds can be scaffolds to bind proteins or to form frameworks to interact with other RNAs. Not surprisingly, dysregulation of certain noncoding RNAs has been shown to be causative of disease. Given this as the background, it is easy to see why it would be useful to develop methods that target RNA and manipulate its biology in rational and predictable ways. The antisense approach has afforded strategies to target RNAs via Watson-Crick base pairing and has typically focused on targeting partially unstructured regions of RNA. Small molecule strategies to target RNA would be desirable not only because compounds could be lead optimized via medicinal chemistry but also because structured regions within an RNA of interest could be targeted to directly interfere with RNA folds that contribute to disease. Additionally, small molecules have historically been the most successful drug candidates. Until recently, the ability to design small molecules that target non-ribosomal RNAs has been elusive, creating the perception that they are "undruggable". In this Account, approaches to demystify targeting RNA with small molecules are described. Rather than bulk screening for compounds that bind to singular

  18. An Analysis of Adenovirus Genomes Using Whole Genome Software Tools

    PubMed Central

    Mahadevan, Padmanabhan

    2016-01-01

    The evolution of sequencing technology has lead to an enormous increase in the number of genomes that have been sequenced. This is especially true in the field of virus genomics. In order to extract meaningful biological information from these genomes, whole genome data mining software tools must be utilized. Hundreds of tools have been developed to analyze biological sequence data. However, only some of these tools are user-friendly to biologists. Several of these tools that have been successfully used to analyze adenovirus genomes are described here. These include Artemis, EMBOSS, pDRAW, zPicture, CoreGenes, GeneOrder, and PipMaker. These tools provide functionalities such as visualization, restriction enzyme analysis, alignment, and proteome comparisons that are extremely useful in the bioinformatics analysis of adenovirus genomes. PMID:28293072

  19. 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

  20. 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).

  1. 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.

  2. 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.

  3. 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.

  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.

  5. 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.

  6. Laboratory Evaluation of Australian Ration Packs.

    DTIC Science & Technology

    1982-09-01

    thiamin, ascorbic acid and energy of rations are included. Daily available nutrients are estimated and evaluated with respect of daily requirement...of rations are included. Daily available nutrients are estimated and evaluated with respect to daily requirements. Some rations were found to be...at the AFFSE were also examined for microbiological quality. TABLE 1 Energy per Gram of Nutrient NUTRIENT kJ/g Protein 17 Fat 37 Carbohydrate 16

  7. 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.

  8. Dual Rationality and Deliberative Agents

    NASA Astrophysics Data System (ADS)

    Debenham, John; Sierra, Carles

    Human agents deliberate using models based on reason for only a minute proportion of the decisions that they make. In stark contrast, the deliberation of artificial agents is heavily dominated by formal models based on reason such as game theory, decision theory and logic—despite that fact that formal reasoning will not necessarily lead to superior real-world decisions. Further the Nobel Laureate Friedrich Hayek warns us of the ‘fatal conceit’ in controlling deliberative systems using models based on reason as the particular model chosen will then shape the system’s future and either impede, or eventually destroy, the subtle evolutionary processes that are an integral part of human systems and institutions, and are crucial to their evolution and long-term survival. We describe an architecture for artificial agents that is founded on Hayek’s two rationalities and supports the two forms of deliberation used by mankind.

  9. Scottish psychoanalysis: a rational religion.

    PubMed

    Miller, Gavin

    2008-01-01

    The ambition to rationally preserve a Christian religious inheritance distinctively informs Scottish psychoanalytic ideas. Scottish psychoanalysis presents the human personality as born into communion with others. The aim of therapy is to restore, preserve, and promote genuinely interpersonal relations. The Scottish psychoanalysis apparent in the work of W. R. D. Fairbairn, Ian Suttie, Hugh Crichton-Miller, and in the philosophy of John Macmurray, is exported to New Zealand, where it is promoted by the New Zealand Association of Psychotherapists. Scottish psychoanalytic ideas also remain effective in post-war Britain: the idea of communion appears in dialogue with other theories in the work of Harry Guntrip, John Macquarrie, R. D. Laing, and Aaron Esterson.

  10. 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.

  11. From rational bubbles to crashes

    NASA Astrophysics Data System (ADS)

    Sornette, D.; Malevergne, Y.

    2001-10-01

    We study and generalize in various ways the model of rational expectation (RE) bubbles introduced by Blanchard and Watson in the economic literature. Bubbles are argued to be the equivalent of Goldstone modes of the fundamental rational pricing equation, associated with the symmetry-breaking introduced by non-vanishing dividends. Generalizing bubbles in terms of multiplicative stochastic maps, we summarize the result of Lux and Sornette that the no-arbitrage condition imposes that the tail of the return distribution is hyperbolic with an exponent μ<1. We then outline the main results of Malevergne and Sornette, who extend the RE bubble model to arbitrary dimensions d: a number d of market time series are made linearly interdependent via d× d stochastic coupling coefficients. We derive the no-arbitrage condition in this context and, with the renewal theory for products of random matrices applied to stochastic recurrence equations, we extend the theorem of Lux and Sornette to demonstrate that the tails of the unconditional distributions associated with such d-dimensional bubble processes follow power laws, with the same asymptotic tail exponent μ<1 for all assets. The distribution of price differences and of returns is dominated by the same power-law over an extended range of large returns. Although power-law tails are a pervasive feature of empirical data, the numerical value μ<1 is in disagreement with the usual empirical estimates μ≈3. We then discuss two extensions (the crash hazard rate model and the non-stationary growth rate model) of the RE bubble model that provide two ways of reconciliation with the stylized facts of financial data.

  12. 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

  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. Exposures from mining and mine tailings

    NASA Astrophysics Data System (ADS)

    Chambers, Douglas B.; Cassaday, Valerie J.; Lowe, Leo M.

    The mining, milling and tailings management of uranium ores results in environmental radiation exposures. This paper describes the sources of radioactive emissions to the environment associated with these activities, reviews the basic approach used to estimate the resultant radiation exposures and presents examples of typical uranium mind and mill facilities. Similar concepts apply to radiation exposures associated with the mining of non-radioactive ores although the magnitudes of the exposures would normally be smaller than those associated with uranium mining.

  15. 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)

  16. 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.

  17. 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…

  18. 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…

  19. 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.

  20. 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…

  1. 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…

  2. 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 for…

  3. Abandoned Mine Lands

    EPA Pesticide Factsheets

    Abandoned Mine Lands are those lands, waters, and surrounding watersheds where extraction, beneficiation, or processing of ores and minerals (excluding coal) has occurred. These lands also include areas where mining or processing activity is inactive.

  4. 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...

  5. 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.

  6. 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.

  7. 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

  8. Proposal for quantum rational secret sharing

    NASA Astrophysics Data System (ADS)

    Maitra, Arpita; De, Sourya Joyee; Paul, Goutam; Pal, Asim K.

    2015-08-01

    A rational secret sharing scheme is a game in which each party responsible for reconstructing a secret tries to maximize his or her utility by obtaining the secret alone. Quantum secret sharing schemes, derived either from quantum teleportation or from quantum error correcting code, do not succeed when we assume rational participants. This is because all existing quantum secret sharing schemes consider that the secret is reconstructed by a party chosen by the dealer. In this paper, for the first time, we propose a quantum secret sharing scheme which is resistant to rational parties. The proposed scheme is fair (everyone gets the secret), is correct, and achieves strict Nash equilibrium.

  9. 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.

  10. Shape Control in Multivariate Barycentric Rational Interpolation

    NASA Astrophysics Data System (ADS)

    Nguyen, Hoa Thang; Cuyt, Annie; Celis, Oliver Salazar

    2010-09-01

    The most stable formula for a rational interpolant for use on a finite interval is the barycentric form [1, 2]. A simple choice of the barycentric weights ensures the absence of (unwanted) poles on the real line [3]. In [4] we indicate that a more refined choice of the weights in barycentric rational interpolation can guarantee comonotonicity and coconvexity of the rational interpolant in addition to a polefree region of interest. In this presentation we generalize the above to the multivariate case. We use a product-like form of univariate barycentric rational interpolants and indicate how the location of the poles and the shape of the function can be controlled. This functionality is of importance in the construction of mathematical models that need to express a certain trend, such as in probability distributions, economics, population dynamics, tumor growth models etc.

  11. 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.

  12. Rational emotive behavior therapy: disputing irrational philosophies.

    PubMed

    Sacks, Susan Bendersky

    2004-05-01

    This article provides an overview of the concepts and techniques of rational emotive behavior therapy to distinguish it from cognitive-behavioral therapy. Rational emotive behavior therapy proposes that psychological disturbance is largely created and maintained through irrational philosophies consisting of internal absolutistic demands. This therapy strives to produce sustained and profound cognitive, emotive, and behavioral change through active, vigorous disputation of underlying irrational philosophies.

  13. 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

  14. 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

  15. 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.

  16. Land Mines (Landminen)

    DTIC Science & Technology

    1978-02-02

    making contact with the safety pin of the pull fuze 42. Two locking bolts held the upper and lower case in position during transport, so that there... safety pin out of the extended striker, thus releasing it. These mines were filled with 200 g of explosives. This type of mine was the model for the...by inserting the detonator slide. However, the mine is not fully armed until the safety pin is removed and reinserted until it makes contact with the

  17. 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.

  18. 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

  19. Genome Sequence of Brevibacillus formosus F12T for a Genome-Sequencing Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria

    PubMed Central

    Wang, Jie-Ping; Liu, Guo-Hong; Chen, Qian-qian; Zhu, Yu-jing; Chen, Zheng; Che, Jian-mei

    2015-01-01

    Brevibacillus formosus F12T is a Gram-positive, spore-forming, and strictly aerobic bacterium. Here, we report the draft 6.215-Mb genome sequence of B. formosus F12T, which will provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria, as well as for the functional gene mining and application of B. formosus. PMID:26205874

  20. 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.

  1. Mine waste technology program

    SciTech Connect

    Wilmoth, R.C.; Powers, T.J.

    1995-10-01

    The Mine Waste Technology Program (MWTP) was initiated to address mining waste generated by active and inactive mining production facilities. In June 1991, an Interagency Agreement was signed between the U.S. Environmental Protection Agency and the Department of Energy which outlined the following activities: To identify and prioritize treatment technologies as candidates for demonstration projects; To propose and conduct large pilot-/field-scale demonstration projects of several innovative technologies that show promise for cost effectively remediating local, regional, and national mine waste problems.

  2. Data mining support systems

    NASA Astrophysics Data System (ADS)

    Zhao, Yinliang; Yao, JingTao; Yao, Yiyu

    2004-04-01

    The main stream of research in data mining (or knowledge discovery in databases) focuses on algorithms and automatic or semi-automatic processes for discovering knowledge hidden in data. In this paper, we adopt a more general and goal oriented view of data mining. Data mining is regarded as a field of study covering the theories, methodologies, techniques, and activities with the goal of discovering new and useful knowledge. One of its objectives is to design and implement data mining systems. A miner solves problems of data mining manually, or semi-automatically by using such systems. However, there is a lack of studies on how to assist a miner in solving data mining problems. From the experiences and lessons of decision support systems, we introduce the concept of data mining support systems (DMSS). We draw an analogy between the field of decision-making and the field of data mining, and between the role of a manager and the role of a data miner. A DMSS is an active and highly interactive computer system that assists data mining activities. The needs and the basic features of DMSS are discussed.

  3. Data mining applications in the context of casemix.

    PubMed

    Koh, H C; Leong, S K

    2001-07-01

    In October 1999, the Singapore Government introduced casemix-based funding to public hospitals. The casemix approach to health care funding is expected to yield significant benefits, including equity and rationality in financing health care, the use of comparative casemix data for quality improvement activities, and the provision of information that enables hospitals to understand their cost behaviour and reinforces the drive for more cost-efficient services. However, there is some concern about the "quicker and sicker" syndrome (that is, the rapid discharge of patients with little regard for the quality of outcome). As it is likely that consequences of premature discharges will be reflected in the readmission data, an analysis of possible systematic patterns in readmission data can provide useful insight into the "quicker and sicker" syndrome. This paper explores potential data mining applications in the context of casemix by using readmission data as an illustration. In particular, it illustrates how data mining can be used to better understand readmission data and to detect systematic patterns, if any. From a technical perspective, data mining (which is capable of analysing complex non-linear and interaction relationships) supplements and complements traditional statistical methods in data analysis. From an applications perspective, data mining provides the technology and methodology to analyse mass volume of data to detect hidden patterns in data. Using readmission data as an illustrative data mining application, this paper explores potential data mining applications in the general casemix context.

  4. Agent-Enriched Data Mining Using an Extendable Framework

    NASA Astrophysics Data System (ADS)

    Albashiri, Kamal Ali; Coenen, Frans

    This paper commences with a discussion of the advantages that Multi-Agent Systems (MAS) can bring to the domain of Knowledge Discovery in Data (KDD), and presents a rational for Agent-Enriched Data Mining (AEDM). A particular challenge of any generic, general purpose, AEDM system is the extensive scope of KDD. To address this challenge the authors suggest that any truly generic AEDM must be readily extendable and propose EMADS, The Extendable Multi-Agent Data mining System. A complete overview of the architecture and agent interaction models of EMADS is presented. The system’s operation is described and illustrated in terms of two KDD scenarios: meta association rule mining and classifier generation. In conclusion the authors suggest that EMADS provides a sound foundation for both KDD research and application based AEDM.

