WorldWideScience

Sample records for cereal genomics resources

  1. Next Generation Characterisation of Cereal Genomes for Marker Discovery

    OpenAIRE

    Paul Visendi; Jacqueline Batley; David Edwards

    2013-01-01

    Cereal crops form the bulk of the world’s food sources, and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis o...

  2. CerealsDB 2.0: an integrated resource for plant breeders and scientists

    Directory of Open Access Journals (Sweden)

    Wilkinson Paul A

    2012-09-01

    Full Text Available Abstract Background Food security is an issue that has come under renewed scrutiny amidst concerns that substantial yield increases in cereal crops are required to feed the world’s booming population. Wheat is of fundamental importance in this regard being one of the three most important crops for both human consumption and livestock feed; however, increase in crop yields have not kept pace with the demands of a growing world population. In order to address this issue, plant breeders require new molecular tools to help them identify genes for important agronomic traits that can be introduced into elite varieties. Studies of the genome using next-generation sequencing enable the identification of molecular markers such as single nucleotide polymorphisms that may be used by breeders to identify and follow genes when breeding new varieties. The development and application of next-generation sequencing technologies has made the characterisation of SNP markers in wheat relatively cheap and straightforward. There is a growing need for the widespread dissemination of this information to plant breeders. Description CerealsDB is an online resource containing a range of genomic datasets for wheat (Triticum aestivum that will assist plant breeders and scientists to select the most appropriate markers for marker assisted selection. CerealsDB includes a database which currently contains in excess of 100,000 putative varietal SNPs, of which several thousand have been experimentally validated. In addition, CerealsDB contains databases for DArT markers and EST sequences, and links to a draft genome sequence for the wheat variety Chinese Spring. Conclusion CerealsDB is an open access website that is rapidly becoming an invaluable resource within the wheat research and plant breeding communities.

  3. Prospects for advancing defense to cereal rusts through genetical genomics.

    Science.gov (United States)

    Ballini, Elsa; Lauter, Nick; Wise, Roger

    2013-01-01

    Rusts are one of the most severe threats to cereal crops because new pathogen races emerge regularly, resulting in infestations that lead to large yield losses. In 1999, a new race of stem rust, Puccinia graminis f. sp. tritici (Pgt TTKSK or Ug99), was discovered in Uganda. Most of the wheat and barley cultivars grown currently worldwide are susceptible to this new race. Pgt TTKSK has already spread northward into Iran and will likely spread eastward throughout the Indian subcontinent in the near future. This scenario is not unique to stem rust; new races of leaf rust (Puccinia triticina) and stripe rust (Puccinia striiformis) have also emerged recently. One strategy for countering the persistent adaptability of these pathogens is to stack complete- and partial-resistance genes, which requires significant breeding efforts in order to reduce deleterious effects of linkage drag. These varied resistance combinations are typically more difficult for the pathogen to defeat, since they would be predicted to apply lower selection pressure. Genetical genomics or expression Quantitative Trait Locus (eQTL) analysis enables the identification of regulatory loci that control the expression of many to hundreds of genes. Integrated deployment of these technologies coupled with efficient phenotyping offers significant potential to elucidate the regulatory nodes in genetic networks that orchestrate host defense responses. The focus of this review will be to present advances in genetical genomic experimental designs and analysis, particularly as they apply to the prospects for discovering partial disease resistance alleles in cereals.

  4. The Genome Atlas Resource

    OpenAIRE

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik; Hansson, Lena; Ussery, David

    2010-01-01

    Abstract. The Genome Atlas is a resource for addressing the challenges of synchronising prokaryotic genomic sequence data from multiple public repositories. This resource can integrate bioinformatic analyses in various data format and quality. Existing open source tools have been used together with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The r...

  5. Prospects for Advancing Defense to Cereal Rusts through Genetical Genomics

    Directory of Open Access Journals (Sweden)

    Elsa eBallini

    2013-05-01

    Full Text Available Rusts are one of the most severe threats to cereal crops because new pathogen races emerge regularly, resulting in infestations that lead to large yield losses. In 1999, a new race of stem rust, Puccinia graminis f. sp. tritici (Pgt TTKSK or Ug99, was discovered in Uganda. Most of the wheat and barley cultivars grown currently worldwide are susceptible to this new race. Pgt TTKSK has already spread northward into Iran and will likely spread eastward throughout the Indian subcontinent in the near future. This scenario is not unique to stem rust; new races of leaf rust (Puccinia triticina and stripe rust (Puccinia striiformis have also emerged recently. One strategy for countering the persistent adaptability of these pathogens is to stack complete- and partial-resistance genes, which requires significant breeding efforts in order to reduce deleterious effects of linkage drag. These varied resistance combinations are typically more difficult for the pathogen to defeat, since they would be predicted to apply lower selection pressure. Genetical genomics or expression Quantitative Trait Locus (eQTL analysis enables the identification of regulatory loci that control the expression of many to hundreds of genes. Integrated deployment of these technologies coupled with efficient phenotyping offers significant potential to elucidate the regulatory nodes in genetic networks that orchestrate host defense responses. The focus of this review will be to present advances in genetical genomic experimental designs and analysis, particularly as they apply to the prospects for discovering partial disease resistance alleles in cereals.

  6. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik;

    2010-01-01

    Abstract. The Genome Atlas is a resource for addressing the challenges of synchronising prokaryotic genomic sequence data from multiple public repositories. This resource can integrate bioinformatic analyses in various data format and quality. Existing open source tools have been used together...... with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  7. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

    DEFF Research Database (Denmark)

    Zhao, Wenming; Wang, Jing; He, Ximiao;

    2004-01-01

    . In addition to comprehensive data from Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS also hosts carefully curated genome information from Oryza sativa L. ssp. japonica and EST sequences available from other cereal crops. In this resource, sequence contigs of indica (93-11) have been further assembled......Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate...... the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGI-RIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis...

  8. WheatGenome.info: A Resource for Wheat Genomics Resource.

    Science.gov (United States)

    Lai, Kaitao

    2016-01-01

    An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ . PMID:26519407

  9. Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals

    Directory of Open Access Journals (Sweden)

    Megan C Shelden

    2013-05-01

    Full Text Available Abiotic stresses such as low water availability and high salinity are major causes of cereal crop yield losses and significantly impact on sustainability. Wheat and barley are two of the most important cereal crops (after maize and rice and are grown in increasingly hostile environments with soil salinity and drought both expected to increase this century, reducing the availability of arable land. Barley and wheat are classified as glycophytes (salt-sensitive, yet they are more salt-tolerant than other cereal crops such as rice and so are good models for studying salt-tolerance in cereals. The exploitation of genetic variation of phenotypic traits through plant breeding could significantly improve growth of cereals in salinity-affected regions, thus leading to improved crop yields. Genetic variation in phenotypic traits for abiotic stress tolerance have been identified in land races and wild germplasm but the molecular basis of these differences is often difficult to determine due to the complex genetic nature of these species. High-throughput functional genomics technologies, such as transcriptomics, metabolomics, proteomics and ionomics are powerful tools for investigating the molecular responses of plants to abiotic stress. The advancement of these technologies has allowed for the identification and quantification of transcript /metabolites in specific cell types and/or tissues. Using these new technologies on plants will provide a powerful tool to uncovering genetic traits in more complex species such as wheat and barley and provide novel insights into the molecular mechanisms of salinity stress tolerance.

  10. Discrimination of Repetitive Sequences Polymorphism in Secale cereale by Genomic In Situ Hybridization-Banding

    Institute of Scientific and Technical Information of China (English)

    Jian-Ping Zhou; Zu-Jun Yang; Guang-Rong Li; Cheng Liu; Zheng-Long Ren

    2008-01-01

    Genomic in situ hybridization banding (GISH-banding), a technique slightly modified from conventional GISH, was used to probe the Chinese native rye (Secale cereale L.) DNA, and enabled us to visualize the Individual rye chromosomes and create a universal reference karyotype of the S. cereale chromosome 1R to 7R. The GISH-banding approach used in the present study was able to discriminate S. cereale chromosomes or segments in the wheat (Triticum aeativum L.) background, including the Triticale, wheat-rye addition and translocation lines. Moreover, the GISH-banding pattern of S.cereale subsp. Afghanicum chromosomes was consistent with that of Chinese native rye cv. Jingzhou rye; whereas the GISH-banding pattem of Secale vavilovli was different from that of S. cereale, indicating that GISH-banding can be used to study evolutionary polymorphism in species or subspecies of Secale. In addition, the production and application of GISH-banding to the study of adenine-thymine-riched heterochromatin is discussed.

  11. Balkan cereals genetic resources in collection of Vavilov Institute of Plant Industry and main directions of cereals breeding in Russia

    OpenAIRE

    LOSKUTOV, Igor

    2014-01-01

    Analysis of information about Balkan cereals collection in VIR passport database is presented. The paper offers the long-term data on the collection of cereal forage crops (barley, oat) studied under diverse conditions at experiment stations of VIR. The selected sources of economically important traits that can be used for main direction of cereal forages breeding are presented

  12. Genomic Resources for Cancer Epidemiology

    Science.gov (United States)

    This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.

  13. Fungal genome resources at NCBI.

    Science.gov (United States)

    Robbertse, B; Tatusova, T

    2011-09-01

    The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools. PMID:22737589

  14. Fungal genome resources at NCBI

    OpenAIRE

    Robbertse, B.; Tatusova, T.

    2011-01-01

    The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/...

  15. Increased understanding of the cereal phytase complement for better mineral bio-availability and resource management

    DEFF Research Database (Denmark)

    Brinch-Pedersen, Henrik; Madsen, Claus Krogh; Holme, Inger Bæksted;

    2014-01-01

    for the bio-availability of micronutrients in human nutrition. The composition and levels of mature grain phytase activity (MGPA) in cereals is of central importance for efficient phytate hydrolysis. The MGPA varies considerably between species. Substantial activity is present in Triticeae tribe cereals like...

  16. NIMH Repository and Genomics Resources (RGR)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The NIMH Repository and Genomics Resource (RGR) stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies....

  17. Resources | Office of Cancer Genomics

    Science.gov (United States)

    OCG provides a variety of scientific and educational resources for both cancer researchers and members of the general public. These resources are divided into the following types: OCG-Supported Resources: Tools, databases, and reagents generated by initiated and completed OCG programs for researchers, educators, and students. (Note: Databases for current OCG programs are available through program-specific data matrices)

  18. Developing genomic resources for the apiaceae

    Science.gov (United States)

    The Apiaceae family includes carrot, celery, cilantro, dill, fennel and numerous other spice and medicinal crops. Carrot is the most economically important member of the Apiaceae with an annual value of $600 M in the United States alone. There are few genomic resources for carrot or other Apiaceae, ...

  19. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution.

    Science.gov (United States)

    Quraishi, Umar Masood; Abrouk, Michael; Murat, Florent; Pont, Caroline; Foucrier, Séverine; Desmaizieres, Gregory; Confolent, Carole; Rivière, Nathalie; Charmet, Gilles; Paux, Etienne; Murigneux, Alain; Guerreiro, Laurent; Lafarge, Stéphane; Le Gouis, Jacques; Feuillet, Catherine; Salse, Jerome

    2011-03-01

    Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.

  20. BREAKFAST CEREALS

    Science.gov (United States)

    This chapter written for the Encyclopedia of Food Sciences and Nutrition summarizes the Cereal Breakfast industry in world up to 2003. The areas covered are the brief history of cereal processing, their classification i.e., ready to eat or hot cereals and their processing methods. It covers the re...

  1. Modeling branching in cereals

    OpenAIRE

    Jochem B. Evers; Vos, Jan

    2013-01-01

    Cereals and grasses adapt their structural development to environmental conditions and the resources available. The primary adaptive response is a variable degree of branching, called tillering in cereals. Especially for heterogeneous plant configurations the degree of tillering varies per plant. Functional–structural plant modeling (FSPM) is a modeling approach allowing simulation of the architectural development of individual plants, culminating in the emergent behavior at the canopy level....

  2. MycoCosm, an Integrated Fungal Genomics Resource

    Energy Technology Data Exchange (ETDEWEB)

    Shabalov, Igor; Grigoriev, Igor

    2012-03-16

    MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

  3. The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse

    OpenAIRE

    Blake, Judith A.; Eppig, Janan T.; Richardson, Joel E.; Davisson, Muriel T.; the Mouse Genome Database Group,

    2000-01-01

    The Mouse Genome Database (MGD) is a comprehensive public database of mouse genomic, genetic and phenotypic information (http://www.informatics.jax.org ). This community database provides information about genes, serves as a mapping resource of the mouse genome, details mammalian orthologs, integrates experimental data, represents standardized mouse nomenclature for genes and alleles, incorporates links to other genomic resources such as sequence data, and includes a variety of additional inf...

  4. BrucellaBase: Genome information resource.

    Science.gov (United States)

    Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Khader, L K M Abdul; Sridhar, Jayavel; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

    2016-09-01

    Brucella sp. causes a major zoonotic disease, brucellosis. Brucella belongs to the family Brucellaceae under the order Rhizobiales of Alphaproteobacteria. We present BrucellaBase, a web-based platform, providing features of a genome database together with unique analysis tools. We have developed a web version of the multilocus sequence typing (MLST) (Whatmore et al., 2007) and phylogenetic analysis of Brucella spp. BrucellaBase currently contains genome data of 510 Brucella strains along with the user interfaces for BLAST, VFDB, CARD, pairwise genome alignment and MLST typing. Availability of these tools will enable the researchers interested in Brucella to get meaningful information from Brucella genome sequences. BrucellaBase will regularly be updated with new genome sequences, new features along with improvements in genome annotations. BrucellaBase is available online at http://www.dbtbrucellosis.in/brucellabase.html or http://59.99.226.203/brucellabase/homepage.html. PMID:27164438

  5. Increasing the Profitability of Energy Cereals by Modifying the Cultivation System; Spannmaal till energi - oekad loensamhet genom anpassning av odlingssystemet

    Energy Technology Data Exchange (ETDEWEB)

    Gunnarsson, Carina; Olsson, Johanna; Lundin, Gunnar; Toro, Alfredo de

    2008-09-15

    The use of cereals and other agricultural crops for energy purposes and the increased demand for food world-wide have increased cereal prices. However since energy prices have also increased, it can still be profitable to use cereals for energy production. To date, the cereals used for bioenergy have usually been grown in the same way as food and feed cereals, but there is scope to tailor the cultivation system to the end product. The overall objective of this project was to improve the profitability of cereal cultivation for energy purposes. Changes to the cultivation system in terms of e.g. choice of crop and cultivar, strategies for fertilisation and crop protection and transport/handling of cereals for bioethanol production or combustion were studied. Timeliness costs associated with bioenergy cereals were also examined. The financial impact of changes in the cultivation system for bioenergy cereals was then examined for three typical farms, located in the provinces of Skaane, Oestergoetland and Uppland. Based on the results obtained, concrete guidelines for farmers were formulated. The average arable area of the typical farms was 203 ha, the farms had a seven-year crop rotation and for all locations winter wheat was the dominant crop but triticale and oats were also included. Two cultivation systems, Traditional and Energy, were examined. In the Energy cultivation system, the winter wheat and triticale were used for bioethanol production in an ethanol plant located in Norrkoeping (Oestergoetland), while the oats were used for combustion in plants close to the typical farms. The results showed that cultivation of bioenergy cereals did not differ greatly from cultivation of food/feed cereals. However, when cultivating cereals for bioethanol production it is important to adapt the nitrogen fertilisation strategy to achieve high starch content together with high yields of the specific cultivar grown. The most important change in the Energy system proved to be

  6. CottonDB: A resource for cotton genome research

    Science.gov (United States)

    CottonDB (http://cottondb.org/) is a database and web resource for cotton genomic and genetic research. Created in 1995, CottonDB was among the first plant genome databases established by the USDA-ARS. Accessed through a website interface, the database aims to be a convenient, inclusive medium of ...

  7. Gramene 2016: comparative plant genomics and pathway resources.

    Science.gov (United States)

    Tello-Ruiz, Marcela K; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A; Huerta, Laura; Keays, Maria; Tang, Y Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J; Jaiswal, Pankaj; Ware, Doreen

    2016-01-01

    Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. PMID:26553803

  8. Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus.

    Science.gov (United States)

    Tamborindeguy, Cecilia; Bereman, Michael S; DeBlasio, Stacy; Igwe, David; Smith, Dawn M; White, Frank; MacCoss, Michael J; Gray, Stewart M; Cilia, Michelle

    2013-01-01

    Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification of aphid genes and proteins mediating virus transmission is critical to develop agriculturally sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Two cyclophilin B proteins, S28 and S29, were identified previously in populations of Schizaphisgraminum that differed in their ability to transmit the RPV strain of Cereal yellow dwarf virus (CYDV-RPV). The presence of S29 was correlated with F2 genotypes that were efficient virus transmitters. The present study revealed the two proteins were isoforms, and a single amino acid change distinguished S28 and S29. The distribution of the two alleles was determined in 12 F2 genotypes segregating for CYDV-RPV transmission capacity and in 11 genetically independent, field-collected S. graminum biotypes. Transmission efficiency for CYDV-RPV was determined in all genotypes and biotypes. The S29 isoform was present in all genotypes or biotypes that efficiently transmit CYDV-RPV and more specifically in genotypes that efficiently transport virus across the hindgut. We confirmed a direct interaction between CYDV-RPV and both S28 and S29 using purified virus and bacterially expressed, his-tagged S28 and S29 proteins. Importantly, S29 failed to interact with a closely related virus that is transported across the aphid midgut. We tested for in vivo interactions using an aphid-virus co-immunoprecipitation strategy coupled with a bottom-up LC-MS/MS analysis using a Q Exactive mass spectrometer. This analysis enabled us to identify a third cyclophilin protein, cyclophilin A, interacting directly or in complex with purified CYDV-RPV. Taken together, these data provide evidence that both cyclophilin A and B interact with CYDV-RPV, and these interactions may be important but not sufficient to mediate virus transport

  9. Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus.

    Directory of Open Access Journals (Sweden)

    Cecilia Tamborindeguy

    Full Text Available Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification of aphid genes and proteins mediating virus transmission is critical to develop agriculturally sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Two cyclophilin B proteins, S28 and S29, were identified previously in populations of Schizaphisgraminum that differed in their ability to transmit the RPV strain of Cereal yellow dwarf virus (CYDV-RPV. The presence of S29 was correlated with F2 genotypes that were efficient virus transmitters. The present study revealed the two proteins were isoforms, and a single amino acid change distinguished S28 and S29. The distribution of the two alleles was determined in 12 F2 genotypes segregating for CYDV-RPV transmission capacity and in 11 genetically independent, field-collected S. graminum biotypes. Transmission efficiency for CYDV-RPV was determined in all genotypes and biotypes. The S29 isoform was present in all genotypes or biotypes that efficiently transmit CYDV-RPV and more specifically in genotypes that efficiently transport virus across the hindgut. We confirmed a direct interaction between CYDV-RPV and both S28 and S29 using purified virus and bacterially expressed, his-tagged S28 and S29 proteins. Importantly, S29 failed to interact with a closely related virus that is transported across the aphid midgut. We tested for in vivo interactions using an aphid-virus co-immunoprecipitation strategy coupled with a bottom-up LC-MS/MS analysis using a Q Exactive mass spectrometer. This analysis enabled us to identify a third cyclophilin protein, cyclophilin A, interacting directly or in complex with purified CYDV-RPV. Taken together, these data provide evidence that both cyclophilin A and B interact with CYDV-RPV, and these interactions may be important but not sufficient to mediate

  10. PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    Bansal Manju

    2011-07-01

    Full Text Available Abstract Background As more and more genomes are being sequenced, an overview of their genomic features and annotation of their functional elements, which control the expression of each gene or transcription unit of the genome, is a fundamental challenge in genomics and bioinformatics. Findings Relative stability of DNA sequence has been used to predict promoter regions in 913 microbial genomic sequences with GC-content ranging from 16.6% to 74.9%. Irrespective of the genome GC-content the relative stability based promoter prediction method has already been proven to be robust in terms of recall and precision. The predicted promoter regions for the 913 microbial genomes have been accumulated in a database called PromBase. Promoter search can be carried out in PromBase either by specifying the gene name or the genomic position. Each predicted promoter region has been assigned to a reliability class (low, medium, high, very high and highest based on the difference between its average free energy and the downstream region. The recall and precision values for each class are shown graphically in PromBase. In addition, PromBase provides detailed information about base composition, CDS and CG/TA skews for each genome and various DNA sequence dependent structural properties (average free energy, curvature and bendability in the vicinity of all annotated translation start sites (TLS. Conclusion PromBase is a database, which contains predicted promoter regions and detailed analysis of various genomic features for 913 microbial genomes. PromBase can serve as a valuable resource for comparative genomics study and help the experimentalist to rapidly access detailed information on various genomic features and putative promoter regions in any given genome. This database is freely accessible for academic and non- academic users via the worldwide web http://nucleix.mbu.iisc.ernet.in/prombase/.

  11. Harnessing the sorghum genome sequence:development of a genome-wide microsattelite (SSR) resource for swift genetic mapping and map based cloning in sorghum

    Science.gov (United States)

    Sorghum is the second cereal crop to have a full genome completely sequenced (Nature (2009), 457:551). This achievement is widely recognized as a scientific milestone for grass genetics and genomics in general. However, the true worth of genetic information lies in translating the sequence informa...

  12. Building a model: developing genomic resources for common milkweed (Asclepias syriaca with low coverage genome sequencing

    Directory of Open Access Journals (Sweden)

    Weitemier Kevin

    2011-05-01

    Full Text Available Abstract Background Milkweeds (Asclepias L. have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L. could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp and 5S rDNA (120 bp sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp, with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae unigenes (median coverage of 0.29× and 66% of single copy orthologs (COSII in asterids (median coverage of 0.14×. From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites and phylogenetics (low-copy nuclear genes studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species

  13. Genome resource for the Indonesian coelacanth, Latimeria menadoensis.

    Science.gov (United States)

    Danke, Joshua; Miyake, Tsutomu; Powers, Thomas; Schein, Jacqueline; Shin, Heesun; Bosdet, Ian; Erdmann, Mark; Caldwell, Roy; Amemiya, Chris T

    2004-03-01

    We have generated a BAC library from the Indonesian coelacanth, Latimeria menadoensis. This library was generated using genomic DNA of nuclei isolated from heart tissue, and has an average insert size of 171 kb. There are a total of 288 384-well microtiter dishes in the library (110,592 clones) and its genomic representation is estimated to encompass > or = 7X coverage based on the amount of DNA presumably cloned in the library as well as via hybridization with probes to a small set of single copy genes. This genomic resource has been made available to the public and should prove useful to the scientific community for many applications, including comparative genomics, molecular evolution and conservation genetics.

  14. Genomic resource development for shellfish of conservation concern.

    Science.gov (United States)

    Timmins-Schiffman, Emma B; Friedman, Carolyn S; Metzger, Dave C; White, Samuel J; Roberts, Steven B

    2013-03-01

    Effective conservation of threatened species depends on the ability to assess organism physiology and population demography. To develop genomic resources to better understand the dynamics of two ecologically vulnerable species in the Pacific Northwest of the United States, larval transcriptomes were sequenced for the pinto abalone, Haliotis kamtschatkana kamtschatkana, and the Olympia oyster, Ostrea lurida. Based on comparative species analysis the Ostrea lurida transcriptome (41 136 contigs) is relatively complete. These transcriptomes represent the first significant contribution to genomic resources for both species. Genes are described based on biological function with particular attention to those associated with temperature change, oxidative stress and immune function. In addition, transcriptome-derived genetic markers are provided. Together, these resources provide valuable tools for future studies aimed at conservation of Haliotis kamtschatkana kamtschatkana, Ostrea lurida and related species.

  15. Quantitative prediction of genome-wide resource allocation in bacteria.

    Science.gov (United States)

    Goelzer, Anne; Muntel, Jan; Chubukov, Victor; Jules, Matthieu; Prestel, Eric; Nölker, Rolf; Mariadassou, Mahendra; Aymerich, Stéphane; Hecker, Michael; Noirot, Philippe; Becher, Dörte; Fromion, Vincent

    2015-11-01

    Predicting resource allocation between cell processes is the primary step towards decoding the evolutionary constraints governing bacterial growth under various conditions. Quantitative prediction at genome-scale remains a computational challenge as current methods are limited by the tractability of the problem or by simplifying hypotheses. Here, we show that the constraint-based modeling method Resource Balance Analysis (RBA), calibrated using genome-wide absolute protein quantification data, accurately predicts resource allocation in the model bacterium Bacillus subtilis for a wide range of growth conditions. The regulation of most cellular processes is consistent with the objective of growth rate maximization except for a few suboptimal processes which likely integrate more complex objectives such as coping with stressful conditions and survival. As a proof of principle by using simulations, we illustrated how calibrated RBA could aid rational design of strains for maximizing protein production, offering new opportunities to investigate design principles in prokaryotes and to exploit them for biotechnological applications. PMID:26498510

  16. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

    OpenAIRE

    Fei, Zhangjun; Joung, Je-Gun; Tang, Xuemei; Zheng, Yi; Huang, Mingyun; Lee, Je Min; McQuinn, Ryan; Tieman, Denise M.; Alba, Rob; Klee, Harry J.; Giovannoni, James J

    2010-01-01

    Tomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. The database is functionally expanded from the previously described Tomato Expression Database by including metabolite profiles as well as large-scale tomato small RNA (sRNA) data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database, respe...

  17. Physical Analysis of the Complex Rye (Secale cereale L.) Alt4 Aluminium (Aluminum) Tolerance Locus Using a Whole-Genome BAC Library of Rye cv. Blanco

    Science.gov (United States)

    Rye is a diploid crop species with many outstanding qualities, and is also important as a source of new traits for wheat and triticale improvement. Here we describe a BAC library of rye cv. Blanco, representing a valuable resource for rye molecular genetic studies. The library provides a 6 × genome ...

  18. AgBase: a functional genomics resource for agriculture

    Directory of Open Access Journals (Sweden)

    Hill David P

    2006-09-01

    Full Text Available Abstract Background Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. Description To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource http://www.agbase.msstate.edu for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO. The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes, return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. Conclusion The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to

  19. The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

    DEFF Research Database (Denmark)

    Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben;

    2013-01-01

    (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to...... assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The...

  20. MorusDB: a resource for mulberry genomics and genome biology.

    Science.gov (United States)

    Li, Tian; Qi, Xiwu; Zeng, Qiwei; Xiang, Zhonghuai; He, Ningjia

    2014-01-01

    Mulberry is an important cultivated plant that has received the attention of biologists interested in sericulture and plant-insect interaction. Morus notabilis, a wild mulberry species with a minimal chromosome number is an ideal material for whole-genome sequencing and assembly. The genome and transcriptome of M. notabilis were sequenced and analyzed. In this article, a web-based and open-access database, the Morus Genome Database (MorusDB), was developed to enable easy-to-access and data mining. The MorusDB provides an integrated data source and an easy accession of mulberry large-scale genomic sequencing and assembly, predicted genes and functional annotations, expressed sequence tags (ESTs), transposable elements (TEs), Gene Ontology (GO) terms, horizontal gene transfers between mulberry and silkworm and ortholog and paralog groups. Transcriptome sequencing data for M. notabilis root, leaf, bark, winter bud and male flower can also be searched and downloaded. Furthermore, MorusDB provides an analytical workbench with some built-in tools and pipelines, such as BLAST, Search GO, Mulberry GO and Mulberry GBrowse, to facilitate genomic studies and comparative genomics. The MorusDB provides important genomic resources for scientists working with mulberry and other Moraceae species, which include many important fruit crops. Designed as a basic platform and accompanied by the SilkDB, MorusDB strives to be a comprehensive platform for the silkworm-mulberry interaction studies. Database URL: http://morus.swu.edu.cn/morusdb.

  1. Floral gene resources from basal angiosperms for comparative genomics research

    Directory of Open Access Journals (Sweden)

    Zhang Xiaohong

    2005-03-01

    Full Text Available Abstract Background The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. Results Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04 generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii many known floral gene homologues have been captured, and (iii phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. Conclusion Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage

  2. Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies.