  5. Using Rational-Emotive Therapy to Prevent Classroom Problems.

    ERIC Educational Resources Information Center

    Webber, Jo; Coleman, Maggie

    1988-01-01

    Teachers are encouraged to utilize rational-emotive therapy to prevent and deal with classroom behavior problems. Rational-emotive therapy is defined, the ABC model of rational thinking briefly explained, types of irrational thinking identified, and suggestions for becoming a rational thinker are offered. Classroom examples are given. (DB)

  6. Rational drug design applied to myeloperoxidase inhibition.

    PubMed

    Van Antwerpen, P; Zouaoui Boudjeltia, K

    2015-06-01

    Rational drug design is a general approach using protein-structure technique in which the discovery of a ligand can be driven either by chance, screening, or rational theory. Myeloperoxidase (MPO) was rapidly identified as a therapeutical target because of its involvement in chronic inflammatory syndromes. In this context, the research of MPO inhibitors was intensified and development of new chemical entities was rationally driven by the research of ligands that enter into the MPO catalytic pocket. Actually, as soon as crystallography data of MPO have become available and its structure was virtually designed, the rational drug design has been applied to this peroxidase. Pharmaceutical industries and academic laboratories apply rational drug design on MPO by either optimizing known inhibitors or searching new molecules by high-throughput virtual screening. By these ways, they were able to find efficient MPO inhibitors and understand their interactions with the enzyme. During this quest of MPO inhibition, it appears that Glu268 is a crucial residue in order to optimize ligand-target interaction. This amino acid should be carefully considered by medicinal chemist when they design inhibitors interfering with MPO activity.

  7. 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

  8. 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.

  9. Changing Conspiracy Beliefs through Rationality and Ridiculing

    PubMed Central

    Orosz, Gábor; Krekó, Péter; Paskuj, Benedek; Tóth-Király, István; Bőthe, Beáta; Roland-Lévy, Christine

    2016-01-01

    Conspiracy theory (CT) beliefs can be harmful. How is it possible to reduce them effectively? Three reduction strategies were tested in an online experiment using general and well-known CT beliefs on a comprehensive randomly assigned Hungarian sample (N = 813): exposing rational counter CT arguments, ridiculing those who hold CT beliefs, and empathizing with the targets of CT beliefs. Several relevant individual differences were measured. Rational and ridiculing arguments were effective in reducing CT, whereas empathizing with the targets of CTs had no effect. Individual differences played no role in CT reduction, but the perceived intelligence and competence of the individual who conveyed the CT belief-reduction information contributed to the success of the CT belief reduction. Rational arguments targeting the link between the object of belief and its characteristics appear to be an effective tool in fighting conspiracy theory beliefs. PMID:27790164

  10. Autonomy, rationality and the wish to die.

    PubMed Central

    Clarke, D M

    1999-01-01

    Although suicide has traditionally carried a negative sanction in Western societies, this is now being challenged, and while there remains substantial public concern surrounding youth and elder suicide, there is a paradoxical push to relax the prohibition under certain circumstances. Central to the arguments behind this are the principles of respect for autonomy and the importance of rationality. It is argued here that the concepts of rationality and autonomy, while valuable, are not strong enough to substantiate a categorical "right to suicide" and that the concepts of "understandability" and "respect" are more useful and able to provide the foundation for responding to a person expressing a wish to die. Roman suicide, sometimes held as an example of "rational suicide", illustrates the effects of culture, tradition and values on the attitudes to, and the practice of, suicide. PMID:10635498

  11. Changing Conspiracy Beliefs through Rationality and Ridiculing.

    PubMed

    Orosz, Gábor; Krekó, Péter; Paskuj, Benedek; Tóth-Király, István; Bőthe, Beáta; Roland-Lévy, Christine

    2016-01-01

    Conspiracy theory (CT) beliefs can be harmful. How is it possible to reduce them effectively? Three reduction strategies were tested in an online experiment using general and well-known CT beliefs on a comprehensive randomly assigned Hungarian sample (N = 813): exposing rational counter CT arguments, ridiculing those who hold CT beliefs, and empathizing with the targets of CT beliefs. Several relevant individual differences were measured. Rational and ridiculing arguments were effective in reducing CT, whereas empathizing with the targets of CTs had no effect. Individual differences played no role in CT reduction, but the perceived intelligence and competence of the individual who conveyed the CT belief-reduction information contributed to the success of the CT belief reduction. Rational arguments targeting the link between the object of belief and its characteristics appear to be an effective tool in fighting conspiracy theory beliefs.

  12. Genome scale engineering techniques for metabolic engineering.

    PubMed

    Liu, Rongming; Bassalo, Marcelo C; Zeitoun, Ramsey I; Gill, Ryan T

    2015-11-01

    Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications.

  13. 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.

  14. Biotreatment of mine drainage

    SciTech Connect

    Bender, J.; Phillips, R.

    1996-12-31

    Several experiments and field tests of microbial mats are described. One study determined the removal rate of Uranium 238 and metals from groundwater by microbial mats. Free floating mats, immobilized mats, excised mats, and pond treatment were examined. Field tests of acid coal mine drainage and precious metal mine drainage are also summarized. The mechanisms of metal removal are briefly described.

  15. Mining outlook in Indonesia

    SciTech Connect

    Not Available

    1984-06-01

    The outlook for mining in Indonesia is presented. Coal appears to be the most promising growth area for Indonesian mining interests, with production slated to reach 1.5 million t/yr by 1985, up from 0.5 million ton in 1983. Also discussed production and trends, aluminum, copper, nickel, silver, gold, tin and iron sands in Indonesia.

  16. Big data mining yields novel insights on cancer.

    PubMed

    Jiang, Peng; Liu, X Shirley

    2015-02-01

    Recent years have seen the rapid growth of large-scale biological data, but the effective mining and modeling of 'big data' for new biological discoveries remains a significant challenge. A new study reanalyzes expression profiles from the Gene Expression Omnibus to make novel discoveries about genes involved in DNA damage repair and genome instability in cancer.

  17. 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.

  18. Mining Deployment Optimization

    NASA Astrophysics Data System (ADS)

    Čech, Jozef

    2016-09-01

    The deployment problem, researched primarily in the military sector, is emerging in some other industries, mining included. The principal decision is how to deploy some activities in space and time to achieve desired outcome while complying with certain requirements or limits. Requirements and limits are on the side constraints, while minimizing costs or maximizing some benefits are on the side of objectives. A model with application to mining of polymetallic deposit is presented. To obtain quick and immediate decision solutions for a mining engineer with experimental possibilities is the main intention of a computer-based tool. The task is to determine strategic deployment of mining activities on a deposit, meeting planned output from the mine and at the same time complying with limited reserves and haulage capacities. Priorities and benefits can be formulated by the planner.

  19. The Rational Hybrid Monte Carlo algorithm

    NASA Astrophysics Data System (ADS)

    Clark, Michael

    2006-12-01

    The past few years have seen considerable progress in algorithmic development for the generation of gauge fields including the effects of dynamical fermions. The Rational Hybrid Monte Carlo (RHMC) algorithm, where Hybrid Monte Carlo is performed using a rational approximation in place the usual inverse quark matrix kernel is one of these developments. This algorithm has been found to be extremely beneficial in many areas of lattice QCD (chiral fermions, finite temperature, Wilson fermions etc.). We review the algorithm and some of these benefits, and we compare against other recent algorithm developements. We conclude with an update of the Berlin wall plot comparing costs of all popular fermion formulations.

  20. 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

  1. [The role of economics in fair rationing].

    PubMed

    Prenzler, A

    2012-10-01

    For several years academic disciplines have discussed the potential conflict between scarcity of funding and fair health care. This review article shows the necessity of involving economic scientists in this discussion as well as their contribution to rationalisation, prioritisation and rationing of health care services. Thereby, it becomes clear that rationing and justice are not a contradiction per se. The interdisciplinary discussion in Germany needs less disciplinary egotism and more willingness to seek solutions and compromises. In this context the procedures followed in other countries can serve as examples.

  2. 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...

  3. 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...

  4. 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

  5. Exploring patterns of epigenetic information with data mining techniques.

    PubMed

    Aguiar-Pulido, Vanessa; Seoane, José A; Gestal, Marcos; Dorado, Julián

    2013-01-01

    Data mining, a part of the Knowledge Discovery in Databases process (KDD), is the process of extracting patterns from large data sets by combining methods from statistics and artificial intelligence with database management. Analyses of epigenetic data have evolved towards genome-wide and high-throughput approaches, thus generating great amounts of data for which data mining is essential. Part of these data may contain patterns of epigenetic information which are mitotically and/or meiotically heritable determining gene expression and cellular differentiation, as well as cellular fate. Epigenetic lesions and genetic mutations are acquired by individuals during their life and accumulate with ageing. Both defects, either together or individually, can result in losing control over cell growth and, thus, causing cancer development. Data mining techniques could be then used to extract the previous patterns. This work reviews some of the most important applications of data mining to epigenetics.

  6. 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…

  7. 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…

  8. 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…

  9. Resource Allocation: Ration, Fashion, or Innovashun?

    ERIC Educational Resources Information Center

    Lourens, Roy

    1986-01-01

    Resource allocation is a key factor in promoting or retarding innovation. In a restrictive economic climate, it is easy to use resource allocation for decremental rationing and to stifle innovative thinking. The technique can also be used to ensure that the institution's human resources are encouraged to identify opportunities for innovation. (MSE)

  10. Rational Solutions for the Fokas System

    NASA Astrophysics Data System (ADS)

    Rao, Ji-Guang; Wang, Li-Hong; Zhang, Yu; He, Jing-Song

    2015-12-01

    Fokas system is the simplest (2+1)-dimensional extension of the nonlinear Schrödinger equation (Eq. (2), Inverse Problems 10 (1994) L19-L22). By using the bilinear transformation method, general rational solutions for the Fokas system are given explicitly in terms of two order-N determinants τn (n = 0, 1) whose elements m(n)i,j (n = 0, 1; 1 ≤ i, j ≤ N) are involved with order-ni and order-nj derivatives. When N = 1, three kinds of rational solution, i.e., fundamental lump and fundamental rogue wave (RW) with n1 = 1, and higher-order rational solution with n1 ≥ 2, are illustrated by explicit formulas from τn (n = 0, 1) and pictures. The fundamental RW is a line RW possessing a line profile on (x, y)-plane, which arises from a constant background with at t ≪ 0 and then disappears into the constant background gradually at t ≫ 0. The fundamental lump is a traveling wave, which can preserve its profile during the propagation on (x, y)-plane. When N ≥ 2 and n1 = n2 = · · · = nN = 1, several specific multi-rational solutions are given graphically. Supported by the National Natural Science Foundation of China under Grant No. 11271210, the K.C. Wong Magna Fund in Ningbo University

  11. 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…

  12. 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…

  13. 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…

  14. Medicine, ethics and religion: rational or irrational?

    PubMed Central

    Orr, R D; Genesen, L B

    1998-01-01

    Savulescu maintains that our paper, which encourages clinicians to honour requests for "inappropriate treatment" is prejudicial to his atheistic beliefs, and therefore wrong. In this paper we clarify and expand on our ideas, and respond to his assertion that medicine, ethics and atheism are objective, rational and true, while religion is irrational and false. PMID:9873978

  15. 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)

  16. 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…

  17. 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)

  18. The Rational-Emotive Approach: A Critique

    ERIC Educational Resources Information Center

    Morris, G. Barry

    1976-01-01

    The critique of Rational-Emotive Therapy aims criticism at Ellis' concept of irrationality, analysis of human behavior and therapeutic techniques. Ellis suggests that his critic's claims lack the support of experimental evidence. He further suggests that an "existential" bias pervades which differs from his own brand of…

  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 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.

  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 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

  1. 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.

  2. 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…

  3. Controlling coal mine bumps

    SciTech Connect

    Goode, C.A.; Campoli, A.A.; Zona, A.

    1984-10-01

    A coal bump or burst is defined as the instantaneous violent failure of a coal pillar(s) from overstress. The causes of coal bumps are not well understood, even though minor disturbances are a daily occurrence in bump prone seams. Lack of knowledge about coal bumps coupled with questionable mining practices can create disastrous consequences. Much of the early work on bumps was documented by US Bureau of Mines (BOM) researchers and operators of mines prone to bumps. In 1954 the BOM published Bulletin 535, This study compares recent events with those findings and suggests measures that can be taken to minimize the potential occurrence and severity of coal bumps.

  4. Draft Genome Sequence of the Thermotolerant Cyanobacterium Desertifilum sp. IPPAS B-1220

    PubMed Central

    Sinetova, Maria A.; Bolatkhan, Kenzhegul; Zayadan, Bolatkhan K.; Ustinova, Vera V.; Kupriyanova, Elena V.; Skrypnik, Alexandra N.; Gogoleva, Natalya E.; Gogolev, Yuriy V.; Los, Dmitry A.

    2016-01-01

    Here, we report the draft genome of the filamentous cyanobacterium Desertifilum sp. strain IPPAS B-1220, isolated from Lake Shar-Nuur, Mongolia. The genome of 6.1 Mb codes for 5,113 genes. Genome mining revealed 10 clusters for the synthesis of bioactive compounds (nonribosomal peptides, polyketides, bacteriocins, and lantipeptides) with potential biotechnological or medical importance. PMID:27856594

  5. 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.

  6. Acid mine drainage

    USGS Publications Warehouse

    Bigham, Jerry M.; Cravotta, Charles A.

    2016-01-01

    Acid mine drainage (AMD) consists of metal-laden solutions produced by the oxidative dissolution of iron sulfide minerals exposed to air, moisture, and acidophilic microbes during the mining of coal and metal deposits. The pH of AMD is usually in the range of 2–6, but mine-impacted waters at circumneutral pH (5–8) are also common. Mine drainage usually contains elevated concentrations of sulfate, iron, aluminum, and other potentially toxic metals leached from rock that hydrolyze and coprecipitate to form rust-colored encrustations or sediments. When AMD is discharged into surface waters or groundwaters, degradation of water quality, injury to aquatic life, and corrosion or encrustation of engineered structures can occur for substantial distances. Prevention and remediation strategies should consider the biogeochemical complexity of the system, the longevity of AMD pollution, the predictive power of geochemical modeling, and the full range of available field technologies for problem mitigation.