    Science.gov (United States)

    Varshney, R K; Beier, U; Khlestkina, E K; Kota, R; Korzun, V; Graner, A; Börner, A

    2007-04-01

    To elucidate the potential of single nucleotide polymorphism (SNP) markers in rye, a set of 48 barley EST (expressed sequence tag) primer pairs was employed to amplify from DNA prepared from five rye inbred lines. A total of 96 SNPs and 26 indels (insertion-deletions) were defined from the sequences of 14 of the resulting amplicons, giving an estimated frequency of 1 SNP per 58 bp and 1 indel per 214 bp in the rye transcriptome. A mean of 3.4 haplotypes per marker with a mean expected heterozygosity of 0.66 were observed. The nucleotide diversity index (pi) was estimated to be in the range 0.0059-0.0530. To improve assay cost-effectiveness, 12 of the 14 SNPs were converted to a cleaved amplified polymorphic sequence (CAPS) format. The resulting 12 SNP loci mapped to chromosomes 1R, 3R, 4R, 5R, 6R, and 7R, at locations consistent with their known map positions in barley. SNP genotypic data were compared with genomic simple sequence repeat (SSR) and EST-derived SSR genotypic data collected from the same templates. This showed a broad equivalence with respect to genetic diversity between these different data types. PMID:17345059

  3. Genomic characterization of the aquaculture resource Mytilus galloprovincialis

    Directory of Open Access Journals (Sweden)

    Maria Murgarella

    2014-06-01

    Full Text Available In the autonomous community of Galicia (NW Spain, M. galloprovincialis is a natural resource of high economic importance to the economy of this region. More than 250,000 MTs of mussels are produced per year, representing 40% of the European production of this bivalve and 80% of the marine aquacultural production of the country. Besides its aquaculture interest, study of the biology M. galloprovincialis may also help to understand better fundamental aspects of molluscan biology. On the other hand, some fascinating features of mediterranean mussels are unique to this species such as its extraordinary resistance to diseases. In fact, in comparison with other bivalves, no records of massive mortality of this organism caused by pathogens has been reported so far. Although some of the molecular components of the innate immune system, responsible of this resistance, have been previously identified and characterized, the genetic mechanisms underlying their diversity are poorly understood. In order to understand better this organism at genome level and search for the genetic basis of its disease resistance, we sequenced its genome at high depth using Illumina technology. After assembling the resulting reads and assisted with transcriptomic data, we annotated its genome sequence. First, we analysed the content of repetitive elements, finding those that are common among molluscs as well as identifying new repeat families unique to M. galloprovincialis. Second, we predicted and annotated its gene repertoire, defining the total number of genes and their density in its genome. Finally, the resulting in silico predicted genes were functionally annotated. Altogether, this information will allow the identification of genes of interest, such as those participating in the innate immunity and will allow us to delve into the possibility of whether their variability has a genetic basis or relies on post-transcriptional events. In addition to this annotation, some

  4. Classifying Cereal Data

    Science.gov (United States)

    The DSQ includes questions about cereal intake and allows respondents up to two responses on which cereals they consume. We classified each cereal reported first by hot or cold, and then along four dimensions: density of added sugars, whole grains, fiber, and calcium.

  5. Learning about the Human Genome. Part 2: Resources for Science Educators. ERIC Digest.

    Science.gov (United States)

    Haury, David L.

    This ERIC Digest identifies how the human genome project fits into the "National Science Education Standards" and lists Human Genome Project Web sites found on the World Wide Web. It is a resource companion to "Learning about the Human Genome. Part 1: Challenge to Science Educators" (Haury 2001). The Web resources and instructional materials can…

  6. The Xenopus ORFeome: A resource that enables functional genomics.

    Science.gov (United States)

    Grant, Ian M; Balcha, Dawit; Hao, Tong; Shen, Yun; Trivedi, Prasad; Patrushev, Ilya; Fortriede, Joshua D; Karpinka, John B; Liu, Limin; Zorn, Aaron M; Stukenberg, P Todd; Hill, David E; Gilchrist, Michael J

    2015-12-15

    Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5' and 3' end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling. PMID:26391338

  7. Oxalate content of cereals and cereal products.

    Science.gov (United States)

    Siener, Roswitha; Hönow, Ruth; Voss, Susanne; Seidler, Ana; Hesse, Albrecht

    2006-04-19

    Detailed knowledge of food oxalate content is of essential importance for dietary treatment of recurrent calcium oxalate urolithiasis. Dietary oxalate can contribute considerably to the amount of urinary oxalate excretion. Because cereal foods play an important role in daily nutrition, the soluble and total oxalate contents of various types of cereal grains, milling products, bread, pastries, and pasta were analyzed using an HPLC-enzyme-reactor method. A high total oxalate content (>50 mg/100 g) was found in whole grain wheat species Triticum durum (76.6 mg/100 g), Triticum sativum (71.2 mg/100 g), and Triticum aestivum (53.3 mg/100 g). Total oxalate content was comparably high in whole grain products of T. aestivum, that is, wheat flakes and flour, as well as in whole grain products of T. durum, that is, couscous, bulgur, and pasta. The highest oxalate content was demonstrated for wheat bran (457.4 mg/100 g). The higher oxalate content in whole grain than in refined grain cereals suggests that oxalic acid is primarily located in the outer layers of cereal grains. Cereals and cereal products contribute to the daily oxalate intake to a considerable extent. Vegetarian diets may contain high amounts of oxalate when whole grain wheat and wheat products are ingested. Recommendations for prevention of recurrence of calcium oxalate stone disease have to take into account the oxalate content of these foodstuffs. PMID:16608223

  8. Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

    Directory of Open Access Journals (Sweden)

    Alessandro M. Varani

    2012-01-01

    Full Text Available The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.

  9. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics.

    Science.gov (United States)

    Fei, Zhangjun; Joung, Je-Gun; Tang, Xuemei; Zheng, Yi; Huang, Mingyun; Lee, Je Min; McQuinn, Ryan; Tieman, Denise M; Alba, Rob; Klee, Harry J; Giovannoni, James J

    2011-01-01

    Tomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. The database is functionally expanded from the previously described Tomato Expression Database by including metabolite profiles as well as large-scale tomato small RNA (sRNA) data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database, respectively, and TFGD provides downloads of all the analyzed results. TFGD is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces and analysis tools, including improved array probe annotations as well as tools to identify co-expressed genes, significantly affected biological processes and biochemical pathways from gene expression data sets and miRNA targets, and to integrate transcript and metabolite profiles, and sRNA and mRNA sequences. The suite of tools and interfaces in TFGD allow intelligent data mining of recently released and continually expanding large-scale tomato functional genomics data sets. TFGD is available at http://ted.bti.cornell.edu. PMID:20965973

  10. GDR (Genome Database for Rosaceae: integrated web resources for Rosaceae genomics and genetics research

    Directory of Open Access Journals (Sweden)

    Ficklin Stephen

    2004-09-01

    Full Text Available Abstract Background Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. Description The Genome Database for Rosaceae (GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. Conclusions The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

  11. The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.

    Science.gov (United States)

    Arnaud, Martha B; Chibucos, Marcus C; Costanzo, Maria C; Crabtree, Jonathan; Inglis, Diane O; Lotia, Adil; Orvis, Joshua; Shah, Prachi; Skrzypek, Marek S; Binkley, Gail; Miyasato, Stuart R; Wortman, Jennifer R; Sherlock, Gavin

    2010-01-01

    The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at aspergillus-curator@genome.stanford.edu.

  12. The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome.

    Science.gov (United States)

    Sjödin, Andreas; Street, Nathaniel Robert; Sandberg, Göran; Gustafsson, Petter; Jansson, Stefan

    2009-06-01

    Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at www.popgenie.org or via www.populusgenome.info.

  13. A new genomic resource dedicated to wood formation in Eucalyptus

    Directory of Open Access Journals (Sweden)

    Couloux Arnaud

    2009-03-01

    Full Text Available Abstract Background Renowned for their fast growth, valuable wood properties and wide adaptability, Eucalyptus species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly. Thus, there is huge potential for marker-assisted breeding programs to improve traits such as wood properties. To this end, the sequencing, analysis and annotation of a large collection of expressed sequences tags (ESTs from genes involved in wood formation in Eucalyptus would provide a valuable resource. Results We report here the normalization and sequencing of a cDNA library from developing Eucalyptus secondary xylem, as well as the construction and sequencing of two subtractive libraries (juvenile versus mature wood and vice versa. A total of 9,222 high quality sequences were collected from about 10,000 cDNA clones. The EST assembly generated a set of 3,857 wood-related unigenes including 2,461 contigs (Cg and 1,396 singletons (Sg that we named 'EUCAWOOD'. About 65% of the EUCAWOOD sequences produced matches with poplar, grapevine, Arabidopsis and rice protein sequence databases. BlastX searches of the Uniref100 protein database allowed us to allocate gene ontology (GO and protein family terms to the EUCAWOOD unigenes. This annotation of the EUCAWOOD set revealed key functional categories involved in xylogenesis. For instance, 422 sequences matched various gene families involved in biosynthesis and assembly of primary and secondary cell walls. Interestingly, 141 sequences were annotated as transcription factors, some of them being orthologs of regulators known to be involved in xylogenesis. The EUCAWOOD dataset was also mined for genomic simple sequence repeat markers, yielding a total of 639 putative microsatellites. Finally, a publicly accessible database was created, supporting multiple queries on the EUCAWOOD dataset. Conclusion In this work, we have identified a

  14. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

    NARCIS (Netherlands)

    L. Shen (Lishuang); M.A. Diroma (Maria Angela); M. Gonzalez (Michael); D. Navarro-Gomez (Daniel); J. Leipzig (Jeremy); M.T. Lott (Marie T.); M. van Oven (Mannis); D.C. Wallace; C.C. Muraresku (Colleen Clarke); Z. Zolkipli-Cunningham (Zarazuela); P.F. Chinnery (Patrick); M. Attimonelli (Marcella); S. Zuchner (Stephan); M.J. Falk (Marni J.); X. Gai (Xiaowu)

    2016-01-01

    textabstractMSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, gene

  15. Generation of EST and Microarray Resources for Functional Genomic Studies on Chicken Intestinal Health

    NARCIS (Netherlands)

    Hemert, van S.; Ebbelaar, B.H.; Smits, M.A.; Rebel, J.M.J.

    2003-01-01

    Expressed sequenced tags (ESTs) and microarray resources have a great impact on the ability to study host response in mice and humans. Unfortunately, these resources are not yet available for domestic farm animals. The aim of this study was to provide genomic resources to study chicken intestinal he

  16. Cereal Crops Research Unit

    Data.gov (United States)

    Federal Laboratory Consortium — The mission of the Cereal Crops Research Unit is to 1) conduct basic research to identify and understand the biological processes affecting the growth, development...

  17. Cereals, Appropriability and Hierarchy

    OpenAIRE

    Mayshar, Joram; Moav, Omer; Neeman, Zvika; Pascali, Luigi

    2015-01-01

    We propose that the development of social hierarchy following the Neolithic Revolution was an outcome of the ability of the emergent elite to appropriate cereal crops from farmers and not a result of land productivity, as argued by conventional theory. We argue that cereals are easier to appropriate than roots and tubers, and that regional differences in the suitability of land for different crops explain therefore differences in the formation of hierarchy and states. A simple model illustrat...

  18. Cereal Box Design: An Interdisciplinary Graphics Activity

    Science.gov (United States)

    Fitzgerald, Mike; Tsosie, Teri

    2012-01-01

    The cereal box design activity is intriguing both for its simplicity and the resourcefulness that it can generate in young people. Also, it lends itself to a variety of curriculums. It covers both consumerism and Design for the Environment (DfE) concepts broadly and in depth. The activity introduces a wide range of topics. They include graphic…

  19. AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

    OpenAIRE

    Legeai, Fabrice; Shigenobu, Shuji; Gauthier, Jean-Pierre; Colbourne, John; Rispe, Claude; Collin, Olivier; Richards, Stephen; Wilson, Alex C. C.; Tagu, Denis

    2010-01-01

    AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search c...

  20. Application of gamma-irradiation to cereals and cereals products

    International Nuclear Information System (INIS)

    Gamma-irradiation may be used on cereals and cereal products to control insect infestation and microbiological problems. Such problems include mould growth, mycotoxin production, pathogens, spore-forming organisms and total microbial load. Deleterious effects of gamma-irradiation arise only at relatively high dose levels with consequences on germination rate, wheat flour dough properties, and cake and noodle quality. Radiation-induced changes to starch have greater impact on behaviour of cereal products than such changes to other cereal components

  1. Future cereal starch bioengineering

    DEFF Research Database (Denmark)

    Blennow, Andreas; Jensen, Susanne Langgård; Shaik, Shahnoor Sultana;

    2013-01-01

    data from cereal ancestors can potentially allow for the reintroduction of cereal traits including, for example, health-promoting carbohydrates that may have been lost during domestication. Raw materials produced in this manner can be processed by clean enzyme-assisted techniques or thermal treatment...... in combination to further functionalize or stabilize the starch polymers. Importantly, such products can be multifunctional in the sense of combined food/material or food/pharma purposes, for example, edible plastics, shape memory materials, and cycloamylose carriers and stabilizers for diverse bioactives......The importance of cereal starch production worldwide cannot be overrated. However, the qualities and resulting values of existing raw and processed starch do not fully meet future demands for environmentally friendly production of renewable, advanced biomaterials, functional foods, and biomedical...

  2. Trichothecenes in cereal grains.

    Science.gov (United States)

    Foroud, Nora A; Eudes, François

    2009-01-01

    Trichothecenes are sesquiterpenoid mycotoxins associated with fusarium head blight (FHB) of cereals, with worldwide economic and health impacts. While various management strategies have been proposed to reduce the mycotoxin risk, breeding towards FHB-resistance appears to be the most effective means to manage the disease, and reduce trichothecene contamination of cereal-based food products. This review provides a brief summary of the trichothecene synthesis in Fusarium species, their toxicity in plants and humans, followed by the current methods of screening and breeding for resistance to FHB and trichothecene accumulation.

  3. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    OpenAIRE

    GIGA Community of Scientists

    2013-01-01

    Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a la...

  4. Development in Rice Genome Research Based on Accurate Genome Sequence

    OpenAIRE

    2008-01-01

    Rice is one of the most important crops in the world. Although genetic improvement is a key technology for the acceleration of rice breeding, a lack of genome information had restricted efforts in molecular-based breeding until the completion of the high-quality rice genome sequence, which opened new opportunities for research in various areas of genomics. The syntenic relationship of the rice genome to other cereal genomes makes the rice genome invaluable for understanding how cereal genomes...

  5. The Integrated Microbial Genomes (IMG) System: An Expanding Comparative Analysis Resource

    Energy Technology Data Exchange (ETDEWEB)

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2009-09-13

    The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through regular releases. Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at .

  6. Online Genome Analysis Resources for Educators, a Comparative Review

    OpenAIRE

    Sarah Grace Prescott

    2012-01-01

    A comparative review of several companies that offer similar kits or services that allow students to isolate DNA (human and others), amplify it by PCR, and in some cases sequence the resulting sample.  The companies include:  Carolina® Biological Supply Company, Bio-Rad®, Edvotek® Inc., Hiram Genomics Store, and 23andMe.

  7. The Global Invertebrate Genomics Alliance (GIGA). 2014. Developing Community Resources to Study Diverse Invertebrate Genomes

    NARCIS (Netherlands)

    Pomponi, S.A.

    2014-01-01

    Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major cha

  8. Cereal Box Totems.

    Science.gov (United States)

    Jones, AnnMarie

    2002-01-01

    Presents a multicultural project used with fourth-grade students in which they created a three-dimensional totem pole using leftover cereal boxes. Discusses in detail how to create the totem pole. Explains that students learned about Northwest American Indians in class. (CMK)

  9. Vernalization in cereals

    OpenAIRE

    Dennis, Elizabeth S.; Peacock, W. James

    2009-01-01

    How vernalization – exposure to a period of cold – induces flowering in Arabidopsis has been intensively investigated at the genetic and moleular levels. Recent papers, including one in BMC Plant Biology, shed light on changes in gene regulation that occur on vernalization in cereals.

  10. Genetic Resources, Genome Mapping and Evolutionary Genomics of the Pig (Sus scrofa

    Directory of Open Access Journals (Sweden)

    Kefei Chen, Tara Baxter, William M. Muir, Martien A. Groenen, Lawrence B. Schook

    2007-01-01

    Full Text Available The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X. As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.

  11. Online Genome Analysis Resources for Educators, a Comparative Review

    Directory of Open Access Journals (Sweden)

    Sarah Grace Prescott

    2012-08-01

    Full Text Available A comparative review of several companies that offer similar kits or services that allow students to isolate DNA (human and others, amplify it by PCR, and in some cases sequence the resulting sample.  The companies include:  Carolina® Biological Supply Company, Bio-Rad®, Edvotek® Inc., Hiram Genomics Store, and 23andMe.

  12. e-Fungi: a data resource for comparative analysis of fungal genomes

    Directory of Open Access Journals (Sweden)

    Hubbard Simon J

    2007-11-01

    Full Text Available Abstract Background The number of sequenced fungal genomes is ever increasing, with about 200 genomes already fully sequenced or in progress. Only a small percentage of those genomes have been comprehensively studied, for example using techniques from functional genomics. Comparative analysis has proven to be a useful strategy for enhancing our understanding of evolutionary biology and of the less well understood genomes. However, the data required for these analyses tends to be distributed in various heterogeneous data sources, making systematic comparative studies a cumbersome task. Furthermore, comparative analyses benefit from close integration of derived data sets that cluster genes or organisms in a way that eases the expression of requests that clarify points of similarity or difference between species. Description To support systematic comparative analyses of fungal genomes we have developed the e-Fungi database, which integrates a variety of data for more than 30 fungal genomes. Publicly available genome data, functional annotations, and pathway information has been integrated into a single data repository and complemented with results of comparative analyses, such as MCL and OrthoMCL cluster analysis, and predictions of signaling proteins and the sub-cellular localisation of proteins. To access the data, a library of analysis tasks is available through a web interface. The analysis tasks are motivated by recent comparative genomics studies, and aim to support the study of evolutionary biology as well as community efforts for improving the annotation of genomes. Web services for each query are also available, enabling the tasks to be incorporated into workflows. Conclusion The e-Fungi database provides fungal biologists with a resource for comparative studies of a large range of fungal genomes. Its analysis library supports the comparative study of genome data, functional annotation, and results of large scale analyses over all the

  13. The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.

    Science.gov (United States)

    Eppig, Janan T; Bult, Carol J; Kadin, James A; Richardson, Joel E; Blake, Judith A; Anagnostopoulos, A; Baldarelli, R M; Baya, M; Beal, J S; Bello, S M; Boddy, W J; Bradt, D W; Burkart, D L; Butler, N E; Campbell, J; Cassell, M A; Corbani, L E; Cousins, S L; Dahmen, D J; Dene, H; Diehl, A D; Drabkin, H J; Frazer, K S; Frost, P; Glass, L H; Goldsmith, C W; Grant, P L; Lennon-Pierce, M; Lewis, J; Lu, I; Maltais, L J; McAndrews-Hill, M; McClellan, L; Miers, D B; Miller, L A; Ni, L; Ormsby, J E; Qi, D; Reddy, T B K; Reed, D J; Richards-Smith, B; Shaw, D R; Sinclair, R; Smith, C L; Szauter, P; Walker, M B; Walton, D O; Washburn, L L; Witham, I T; Zhu, Y

    2005-01-01

    The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.

  14. CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips.

    Directory of Open Access Journals (Sweden)

    Hamed Heydari

    Full Text Available Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1 annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2 access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3 advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB, Pairwise Genome Comparison (PGC tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.

  15. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    KAUST Repository

    Bracken-Grissom, Heather

    2013-12-12

    Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site () has been launched to facilitate this collaborative venture.

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

    Science.gov (United States)

    Tatusova, Tatiana

    2016-01-01

    The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI website, text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Comparative genome analysis tools lead to further understanding of evolution processes quickening the pace of discovery. Recent technological innovations have ignited an explosion in genome sequencing that has fundamentally changed our understanding of the biology of living organisms. This huge increase in DNA sequence data presents new challenges for the information management system and the visualization tools. New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data. PMID:27115625

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

    Science.gov (United States)

    Tatusova, Tatiana

    2016-01-01

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

  18. Hyperphosphorylation of cereal starch

    DEFF Research Database (Denmark)

    Carciofi, Massimiliano; Shaik, Shahnoor Sultana; Jensen, Susanne Langgård;

    2011-01-01

    phosphate compared with potato tuber starch and in order to investigate the effect of increased endosperm starch phosphate, the potato starch phosphorylating enzyme glucan water dikinase (StGWD) was overexpressed specifically in the developing barley endosperm. StGWD overexpressors showed wild......Plant starch is naturally phosphorylated at a fraction of the C6 and the C3 hydroxyl groups during its biosynthesis in plastids. Starch phosphate esters are important in starch metabolism and they also generate specific industrial functionality. Cereal grains starch contains little starch bound......-type phenotype. Transgenic cereal grains synthesized starch with higher starch bound phosphate content (7.5 (±0.67) nmol/mg) compared to control lines (0.8 (±0.05) nmol/mg) with starch granules showing altered morphology and lower melting enthalpy. Our data indicate specific action of GWD during starch...

  19. Zinc biofortification of cereals

    DEFF Research Database (Denmark)

    Palmgren, Michael; Clemens, Stephan; Williams, Lorraine E.;

    2008-01-01

    The goal of biofortification is to develop plants that have an increased content of bioavailable nutrients in their edible parts. Cereals serve as the main staple food for a large proportion of the world population but have the shortcoming, from a nutrition perspective, of being low in zinc...... and other essential nutrients. Major bottlenecks in plant biofortification appear to be the root-shoot barrier and - in cereals - the process of grain filling. New findings demonstrate that the root-shoot distribution of zinc is controlled mainly by heavy metal transporting P1B-ATPases and the metal...... tolerance protein (MTP) family. A greater understanding of zinc transport is important to improve crop quality and also to help alleviate accumulation of any toxic metals....

  20. A whole-genome, radiation hybrid mapping resource of hexaploid wheat.

    Science.gov (United States)

    Tiwari, Vijay K; Heesacker, Adam; Riera-Lizarazu, Oscar; Gunn, Hilary; Wang, Shichen; Wang, Yi; Gu, Young Q; Paux, Etienne; Koo, Dal-Hoe; Kumar, Ajay; Luo, Ming-Cheng; Lazo, Gerard; Zemetra, Robert; Akhunov, Eduard; Friebe, Bernd; Poland, Jesse; Gill, Bikram S; Kianian, Shahryar; Leonard, Jeffrey M

    2016-04-01

    Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species. PMID:26945524

  1. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

    Directory of Open Access Journals (Sweden)

    Kumar Ajay

    2012-11-01

    scaffolds of the D-genome. Conclusions The RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.

  2. CMD: a Cotton Microsatellite Database resource for Gossypium genomics

    Directory of Open Access Journals (Sweden)

    Liu Shaolin

    2006-05-01

    Full Text Available Abstract Background The Cotton Microsatellite Database (CMD http://www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. Description At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. Conclusion The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.

  3. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

    Directory of Open Access Journals (Sweden)

    Jorge Duitama

    Full Text Available Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

  4. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

    Science.gov (United States)

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  5. Natural and artificial mutants as valuable resources for functional genomics and molecular breeding

    Directory of Open Access Journals (Sweden)

    Shu-Ye Jiang, Srinivasan Ramachandran

    2010-01-01

    Full Text Available With the completion of rice genome sequencing, large collection of expression data and the great efforts in annotating rice genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. In this study, we have reviewed currently employed tools to generate such mutant populations. These tools include natural, physical, chemical, tissue culture, T-DNA, transposon or gene silencing based mutagenesis. We also reviewed how these tools were used to generate a large collection of mutants and how these mutants can be screened and detected for functional analysis of a gene. The data suggested that the current population of mutants might be large enough to tag all predicted genes. However, the collection of flanking sequencing tags (FSTs is limited due to the relatively higher cost. Thus, we have proposed a new strategy to generate gene-silencing mutants at the genome-wide level. Due to the large collection of insertion mutants, the next step to rice functional genomics should be focusing on functional characterization of tagged genes by detailed survey of corresponding mutants. Additionally, we also evaluated the utilization of these mutants as valuable resources for molecular breeding.

  6. A diploid wheat TILLING resource for wheat functional genomics

    Directory of Open Access Journals (Sweden)

    Rawat Nidhi

    2012-11-01

    Full Text Available Abstract Background Triticum monococcum L., an A genome diploid einkorn wheat, was the first domesticated crop. As a diploid, it is attractive genetic model for the study of gene structure and function of wheat-specific traits. Diploid wheat is currently not amenable to reverse genetics approaches such as insertion mutagenesis and post-transcriptional gene silencing strategies. However, TILLING offers a powerful functional genetics approach for wheat gene analysis. Results We developed a TILLING population of 1,532 M2 families using EMS as a mutagen. A total of 67 mutants were obtained for the four genes studied. Waxy gene mutation frequencies are known to be 1/17.6 - 34.4 kb DNA in polyploid wheat TILLING populations. The T. monococcum diploid wheat TILLING population had a mutation frequency of 1/90 kb for the same gene. Lignin biosynthesis pathway genes- COMT1, HCT2, and 4CL1 had mutation frequencies of 1/86 kb, 1/92 kb and 1/100 kb, respectively. The overall mutation frequency of the diploid wheat TILLING population was 1/92 kb. Conclusion The mutation frequency of a diploid wheat TILLING population was found to be higher than that reported for other diploid grasses. The rate, however, is lower than tetraploid and hexaploid wheat TILLING populations because of the higher tolerance of polyploids to mutations. Unlike polyploid wheat, most mutants in diploid wheat have a phenotype amenable to forward and reverse genetic analysis and establish diploid wheat as an attractive model to study gene function in wheat. We estimate that a TILLING population of 5, 520 will be needed to get a non-sense mutation for every wheat gene of interest with 95% probability.

  7. Genetic transformation of major cereal crops.

    Science.gov (United States)

    Ji, Qing; Xu, Xing; Wang, Kan

    2013-01-01

    Of the more than 50,000 edible plant species in the world, at least 10,000 species are cereal grains. Three major cereal crops, rice (Oryza sativa), maize (Zea mays), and wheat (Triticum sp.), provide two-thirds of the world's food energy intake. Although crop yields have improved tremendously thanks to technological advances in the past 50 years, population increases and climate changes continue to threaten the sustainability of current crop productions. Whereas conventional and marker-assisted breeding programs continue to play a major role in crop improvement, genetic engineering has drawn an intense worldwide interest from the scientific community. In the past decade, genetic transformation technologies have revolutionized agricultural practices and millions of hectares of biotech crops have been cultured. Because of its unique ability to insert well-characterized gene sequences into the plant genome, genetic engineering can also provide effective tools to address fundamental biological questions. This technology is expected to continue to be an indispensable approach for both basic and applied research. Here, we overview briefly the development of the genetic transformation in the top seven cereals, namely maize, rice, wheat, barley (Hordeum vulgare), sorghum (Sorghum sp.), oat (Avena sativa), and millets. The advantages and disadvantages of the two major transformation methods, Agrobacterium tumefaciens-mediated and biolistic methods, are also discussed.

  8. Prospects and Challenges for the Conservation of Farm Animal Genomic Resources, 2015-2025

    Directory of Open Access Journals (Sweden)

    Michael William Bruford

    2015-10-01

    Full Text Available Livestock conservation practice is changing rapidly in light of policy, climate change and market demands. The last decade saw a step change in technological and analytical approaches to define, manage and conserve Farm Animal Genomic Resources (FAnGR. These changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and the methodologies needed to exploit new, multidimensional data. The ESF Genomic Resources program final conference addressed these problems attempting to contribute to the development of the research and policy agenda for the next decade. We broadly identified four areas related to methodological and analytical challenges, data management and conservation. The overall conclusion is that there is a need for the use of current state-of-the-art tools to characterise the state of genomic resources in non-commercial and local breeds. The livestock genomic sector, which has been relatively well-organised in applying such methodologies so far, needs to make a concerted effort in the coming decade to enable to the democratisation of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.

  9. A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy.

    Science.gov (United States)

    Brenton, Zachary W; Cooper, Elizabeth A; Myers, Mathew T; Boyles, Richard E; Shakoor, Nadia; Zielinski, Kelsey J; Rauh, Bradley L; Bridges, William C; Morris, Geoffrey P; Kresovich, Stephen

    2016-09-01

    With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production.