  7. Upper Animas Mining District

    EPA Pesticide Factsheets

    Web page provides narrative of What's New?, Site Description, Site Risk, Cleanup Progress, Community Involvement, Next Steps, Site Documents, FAQ, Contacts and LInks for the Upper Animas Mining District site in San Juan County, Colorado.

  8. 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.

  9. 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).

  10. 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.

  11. 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.

  12. Competency to Proceed to Trial Evaluations and Rational Understanding.

    PubMed

    Ragatz, Laurie; Vitacco, Michael J; Tross, Rozanna

    2015-12-01

    In Dusky v. United States, the United States Supreme Court established "rational understanding" as a necessary component of a defendant's competency to stand trial. Yet, rational understanding has engendered misunderstanding, stemming from inconsistent court rulings and lack of systematic attention given to definitions of rationality. The purpose of this article is to assist with the conceptualization of rational understanding as it relates to competency to proceed to trial. This will be accomplished through a review of legal decisions and scholarly papers that provide various definitions of rationality. We discuss the suitability of standardized instruments of competency and how they may assist in providing a valid metric for evaluating rational abilities. We also provide discussion of how case law, in conjunction with psycholegal research, can be used to gain nuanced insight into operationalizations of rational understanding. By gaining a thorough understanding of rationality in competency to proceed to trial evaluations, clinicians may improve on the quality and foundation of their evaluations.

  13. The Continuing Quest for Rationality in Curriculum Practice.

    ERIC Educational Resources Information Center

    Gay, Geneva

    1979-01-01

    Suggests that understanding different conceptual models of curriculum making will increase the effectiveness and rationality of the development process. Presents four commonly used models of curriculum development: empiricism, rationalism, pragmatism, and humanism. (Author/JM)

  14. 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.

  15. The origin of bounded rationality and intelligence.

    PubMed

    Lo, Andrew W

    2013-09-01

    Rational economic behavior in which individuals maximize their own self-interest is only one of many possible types of behavior that arise from natural selection. Given an initial population of individuals, each assigned a purely arbitrary behavior with respect to a binary choice problem, and assuming that offspring behave identically to their parents, only those behaviors linked to reproductive success will survive, and less successful behaviors will disappear exponentially fast. This framework yields a single evolutionary explanation for the origin of several behaviors that have been observed in organisms ranging from bacteria to humans, including risk-sensitive foraging, risk aversion, loss aversion, probability matching, randomization, and diversification. The key to understanding which types of behavior are more likely to survive is how behavior affects reproductive success in a given population's environment. From this perspective, intelligence is naturally defined as behavior that increases the likelihood of reproductive success, and bounds on rationality are determined by physiological and environmental constraints.

  16. 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.

  17. 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.

  18. Innovative Ration Preservation via Supercritical Carbon Dioxide

    DTIC Science & Technology

    2012-07-01

    regarded as safe (GRAS) treatment and a novel alternative to traditional thermal processing, which can cause product quality degradation. The CO2 is...reactions continuously occur in food, causing constant changes. Food enzymes and microbes are associated with loss of product quality such as browning...components can also cause product quality degradation. There is a critical need in combat rations for a generally regarded as safe (GRAS), non

  19. The Long Life Ration Packet (LLRP)

    DTIC Science & Technology

    1991-02-18

    50 202 Coffee, cream and sugar 13 52 Total 353 1540 MENU 2 Beef Stew 140 692 Granola bar 43 209 Chocolate covered cookie 43 226 Caramels 35 149 Cocoa ...jelly chocolate icing Fruit cocktail Coffee Coffee Sugar cookies Cocoa Tea Coffee Orange beverage Tea Fruit punch beverage 10 Gross weight/ration 3.639...Chicken Stew Pork with Escalloped Corn Flake Bar, Orange Enriched Sweet Chocolate Potatoes Flavored Bar with Almonds Fruitcake Bar Cocoa Beverage

  20. Integrable mappings via rational elliptic surfaces

    NASA Astrophysics Data System (ADS)

    Tsuda, Teruhisa

    2004-02-01

    We present a geometric description of the QRT map (which is an integrable mapping introduced by Quispel, Roberts and Thompson) in terms of the addition formula of a rational elliptic surface. By this formulation, we classify all the cases when the QRT map is periodic; and show that its period is 2, 3, 4, 5 or 6. A generalization of the QRT map which acts birationally on a pencil of K3 surfaces, or Calabi-Yau manifolds, is also presented.

  1. China rationalizes its renewable energy policy

    SciTech Connect

    Su, Jack H.; Hui, Simone S.; Tsen, Kevin H.

    2010-04-15

    China's over-reliance on thermal power generation, especially coal-fired power stations, is well-documented. While nuclear power continues as an option to coal, China's strides in renewable energy are unprecedented. Recent amendments to the Renewable Energy Law, first promulgated in 2006, attempt to rationalize the regulatory regime governing wind, solar, hydropower and biomass projects in China, currently fraught with inadequate interconnection and tariff shock issues. (author)

  2. 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.

  3. 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.

  4. Regret and the rationality of choices

    PubMed Central

    Bourgeois-Gironde, Sacha

    2010-01-01

    Regret helps to optimize decision behaviour. It can be defined as a rational emotion. Several recent neurobiological studies have confirmed the interface between emotion and cognition at which regret is located and documented its role in decision behaviour. These data give credibility to the incorporation of regret in decision theory that had been proposed by economists in the 1980s. However, finer distinctions are required in order to get a better grasp of how regret and behaviour influence each other. Regret can be defined as a predictive error signal but this signal does not necessarily transpose into a decision-weight influencing behaviour. Clinical studies on several types of patients show that the processing of an error signal and its influence on subsequent behaviour can be dissociated. We propose a general understanding of how regret and decision-making are connected in terms of regret being modulated by rational antecedents of choice. Regret and the modification of behaviour on its basis will depend on the criteria of rationality involved in decision-making. We indicate current and prospective lines of research in order to refine our views on how regret contributes to optimal decision-making. PMID:20026463

  5. QuadBase2: web server for multiplexed guanine quadruplex mining and visualization.

    PubMed

    Dhapola, Parashar; Chowdhury, Shantanu

    2016-07-08

    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.

  6. 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

  7. Rationalization and the Role of the School Counselor.

    ERIC Educational Resources Information Center

    Clark, Arthur J.

    1995-01-01

    Examines rationalization in counselors' interactions with students, parents, and teachers--provides examples of each kind of interaction. Describes the dynamics of rationalization in the schools and outlines interventions that may be used with students, parents, and teachers. Also explores counselors' use of rationalization and gives examples of…

  8. 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…

  9. Should informed consent be based on rational beliefs?

    PubMed Central

    Savulescu, J; Momeyer, R W

    1997-01-01

    Our aim is to expand the regulative ideal governing consent. We argue that consent should not only be informed but also based on rational beliefs. We argue that holding true beliefs promotes autonomy. Information is important insofar as it helps a person to hold the relevant true beliefs. But in order to hold the relevant true beliefs, competent people must also think rationally. Insofar as information is important, rational deliberation is important. Just as physicians should aim to provide relevant information regarding the medical procedures prior to patients consenting to have those procedures, they should also assist patients to think more rationally. We distinguish between rational choice/action and rational belief. While autonomous choice need not necessarily be rational, it should be based on rational belief. The implication for the doctrine of informed consent and the practice of medicine is that, if physicians are to respect patient autonomy and help patients to choose and act more rationally, not only must they provide information, but they should care more about the theoretical rationality of their patients. They should not abandon their patients to irrationality. They should help their patients to deliberate more effectively and to care more about thinking rationally. We illustrate these arguments in the context of Jehovah's Witnesses refusing life-saving blood transfusions. Insofar as Jehovah's Witnesses should be informed of the consequences of their actions, they should also deliberate rationally about these consequences. PMID:9358347

  10. 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…

  11. Recent advances in genome-based polyketide discovery.

    PubMed

    Helfrich, Eric J N; Reiter, Silke; Piel, Jörn

    2014-10-01

    Polyketides are extraordinarily diverse secondary metabolites of great pharmacological value and with interesting ecological functions. The post-genomics era has led to fundamental changes in natural product research by inverting the workflow of secondary metabolite discovery. As opposed to traditional bioactivity-guided screenings, genome mining is an in silico method to screen and analyze sequenced genomes for natural product biosynthetic gene clusters. Since genes for known compounds can be recognized at the early computational stage, genome mining presents an opportunity for dereplication. This review highlights recent progress in bioinformatics, pathway engineering and chemical analytics to extract the biosynthetic secrets hidden in the genome of both well-known natural product sources as well as previously neglected bacteria.

  12. 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/.

  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. Rational-spline approximation with automatic tension adjustment

    NASA Technical Reports Server (NTRS)

    Schiess, J. R.; Kerr, P. A.

    1984-01-01

    An algorithm for weighted least-squares approximation with rational splines is presented. A rational spline is a cubic function containing a distinct tension parameter for each interval defined by two consecutive knots. For zero tension, the rational spline is identical to a cubic spline; for very large tension, the rational spline is a linear function. The approximation algorithm incorporates an algorithm which automatically adjusts the tension on each interval to fulfill a user-specified criterion. Finally, an example is presented comparing results of the rational spline with those of the cubic spline.

  16. 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.

  17. Digital family histories for data mining.

    PubMed

    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.

  18. Longwall mining system

    SciTech Connect

    Guay, P.J.; Ludlow, J.E.; Peake, C.V.

    1983-05-10

    A longwall mining system includes a bidirectional shearer and a roof supporting structure. The shearer includes a pair of angled floor drums, a pivotable roof drum and a loading conveyor. Each drum has a plurality of picks disposed about the drum surface for cutting a material to be mined and a plurality of vanes disposed on the drum surface for carrying the cut material to the loading conveyor. The roof supporting structure includes a load carrying shield which is braced by a pair of supports. The supports are located under the shield in a position between the shearer and a face conveyor. The face conveyor, which is fed by the loading conveyor, carries the mined material to main conveyor for haulage to the outside.

  19. 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

  20. 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)

  1. Genomic dissection of the seed

    PubMed Central

    Becker, Michael G.; Hsu, Ssu-Wei; Harada, John J.; Belmonte, Mark F.

    2014-01-01

    Seeds play an integral role in the global food supply and account for more than 70% of the calories that we consume on a daily basis. To meet the demands of an increasing population, scientists are turning to seed genomics research to find new and innovative ways to increase food production. Seed genomics is evolving rapidly, and the information produced from seed genomics research has exploded over the past two decades. Advances in modern sequencing strategies that profile every molecule in every cell, tissue, and organ and the emergence of new model systems have provided the tools necessary to unravel many of the biological processes underlying seed development. Despite these advances, the analyses and mining of existing seed genomics data remain a monumental task for plant biologists. This review summarizes seed region and subregion genomic data that are currently available for existing and emerging oilseed models. We provide insight into the development of tools on how to analyze large-scale datasets. PMID:25309563

  2. 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

  3. A data mining method to facilitate SAR transfer.

    PubMed

    Wassermann, Anne Mai; Bajorath, Jürgen

    2011-08-22

    A challenging practical problem in medicinal chemistry is the transfer of SAR information from one chemical series to another. Currently, there are no computational methods available to rationalize or support this process. Herein, we present a data mining approach that enables the identification of alternative analog series with different core structures, corresponding substitution patterns, and comparable potency progression. Scaffolds can be exchanged between these series and new analogs suggested that incorporate preferred R-groups. The methodology can be applied to search for alternative analog series if one series is known or, alternatively, to systematically assess SAR transfer potential in compound databases.

  4. 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.

  5. Computational Methods Applied to Rational Drug Design.

    PubMed

    Ramírez, David

    2016-01-01

    Due to the synergic relationship between medical chemistry, bioinformatics and molecular simulation, the development of new accurate computational tools for small molecules drug design has been rising over the last years. The main result is the increased number of publications where computational techniques such as molecular docking, de novo design as well as virtual screening have been used to estimate the binding mode, site and energy of novel small molecules. In this work I review some tools, which enable the study of biological systems at the atomistic level, providing relevant information and thereby, enhancing the process of rational drug design.

  6. Laboratory Evaluation of Australian Ration Packs

    DTIC Science & Technology

    1993-08-01

    Procurement of CRIM 11 2.2.2 Controlled Storage Conditions 11 2.2.3 Ration Chocolate 12 2.2.4 Data Collection and Interpretation 12 2.3 Analytical...Fortified Chocolate Trial 21 3.1.3 Ascorbyl Palmitate Fortified Chocolate Trial 21 3.1.4 IMCR Main Meal Trial 21 3.1.5 CRIOM Soup Powder Trial 21... chocolate and coffee for the storage stability of ascorbic acid and hiamine. "* EFR fruit candy for the storage stability of ascorbic acid. "* Combat

  7. Rational design and synthesis of Janus composites.

    PubMed

    Liang, Fuxin; Zhang, Chengliang; Yang, Zhenzhong

    2014-10-29

    Janus composites with two different components divided on the same object have gained growing interest in many fields, such as solid emulsion stabilizers, sensors, optical probes and self-propellers. Over the past twenty years, various synthesis methods have been developed including Pickering emulsion interfacial modification, block copolymer self-assembly, microfluidics, electro co-jetting, and swelling emulsion polymerization. Anisotropic shape and asymmetric spatial distribution of compositions and functionalities determine their unique performances. Rational design and large scale synthesis of functional Janus materials are crucial for the systematical characterization of performance and exploitation of practical applications.

  8. Computational Methods Applied to Rational Drug Design

    PubMed Central

    Ramírez, David

    2016-01-01

    Due to the synergic relationship between medical chemistry, bioinformatics and molecular simulation, the development of new accurate computational tools for small molecules drug design has been rising over the last years. The main result is the increased number of publications where computational techniques such as molecular docking, de novo design as well as virtual screening have been used to estimate the binding mode, site and energy of novel small molecules. In this work I review some tools, which enable the study of biological systems at the atomistic level, providing relevant information and thereby, enhancing the process of rational drug design. PMID:27708723

  9. Rational defect introduction in silicon nanowires.

    PubMed

    Shin, Naechul; Chi, Miaofang; Howe, Jane Y; Filler, Michael A

    2013-05-08

    The controlled introduction of planar defects, particularly twin boundaries and stacking faults, in group IV nanowires remains challenging despite the prevalence of these structural features in other nanowire systems (e.g., II-VI and III-V). Here we demonstrate how user-programmable changes to precursor pressure and growth temperature can rationally generate both transverse twin boundaries and angled stacking faults during the growth of <111> oriented Si nanowires. We leverage this new capability to demonstrate prototype defect superstructures. These findings yield important insight into the mechanism of defect generation in semiconductor nanowires and suggest new routes to engineer the properties of this ubiquitous semiconductor.

  10. 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

  11. Mining the Social Mediome

    PubMed Central

    Asch, David A.; Rader, Daniel J.; Merchant, Raina

    2015-01-01

    The experiences and behaviors revealed in our everyday lives provide as much insight into health and disease as any analysis of our genome could ever produce. These characteristics are not found in the genome, but may be revealed in our online activities which make up our social mediome. PMID:26341614

  12. Abandoned Mine Lands: Site Information

    EPA Pesticide Factsheets

    A catalogue of mining sites proposed for and listed on the NPL as well as mining sites being cleaned up using the Superfund Alternative Approach. Also mine sites not on the NPL but that have had removal or emergency response cleanup actions.

  13. 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....

  14. Humanitarian Consequences of Land Mines.

    ERIC Educational Resources Information Center

    Rutherford, Ken

    1997-01-01

    Investigates the human and economic consequences of the continuing use and abandonment of land mines. Discusses the reasons for the worldwide proliferation (over 85 million uncleared mines in at least 62 countries) and the legal complexities in curtailing their use. Includes a brief account by a land-mine victim. (MJP)

  15. 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)

  16. Under-mining health: environmental justice and mining in India.

    PubMed

    Saha, Shubhayu; Pattanayak, Subhrendu K; Sills, Erin O; Singha, Ashok K

    2011-01-01

    Despite the potential for economic growth, extractive mineral industries can impose negative health externalities in mining communities. We estimate the size of these externalities by combining household interviews with mine location and estimating statistical functions of respiratory illness and malaria among villagers living along a gradient of proximity to iron-ore mines in rural India. Two-stage regression modeling with cluster corrections suggests that villagers living closer to mines had higher respiratory illness and malaria-related workday loss, but the evidence for mine workers is mixed. These findings contribute to the thin empirical literature on environmental justice and public health in developing countries.

  17. Genomic Testing

    MedlinePlus

    ... Services released a report identifying gaps in the regulation, oversight, and usefulness of genetic testing. They expressed ... December 20, 2016 Content source: Center for Surveillance, Epidemiology and Laboratory Services (CSELS) , Public Health Genomics Email ...

  18. 76 FR 70075 - Proximity Detection Systems for Continuous Mining Machines in Underground Coal Mines

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-10

    ... Mining Machines in Underground Coal Mines AGENCY: Mine Safety and Health Administration, Labor. ACTION... addressing Proximity Detection Systems for Continuous Mining Machines in Underground Coal Mines. This... Continuous Mining Machines in Underground Coal Mines. MSHA conducted hearings on October 18, October...

  19. Phenotype mining in CNV carriers from a population cohort†

    PubMed Central

    Pietiläinen, Olli P. H.; Rehnström, Karola; Jakkula, Eveliina; Service, Susan K.; Congdon, Eliza; Tilgmann, Carola; Hartikainen, Anna-Liisa; Taanila, Anja; Heikura, Ulla; Paunio, Tiina; Ripatti, Samuli; Jarvelin, Marjo-Riitta; Isohanni, Matti; Sabatti, Chiara; Palotie, Aarno; Freimer, Nelson B.; Peltonen, Leena

    2011-01-01

    Phenotype mining is a novel approach for elucidating the genetic basis of complex phenotypic variation. It involves a search of rich phenotype databases for measures correlated with genetic variation, as identified in genome-wide genotyping or sequencing studies. An initial implementation of phenotype mining in a prospective unselected population cohort, the Northern Finland 1966 Birth Cohort (NFBC1966), identifies neurodevelopment-related traits—intellectual deficits, poor school performance and hearing abnormalities—which are more frequent among individuals with large (>500 kb) deletions than among other cohort members. Observation of extensive shared single nucleotide polymorphism haplotypes around deletions suggests an opportunity to expand phenotype mining from cohort samples to the populations from which they derive. PMID:21505072

  20. Rational Decision-Making in Inhibitory Control

    PubMed Central

    Shenoy, Pradeep; Yu, Angela J.

    2011-01-01

    An important aspect of cognitive flexibility is inhibitory control, the ability to dynamically modify or cancel planned actions in response to changes in the sensory environment or task demands. We formulate a probabilistic, rational decision-making framework for inhibitory control in the stop signal paradigm. Our model posits that subjects maintain a Bayes-optimal, continually updated representation of sensory inputs, and repeatedly assess the relative value of stopping and going on a fine temporal scale, in order to make an optimal decision on when and whether to go on each trial. We further posit that they implement this continual evaluation with respect to a global objective function capturing the various reward and penalties associated with different behavioral outcomes, such as speed and accuracy, or the relative costs of stop errors and go errors. We demonstrate that our rational decision-making model naturally gives rise to basic behavioral characteristics consistently observed for this paradigm, as well as more subtle effects due to contextual factors such as reward contingencies or motivational factors. Furthermore, we show that the classical race model can be seen as a computationally simpler, perhaps neurally plausible, approximation to optimal decision-making. This conceptual link allows us to predict how the parameters of the race model, such as the stopping latency, should change with task parameters and individual experiences/ability. PMID:21647306

  1. Ritual and rational action in hospitals.

    PubMed

    Chapman, G E

    1983-01-01

    Menzies argues that nursing hierarchies and ritual practices protect nurses from the anxieties provoked by encountering human suffering. This proposition is examined with particular reference to ritual practices in nursing. It is argued that Menzies studied nurses in isolation from the societal and subcultural norms and values which direct hospital activity. Her psychodynamic model is contrasted with a sociological model of human conduct and action. The characteristics of ritual and rational action, and the difference between non-rational and irrational rituals, is explored. The findings of three 5-month periods of participant observation are presented as illustrative case material to support the authors view, that ritual procedures are not only defence mechanisms against anxiety, but social acts which generate and convey meaning. Ritual practices described in this analysis include rituals surrounding birth, death, status and power. It is concluded that if nurses wish to change or alter ritual nursing practices in hospital it is necessary to understand their social as well as their psychological meaning.

  2. Liberal rationalism and medical decision-making.

    PubMed

    Savulescu, Julian

    1997-04-01

    I contrast Robert Veatch's recent liberal vision of medical decision-making with a more rationalist liberal model. According to Veatch, physicians are biased in their determination of what is in their patient's overall interests in favour of their medical interests. Because of the extent of this bias, we should abandon the practice of physicians offering what they guess to be the best treatment option. Patients should buddy up with physicians who share the same values -- 'deep value pairing'. The goal of choice is maximal promotion of patient values. I argue that if subjectivism about value and valuing is true, this move is plausible. However, if objectivism about value is true -- that there really are states which are good for people regardless of whether they desire to be in them -- then we should accept a more rationalist liberal alternative. According to this alternative, what is required to decide which course is best is rational dialogue between physicians and patients, both about the patient's circumstances and her values, and not the seeking out of people, physicians or others, who share the same values. Rational discussion requires that physicians be reasonable and empathic. I describe one possible account of a reasonable physician.

  3. 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.

  4. Rational recovery: alternative to AA for addiction?

    PubMed

    Galanter, M; Egelko, S; Edwards, H

    1993-01-01

    Rational Recovery (RR) is a new self-help movement for substance abusers, with a cognitive orientation. It has been suggested as an alternative to Alcoholics Anonymous. This study was designed to examine the nature of RR and its impact on those who join. A national sample of 433 substance-abusing people attending 63 established RR groups was evaluated, using codable self-report questionnaires completed at RR meetings. Members were mostly men with college experience who had previously attended AA. Among recruits who attended their first RR meeting in the last month, 38% were abstinent in the last month. Among members who had joined 3 or more months before, 73% were abstinent in the last month; they had attended an average of 4.1 RR meetings in that month, and carried out exercises at home based on Rational Emotive Therapy. Among those who joined 6 or more months before, 58% reported at least 6 months of abstinence. Among members with a history of heavy cocaine use, the portion reporting abstinence in the last month was not significantly different from those who had never used cocaine. The minority of members who were engaged for 3 months were still drinking, though, and did so on an average of 9.9 days in the last month. RR succeeded in engaging substance abusers and promoting abstinence among many of them while presenting a cognitive orientation that is different from the spiritual one of AA. Its utility in substance abuse treatment warrants further assessment.

  5. Scattering in three dimensions from rational maps

    NASA Astrophysics Data System (ADS)

    Cachazo, Freddy; He, Song; Yuan, Ellis Ye

    2013-10-01

    The complete tree-level S-matrix of four dimensional super Yang-Mills and supergravity has compact forms as integrals over the moduli space of certain rational maps. In this note we derive formulas for amplitudes in three dimensions by using the fact that when amplitudes are dressed with proper wave functions dimensional reduction becomes straightforward. This procedure leads to formulas in terms of rational maps for three dimensional maximally supersymmetric Yang-Mills and gravity theories. The integrand of the new formulas contains three basic structures: Parke-Taylor-like factors, Vandermonde determinants and resultants. Integrating out some of the Grassmann directions produces formulas for theories with less than maximal supersymmetry, which exposes yet a fourth kind of structure. Combining all four basic structures we start a search for consistent S-matrices in three dimensions. Very nicely, the most natural ones are those corresponding to ABJM and BLG theories. We also make a connection between the power of a resultant in the integrand, representations of the Poincaré group, infrared behavior and conformality of a theory. Extensions to other theories in three dimensions and to arbitrary dimensions are also discussed.

  6. 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

  7. Integrative data-mining tools to link gene and function.

    PubMed

    El Yacoubi, Basma; de Crécy-Lagard, Valérie

    2014-01-01

    Information derived from genomic and post-genomic data can be efficiently used to link gene and function. Several web-based platforms have been developed to mine these types of data by integrating different tools. This method paper is designed to allow the user to navigate these platforms in order to make functional predictions. The main focus is on phylogenetic distribution and physical clustering tools, but other tools such as pathway reconstruction, gene fusions, and analysis of high-throughput experimental data are also surveyed.

  8. Grants Mining District

    EPA Pesticide Factsheets

    The Grants Mineral Belt was the focus of uranium extraction and production activities from the 1950s until the late 1990s. EPA is working with state, local, and federal partners to assess and address health risks and environmental effects of the mines

  9. Bioremediation of mine water.

    PubMed

    Klein, Robert; Tischler, Judith S; Mühling, Martin; Schlömann, Michael

    2014-01-01

    Caused by the oxidative dissolution of sulfide minerals, mine waters are often acidic and contaminated with high concentrations of sulfates, metals, and metalloids. Because the so-called acid mine drainage (AMD) affects the environment or poses severe problems for later use, treatment of these waters is required. Therefore, various remediation strategies have been developed to remove soluble metals and sulfates through immobilization using physical, chemical, and biological approaches. Conventionally, iron and sulfate-the main pollutants in mine waters-are removed by addition of neutralization reagents and subsequent chemical iron oxidation and sulfate mineral precipitation. Biological treatment strategies take advantage of the ability of microorganisms that occur in mine waters to metabolize iron and sulfate. As a rule, these can be grouped into oxidative and reductive processes, reflecting the redox state of mobilized iron (reduced form) and sulfur (oxidized form) in AMD. Changing the redox states of iron and sulfur results in iron and sulfur compounds with low solubility, thus leading to their precipitation and removal. Various techniques have been developed to enhance the efficacy of these microbial processes, as outlined in this review.

  10. Pneumatic stowing seals mines

    SciTech Connect

    Brezovec, D.

    1983-11-01

    A pneumatic stowing technique has been used in the US to seal entries to abandoned mines. Limestone mixed with dry cement or bentonite is blown into the opening. Sealing can be accomplished in much less time than with traditional concrete block/clay plug methods.

  11. 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].

  12. 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,…

  13. 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.

  14. 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…

  15. Mining (except Oil and Gas) Sector (NAICS 212)

    EPA Pesticide Factsheets

    EPA Regulatory and enforcement information for the mining sector, including metal mining & nonmetallic mineral mining and quarrying. Includes information about asbestos, coal mining, mountaintop mining, Clean Water Act section 404, and abandoned mine lands

  16. Technologies for Decreasing Mining Losses

    NASA Astrophysics Data System (ADS)

    Valgma, Ingo; Väizene, Vivika; Kolats, Margit; Saarnak, Martin

    2013-12-01

    In case of stratified deposits like oil shale deposit in Estonia, mining losses depend on mining technologies. Current research focuses on extraction and separation possibilities of mineral resources. Selective mining, selective crushing and separation tests have been performed, showing possibilities of decreasing mining losses. Rock crushing and screening process simulations were used for optimizing rock fractions. In addition mine backfilling, fine separation, and optimized drilling and blasting have been analyzed. All tested methods show potential and depend on mineral usage. Usage in addition depends on the utilization technology. The questions like stability of the material flow and influences of the quality fluctuations to the final yield are raised.