  10. Resources

    Science.gov (United States)

    ... palate - resources Colon cancer - resources Cystic fibrosis - resources Depression - resources Diabetes - resources Digestive disease - resources Drug abuse - resources Eating disorders - resources Elder care - resources Epilepsy - resources Family troubles - ...

  11. Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus).

    Science.gov (United States)

    Thanh, Nguyen Minh; Jung, Hyungtaek; Lyons, Russell E; Njaci, Isaac; Yoon, Byoung-Ha; Chand, Vincent; Tuan, Nguyen Viet; Thu, Vo Thi Minh; Mather, Peter

    2015-10-01

    Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478bp and N50 length of 506bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species. PMID:25979246

  12. Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome

    Directory of Open Access Journals (Sweden)

    Kelley Joanna L

    2012-11-01

    Full Text Available Abstract Background Elucidating the genomic basis of adaptation and speciation is a major challenge in natural systems with large quantities of environmental and phenotypic data, mostly because of the scarcity of genomic resources for non-model organisms. The Atlantic molly (Poecilia mexicana, Poeciliidae is a small livebearing fish that has been extensively studied for evolutionary ecology research, particularly because this species has repeatedly colonized extreme environments in the form of caves and toxic hydrogen sulfide containing springs. In such extreme environments, populations show strong patterns of adaptive trait divergence and the emergence of reproductive isolation. Here, we used RNA-sequencing to assemble and annotate the first transcriptome of P. mexicana to facilitate ecological genomics studies in the future and aid the identification of genes underlying adaptation and speciation in the system. Description We provide the first annotated reference transcriptome of P. mexicana. Our transcriptome shows high congruence with other published fish transcriptomes, including that of the guppy, medaka, zebrafish, and stickleback. Transcriptome annotation uncovered the presence of candidate genes relevant in the study of adaptation to extreme environments. We describe general and oxidative stress response genes as well as genes involved in pathways induced by hypoxia or involved in sulfide metabolism. To facilitate future comparative analyses, we also conducted quantitative comparisons between P. mexicana from different river drainages. 106,524 single nucleotide polymorphisms were detected in our dataset, including potential markers that are putatively fixed across drainages. Furthermore, specimens from different drainages exhibited some consistent differences in gene regulation. Conclusions Our study provides a valuable genomic resource to study the molecular underpinnings of adaptation to extreme environments in replicated sulfide

  13. StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

    Science.gov (United States)

    Zheng, Wenning; Tan, Tze King; Paterson, Ian C; Mutha, Naresh V R; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A; Jakubovics, Nicholas S; Choo, Siew Woh

    2016-01-01

    The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my. PMID:27138013

  14. StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

    Science.gov (United States)

    Zheng, Wenning; Tan, Tze King; Paterson, Ian C; Mutha, Naresh V R; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A; Jakubovics, Nicholas S; Choo, Siew Woh

    2016-01-01

    The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my.

  15. RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA.

    Science.gov (United States)

    Chen, Lei; Ai, Peng; Zhang, Jinfeng; Deng, Qiming; Wang, Shiquan; Li, Shuangcheng; Zhu, Jun; Li, Ping; Zheng, Aiping

    2016-01-01

    Rice [Oryza sativa (L.)] feeds more than half of the world's population. Rhizoctonia solaniis a major fungal pathogen of rice causing extreme crop losses in all rice-growing regions of the world. R. solani AG1 IA is a major cause of sheath blight in rice. In this study, we constructed a comprehensive and user-friendly web-based database, RSIADB, to analyse its draft genome and transcriptome. The database was built using the genome sequence (10,489 genes) and annotation information for R. solani AG1 IA. A total of six RNAseq samples of R. solani AG1 IA were also analysed, corresponding to 10, 18, 24, 32, 48 and 72 h after infection of rice leaves. The RSIADB database enables users to search, browse, and download gene sequences for R. solani AG1 IA, and mine the data using BLAST, Sequence Extractor, Browse and Construction Diagram tools that were integrated into the database. RSIADB is an important genomic resource for scientists working with R. solani AG1 IA and will assist researchers in analysing the annotated genome and transcriptome of this pathogen. This resource will facilitate studies on gene function, pathogenesis factors and secreted proteins, as well as provide an avenue for comparative analyses of genes expressed during different stages of infection. Database URL:http://genedenovoweb.ticp.net:81/rsia/index.php.

  16. RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA.

    Science.gov (United States)

    Chen, Lei; Ai, Peng; Zhang, Jinfeng; Deng, Qiming; Wang, Shiquan; Li, Shuangcheng; Zhu, Jun; Li, Ping; Zheng, Aiping

    2016-01-01

    Rice [Oryza sativa (L.)] feeds more than half of the world's population. Rhizoctonia solaniis a major fungal pathogen of rice causing extreme crop losses in all rice-growing regions of the world. R. solani AG1 IA is a major cause of sheath blight in rice. In this study, we constructed a comprehensive and user-friendly web-based database, RSIADB, to analyse its draft genome and transcriptome. The database was built using the genome sequence (10,489 genes) and annotation information for R. solani AG1 IA. A total of six RNAseq samples of R. solani AG1 IA were also analysed, corresponding to 10, 18, 24, 32, 48 and 72 h after infection of rice leaves. The RSIADB database enables users to search, browse, and download gene sequences for R. solani AG1 IA, and mine the data using BLAST, Sequence Extractor, Browse and Construction Diagram tools that were integrated into the database. RSIADB is an important genomic resource for scientists working with R. solani AG1 IA and will assist researchers in analysing the annotated genome and transcriptome of this pathogen. This resource will facilitate studies on gene function, pathogenesis factors and secreted proteins, as well as provide an avenue for comparative analyses of genes expressed during different stages of infection. Database URL:http://genedenovoweb.ticp.net:81/rsia/index.php. PMID:27022158

  17. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

    OpenAIRE

    Bruford, Michael W.; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J; Andreia J Amaral; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel

    2015-01-01

    Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional dat...

  18. GeneSeer: A sage for gene names and genomic resources

    OpenAIRE

    Tully Tim; Olson Andrew J; Sachidanandam Ravi

    2005-01-01

    Abstract Background Independent identification of genes in different organisms and assays has led to a multitude of names for each gene. This balkanization makes it difficult to use gene names to locate genomic resources, homologs in other species and relevant publications. Methods We solve the naming problem by collecting data from a variety of sources and building a name-translation database. We have also built a table of homologs across several model organisms: H. sapiens, M. musculus, R. ...

  19. Panzea: a database and resource for molecular and functional diversity in the maize genome

    OpenAIRE

    Zhao, Wei; Canaran, Payan; Jurkuta, Rebecca; Fulton, Theresa; Glaubitz, Jeffrey; Buckler, Edward; Doebley, John; Gaut, Brandon; Goodman, Major; Holland, Jim; Kresovich, Stephen; McMullen, Michael; Stein, Lincoln; Ware, Doreen

    2005-01-01

    Serving as a community resource, Panzea () is the bioinformatics arm of the Molecular and Functional Diversity in the Maize Genome project. Maize, a classical model for genetic studies, is an important crop species and also the most diverse crop species known. On average, two randomly chosen maize lines have one single-nucleotide polymorphism every ∼100 bp; this divergence is roughly equivalent to the differences between humans and chimpanzees. This exceptional genotypic diversity underlies t...

  20. NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

    Science.gov (United States)

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

    2016-01-01

    Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

  1. NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

    Science.gov (United States)

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

    2016-01-01

    Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

  2. Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.)

    Science.gov (United States)

    The rapid advancement in high-throughput SNP genotyping technologies along with next generation sequencing (NGS) platforms has decreased the cost, improved the quality of large-scale genome surveys, and allowed specialty crops with limited genomic resources such as carrot (Daucus carota) to access t...

  3. More protein in cereals?

    International Nuclear Information System (INIS)

    Ways in which the protein content of plant crops may be raised by the use of nuclear radiation are to be discussed at a symposium in Vienna in June next year, organized by the joint Food and Agriculture Organization/Agency Division of Atomic Energy in Food and Agriculture. Plant crops - especially cereal grains - are the basic food and protein source of most of the world's population, particularly in less-developed countries. But their natural protein content is low; increasing the quantity and nutritional quality of plant protein is potentially the most feasible way to combat widespread protein malnutrition. This improvement in seed stock can be achieved by plant breeding methods in which nuclear irradiation techniques are used to induce mutations in grain, and other isotopic techniques can be used to select only those mutants which have the desired properties. The scientists who attend the symposium will have an opportunity to review what mutation plant breeders have achieved, the application of nuclear techniques to screening for protein and amino-acid content and nutritional value, and isotopic methods which contribute to research in plant nutrition and physiology. (author)

  4. The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond1

    Science.gov (United States)

    Mueller, Lukas A.; Solow, Teri H.; Taylor, Nicolas; Skwarecki, Beth; Buels, Robert; Binns, John; Lin, Chenwei; Wright, Mark H.; Ahrens, Robert; Wang, Ying; Herbst, Evan V.; Keyder, Emil R.; Menda, Naama; Zamir, Dani; Tanksley, Steven D.

    2005-01-01

    The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of phenotypic information for a mutagenized tomato population, and associated tools such as real-time quantitative trait loci. Recently, the International Solanaceae Project (SOL) was formed as an umbrella organization for Solanaceae research in over 30 countries to address important questions in plant biology. The first cornerstone of the SOL project is the sequencing of the entire euchromatic portion of the tomato genome. SGN is collaborating with other bioinformatics centers in building the bioinformatics infrastructure for the tomato sequencing project and implementing the bioinformatics strategy of the larger SOL project. The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond. PMID:16010005

  5. Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing.

    Science.gov (United States)

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology.

  6. GeneSeer: A sage for gene names and genomic resources

    Directory of Open Access Journals (Sweden)

    Tully Tim

    2005-09-01

    Full Text Available Abstract Background Independent identification of genes in different organisms and assays has led to a multitude of names for each gene. This balkanization makes it difficult to use gene names to locate genomic resources, homologs in other species and relevant publications. Methods We solve the naming problem by collecting data from a variety of sources and building a name-translation database. We have also built a table of homologs across several model organisms: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae, S. pombe and A. thaliana. This allows GeneSeer to draw phylogenetic trees and identify the closest homologs. This, in turn, allows the use of names from one species to identify homologous genes in another species. A website http://geneseer.cshl.org/ is connected to the database to allow user-friendly access to our tools and external genomic resources using familiar gene names. Conclusion GeneSeer allows access to gene information through common names and can map sequences to names. GeneSeer also allows identification of homologs and paralogs for a given gene. A variety of genomic data such as sequences, SNPs, splice variants, expression patterns and others can be accessed through the GeneSeer interface. It is freely available over the web http://geneseer.cshl.org/ and can be incorporated in other tools through an http-based software interface described on the website. It is currently used as the search engine in the RNAi codex resource, which is a portal for short hairpin RNA (shRNA gene-silencing constructs.

  7. Combined use of genetic and genomics resources to understand virus resistance and fruit quality traits in melon.

    Science.gov (United States)

    Argyris, Jason M; Pujol, Marta; Martín-Hernández, Ana Montserrat; Garcia-Mas, Jordi

    2015-09-01

    The availability of the genome sequence of many crop species during the past few years has opened a new era in plant biology, allowing for the performance of massive genomic studies in plant species other than the classical models Arabidopsis and rice. One of these crop species is melon (Cucumis melo), a cucurbit of high economic value that has become an interesting model for the study of biological processes such as fruit ripening, sex determination and phloem transport. The recent availability of the melon genome sequence, together with a number of genetic and genomic resources, provides powerful tools that can be used to assist in the main melon breeding targets, namely disease resistance and fruit quality. In this review, we will describe recent data obtained combining the use of a melon near isogenic line (NIL) population and genomic resources to gain insight into agronomically important traits as fruit ripening, resistance to Cucumber Mosaic virus (CMV) and the accumulation of sugars in fruits.

  8. A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

    Directory of Open Access Journals (Sweden)

    Jose L. Pruneda-Paz

    2014-07-01

    Full Text Available Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1 that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.

  9. Genomic Resources for Water Yam (Dioscorea alata L.: Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries.

    Directory of Open Access Journals (Sweden)

    Christopher A Saski

    Full Text Available The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp. is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS profiles on two yam (Dioscorea alata L. genotypes (TDa 95/00328 and TDa 95-310 was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using

  10. Priority regions for research on dryland cereals and legumes

    Science.gov (United States)

    Hyman, Glenn; Barona, Elizabeth; Biradar, Chandrashekhar; Guevara, Edward; Dixon, John; Beebe, Steve; Castano, Silvia Elena; Alabi, Tunrayo; Gumma, Murali Krishna; Sivasankar, Shoba; Rivera, Ovidio; Espinosa, Herlin; Cardona, Jorge

    2016-01-01

    Dryland cereals and legumes  are important crops in farming systems across the world.  Yet they are frequently neglected among the priorities for international agricultural research and development, often due to lack of information on their magnitude and extent. Given what we know about the global distribution of dryland cereals and legumes, what regions should be high priority for research and development to improve livelihoods and food security? This research evaluated the geographic dimensions of these crops and the farming systems where they are found worldwide. The study employed geographic information science and data to assess the key farming systems and regions for these crops. Dryland cereal and legume crops should be given high priority in 18 farming systems worldwide, where their cultivated area comprises more than 160 million ha. These regions include the dryer areas of South Asia, West and East Africa, the Middle East and North Africa, Central America and other parts of Asia. These regions are prone to drought and heat stress, have limiting soil constraints, make up half of the global population and account for 60 percent of the global poor and malnourished. The dryland cereal and legume crops and farming systems merit more research and development attention to improve productivity and address development problems. This project developed an open access dataset and information resource that provides the basis for future analysis of the geographic dimensions of dryland cereals and legumes. PMID:27303632

  11. Exploiting genomics resources to identify candidate genes underlying antioxidants content in tomato fruit

    Directory of Open Access Journals (Sweden)

    Roberta eCalafiore

    2016-04-01

    Full Text Available The tomato is a model species for fleshy fruit development and ripening, as well as for genomics studies of others Solanaceae. Many genetic and genomics resources, including databases for sequencing, transcriptomics and metabolomics data, have been developed and are today available. The purpose of the present work was to uncover new genes and/or alleles that determine ascorbic acid and carotenoids accumulation, by exploiting one Solanum pennellii introgression lines (IL7-3 harboring quantitative trait loci (QTL that increase the content of these metabolite in the fruit. The higher ascorbic acid and carotenoids content in IL7-3 was confirmed at three fruit developmental stages. The tomato genome reference sequence and the recently released S. pennellii genome sequence were investigated to identify candidate genes that might control ascorbic acid and carotenoids accumulation. First of all, a refinement of the wild region borders in the IL7-3 was achieved by analyzing CAPS markers designed in our laboratory. Afterwards, six candidate genes associated to ascorbic acid and one with carotenoids metabolism were identified exploring the annotation and the Gene Ontology terms of genes included in the region. Variants between the sequence of the wild and the cultivated alleles of these genes were investigated for their functional relevance and their potential effects on the protein sequences were predicted. Transcriptional levels of candidate genes in the introgression region were extracted from RNA-Seq data available for the entire S. pennellii introgression lines collection and verified by Real-Time qPCR. Finally, seven IL7-3 sub-lines were genotyped using 28 species-specific markers and then were evaluated for metabolites content. These analyses evidenced a significant decrease in transcript abundance for one 9-cis-epoxycarotenoid dioxygenase and one L-ascorbate oxidase homolog, whose role in the accumulation of carotenoids and ascorbic acid is

  12. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.