  17. 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.

  18. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.

    PubMed

    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.

  19. The UCSC Genome Browser Database: update 2006.

    PubMed

    Hinrichs, A S; Karolchik, D; Baertsch, R; Barber, G P; Bejerano, G; Clawson, H; Diekhans, M; Furey, T S; Harte, R A; Hsu, F; Hillman-Jackson, J; Kuhn, R M; Pedersen, J S; Pohl, A; Raney, B J; Rosenbloom, K R; Siepel, A; Smith, K E; Sugnet, C W; Sultan-Qurraie, A; Thomas, D J; Trumbower, H; Weber, R J; Weirauch, M; Zweig, A S; Haussler, D; Kent, W J

    2006-01-01

    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

  20. Chemical data mining of the NCI human tumor cell line database.

    PubMed

    Wang, Huijun; Klinginsmith, Jonathan; Dong, Xiao; Lee, Adam C; Guha, Rajarshi; Wu, Yuqing; Crippen, Gordon M; Wild, David J

    2007-01-01

    The NCI Developmental Therapeutics Program Human Tumor cell line data set is a publicly available database that contains cellular assay screening data for over 40 000 compounds tested in 60 human tumor cell lines. The database also contains microarray assay gene expression data for the cell lines, and so it provides an excellent information resource particularly for testing data mining methods that bridge chemical, biological, and genomic information. In this paper we describe a formal knowledge discovery approach to characterizing and data mining this set and report the results of some of our initial experiments in mining the set from a chemoinformatics perspective.

  1. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  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. Mining-Induced Coal Permeability Change Under Different Mining Layouts

    NASA Astrophysics Data System (ADS)

    Zhang, Zetian; Zhang, Ru; Xie, Heping; Gao, Mingzhong; Xie, Jing

    2016-09-01

    To comprehensively understand the mining-induced coal permeability change, a series of laboratory unloading experiments are conducted based on a simplifying assumption of the actual mining-induced stress evolution processes of three typical longwall mining layouts in China, i.e., non-pillar mining (NM), top-coal caving mining (TCM) and protective coal-seam mining (PCM). A theoretical expression of the mining-induced permeability change ratio (MPCR) is derived and validated by laboratory experiments and in situ observations. The mining-induced coal permeability variation under the three typical mining layouts is quantitatively analyzed using the MPCR based on the test results. The experimental results show that the mining-induced stress evolution processes of different mining layouts do have an influence on the mechanical behavior and evolution of MPCR of coal. The coal mass in the PCM simulation has the lowest stress concentration but the highest peak MPCR (approximately 4000 %), whereas the opposite trends are observed for the coal mass under NM. The results of the coal mass under TCM fall between those for PCM and NM. The evolution of the MPCR of coal under different layouts can be divided into three sections, i.e., stable increasing section, accelerated increasing section and reducing section, but the evolution processes are slightly different for the different mining layouts. A coal bed gas intensive extraction region is recommended based on the MPCR distribution of coal seams obtained by simplifying assumptions and the laboratory testing results. The presented results are also compared with existing conventional triaxial compression test results to fully comprehend the effect of actual mining-induced stress evolution on coal property tests.

  4. 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.

  5. Skyrmion vibration modes within the rational map ansatz

    SciTech Connect

    Lin, W. T.; Piette, B.

    2008-06-15

    We study the vibration modes of the Skyrme model within the rational map ansatz. We show that the vibrations of the radial profiles and the rational maps are decoupled and we consider explicitly the cases B=1, B=2, and B=4. We then compare our results with the vibration modes obtained numerically by Barnes et al. and show that qualitatively the rational map reproduces the vibration modes obtained numerically but that the vibration frequencies of these modes do not match very well.

  6. Point Shifts in Rational Interpolation with Optimized Denominator

    DTIC Science & Technology

    2001-07-01

    estimate hr - f’Ik. and hr - f"Il. Schneider and Werner [14] have noticed that every rational interpolant R E lZNN, written in its barycentric form R...UNCLASSIFIED Defense Technical Information Center Compilation Part Notice ADP013753 TITLE: Point Shifts in Rational Interpolation with Optimized...report: ADP013708 thru ADP013761 UNCLASSIFIED Point shifts in rational interpolation with optimized denominator Jean-Paul Berrut D~partement de

  7. 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

  8. Rational elicitation of cold-sensitive phenotypes

    PubMed Central

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

    2016-01-01

    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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. An appraisal of rational-emotive therapy.

    PubMed

    Haaga, D A; Davison, G C

    1993-04-01

    Albert Ellis's rational-emotive therapy (RET) is scrutinized on several conceptual and empirical grounds, including its reliance on constructive assessment and its ethical stance. Its professional impact thus far exceeds its scientific status. Opinion varies on how even to define irrational beliefs; 1 consequence is problems in assessing them. Meta-analytic reviews provide support for the general utility of RET, but more qualitative reviews question both the internal and external validity of much of the published research. Lacking are process studies that can shed light on the mechanisms of therapeutic change, a situation likely due to the complexity of RET and to a lack of consensus as well about its very definition. Perhaps more progress can be achieved by forsaking studies of RET as a package and shifting instead to examination of specific therapeutic tactics in particular circumstances.

  14. Text Mining for Neuroscience

    NASA Astrophysics Data System (ADS)

    Tirupattur, Naveen; Lapish, Christopher C.; Mukhopadhyay, Snehasis

    2011-06-01

    Text mining, sometimes alternately referred to as text analytics, refers to the process of extracting high-quality knowledge from the analysis of textual data. Text mining has wide variety of applications in areas such as biomedical science, news analysis, and homeland security. In this paper, we describe an approach and some relatively small-scale experiments which apply text mining to neuroscience research literature to find novel associations among a diverse set of entities. Neuroscience is a discipline which encompasses an exceptionally wide range of experimental approaches and rapidly growing interest. This combination results in an overwhelmingly large and often diffuse literature which makes a comprehensive synthesis difficult. Understanding the relations or associations among the entities appearing in the literature not only improves the researchers current understanding of recent advances in their field, but also provides an important computational tool to formulate novel hypotheses and thereby assist in scientific discoveries. We describe a methodology to automatically mine the literature and form novel associations through direct analysis of published texts. The method first retrieves a set of documents from databases such as PubMed using a set of relevant domain terms. In the current study these terms yielded a set of documents ranging from 160,909 to 367,214 documents. Each document is then represented in a numerical vector form from which an Association Graph is computed which represents relationships between all pairs of domain terms, based on co-occurrence. Association graphs can then be subjected to various graph theoretic algorithms such as transitive closure and cycle (circuit) detection to derive additional information, and can also be visually presented to a human researcher for understanding. In this paper, we present three relatively small-scale problem-specific case studies to demonstrate that such an approach is very successful in

  15. 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.

  16. Monotone data visualization using rational trigonometric spline interpolation.

    PubMed

    Ibraheem, Farheen; Hussain, Maria; Hussain, Malik Zawwar

    2014-01-01

    Rational cubic and bicubic trigonometric schemes are developed to conserve monotonicity of curve and surface data, respectively. The rational cubic function has four parameters in each subinterval, while the rational bicubic partially blended function has eight parameters in each rectangular patch. The monotonicity of curve and surface data is retained by developing constraints on some of these parameters in description of rational cubic and bicubic trigonometric functions. The remaining parameters are kept free to modify the shape of curve and surface if required. The developed algorithm is verified mathematically and demonstrated graphically.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. Alchemy and mining: metallogenesis and prospecting in early mining books.

    PubMed

    Dym, Warren Alexander

    2008-11-01

    Historians have assumed that alchemy had a close association with mining, but exactly how and why miners were interested in alchemy remains unclear. This paper argues that alchemical theory began to be synthesised with classical and Christian theories of the earth in mining books after 1500, and served an important practical function. The theory of metals that mining officials addressed spoke of mineral vapours (Witterungen) that left visible markings on the earth's surface. The prospector searched for mineral ore in part by studying these indications. Mineral vapours also explained the functioning of the dowsing rod, which prospectors applied to the discovery of ore. Historians of early chemistry and mining have claimed that mining had a modernising influence by stripping alchemy of its theoretical component, but this paper shows something quite to the contrary: mining officials may have been sceptical of the possibility of artificial transmutation, but they were interested in a theory of the earth that could translate into prospecting knowledge.

  2. Alma Data Mining Toolkit

    NASA Astrophysics Data System (ADS)

    Friedel, Douglas; Looney, Leslie; Teuben, Peter J.; Pound, Marc W.; Rauch, Kevin P.; Mundy, Lee; Harris, Robert J.; Xu, Lisa

    2016-06-01

    ADMIT (ALMA Data Mining Toolkit) is a Python based pipeline toolkit for the creation and analysis of new science products from ALMA data. ADMIT quickly provides users with a detailed overview of their science products, for example: line identifications, line 'cutout' cubes, moment maps, and emission type analysis (e.g., feature detection). Users can download the small ADMIT pipeline product (< 20MB), analyze the results, then fine-tune and re-run the ADMIT pipeline (or any part thereof) on their own machines and interactively inspect the results. ADMIT has both a web browser and command line interface available for this purpose. By analyzing multiple data cubes simultaneously, data mining between many astronomical sources and line transitions are possible. Users are also able to enhance the capabilities of ADMIT by creating customized ADMIT tasks satisfying any special processing needs. We will present some of the salient features of ADMIT and example use cases.

  3. Mine roof support

    SciTech Connect

    Bollmann, A.

    1981-02-24

    A mine roof support has a base and a roof shield pivoted to the base and carrying at its upper end a pivoted cap which is urged upwardly against the mine roof by a hydraulic pit prop reacting between the cap and the base. The lower end of the roof shield is connected to the base by two links each having a pivot cooperating with a pivot on the roof shield, and a pivot cooperating with a pivot on the base. In addition, the base and/or the lower end of the roof shield has an auxiliary for each link and each link has an auxiliary pivot which can be connected with one of the auxiliary pivots of the base or lower end.

  4. Multievidence microarray mining.

    PubMed

    Seifert, Martin; Scherf, Matthias; Epple, Anton; Werner, Thomas

    2005-10-01

    Microarray mining is a challenging task because of the superposition of several processes in the data. We believe that the combination of microarray data-based analyses (statistical significance analysis of gene expression) with array-independent analyses (literature-mining and promoter analysis) enables some of the problems of traditional array analysis to be overcome. As a proof-of-principle, we revisited publicly available microarray data derived from an experiment with platelet-derived growth factor (PDGF)-stimulated fibroblasts. Our strategy revealed results beyond the detection of the major metabolic pathway known to be linked to the PDGF response: we were able to identify the crosstalking regulatory networks underlying the metabolic pathway without using a priori knowledge about the experiment.

  5. Phosphate Mines, Jordan

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Jordan's leading industry and export commodities are phosphate and potash, ranked in the top three in the world. These are used to make fertilizer. The Jordan Phosphate Mines Company is the sole producer, having started operations in 1935. In addition to mining activities, the company produces phosphoric acid (for fertilizers, detergents, pharmaceuticals), diammonium phosphate (for fertilizer), sulphuric acid (many uses), and aluminum fluoride (a catalyst to make aluminum and magnesium).

    The image covers an area of 27.5 x 49.4 km, was acquired on September 17, 2005, and is located near 30.8 degrees north latitude, 36.1 degrees east 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.

  6. Mining in chemometrics.

    PubMed

    Mutihac, Lucia; Mutihac, Radu

    2008-03-31

    Some of the increasingly spread data mining methods in chemometrics like exploratory data analysis, artificial neural networks, pattern recognition, and digital image processing with their highs and lows along with some of their representative applications are discussed. The development of more complex analytical instruments and the need to cope with larger experimental data sets have demanded for new approaches in data analysis, which have led to advanced methods in experimental design and data processing. Hypothesis-driven methods typified by inferential statistics have been gradually complemented or even replaced by data-driven model-free methods that seek for structure in data without reference to the experimental protocol or prior hypotheses. The emphasis is put on the ability of data mining methods to solve multivariate-multiresponse problems on the basis of experimental data and minimal statistical assumptions only, in contrast to classical methods, which require predefined priors to be tested against some null-hypothesis.

  7. 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).

  8. Drum cutter mining machine

    SciTech Connect

    Oberste-beulmann, K.; Schupphaus, H.

    1980-02-19

    A drum cutter mining machine includes a machine frame with a winch having a drive wheel to engage a rack or chain which extends along the path of travel by the mining machine to propel the machine along a mine face. The mining machine is made up of discrete units which include a machine body and machine housings joined to opposite sides of the machine body. The winch is either coupled through a drive train with a feed drive motor or coupled to the drive motor for cutter drums. The machine housings each support a pivot shaft coupled by an arm to a drum cutter. One of these housings includes a removable end cover and a recess adapted to receive a support housing for a spur gear system used to transmit torque from a feed drive motor to a reduction gear system which is, in turn, coupled to the drive wheel of the winch. In one embodiment, a removable end cover on the machine housing provides access to the feed drive motor. The feed drive motor is arranged so that the rotational axis of its drive output shaft extends transversely to the stow side of the machine frame. In another embodiment, the reduction gear system is arranged at one side of the pivot shaft for the cutter drum while the drive motor therefor is arranged at the other side of the pivot shaft and coupled thereto through the spur gear system. In a further embodiment, the reduction gear system is disposed between the feed motor and the pivot shaft.

  9. National Underground Mines Inventory

    DTIC Science & Technology

    1983-10-01

    that the contents necessaZiy reflect the views and policies of the Federal Emergency Management Agency. FINAL REPORT RTI/2506/OO-O1F NATIONAL...UNDERGROUND MINES INVENTORY Prepared by: M. Wright R. Chessin K. Reeves S. York, III Prepared for: Federal Emergency Management Agency Washington , D.C. 20472...Emergency Management Agency October 1983 Washington , DC 20472 I. NUMBEROFPAGES 80 14. MONITORING AGENCY NAME A ADORESS(1lierent bum Controflhi Office

  10. Germany knows mining

    SciTech Connect

    2006-11-15

    Whether it is the nuance of precision or robust rock breaking strength, German suppliers have the expertise. Germany has about 120 companies in the mining equipment industry, employing some 16,000 people. The article describes some recent developments of the following companies: DBT, Liebherr, Atlas Copco, BASF, Boart Longyear, Eickhoff, IBS, Maschinenfabrik Glueckauf, Komatsu, TAKRA, Terex O & R, Thyssen Krupp Foerdertechnik and Wirtgen. 7 photos.

  11. NVESD mine lane facility

    NASA Astrophysics Data System (ADS)

    Habersat, James D.; Marshall, Christopher; Maksymonko, George

    2003-09-01

    The NVESD Mine Lane Facility has recently undergone an extensive renovation. It now consists of an indoor, dry lane portion, a greenhouse portion with moisture-controlled lanes, a control room, and two outdoor lanes. The indoor structure contains six mine lanes, each approximately 2.5m (width) × 1.2m (depth) × 33m(length). These lanes contain six different soil types: magnetite/sand, silt, crusher run gravel (bluestone gravel), bank run gravel (tan gravel), red clay, and white sand. An automated trolley system is used for mounting the various mine detection systems and sensors under test. Data acquisition and data logging is fully automated. The greenhouse structure was added to provide moisture controlled lanes for measuring the effect of moisture on sensor effectiveness. A gantry type crane was installed to permit remotely controlled positioning of a sensor package over any portion of the greenhouse lanes at elevations from ground level up to 5m without shadowing the target area. The roof of the greenhouse is motorized, and can be rolled back to allow full solar loading. A control room overlooking the lanes is complete with recording and monitoring devices and contains controls to operate the trolleys. A facility overview is presented and typical results from recent data collection exercises are presented.

  12. Data Mining and Analysis

    NASA Technical Reports Server (NTRS)

    Samms, Kevin O.

    2015-01-01

    The Data Mining project seeks to bring the capability of data visualization to NASA anomaly and problem reporting systems for the purpose of improving data trending, evaluations, and analyses. Currently NASA systems are tailored to meet the specific needs of its organizations. This tailoring has led to a variety of nomenclatures and levels of annotation for procedures, parts, and anomalies making difficult the realization of the common causes for anomalies. Making significant observations and realizing the connection between these causes without a common way to view large data sets is difficult to impossible. In the first phase of the Data Mining project a portal was created to present a common visualization of normalized sensitive data to customers with the appropriate security access. The tool of the visualization itself was also developed and fine-tuned. In the second phase of the project we took on the difficult task of searching and analyzing the target data set for common causes between anomalies. In the final part of the second phase we have learned more about how much of the analysis work will be the job of the Data Mining team, how to perform that work, and how that work may be used by different customers in different ways. In this paper I detail how our perspective has changed after gaining more insight into how the customers wish to interact with the output and how that has changed the product.

  13. Organizational Data Mining

    NASA Astrophysics Data System (ADS)

    Nemati, Hamid R.; Barko, Christopher D.

    Many organizations today possess substantial quantities of business information but have very little real business knowledge. A recent survey of 450 business executives reported that managerial intuition and instinct are more prevalent than hard facts in driving organizational decisions. To reverse this trend, businesses of all sizes would be well advised to adopt Organizational Data Mining (ODM). ODM is defined as leveraging Data Mining tools and technologies to enhance the decision-making process by transforming data into valuable and actionable knowledge to gain a competitive advantage. ODM has helped many organizations optimize internal resource allocations while better understanding and responding to the needs of their customers. The fundamental aspects of ODM can be categorized into Artificial Intelligence (AI), Information Technology (IT), and Organizational Theory (OT), with OT being the key distinction between ODM and Data Mining. In this chapter, we introduce ODM, explain its unique characteristics, and report on the current status of ODM research. Next we illustrate how several leading organizations have adopted ODM and are benefiting from it. Then we examine the evolution of ODM to the present day and conclude our chapter by contemplating ODM's challenging yet opportunistic future.

  14. 30 CFR 77.1200 - Mine map.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Mine map. 77.1200 Section 77.1200 Mineral... SAFETY STANDARDS, SURFACE COAL MINES AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Maps § 77.1200 Mine map. The operator shall maintain an accurate and up-to-date map of the mine, on a scale of not...

  15. 30 CFR 75.203 - Mining methods.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Mining methods. 75.203 Section 75.203 Mineral... SAFETY STANDARDS-UNDERGROUND COAL MINES Roof Support § 75.203 Mining methods. (a) The method of mining... used to maintain the projected direction of mining in entries, rooms, crosscuts and pillar splits....

  16. 30 CFR 75.203 - Mining methods.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Mining methods. 75.203 Section 75.203 Mineral... SAFETY STANDARDS-UNDERGROUND COAL MINES Roof Support § 75.203 Mining methods. (a) The method of mining... used to maintain the projected direction of mining in entries, rooms, crosscuts and pillar splits....

  17. 30 CFR 75.203 - Mining methods.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Mining methods. 75.203 Section 75.203 Mineral... SAFETY STANDARDS-UNDERGROUND COAL MINES Roof Support § 75.203 Mining methods. (a) The method of mining... used to maintain the projected direction of mining in entries, rooms, crosscuts and pillar splits....

  18. 30 CFR 75.203 - Mining methods.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Mining methods. 75.203 Section 75.203 Mineral... SAFETY STANDARDS-UNDERGROUND COAL MINES Roof Support § 75.203 Mining methods. (a) The method of mining... used to maintain the projected direction of mining in entries, rooms, crosscuts and pillar splits....

  19. 30 CFR 75.203 - Mining methods.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Mining methods. 75.203 Section 75.203 Mineral... SAFETY STANDARDS-UNDERGROUND COAL MINES Roof Support § 75.203 Mining methods. (a) The method of mining... used to maintain the projected direction of mining in entries, rooms, crosscuts and pillar splits....

  20. Protein Kinase Target Discovery From Genome-Wide Messenger RNA Expression Profiling

    PubMed Central

    Ma’ayan, Avi; He, John C.

    2010-01-01

    Genome-wide messenger RNA profiling provides a snapshot of the global state of the cell under different experimental conditions such as diseased versus normal cellular states. However, because measurements are in the form of quantitative changes in messenger RNA levels, such experimental data does not provide direct understanding of the regulatory molecular mechanisms responsible for the observed changes. Identifying potential cell signaling regulatory mechanisms responsible for changes in gene expression under different experimental conditions or in different tissues has been the focus of many computational systems biology studies. Most popular approaches include promoter analysis, gene ontology, or pathway enrichment analysis, as well as reverse engineering of networks from messenger RNA expression data. Here we present a rational approach for identifying and ranking protein kinases that are likely responsible for observed changes in gene expression. By combining promoter analysis; data from various chromatin immunoprecipitation studies such as chromatin immunoprecipitation sequencing, chromatin immunoprecipitation coupled with paired-end ditag, and chromatin immunoprecipitation-on-chip; protein-protein interactions; and kinase-protein phosphorylation reactions collected from the literature, we can identify and rank candidate protein kinases for knock-down, or other types of functional validations, based on genome-wide changes in gene expression. We describe how protein kinase candidate identification and ranking can be made robust by cross-validation with phosphoproteomics data as well as through a literature-based text-mining approach. In conclusion, data integration can produce robust candidate rankings for understanding cell regulation through identification of protein kinases responsible for gene expression changes, and thus rapidly advancing drug target discovery and unraveling drug mechanisms of action. PMID:20687179

  1. Genome mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome maps can be thought of much like road maps except that, instead of traversing across land, they traverse across the chromosomes of an organism. Genetic markers serve as landmarks along the chromosome and provide researchers information as to how close they may be to a gene or region of inter...

  2. Ground control for highwall mining

    SciTech Connect

    Zipf, R.K.; Mark, C.

    2007-09-15

    Perhaps the greatest risk to both equipment and personnel associated with highwall mining is from ground control. The two most significant ground control hazards are rock falls from highwall and equipment entrapment underground. In the central Appalachians, where the majority of highwall mining occurs in the USA, hillseams (or mountain cracks) are the most prominent structure that affects highwall stability. The article discusses measures to minimise the risk of failure associated with hillstreams. A 'stuck' or trapped highwall miner, and the ensuring retrieval or recovery operation, can be extremely disruptive to the highwall mining process. Most entrapment, are due to roof falls in the hole. The options for recovery are surface retrieval, surface excavation or underground recovery. Proper pillar design is essential to maintain highwall stability and prevent entrapments. NIOSH has developed the Analysis of Retreat Mining Pillar stability-Highwall Mining (ARMPS-HWM) computer program to help mine planners with this process. 10 figs.

  3. Economics of mining law

    USGS Publications Warehouse

    Long, K.R.

    1995-01-01

    Modern mining law, by facilitating socially and environmentally acceptable exploration, development, and production of mineral materials, helps secure the benefits of mineral production while minimizing environmental harm and accounting for increasing land-use competition. Mining investments are sunk costs, irreversibly tied to a particular mineral site, and require many years to recoup. Providing security of tenure is the most critical element of a practical mining law. Governments owning mineral rights have a conflict of interest between their roles as a profit-maximizing landowner and as a guardian of public welfare. As a monopoly supplier, governments have considerable power to manipulate mineral-rights markets. To avoid monopoly rent-seeking by governments, a competitive market for government-owned mineral rights must be created by artifice. What mining firms will pay for mineral rights depends on expected exploration success and extraction costs. Landowners and mining firms will negotlate respective shares of anticipated differential rents, usually allowing for some form of risk sharing. Private landowners do not normally account for external benefits or costs of minerals use. Government ownership of mineral rights allows for direct accounting of social prices for mineral-bearing lands and external costs. An equitable and efficient method is to charge an appropriate reservation price for surface land use, net of the value of land after reclamation, and to recover all or part of differential rents through a flat income or resource-rent tax. The traditional royalty on gross value of production, essentially a regressive income tax, cannot recover as much rent as a flat income tax, causes arbitrary mineral-reserve sterilization, and creates a bias toward development on the extensive margin where marginal environmental costs are higher. Mitigating environmental costs and resolving land-use conflicts require local evaluation and planning. National oversight ensures

  4. 30 CFR 819.21 - Auger mining: Protection of underground mining.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Auger mining: Protection of underground mining. 819.21 Section 819.21 Mineral Resources OFFICE OF SURFACE MINING RECLAMATION AND ENFORCEMENT... STANDARDS-AUGER MINING § 819.21 Auger mining: Protection of underground mining. Auger holes shall not...

  5. 30 CFR 77.1712 - Reopening mines; notification; inspection prior to mining.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... to mining. 77.1712 Section 77.1712 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... prior to mining. Prior to reopening any surface coal mine after it has been abandoned or declared... an authorized representative of the Secretary before any mining operations in such mine...

  6. 30 CFR 49.4 - Alternative mine rescue capability for special mining conditions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... mining conditions. 49.4 Section 49.4 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT... special mining conditions. (a) If an underground mine is operating under special mining conditions, the... review and approval. (c) To be considered “operating under special mining conditions,” the operator...

  7. 30 CFR 819.21 - Auger mining: Protection of underground mining.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Auger mining: Protection of underground mining. 819.21 Section 819.21 Mineral Resources OFFICE OF SURFACE MINING RECLAMATION AND ENFORCEMENT... STANDARDS-AUGER MINING § 819.21 Auger mining: Protection of underground mining. Auger holes shall not...

  8. 30 CFR 77.1712 - Reopening mines; notification; inspection prior to mining.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... to mining. 77.1712 Section 77.1712 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... prior to mining. Prior to reopening any surface coal mine after it has been abandoned or declared... an authorized representative of the Secretary before any mining operations in such mine...

  9. 30 CFR 77.1712 - Reopening mines; notification; inspection prior to mining.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... to mining. 77.1712 Section 77.1712 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... prior to mining. Prior to reopening any surface coal mine after it has been abandoned or declared... an authorized representative of the Secretary before any mining operations in such mine...

  10. 30 CFR 819.21 - Auger mining: Protection of underground mining.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Auger mining: Protection of underground mining. 819.21 Section 819.21 Mineral Resources OFFICE OF SURFACE MINING RECLAMATION AND ENFORCEMENT... STANDARDS-AUGER MINING § 819.21 Auger mining: Protection of underground mining. Auger holes shall not...

  11. 30 CFR 819.21 - Auger mining: Protection of underground mining.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Auger mining: Protection of underground mining. 819.21 Section 819.21 Mineral Resources OFFICE OF SURFACE MINING RECLAMATION AND ENFORCEMENT... STANDARDS-AUGER MINING § 819.21 Auger mining: Protection of underground mining. Auger holes shall not...

  12. 30 CFR 819.21 - Auger mining: Protection of underground mining.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Auger mining: Protection of underground mining. 819.21 Section 819.21 Mineral Resources OFFICE OF SURFACE MINING RECLAMATION AND ENFORCEMENT... STANDARDS-AUGER MINING § 819.21 Auger mining: Protection of underground mining. Auger holes shall not...