    Science.gov (United States)

    Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu

    2016-06-01

    MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.

  13. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.

    Science.gov (United States)

    Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu

    2016-06-01

    MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources. PMID:26919060

  14. Drought tolerance in potato (S. tuberosum L.): Can we learn from drought tolerance research in cereals?

    Science.gov (United States)

    Monneveux, Philippe; Ramírez, David A; Pino, María-Teresa

    2013-05-01

    Drought tolerance is a complex trait of increasing importance in potato. Our knowledge is summarized concerning drought tolerance and water use efficiency in this crop. We describe the effects of water restriction on physiological characteristics, examine the main traits involved, report the attempts to improve drought tolerance through in vitro screening and marker assisted selection, list the main genes involved and analyze the potential interest of native and wild potatoes to improve drought tolerance. Drought tolerance has received more attention in cereals than in potato. The review compares these crops for indirect selection methods available for assessment of drought tolerance related traits, use of genetic resources, progress in genomics, application of water saving techniques and availability of models to anticipate the effects of climate change on yield. It is concluded that drought tolerance improvement in potato could greatly benefit from the transfer of research achievements in cereals. Several promising research directions are presented, such as the use of fluorescence, reflectance, color and thermal imaging and stable isotope techniques to assess drought tolerance related traits, the application of the partial root-zone drying technique to improve efficiency of water supply and the exploitation of stressful memory to enhance hardiness.

  15. [Wholegrain cereals and sanitary benefits].

    Science.gov (United States)

    Ortega, Rosa M; Aparicio Vizuete, Aránzazu; Jiménez Ortega, Ana Isabel; Rodríguez Rodríguez, Elena

    2015-07-18

    Objetivos: las guías alimentarias para conseguir una alimentación correcta establecen como aconsejable tomar tres o más raciones de cereales integrales de grano completo al día. Sin embargo, la norma es poco conocida en nuestro entorno, afectando el incumplimiento a la práctica totalidad de la población. Por ello, el objetivo de la presente revisión es analizar los beneficios nutricionales y sanitarios asociados al consumo de cereales de grano completo y las posibles ventajas que podrían derivarse del cumplimiento con consumo aconsejado para estos alimentos. Métodos: búsqueda bibliográfica en relación con el tema. Resultados: los cereales de grano completo aportan cantidades elevadas de hidratos de carbono, fibra, vitaminas y minerales, cuya contribución a la dieta media ayuda a alcanzar las ingestas recomendadas y los objetivos nutricionales vigentes, por lo que su consumo en la cantidad aconsejada supone un beneficio nutricional. Por otra parte, diversos estudios señalan que un aumento en el consumo de cereales de grano completo se asocia con una protección frente al padecimiento de diversas enfermedades crónico-degenerativas (cardiovasculares, diabetes, síndrome metabólico y cáncer), ayudando en el mantenimiento de la salud digestiva y del peso corporal. Estos resultados pueden ser debidos al aporte de nutrientes, fibra y fitoquímicos, procedente de estos alimentos, así como al desplazamiento de la dieta de otros productos con un perfil nutricional menos conveniente, teniendo en cuenta la composición de la dieta media española. De hecho, el consumo de cereales de grano completo ha sido relacionado con una posible mejora en la microbiota intestinal y una mayor protección antioxidante. Pese a estas ventajas, el consumo de cereales es mirado con recelo por diversos individuos, especialmente por aquellas personas preocupadas por el control de peso, y los beneficios adicionales asociados al consumo de cereales de grano completo no son

  16. Antioxidant Properties of Whole Grain Cereals

    OpenAIRE

    Čukelj, Nikolina; Novotny, Dubravka; Ćurić, Duška

    2010-01-01

    Cereals have a long history of use by humans. Cereals and cereal products are staple foods, and are important source of energy, carbohydrate, protein, fibre, vitamins (E, B) and minerals (Zn, Mg, Fe) in both developed and developing countries. The health aspects of whole grain cereals have long been known, but the antioxidant profile of whole grains has only recently been introduced to the antioxidant research community where mostly fruits and vegetables are in focus. In vitro experiments con...

  17. Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design

    Directory of Open Access Journals (Sweden)

    Malloch Gaynor

    2007-11-01

    Full Text Available Abstract Background The green peach aphid, Myzus persicae (Sulzer, is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. Results Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs. Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection. The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. Furthermore, 2423 genes that are novel to science and potentially aphid-specific were identified. Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. Conclusion New genomic resources have been developed for M. persicae, an agriculturally important insect pest. These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. These resources will help elucidate the adaptations that allow M. persicae to develop compatible

  18. Detection methods for mycotoxins in cereal grains and cereal products

    Directory of Open Access Journals (Sweden)

    Pascale Michelangelo N.

    2009-01-01

    Full Text Available Analytical methods for mycotoxins in cereals and cereal-based products require three major steps, including extraction, clean-up (to eliminate interferences from the extract and concentrate the analyte, and detection/determination of the toxin (by using suitable analytical instruments/technologies. Clean-up is essential for the analysis of mycotoxins at trace levels, and involves the use of solid phase extraction and multifunctional (e.g. MycoSep® or immunoaffinity columns. Different chromatographic methods are commonly used for quantitative determination of mycotoxins, including gas-chromatography (GC coupled with electron capture, flame ionization or mass spectrometry (MS detectors (mainly for type-A trichothecenes, and high-performance liquid chromatography (HPLC coupled with ultraviolet, diode array, fluorescence or MS detectors. The choice of method depends on the matrix and the mycotoxin to be analyzed. Liquid chromatography-tandem mass spectrometry (LC-MS/MS is spreading rapidly as a promising technique for simultaneous screening, identification and quantitative determination of a large number of mycotoxins. In addition, commercial immunometric assays, such as enzyme-linked immunosorbent assays (ELISA, are frequently used for screening purposes as well. Recently, a variety of emerging methods have been proposed for the analysis of mycotoxins in cereals based on novel technologies, including immunochromatography (i.e. lateral flow devices, fluorescence polarization immunoassays (FPIA, infrared spectroscopy (FT-NIR, molecularly imprinted polymers (MIPs and optical biosensors.

  19. Cereals Market in Romania under the Impact of the Common Agricultural Policy

    Directory of Open Access Journals (Sweden)

    Florentina CONSTANTIN

    2013-12-01

    Full Text Available The aim of this paper is to analyses the cereals market after Romania accession to European Union. Thus, I considered necessary and appropriate to achieve the dynamic analysis of production, prices, trade, consumption, and self-sufficiency that provides an overview on the evolution of the cereals market in Romania, in the European context, starting from resources representing the demand, to the uses that represent the supply. I also point out the main mechanisms and support instruments for the cereals market under the Common Agriculture Policy, in the period 2007-2013 and towards 2014-2020.

  20. Microbiological Spoilage of Cereal Products

    Science.gov (United States)

    Cook, Frederick K.; Johnson, Billie L.

    A wide range of cereal products, including bakery items, refrigerated dough, fresh pasta products, dried cereal products, snack foods, and bakery mixes, are manufactured for food consumption. These products are subject to physical, chemical, and microbiological spoilage that affects the taste, aroma, leavening, appearance, and overall quality of the end consumer product. Microorganisms are ubiquitous in nature and have the potential for causing food spoilage and foodborne disease. However, compared to other categories of food products, bakery products rarely cause food poisoning. The heat that is applied during baking or frying usually eliminates pathogenic and spoilage microorganisms, and low moisture contributes to product stability. Nevertheless, microbiological spoilage of these products occurs, resulting in substantial economic losses.

  1. Cereals Market in Romania under the Impact of the Common Agricultural Policy

    OpenAIRE

    Constantin, Florentina

    2013-01-01

    The aim of this paper is to analyses the cereals market after Romania accession to European Union. Thus, I considered necessary and appropriate to achieve the dynamic analysis of production, prices, trade, consumption, and self-sufficiency that provides an overview on the evolution of the cereals market in Romania, in the European context, starting from resources representing the demand, to the uses that represent the supply. I also point out the main mechanisms and support instruments for th...

  2. Sequencing and annotation of the Wolbachia endosymbiont of Diaphorina citri by the CG-HLB Genome Resources group reveals candidate sources of interaction with the insect host

    OpenAIRE

    Saha, Surya; Hunter, Wayne; Lindeberg, Magdalen

    2014-01-01

    The Citrus Greening – Huanglongbing (CG-HLB) Genome Resources group serves as a bioinformatics resource for diverse projects related to the biology of CG-HLB.  A major recent project concerns the generation and annotation of a draft genome sequence for the Wolbachia endosymbiont (wDi) of the Asian citrus psyllid, of particular interest given the potential for control of psyllid behavior through manipulation of its bacterial endosymbionts.   The Wolbachia draft genome was assembled and contigs...

  3. Genomics of Sorghum

    OpenAIRE

    Paterson, Andrew H.

    2008-01-01

    Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relatin...

  4. GenomicusPlants: a web resource to study genome evolution in flowering plants.

    Science.gov (United States)

    Louis, Alexandra; Murat, Florent; Salse, Jérôme; Crollius, Hugues Roest

    2015-01-01

    Comparative genomics combined with phylogenetic reconstructions are powerful approaches to study the evolution of genes and genomes. However, the current rapid expansion of the volume of genomic information makes it increasingly difficult to interrogate, integrate and synthesize comparative genome data while taking into account the maximum breadth of information available. GenomicusPlants (http://www.genomicus.biologie.ens.fr/genomicus-plants) is an extension of the Genomicus webserver that addresses this issue by allowing users to explore flowering plant genomes in an intuitive way, across the broadest evolutionary scales. Extant genomes of 26 flowering plants can be analyzed, as well as 23 ancestral reconstructed genomes. Ancestral gene order provides a long-term chronological view of gene order evolution, greatly facilitating comparative genomics and evolutionary studies. Four main interfaces ('views') are available where: (i) PhyloView combines phylogenetic trees with comparisons of genomic loci across any number of genomes; (ii) AlignView projects loci of interest against all other genomes to visualize its topological conservation; (iii) MatrixView compares two genomes in a classical dotplot representation; and (iv) Karyoview visualizes chromosome karyotypes 'painted' with colours of another genome of interest. All four views are interconnected and benefit from many customizable features.

  5. [Development of cereal bar with pineapple skin].

    Science.gov (United States)

    Fonseca, Renata Siqueira; Del Santo, Victor Rogério; Souza, Gilberto Batista de; Pereira, Cíntia Alessandra Matiucci

    2011-06-01

    The cereal bars are multi-component products consisting of cereals, dried fruit and syrup binder and may be added to the consumable parts of fruits and vegetables which usually are not exploited and have high nutritional value, thereby reducing food waste. It was developed a jam with pineapple skin, which it was utilized in 13.5% in the cereal bar formulation. The cereal bar was sensorial evaluated and had its centesimal and mineral composition determined. The new product achieved average of 8.3 for global impression using 9 points hedonic scale, 91% of acceptance rate and 67% of purchase intent. In this first use of pineapple skin jam as food ingredient it can be concluded that its aggregation in the cereal bar formula is feasible, making an accepted product with fibers, proteins and minerals, as an alternative to traditional cereal bars.

  6. Knowledge of cereals among primary school students

    OpenAIRE

    Murko, Ana

    2015-01-01

    In human diet cereals represent an important source of carbohydrates, proteins, vitamins, and elements, which are needed for healthy growth and development. This thesis is thus focused on knowledge of cereals among primary school students. We were assessing the knowledge of different cereals among primary school students based on their age and type of environment they live in. Beside these two variables, we took into consideration also their gender. 240 primary school students from sixth ...

  7. Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

    OpenAIRE

    Matsukura, C; Aoki, K.; Fukuda, N.; Mizoguchi, T.; Asamizu, E; Saito, T.; Shibata, D.; Ezura, H.

    2008-01-01

    Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu ) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studie...