  13. Draft Genome Sequence of Marine Sponge Symbiont Pseudoalteromonas luteoviolacea IPB1, Isolated from Hilo, Hawaii.

    PubMed

    Sakai-Kawada, Francis E; Yakym, Christopher J; Helmkampf, Martin; Hagiwara, Kehau; Ip, Courtney G; Antonio, Brandi J; Armstrong, Ellie; Ulloa, Wesley J; Awaya, Jonathan D

    2016-09-22

    We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain IPB1 that was isolated from the Hawaiian marine sponge Iotrochota protea Genome mining complemented with bioassay studies will elucidate secondary metabolite biosynthetic pathways and will help explain the ecological interaction between host sponge and microorganism.

  14. 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...

  15. Genomic prediction contributing to a promising global strategy to turbocharge gene banks

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The 7.4 million plant accessions in genebanks are largely underutilized due to various resource constraints, but current genomic and analytic technologies are enabling us to mine this natural heritage. Here we report a proof-of-concept study to integrate genomic prediction into a broad germplasm eva...

  16. 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...

  17. Genome Sequence of the Acidophilic Iron Oxidizer Ferrimicrobium acidiphilum Strain T23T.

    PubMed

    Eisen, Sebastian; Poehlein, Anja; Johnson, D Barrie; Daniel, Rolf; Schlömann, Michael; Mühling, Martin

    2015-04-30

    Extremely acidophilic iron-oxidizing bacteria have largely been characterized for the phyla Proteobacteria and Nitrospira. Here, we report the draft genome of an iron-oxidizing and -reducing heterotrophic mesophile of the Actinobacteria, Ferrimicrobium acidiphilum, which was isolated from an abandoned pyrite mine. The genome sequence comprises 3.08 Mb.

  18. Genome cartography: charting the apicomplexan genome.

    PubMed

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology.

  19. New Equipment for Mine Safety

    NASA Technical Reports Server (NTRS)

    1983-01-01

    While planning for the space shuttle, Bendix Corporation with the help of Johnson Space Center expanded the anthropometric data base for aerospace and nonaerospace use in clothing, workplace, etc. The result was the Anthropometric Source Book which was later utilized by the U.S. Bureau of Mines in designing advanced mining systems. The book was particularly valuable in the design of a remote cab used in mining.

  20. Data Mining in Social Media

    NASA Astrophysics Data System (ADS)

    Barbier, Geoffrey; Liu, Huan

    The rise of online social media is providing a wealth of social network data. Data mining techniques provide researchers and practitioners the tools needed to analyze large, complex, and frequently changing social media data. This chapter introduces the basics of data mining, reviews social media, discusses how to mine social media data, and highlights some illustrative examples with an emphasis on social networking sites and blogs.

  1. Genomics and Bioinformatics of Parkinson's Disease

    PubMed Central

    Scholz, Sonja W.; Mhyre, Tim; Ressom, Habtom; Shah, Salim; Federoff, Howard J.

    2012-01-01

    Within the last two decades, genomics and bioinformatics have profoundly impacted our understanding of the molecular mechanisms of Parkinson's disease (PD). From the description of the first PD gene in 1997 until today, we have witnessed the emergence of new technologies that have revolutionized our concepts to identify genetic mechanisms implicated in human health and disease. Driven by the publication of the human genome sequence and followed by the description of detailed maps for common genetic variability, novel applications to rapidly scrutinize the entire genome in a systematic, cost-effective manner have become a reality. As a consequence, about 30 genetic loci have been unequivocally linked to the pathogenesis of PD highlighting essential molecular pathways underlying this common disorder. Herein we discuss how neurogenomics and bioinformatics are applied to dissect the nature of this complex disease with the overall aim of developing rational therapeutic interventions. PMID:22762024

  2. 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.…

  3. Early Developmental Trajectories toward Concepts of Rational Numbers

    ERIC Educational Resources Information Center

    Kainulainen, Mikko; McMullen, Jake; Lehtinen, Erno

    2017-01-01

    Difficulties with rational numbers have been explained by a natural number bias, where concepts of natural numbers are inappropriately applied to rational numbers. Overcoming this difficulty may require a radical restructuring of previous knowledge. In order to capture this development, we examined third- to fifth-grade students' understanding of…

  4. 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…

  5. 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…

  6. Convexity preserving C2 rational quadratic trigonometric spline

    NASA Astrophysics Data System (ADS)

    Dube, Mridula; Tiwari, Preeti

    2012-09-01

    A C2 rational quadratic trigonometric spline interpolation has been studied using two kind of rational quadratic trigonometric splines. It is shown that under some natural conditions the solution of the problem exits and is unique. The necessary and sufficient condition that constrain the interpolation curves to be convex in the interpolating interval or subinterval are derived.

  7. Number Sense in the Transition from Natural to Rational Numbers

    ERIC Educational Resources Information Center

    Van Hoof, Jo; Verschaffel, Lieven; Van Dooren, Wim

    2017-01-01

    Background: Rational numbers are of critical importance both in mathematics and in other fields of science. However, they form a stumbling block for learners. One widely known source of the difficulty learners have with rational numbers is the natural number bias, that is the tendency to (inappropriately) apply natural number properties in…

  8. Rational-emotive therapy and depression: a clinical case study.

    PubMed

    Horton, A M; Johnson, C H

    1980-12-01

    Rational-emotive group and bibliotherapy were used to treat a depressed patient in a clinical setting. Psychological test data document a dramatic improvement. It is suggested that rational-emotive therapy may prove efficacious for the treatment of some depressed patients in clinical settings.

  9. 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…

  10. Mining's impact on groundwater assessed

    NASA Astrophysics Data System (ADS)

    Detailed studies have indicated that groundwater is contaminated in the immediate vicinity of many mines in the eastern United States. However, no underground mines and very few refuse disposal areas have monitoring systems that can provide adequate warning of impending threats to groundwater quality.This was one of the conclusions of a 3-year study by Geraghty & Miller, Inc., a firm of consulting groundwater geologists and hydrologists based in Syosset, New York. The study focused on mines east of the 100th meridian. These mines will produce an estimated 1.1 billion tons of coal and 200 million tons of waste by 1985.

  11. Data Mining for Financial Applications

    NASA Astrophysics Data System (ADS)

    Kovalerchuk, Boris; Vityaev, Evgenii

    This chapter describes Data Mining in finance by discussing financial tasks, specifics of methodologies and techniques in this Data Mining area. It includes time dependence, data selection, forecast horizon, measures of success, quality of patterns, hypothesis evaluation, problem ID, method profile, attribute-based and relational methodologies. The second part of the chapter discusses Data Mining models and practice in finance. It covers use of neural networks in portfolio management, design of interpretable trading rules and discovering money laundering schemes using decision rules and relational Data Mining methodology.

  12. Data mining applications in healthcare.

    PubMed

    Koh, Hian Chye; Tan, Gerald

    2005-01-01

    Data mining has been used intensively and extensively by many organizations. In healthcare, data mining is becoming increasingly popular, if not increasingly essential. Data mining applications can greatly benefit all parties involved in the healthcare industry. For example, data mining can help healthcare insurers detect fraud and abuse, healthcare organizations make customer relationship management decisions, physicians identify effective treatments and best practices, and patients receive better and more affordable healthcare services. The huge amounts of data generated by healthcare transactions are too complex and voluminous to be processed and analyzed by traditional methods. Data mining provides the methodology and technology to transform these mounds of data into useful information for decision making. This article explores data mining applications in healthcare. In particular, it discusses data mining and its applications within healthcare in major areas such as the evaluation of treatment effectiveness, management of healthcare, customer relationship management, and the detection of fraud and abuse. It also gives an illustrative example of a healthcare data mining application involving the identification of risk factors associated with the onset of diabetes. Finally, the article highlights the limitations of data mining and discusses some future directions.

  13. Mate choice in fruit flies is rational and adaptive

    PubMed Central

    Arbuthnott, Devin; Fedina, Tatyana Y.; Pletcher, Scott D.; Promislow, Daniel E. L.

    2017-01-01

    According to rational choice theory, beneficial preferences should lead individuals to sort available options into linear, transitive hierarchies, although the extent to which non-human animals behave rationally is unclear. Here we demonstrate that mate choice in the fruit fly Drosophila melanogaster results in the linear sorting of a set of diverse isogenic female lines, unambiguously demonstrating the hallmark of rational behaviour, transitivity. These rational choices are associated with direct benefits, enabling males to maximize offspring production. Furthermore, we demonstrate that female behaviours and cues act redundantly in mate detection and assessment, as rational mate choice largely persists when visual or chemical sensory modalities are impaired, but not when both are impaired. Transitivity in mate choice demonstrates that the quality of potential mates varies significantly among genotypes, and that males and females behave in such a way as to facilitate adaptive mate choice. PMID:28094789

  14. On the denominator values and barycentric weights of rational interpolants

    NASA Astrophysics Data System (ADS)

    Polezzi, M.; Sri Ranga, A.

    2007-03-01

    We improve upon the method of Zhu and Zhu [A method for directly finding the denominator values of rational interpolants, J. Comput. Appl. Math. 148 (2002) 341-348] for finding the denominator values of rational interpolants, reducing considerably the number of arithmetical operations required for their computation. In a second stage, we determine the points (if existent) which can be discarded from the rational interpolation problem. Furthermore, when the interpolant has a linear denominator, we obtain a formula for the barycentric weights which is simpler than the one found by Berrut and Mittelmann [Matrices for the direct determination of the barycentric weights of rational interpolation, J. Comput. Appl. Math. 78 (1997) 355-370]. Subsequently, we give a necessary and sufficient condition for the rational interpolant to have a pole.

  15. Text mining in livestock animal science: introducing the potential of text mining to animal sciences.

    PubMed

    Sahadevan, S; Hofmann-Apitius, M; Schellander, K; Tesfaye, D; Fluck, J; Friedrich, C M

    2012-10-01

    In biological research, establishing the prior art by searching and collecting information already present in the domain has equal importance as the experiments done. To obtain a complete overview about the relevant knowledge, researchers mainly rely on 2 major information sources: i) various biological databases and ii) scientific publications in the field. The major difference between the 2 information sources is that information from databases is available, typically well structured and condensed. The information content in scientific literature is vastly unstructured; that is, dispersed among the many different sections of scientific text. The traditional method of information extraction from scientific literature occurs by generating a list of relevant publications in the field of interest and manually scanning these texts for relevant information, which is very time consuming. It is more than likely that in using this "classical" approach the researcher misses some relevant information mentioned in the literature or has to go through biological databases to extract further information. Text mining and named entity recognition methods have already been used in human genomics and related fields as a solution to this problem. These methods can process and extract information from large volumes of scientific text. Text mining is defined as the automatic extraction of previously unknown and potentially useful information from text. Named entity recognition (NER) is defined as the method of identifying named entities (names of real world objects; for example, gene/protein names, drugs, enzymes) in text. In animal sciences, text mining and related methods have been briefly used in murine genomics and associated fields, leaving behind other fields of animal sciences, such as livestock genomics. The aim of this work was to develop an information retrieval platform in the livestock domain focusing on livestock publications and the recognition of relevant data from

  16. Uranium Mines and Mills Location Database

    EPA Pesticide Factsheets

    The Uranium Mines and Mills location database identifies and shows the location of active and inactive uranium mines and mills, as well as mines which principally produced other minerals, but were known to have uranium in the ore.

  17. Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis.

    PubMed

    Christen, Matthias; Deutsch, Samuel; Christen, Beat

    2015-08-21

    Recent advances in synthetic biology have resulted in an increasing demand for the de novo synthesis of large-scale DNA constructs. Any process improvement that enables fast and cost-effective streamlining of digitized genetic information into fabricable DNA sequences holds great promise to study, mine, and engineer genomes. Here, we present Genome Calligrapher, a computer-aided design web tool intended for whole genome refactoring of bacterial chromosomes for de novo DNA synthesis. By applying a neutral recoding algorithm, Genome Calligrapher optimizes GC content and removes obstructive DNA features known to interfere with the synthesis of double-stranded DNA and the higher order assembly into large DNA constructs. Subsequent bioinformatics analysis revealed that synthesis constraints are prevalent among bacterial genomes. However, a low level of codon replacement is sufficient for refactoring bacterial genomes into easy-to-synthesize DNA sequences. To test the algorithm, 168 kb of synthetic DNA comprising approximately 20 percent of the synthetic essential genome of the cell-cycle bacterium Caulobacter crescentus was streamlined and then ordered from a commercial supplier of low-cost de novo DNA synthesis. The successful assembly into eight 20 kb segments indicates that Genome Calligrapher algorithm can be efficiently used to refactor difficult-to-synthesize DNA. Genome Calligrapher is broadly applicable to recode biosynthetic pathways, DNA sequences, and whole bacterial genomes, thus offering new opportunities to use synthetic biology tools to explore the functionality of microbial diversity. The Genome Calligrapher web tool can be accessed at https://christenlab.ethz.ch/GenomeCalligrapher  .

  18. 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.

  19. 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.

  20. Mining the oocyte transcriptome.

    PubMed

    Andreu-Vieyra, Claudia; Lin, Yi-Nan; Matzuk, Martin M

    2006-01-01

    Mammalian folliculogenesis and oocyte physiology are complex and not fully understood. However, major advances over the past 15 years in our ability to create and study in vivo models have improved our understanding of these essential physiological processes. More recently, the availability of vast arrays of DNA sequence information in the forms of "complete" genomes, expressed sequence tag libraries and microarray data from reproductive tissues have stimulated the discovery of new information through genome scanning, prediction programs and in silico screening techniques. These technological improvements will help to expand our understanding of folliculogenesis and oocyte physiology and improve human reproductive health.