  8. De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia.

    Science.gov (United States)

    Singh, Rakesh; Kumar, Rajesh; Mahato, Ajay Kumar; Paliwal, Ritu; Singh, Amit Kumar; Kumar, Sundeep; Marla, Soma S; Kumar, Ashok; Singh, Nagendra K

    2016-09-01

    Tinospora cordifolia is known for its medicinal properties owing to the presence of useful constituents such as terpenes, glycosides, steroids, alkaloids, and flavonoids belonging to secondary metabolism origin. However, there is little information available pertaining to critical genomic elements (ESTs, molecular markers) necessary for judicious exploitation of its germplasm. We employed 454 GS-FLX pyrosequencing of entire transcripts and altogether ∼25 K assembled transcripts or Expressed sequence tags (ESTs) were identified. As the interest in T. cordifolia is primarily due to its secondary metabolite constituents, the ESTs pertaining to terpenoids biosynthetic pathway were identified in the present study. Additionally, several ESTs were assigned to different transcription factor families. To validate our transcripts dataset, the novel EST-SSR markers were generated to assess the genetic diversity among germplasm of T. cordifolia. These EST-SSR markers were found to be polymorphic and the dendrogram based on dice similarity index revealed three distinct clustering of accessions. The present study demonstrates effectiveness in using both NEWBLER and MIRA sequence read assembler software for enriching transcript-dataset and thus enables better exploitation of EST resources for mining candidate genes and designing molecular markers. PMID:27465295

  9. Evaluation of Breakfast Cereals and Cereal Advertising by a Young Adult Audience.

    Science.gov (United States)

    Gagnard, Alice

    A study examined the knowledge of and attitudes toward nutrition in general and specifically toward cold breakfast cereals and cereal advertising with different creative appeals. Subjects, 117 undergraduate university students, completed a questionnaire about their use of cold breakfast cereal and their sources of information about nutrition.…

  10. Possible Roles for Polycomb Repressive Complex 2 in Cereal Endosperm

    Directory of Open Access Journals (Sweden)

    Kaoru eTonosaki

    2015-03-01

    Full Text Available The Polycomb Repressive Complex 2 (PRC2 is an evolutionarily conserved multimeric protein complex in both plants and animals. In contrast to animals, plants have evolved a range of different components of PRC2 and form diverse complexes that act in the control of key regulatory genes at many stages of development during the life cycle. A number of studies, particularly in the model species Arabidopsis thaliana, have highlighted the role of PRC2 and of epigenetic controls via parent-of-origin specific gene expression for endosperm development. However, recent research in cereal plants has revealed that although some components of PRC2 show evolutionary conservation with respect to parent-of-origin specific gene expression patterns, the identity of the imprinted genes encoding PRC2 components is not conserved. This disparity may reflect the facts that cereal plant genomes have undergone different patterns of duplication during evolution compared to Arabidopsis thaliana and that the endosperm development program is not identical in monocots and eudicots. In this context, we focus this review on the expression of imprinted PRC2 genes and their roles in endosperm development in cereals.

  11. Cold acclimation and vegetative/reproductive transition in winter cereals

    Directory of Open Access Journals (Sweden)

    Mohsen Janmohammadi

    2012-12-01

    Full Text Available Cereals display a broad capacity range to survive low temperatures (LT and frost condition. Exposure of winter cereals to low, nonfreezing temperatures during the autumn and before freezing injury occurs can induces various changes in genome, transcriptome, proteome, and metabolom levels in plant cells, by which plants are able to adjust their metabolism to LT and improve their freezing tolerance (FT. The difference between the cultivars can be interpreted by hardening conditions and the different mode and severity of changes occurred in each levels during cold acclimation. FT in cereals is dependent upon phonological development and the highest level of FT only acquires during the vegetative stage and plants by initiation of the reproductive phase lose the ability for hardening. Phonological growth is controlled by the developmental genes (vernalization, photoperiod, etc. which regulate the vegetative/reproductive transition and consequently determine the duration and level of FT expression. Furthermore under filed condition winter survival is also determined by the acclimation temperature of locations that may affect phenological development and delay the beginning of reproductive growth.

  12. Diversity of tri-functional histidine biosynthesis gene (his) in cereal Phaeosphaeria species

    Science.gov (United States)

    The full length genomic sequences of tri-functional histidine biosynthesis (his) gene were obtained and compared from cereal Phaeosphaeria species by PCR amplification. The his gene coding sequence in wheat-biotype P. nodorum (PN-w) was 2697 bp in size. The his genes in barley-biotype P. nodorum (PN...

  13. CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes

    Directory of Open Access Journals (Sweden)

    Moreau Yves

    2007-10-01

    Gène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. Conclusion To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.

  14. Shakespeare Cereals: A Popular Culture Exercise.

    Science.gov (United States)

    Schiff, Peter

    1997-01-01

    Offers an exercise involving popular culture to help students experience the contemporary power of Shakespeare. Explains that after reading a Shakespeare play, students develop new cereal brands based upon the work's plot, characters, or themes, afterward naming, designing, creating, and displaying the cereal package. Combines literary analysis,…

  15. Genomic resources for the brown planthopper, Nilaparvata lugens: Transcriptome pyrosequencing and microarray design

    Institute of Scientific and Technical Information of China (English)

    Chris Bass; Martin Bay Hebsgaard; Joseph Hughes

    2012-01-01

    The brown planthopper,Nilaparvata lugens is a pest of cultivated rice throughout Asia and is controlled using insecticides and/or resistant rice varieties.This species has developed resistance to many classes of insecticide and biotypes have developed that are virulent against formerly resistant rice cultivars.Insects use a suite of detoxification enzymes,including cytochrome P450s,glutathione S-transferases and carboxyl/cholinesterases to defend themselves against plant secondary metabolites and pesticides.Pyrosequencing on the Roche 454-FLX platform was used to produce a substantial expressed sequence tag (EST) dataset to complement the existing Sanger sequenced ESTs in GenBank.A total of 78 959 reads were combined with the 37 392 publically available Sanger ESTs; these assembled into 8 911 contigs and 10 620 singletons.Analysis of the distribution of tentative unique genes (TUGs) with the gene ontology for biological processes and molecular functions suggests that the 454 and Sanger EST assembly is broadly representative of the N.lugens transcriptome.The brown planthopper transcriptome was found to contain 31 TUGs encoding P450s,nine encoding glutathione S-transferases and 26 encoding carboxyl/cholinesterases and many of these are putatively involved in the detoxification of xenobiotics.The Agilent eArray platform was used to construct an oligonucleotide microarray populated with probes for ~ 19 000 unigene sequences,including all those known to encode detoxification enzymes.The genomic resources developed in this study will be useful to the community studying this crop pest and will help elucidate the molecular mechanism underlying insecticide resistance and planthopper adaptation to resistant rice cultivars.

  16. Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis.

    Science.gov (United States)

    Aliyeva-Schnorr, Lala; Stein, Nils; Houben, Andreas

    2016-05-01

    Crop wild relatives are considered as important genetic resources of allelic diversity for domesticated crop species. Their utilization in breeding programs, however, is often limited due to crossing barriers and genome incompatibilities. Wild relatives of barley possess attractive properties and hence allelic diversity for adapting barley better to changing environmental conditions. Therefore, gaining a better knowledge about genomic synteny between cultivated barley and wild relatives of the same genus is an important task. To visualize genomic collinearity in related species, 22 genomic single-copy and 14 complementary DNA (cDNA) chromosome 3H-specific probes were mapped to the chromosomes of Hordeum bulbosum, Hordeum marinum, Hordeum pubiflorum, Hordeum murinum, and Secale cereale by fluorescent in situ hybridization (FISH). Most probes showed reliable signals confirming homoeology between cultivated barley and related species. Differences in order and position of FISH markers demonstrated sequence movements or small-scale chromosomal rearrangements within genus Hordeum and confirmed interchromosomal rearrangements between barley and rye. Comparison between repeat-free genomic and cDNA probes showed that gene-containing single-copy genomic DNA (gDNA) probes are performing more reliably for FISH-based analysis of synteny.

  17. HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization.

    Directory of Open Access Journals (Sweden)

    Sahar Abubucker

    Full Text Available A vast majority of the burden from neglected tropical diseases result from helminth infections (nematodes and platyhelminthes. Parasitic helminthes infect over 2 billion, exerting a high collective burden that rivals high-mortality conditions such as AIDS or malaria, and cause devastation to crops and livestock. The challenges to improve control of parasitic helminth infections are multi-fold and no single category of approaches will meet them all. New information such as helminth genomics, functional genomics and proteomics coupled with innovative bioinformatic approaches provide fundamental molecular information about these parasites, accelerating both basic research as well as development of effective diagnostics, vaccines and new drugs. To facilitate such studies we have developed an online resource, HelmCoP (Helminth Control and Prevention, built by integrating functional, structural and comparative genomic data from plant, animal and human helminthes, to enable researchers to develop strategies for drug, vaccine and pesticide prioritization, while also providing a useful comparative genomics platform. HelmCoP encompasses genomic data from several hosts, including model organisms, along with a comprehensive suite of structural and functional annotations, to assist in comparative analyses and to study host-parasite interactions. The HelmCoP interface, with a sophisticated query engine as a backbone, allows users to search for multi-factorial combinations of properties and serves readily accessible information that will assist in the identification of various genes of interest. HelmCoP is publicly available at: http://www.nematode.net/helmcop.html.

  18. A contig-based strategy for the genome-wide discovery of microRNAs without complete genome resources.

    Directory of Open Access Journals (Sweden)

    Jun-Zhi Wen

    Full Text Available MicroRNAs (miRNAs are important regulators of many cellular processes and exist in a wide range of eukaryotes. High-throughput sequencing is a mainstream method of miRNA identification through which it is possible to obtain the complete small RNA profile of an organism. Currently, most approaches to miRNA identification rely on a reference genome for the prediction of hairpin structures. However, many species of economic and phylogenetic importance are non-model organisms without complete genome sequences, and this limits miRNA discovery. Here, to overcome this limitation, we have developed a contig-based miRNA identification strategy. We applied this method to a triploid species of edible banana (GCTCV-119, Musa spp. AAA group and identified 180 pre-miRNAs and 314 mature miRNAs, which is three times more than those were predicted by the available dataset-based methods (represented by EST+GSS. Based on the recently published miRNA data set of Musa acuminate, the recall rate and precision of our strategy are estimated to be 70.6% and 92.2%, respectively, significantly better than those of EST+GSS-based strategy (10.2% and 50.0%, respectively. Our novel, efficient and cost-effective strategy facilitates the study of the functional and evolutionary role of miRNAs, as well as miRNA-based molecular breeding, in non-model species of economic or evolutionary interest.

  19. FveGD: an online resource for diploid strawberry (fragaria vesca) genomics data

    Science.gov (United States)

    Fragaria vesca, a diploid strawberry species commonly known as the alpine or woodland strawberry, is a versatile experimental plant system that is an emerging model for the Rosaceae family. An ancestral F. vesca genome contributed to the genome of the octoploid dessert strawberry (F. xananassa) and...

  20. CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome data

    Directory of Open Access Journals (Sweden)

    Hüser Andrea T

    2007-11-01

    Full Text Available Abstract Background The introduction of high-throughput genome sequencing and post-genome analysis technologies, e.g. DNA microarray approaches, has created the potential to unravel and scrutinize complex gene-regulatory networks on a large scale. The discovery of transcriptional regulatory interactions has become a major topic in modern functional genomics. Results To facilitate the analysis of gene-regulatory networks, we have developed CoryneCenter, a web-based resource for the systematic integration and analysis of genome, transcriptome, and gene regulatory information for prokaryotes, especially corynebacteria. For this purpose, we extended and combined the following systems into a common platform: (1 GenDB, an open source genome annotation system, (2 EMMA, a MAGE compliant application for high-throughput transcriptome data storage and analysis, and (3 CoryneRegNet, an ontology-based data warehouse designed to facilitate the reconstruction and analysis of gene regulatory interactions. We demonstrate the potential of CoryneCenter by means of an application example. Using microarray hybridization data, we compare the gene expression of Corynebacterium glutamicum under acetate and glucose feeding conditions: Known regulatory networks are confirmed, but moreover CoryneCenter points out additional regulatory interactions. Conclusion CoryneCenter provides more than the sum of its parts. Its novel analysis and visualization features significantly simplify the process of obtaining new biological insights into complex regulatory systems. Although the platform currently focusses on corynebacteria, the integrated tools are by no means restricted to these species, and the presented approach offers a general strategy for the analysis and verification of gene regulatory networks. CoryneCenter provides freely accessible projects with the underlying genome annotation, gene expression, and gene regulation data. The system is publicly available at http://www.CoryneCenter.de.

  1. Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource

    Directory of Open Access Journals (Sweden)

    Vergnaud Gilles

    2004-01-01

    Full Text Available Abstract Background Polymorphic tandem repeat typing is a new generic technology which has been proved to be very efficient for bacterial pathogens such as B. anthracis, M. tuberculosis, P. aeruginosa, L. pneumophila, Y. pestis. The previously developed tandem repeats database takes advantage of the release of genome sequence data for a growing number of bacteria to facilitate the identification of tandem repeats. The development of an assay then requires the evaluation of tandem repeat polymorphism on well-selected sets of isolates. In the case of major human pathogens, such as S. aureus, more than one strain is being sequenced, so that tandem repeats most likely to be polymorphic can now be selected in silico based on genome sequence comparison. Results In addition to the previously described general Tandem Repeats Database, we have developed a tool to automatically identify tandem repeats of a different length in the genome sequence of two (or more closely related bacterial strains. Genome comparisons are pre-computed. The results of the comparisons are parsed in a database, which can be conveniently queried over the internet according to criteria of practical value, including repeat unit length, predicted size difference, etc. Comparisons are available for 16 bacterial species, and the orthopox viruses, including the variola virus and three of its close neighbors. Conclusions We are presenting an internet-based resource to help develop and perform tandem repeats based bacterial strain typing. The tools accessible at http://minisatellites.u-psud.fr now comprise four parts. The Tandem Repeats Database enables the identification of tandem repeats across entire genomes. The Strain Comparison Page identifies tandem repeats differing between different genome sequences from the same species. The "Blast in the Tandem Repeats Database" facilitates the search for a known tandem repeat and the prediction of amplification product sizes. The "Bacterial

  2. Antarctic notothenioid fishes: genomic resources and strategies for analyzing an adaptive radiation.

    Science.gov (United States)

    Detrich, H W; Amemiya, Chris T

    2010-12-01

    The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species-flock in the cold Southern Ocean that surrounds Antarctica. To facilitate genome-level studies of the diversification of these fishes, we present estimates of the genome sizes of 11 Antarctic species and describe the production of high-quality bacterial artificial chromosome (BAC) libraries for two, the red-blooded notothen Notothenia coriiceps and the white-blooded icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families (e.g., the crown group Channichthyidae [icefishes]), was accompanied by genome expansion. Six species from the basal family Nototheniidae had C-values between 0.98 and 1.20 pg, a range that is consistent with the genome sizes of proposed outgroups (e.g., percids) of the notothenioid suborder. In contrast, four icefishes had C-values in the range 1.66-1.83 pg. The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprise 12× and 10× coverage of the respective genomes and have average insert sizes of 138 and 168 kb. Paired BAC-end reads representing ∼0.1% of each genome showed that the repetitive element landscapes of the two genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The availability of these high-quality and well-characterized BAC libraries sets the stage for targeted genomic analyses of the unusual anatomical and physiological adaptations of the notothenioids, some of which mimic human diseases. Here we consider the evolution of secondary pelagicism by various taxa of the group and illustrate the utility of Antarctic icefishes as an evolutionary-mutant model of human osteopenia (low-mineral density of bones).