  1. Genomic analysis of the eukaryotic protein kinase superfamily: a perspective

    PubMed Central

    Hanks, Steven K

    2003-01-01

    Protein kinases with a conserved catalytic domain make up one of the largest 'superfamilies' of eukaryotic proteins and play many key roles in biology and disease. Efforts to identify and classify all the members of the eukaryotic protein kinase superfamily have recently culminated in the mining of essentially complete human genome data. PMID:12734000

  2. Personal genomics services: whose genomes?

    PubMed Central

    Gurwitz, David; Bregman-Eschet, Yael

    2009-01-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below. PMID:19259127

  3. MINE WASTE TECHNOLOGY PROGRAM - UNDERGROUND MINE SOURCE CONTROL DEMONSTRATION PROJECT

    EPA Science Inventory

    This report presents results of the Mine Waste Technology Program Activity III, Project 8, Underground Mine Source Control Demonstration Project implemented and funded by the U. S. Environmental Protection Agency (EPA) and jointly administered by EPA and the U. S. Department of E...

  4. 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

  5. Draft Genome Sequence of a Novel Acidophilic Iron-Oxidizing Firmicutes Species, “Acidibacillus ferrooxidans” (SLC66T)

    PubMed Central

    Ñancucheo, Ivan; Oliveira, Renato; Dall’Agnol, Hivana; Johnson, D. Barrie; Grail, Barry; Holanda, Roseanne; Nunes, Gisele Lopes; Cuadros-Orellana, Sara

    2016-01-01

    Here, we present the draft genome sequence of the type strain of “Acidibacillus ferrooxidans,” a mesophilic, heterotrophic, and acidophilic bacterium that was isolated from mine spoilage subjected to accelerated weathering in humidity cell tests carried out by the former U.S. Bureau of Mines in Salt Lake City, UT. PMID:27198020

  6. 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

  7. Ancient genomics.

    PubMed

    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

    2015-01-19

    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.

  8. Mining the Home Environment

    PubMed Central

    Cook, Diane J.; Krishnan, Narayanan

    2014-01-01

    Individuals spend a majority of their time in their home or workplace and for many, these places are our sanctuaries. As society and technology advance there is a growing interest in improving the intelligence of the environments in which we live and work. By filling home environments with sensors and collecting data during daily routines, researchers can gain insights on human daily behavior and the impact of behavior on the residents and their environments. In this article we provide an overview of the data mining opportunities and challenges that smart environments provide for researchers and offer some suggestions for future work in this area. PMID:25506128

  9. Respiratory cancers in mining

    SciTech Connect

    Reger, R.B.; Morgan, W.K. )

    1993-01-01

    The issue of carcinogenicity among mine workers and among workers in selected nonmining industries is examined. In the late 19th century, a high frequency of lung cancers was noted among metal miners in Bohemia, which probably related to their exposure to radon. Subsequently, other substances, including arsenic, asbestos, chromates, nickel, and chloroethers, have been linked causally to lung cancer. The IARC classification of substances as carcinogens is summarized, and the epidemiologic studies of humans employed in occupations with high rates of lung cancer due to carcinogen exposures are reviewed. 146 refs.

  10. Hydraulic mining method

    DOEpatents

    Huffman, Lester H.; Knoke, Gerald S.

    1985-08-20

    A method of hydraulically mining an underground pitched mineral vein comprising drilling a vertical borehole through the earth's lithosphere into the vein and drilling a slant borehole along the footwall of the vein to intersect the vertical borehole. Material is removed from the mineral vein by directing a high pressure water jet thereagainst. The resulting slurry of mineral fragments and water flows along the slant borehole into the lower end of the vertical borehole from where it is pumped upwardly through the vertical borehole to the surface.

  11. Airflow obstruction and mining

    SciTech Connect

    Stenton, S.C.; Hendrick, D.J. )

    1993-01-01

    Bronchitis and emphysema have long been described as diseases of miners, but the precise contribution of occupational exposures to coal and other mine dusts in causing these disorders, as opposed to cofactors such as social class, environmental pollution, and cigarette smoking, has not been fully defined. Epidemiologic studies have attempted, with varying degrees of success, to determine the incidence and severity of chronic obstructive pulmonary diseases in miners as compared to the general population. The results from these studies, and those in other nonmining industries with dust exposures, are examined. 98 refs.

  12. Web data mining

    NASA Astrophysics Data System (ADS)

    Wibonele, Kasanda J.; Zhang, Yanqing

    2002-03-01

    A web data mining system using granular computing and ASP programming is proposed. This is a web based application, which allows web users to submit survey data for many different companies. This survey is a collection of questions that will help these companies develop and improve their business and customer service with their clients by analyzing survey data. This web application allows users to submit data anywhere. All the survey data is collected into a database for further analysis. An administrator of this web application can login to the system and view all the data submitted. This web application resides on a web server, and the database resides on the MS SQL server.

  13. Mineral mining installation

    SciTech Connect

    Plevak, L.; Weirich, W.

    1982-04-20

    A longwall mineral mining installation has a longwall conveyor and a plurality of roof support units positioned side-by-side at the goaf side of the conveyor. The hydraulic appliances of the roof support units, such as their hydraulic props, hydraulic advance rams and hydraulic control valves, are supplied with pressurized hydraulic fluid from hydraulic supply lines which run along the goaf side of the conveyor. A plurality of flat, platelike intermediate members are provided at the goaf side of the conveyor. These intermediate members are formed with internal ducts for feeding the hydraulic fluid from the supply lines to the hydraulic appliances of the roof support units.

  14. Prostate cancer invasion and metastasis: Insights from mining genomic data

    DOE PAGES

    Hudson, Bryan D.; Kulp, Kristen S.; Loots, Gabriela G.

    2013-07-22

    Prostate cancer (PCa) is the second most commonly diagnosed malignancy in men in the Western world and the second leading cause of cancer-related deaths among men worldwide. Although most cancers have the potential to metastasize under appropriate conditions, PCa favors the skeleton as a primary site of metastasis, suggesting that the bone microenvironment is conducive to its growth. PCa metastasis proceeds through a complex series of molecular events that include angiogenesis at the site of the original tumor, local migration within the primary site, intravasation into the blood stream, survival within the circulation, extravasation of the tumor cells to themore » target organ and colonization of those cells within the new site. In turn, each one of these steps involves a complicated chain of events that utilize multiple protein–protein interactions, protein signaling cascades and transcriptional changes. Despite the urgent need to improve current biomarkers for diagnosis, prognosis and drug resistance, advances have been slow. Global gene expression methods such as gene microarrays and RNA sequencing enable the study of thousands of genes simultaneously and allow scientists to examine molecular pathways of cancer pathogenesis. In this review, we summarize the current literature that explored high-throughput transcriptome analysis toward the advancement of biomarker discovery for PCa. Novel biomarkers are strongly needed to enable more accurate detection of PCa, improve prediction of tumor aggressiveness and facilitate the discovery of new therapeutic targets for tailored medicine. Furthermore, promising molecular markers identified from gene expression profiling studies include HPN, CLU1, WT1, WNT5A, AURKA and SPARC.« less

  15. Prostate cancer invasion and metastasis: Insights from mining genomic data

    SciTech Connect

    Hudson, Bryan D.; Kulp, Kristen S.; Loots, Gabriela G.

    2013-07-22

    Prostate cancer (PCa) is the second most commonly diagnosed malignancy in men in the Western world and the second leading cause of cancer-related deaths among men worldwide. Although most cancers have the potential to metastasize under appropriate conditions, PCa favors the skeleton as a primary site of metastasis, suggesting that the bone microenvironment is conducive to its growth. PCa metastasis proceeds through a complex series of molecular events that include angiogenesis at the site of the original tumor, local migration within the primary site, intravasation into the blood stream, survival within the circulation, extravasation of the tumor cells to the target organ and colonization of those cells within the new site. In turn, each one of these steps involves a complicated chain of events that utilize multiple protein–protein interactions, protein signaling cascades and transcriptional changes. Despite the urgent need to improve current biomarkers for diagnosis, prognosis and drug resistance, advances have been slow. Global gene expression methods such as gene microarrays and RNA sequencing enable the study of thousands of genes simultaneously and allow scientists to examine molecular pathways of cancer pathogenesis. In this review, we summarize the current literature that explored high-throughput transcriptome analysis toward the advancement of biomarker discovery for PCa. Novel biomarkers are strongly needed to enable more accurate detection of PCa, improve prediction of tumor aggressiveness and facilitate the discovery of new therapeutic targets for tailored medicine. Furthermore, promising molecular markers identified from gene expression profiling studies include HPN, CLU1, WT1, WNT5A, AURKA and SPARC.

  16. Bacterial genome mining of enzymatic tools for alkyne biosynthesis

    PubMed Central

    Zhu, Xuejun; Su, Michael; Manickam, Kadhirvel; Zhang, Wenjun

    2015-01-01

    The alkyne is an important functionality widely used in material science, pharmaceutical science, and chemical biology, but the importance of this functionality is contrasted by the very limited number of enzymes known to be involved in alkyne biosynthesis. We recently reported the first known carrier protein-dependent pathway for terminal alkyne formation, and in silico analysis suggested that this mechanism could be widespread in bacteria. In this paper, we screened additional homologous gene cassettes presumed to be involved in alkyne biosynthesis using both in vitro biochemical study and an E. coli-polyketide synthase (PKS) reporting system for in vivo analysis. We discovered and characterized a new terminal alkyne biosynthetic pathway comprised of TtuA, B, and C from Teredinibacter turnerae T7901. While the acyl-CoA ligase homolog (TtuA) demonstrated promiscuity in the activation and loading of medium-chain fatty acids onto the carrier protein (TtuC), the desaturase homolog (TtuB) showed stringent substrate specificity towards C10 fatty acyl moieties. In addition, TtuB was demonstrated to be a bifunctional desaturase/acetylenase that efficiently catalyzed two sequential O2-dependent dehydrogenation reactions. A novel terminal-alkyne bearing polyketide was further produced upon co-expression of ttuABC and a PKS gene in E. coli. The discovery and characterization of TtuA, B, and C provides us with a new bifunctional desaturase/acetylenase for mechanistic and structural study and expands the scarce enzyme inventory for the biosynthesis of the alkyne functionality, which has important applications in synthetic and chemical biology. PMID:26441143

  17. Investigating the control of chlorophyll degradation by genomic correlation mining

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 regulat...

  18. A comparative study of nitrilases identified by genome mining.

    PubMed

    Kaplan, Ondřej; Veselá, Alicja B; Petříčková, Alena; Pasquarelli, Fabrizia; Pičmanová, Martina; Rinágelová, Anna; Bhalla, Tek Chand; Pátek, Miroslav; Martínková, Ludmila

    2013-07-01

    Escherichia coli strains expressing different nitrilases transformed nitriles or KCN. Six nitrilases (from Aspergillus niger (2), A. oryzae, Neurospora crassa, Arthroderma benhamiae, and Nectria haematococca) were arylacetonitrilases, two enzymes (from A. niger and Penicillium chrysogenum) were cyanide hydratases and the others (from P. chrysogenum, P. marneffei, Gibberella moniliformis, Meyerozyma guilliermondi, Rhodococcus rhodochrous, and R. ruber) preferred (hetero)aromatic nitriles as substrates. Promising nitrilases for the transformation of industrially important substrates were found: the nitrilase from R. ruber for 3-cyanopyridine, 4-cyanopyridine and bromoxynil, the nitrilases from N. crassa and A. niger for (R,S)-mandelonitrile, and the cyanide hydratase from A. niger for KCN and 2-cyanopyridine.

  19. Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativa L.).

    PubMed

    Ashkani, Sadegh; Yusop, Mohd Rafii; Shabanimofrad, Mahmoodreza; Azady, Amin; Ghasemzadeh, Ali; Azizi, Parisa; Latif, Mohammad Abdul

    2015-01-01

    Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.

  20. Rational Emotive Behavior Therapy (REBT), Irrational and Rational Beliefs, and the Mental Health of Athletes

    PubMed Central

    Turner, Martin J.

    2016-01-01

    In this article Rational Emotive Behavior Therapy (REBT) is proposed as a potentially important framework for the understanding and promotion of mental health in athletes. Cognitive-behavioral approaches predominate in the provision of sport psychology, and often form the backbone of psychological skills training for performance enhancement and maintenance. But far from being solely performance-focused, the cognitive-behavioral approach to sport psychology can restore, promote, and maintain mental health. This review article presents REBT (Ellis, 1957), the original cognitive behavioral therapy, as a valuable approach to addressing mental health issues in sport. REBT holds that it is not events that directly cause emotions and behaviors. Rather, it is one’s beliefs about the events that lead to emotional and behavioral reactivity. Further, REBT distinguishes between rational and irrational beliefs, and suggests that in response to failure, maltreatment, and misfortune, people can react with either healthy or unhealthy emotional and behavioral responses. The extant research indicates that irrational beliefs lead to unhealthy negative emotions, a range of pathological conditions, and a host of maladaptive behaviors that undermine mental health. Therefore, REBT proposes a process for the reduction of irrational beliefs and the promotion of rational beliefs. The use of REBT in sport is seldom reported in literature, but research is growing. This review article proposes three important areas of investigation that will aid the understanding of irrational beliefs and the application of REBT within sport. These areas are: (1) the influence of irrational beliefs and REBT on the mental health of athletes, (2) the influence of irrational beliefs and REBT on athletic performance, (3) the origins and development of irrational beliefs in athletes. Each area is discussed in turn, offering a critical and progressive review of the literature as well as highlighting research