  3. Cereal grains and coronary heart disease.

    Science.gov (United States)

    Truswell, A S

    2002-01-01

    Cereal grains and their products provide around 30% of total energy intake in British adults, (much more than any of the other major food groups). Coronary heart disease (CHD) is the largest single cause of death in Britain and many other Western countries. This review examines the question whether there is a relation between cereal consumption and CHD. Several of the nutrients in cereals have known potential for reducing risk factors for CHD: the linoleic acid, fibre, vitamin E, selenium and folate. Cereals also contain phytoestrogens of the lignan family and several phenolic acids with antioxidant properties. Processing generally reduces the content of these nutrients and bioprotective substances. Although cereals at the farm gate are very low in salt, processed cereal foods, eg bread and some breakfast cereals, are high-salt foods and thus could contribute to raising blood pressure. Human experiments have clearly shown that oat fibre tends to lower plasma total and LDL cholesterol but wheat fibre does not. Rice bran and barley may also lower cholesterol but most people do not eat enough barley to have an effect. Cereal foods with low glycaemic index such as pasta and oats are beneficial for people with diabetes and might lower plasma lipids. Between 1996 and 2001 an accumulation of five very large cohort studies in the USA, Finland and Norway have all reported that subjects consuming relatively large amounts of whole grain cereals have significantly lower rates of CHD. This confirms an earlier report from a small British cohort. The protective effect does not seem to be due to cholesterol-lowering. While cohort studies have shown this consistent protective effect of whole grain cereals, there has been (only one) randomised controlled secondary prevention trial of advice to eat more cereal fibre. In this there was no reduction of the rate of reinfarction. The trial had some weaknesses, eg there were eight different diets, compliance was not checked objectively

  4. Breakfast Cereals: The Extreme Food Industry

    OpenAIRE

    Connor, John M.

    1996-01-01

    The purpose of my talk today is to review several aspects of the market structure, strategic rivalry, and economic performance of the ready-to-eat cereals industry. To do so, I will at times take a long historical view of the breakfast cereals industry because many of the behaviors we observe today seem to me to be imbedded in habits of business rivalry that were learned many decades ago and yet persist today. My perspective on the RTE breakfast cereals industry is informed by nearly twenty y...

  5. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

    Science.gov (United States)

    Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andrés; Álvarez-Dios, José Antonio; Cabaleiro, Santiago; Caamaño, Rubén; Martínez, Paulino; Bouza, Carmen

    2016-01-01

    Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species. PMID:26901189

  6. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot.

    Science.gov (United States)

    Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andrés; Álvarez-Dios, José Antonio; Cabaleiro, Santiago; Caamaño, Rubén; Martínez, Paulino; Bouza, Carmen

    2016-01-01

    Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species. PMID:26901189

  7. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

    Directory of Open Access Journals (Sweden)

    Diego Robledo

    2016-02-01

    Full Text Available Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs. Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.

  8. InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data

    Institute of Scientific and Technical Information of China (English)

    Christopher G.Love; Ambrose E.Andongabo; Jun Wang; Pierre W.C.Carion; Christopher J.Rawlings; Graham J.King

    2012-01-01

    Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research.InterStoreDB is a suite of integrated databases designed to assist in this process.The individual databases are species independent and generic in design,providing access to curated datasets relating to plant populations,phenotypic traits,genetic maps,marker loci and QTL,with links to functional gene annotation and genomic sequence data.Each component database provides access to associated metadata,including data provenance and parameters used in analyses,thus providing users with information to evaluate the relative worth of any associations identified.The databases include CropStoreDB,for management of population,genetic map,QTL and trait measurement data,SeqStoreDB for sequence-related data and AlignStoreDB,which stores sequence alignment information,and allows navigation between genetic and genomic datasets.Genetic maps are visualized and compared using the CMAP tool,and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser.This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal.We demonstrate the value of InterStoreDB as a tool for Brassica research.InterStoreDB is available from:http:llwww.interstoredb.org

  9. Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources

    Directory of Open Access Journals (Sweden)

    Waugh Robbie

    2010-12-01

    Full Text Available Abstract Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B. However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.

  10. Iron in Breakfast Cereal. Demonstrations for National Chemistry Week 2004

    Science.gov (United States)

    Jacobsen, Erica K.; Maynard, James

    2004-11-01

    Cereal manufacturers have a few choices for how they include iron in their products. Some cereal manufacturers prefer to add particles of pure iron metal (called elemental iron or reduced iron) because elemental iron is stable in storage and does not affect the cereal's flavor. General Mills' brand-name "Total" is one such cereal. The addition of this strongly magnetic form of iron allows "Total" cereal to be used in the two demonstrations described in this article. In the first, a flake of "Total" cereal is inserted between the two poles of a permanent magnet. The iron in the cereal allows the flake to remain suspended between the two poles. The second uses crushed "Total" cereal and a neodymium magnet. The crushed cereal is scattered over clear Plexiglas and the magnet can be moved around underneath. This drags the iron filings through the crushed cereal.

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

    Directory of Open Access Journals (Sweden)

    Sharpton Thomas J

    2012-10-01

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

  12. Food Microscopy and the Nutritional Quality of Cereal Foods

    OpenAIRE

    Yiu, Suk Hing

    1993-01-01

    The nutritional quality of cereal foods is directly related to the nature of nutrient storage in cereal grains. Most cereal nutrients, such as carbohydrates and minerals , are st ructurally bound. Processing alters the structural organization of the cereal grain. Results obtained from many nutritional studies indicate that the structure and physical form of a cereal food greatly influence the availability of its nutrients. Using oats and wheat as examples, this review demonstrates how micr...

  13. Winter and Spring Cereal Production in the Maritimes

    OpenAIRE

    Nelson, Karen; MacKenzie, Joanna; Hammermeister, Andy

    2010-01-01

    Organic producers have expressed an interest in diversifying their crop rotations through the inclusion of winter cereals. Winter cereals have many potential benefits, as they provide soil cover over the winter months, can often out-compete weeds in the spring and can be harvested earlier than other cereal crops. This study aimed to evaluate the effect of management history on the performance of winter cereals versus spring cereals.

  14. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics.

    Science.gov (United States)

    Mustafiz, Ananda; Kumari, Sumita; Karan, Ratna

    2016-06-01

    Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population. PMID:27252584

  15. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics.

    Science.gov (United States)

    Mustafiz, Ananda; Kumari, Sumita; Karan, Ratna

    2016-06-01

    Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.

  16. Reactivity of lipids during cereal processing

    OpenAIRE

    Lehtinen, Pekka

    2003-01-01

    The study elucidates factors affecting the reactivity of lipids in multiphase food systems, such as processed cereal food products. By using oat and oat products as model materials, both enzymatic and non-enzymatic lipid reactions were studied in aqueous suspensions and in dry flour. The information obtained can be used to improve existing cereal processing schemes and to develop new processing technologies for obtaining high quality food products with enhanced shelf stability. In aqueous...

  17. Panzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome

    Science.gov (United States)

    Maize, a classical model for genetic studies, is an important agronomic crop, and the genome is known to contain many natural differences in the DNA between different strains. On average, two randomly chosen maize lines have an average of one single nucleotide polymorphism (SNP) every ~100 bp; this...

  18. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

    Science.gov (United States)

    Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha; Dhanda, Sandeep Kumar; Sehgal, Manika; Khan, Md. Shoaib; Monga, Isha; Dar, Showkat Ahmad; Singh, Sandeep; Nagpal, Gandharva; Usmani, Salman Sadullah; Thakur, Anamika; Kaur, Gazaldeep; Sharma, Shivangi; Bhardwaj, Aman; Qureshi, Abid; Raghava, Gajendra Pal Singh; Kumar, Manoj

    2016-01-01

    Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates. PMID:27633273

  19. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis.

    Science.gov (United States)

    Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha; Dhanda, Sandeep Kumar; Sehgal, Manika; Khan, Md Shoaib; Monga, Isha; Dar, Showkat Ahmad; Singh, Sandeep; Nagpal, Gandharva; Usmani, Salman Sadullah; Thakur, Anamika; Kaur, Gazaldeep; Sharma, Shivangi; Bhardwaj, Aman; Qureshi, Abid; Raghava, Gajendra Pal Singh; Kumar, Manoj

    2016-01-01

    Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates.

  20. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis.

    Science.gov (United States)

    Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha; Dhanda, Sandeep Kumar; Sehgal, Manika; Khan, Md Shoaib; Monga, Isha; Dar, Showkat Ahmad; Singh, Sandeep; Nagpal, Gandharva; Usmani, Salman Sadullah; Thakur, Anamika; Kaur, Gazaldeep; Sharma, Shivangi; Bhardwaj, Aman; Qureshi, Abid; Raghava, Gajendra Pal Singh; Kumar, Manoj

    2016-01-01

    Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates. PMID:27633273

  1. Black raspberry genomic and genetic resource development to enable cultivar improvement

    Science.gov (United States)

    This project incorporates use of phenotypic, genotypic and genomic data to advance and streamline identification of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis L.). A lack of adapted, disease resistant cultivars has...

  2. Carotenoids in Staple Cereals: Metabolism, Regulation, and Genetic Manipulation.

    Science.gov (United States)

    Zhai, Shengnan; Xia, Xianchun; He, Zhonghu

    2016-01-01

    Carotenoids play a critical role in animal and human health. Animals and humans are unable to synthesize carotenoids de novo, and therefore rely upon diet as sources of these compounds. However, major staple cereals often contain only small amounts of carotenoids in their grains. Consequently, there is considerable interest in genetic manipulation of carotenoid content in cereal grain. In this review, we focus on carotenoid metabolism and regulation in non-green plant tissues, as well as genetic manipulation in staple cereals such as rice, maize, and wheat. Significant progress has been made in three aspects: (1) seven carotenogenes play vital roles in carotenoid regulation in non-green plant tissues, including 1-deoxyxylulose-5-phosphate synthase influencing isoprenoid precursor supply, phytoene synthase, β-cyclase, and ε-cyclase controlling biosynthesis, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase and carotenoid cleavage dioxygenases responsible for degradation, and orange gene conditioning sequestration sink; (2) provitamin A-biofortified crops, such as rice and maize, were developed by either metabolic engineering or marker-assisted breeding; (3) quantitative trait loci for carotenoid content on chromosomes 3B, 7A, and 7B were consistently identified, eight carotenogenes including 23 loci were detected, and 10 gene-specific markers for carotenoid accumulation were developed and applied in wheat improvement. A comprehensive and deeper understanding of the regulatory mechanisms of carotenoid metabolism in crops will be beneficial in improving our precision in improving carotenoid contents. Genomic selection and gene editing are emerging as transformative technologies for provitamin A biofortification. PMID:27559339

  3. Carotenoids in Staple Cereals: Metabolism, Regulation, and Genetic Manipulation

    Science.gov (United States)

    Zhai, Shengnan; Xia, Xianchun; He, Zhonghu

    2016-01-01

    Carotenoids play a critical role in animal and human health. Animals and humans are unable to synthesize carotenoids de novo, and therefore rely upon diet as sources of these compounds. However, major staple cereals often contain only small amounts of carotenoids in their grains. Consequently, there is considerable interest in genetic manipulation of carotenoid content in cereal grain. In this review, we focus on carotenoid metabolism and regulation in non-green plant tissues, as well as genetic manipulation in staple cereals such as rice, maize, and wheat. Significant progress has been made in three aspects: (1) seven carotenogenes play vital roles in carotenoid regulation in non-green plant tissues, including 1-deoxyxylulose-5-phosphate synthase influencing isoprenoid precursor supply, phytoene synthase, β-cyclase, and ε-cyclase controlling biosynthesis, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase and carotenoid cleavage dioxygenases responsible for degradation, and orange gene conditioning sequestration sink; (2) provitamin A-biofortified crops, such as rice and maize, were developed by either metabolic engineering or marker-assisted breeding; (3) quantitative trait loci for carotenoid content on chromosomes 3B, 7A, and 7B were consistently identified, eight carotenogenes including 23 loci were detected, and 10 gene-specific markers for carotenoid accumulation were developed and applied in wheat improvement. A comprehensive and deeper understanding of the regulatory mechanisms of carotenoid metabolism in crops will be beneficial in improving our precision in improving carotenoid contents. Genomic selection and gene editing are emerging as transformative technologies for provitamin A biofortification. PMID:27559339

  4. Development of genomic resources for the prairie vole (Microtus ochrogaster: construction of a BAC library and vole-mouse comparative cytogenetic map

    Directory of Open Access Journals (Sweden)

    Young Larry J

    2010-01-01

    Full Text Available Abstract Background The prairie vole (Microtus ochrogaster is a premier animal model for understanding the genetic and neurological basis of social behaviors. Unlike other biomedical models, prairie voles display a rich repertoire of social behaviors including the formation of long-term pair bonds and biparental care. However, due to a lack of genomic resources for this species, studies have been limited to a handful of candidate genes. To provide a substrate for future development of genomic resources for this unique model organism, we report the construction and characterization of a bacterial artificial chromosome (BAC library from a single male prairie vole and a prairie vole-mouse (Mus musculus comparative cytogenetic map. Results We constructed a prairie vole BAC library (CHORI-232 consisting of 194,267 recombinant clones with an average insert size of 139 kb. Hybridization-based screening of the gridded library at 19 loci established that the library has an average depth of coverage of ~10×. To obtain a small-scale sampling of the prairie vole genome, we generated 3884 BAC end-sequences totaling ~2.8 Mb. One-third of these BAC-end sequences could be mapped to unique locations in the mouse genome, thereby anchoring 1003 prairie vole BAC clones to an orthologous position in the mouse genome. Fluorescence in situ hybridization (FISH mapping of 62 prairie vole clones with BAC-end sequences mapping to orthologous positions in the mouse genome was used to develop a first-generation genome-wide prairie vole-mouse comparative cytogenetic map. While conserved synteny was observed between this pair of rodent genomes, rearrangements between the prairie vole and mouse genomes were detected, including a minimum of five inversions and 16 inter-chromosomal rearrangements. Conclusions The construction of the prairie vole BAC library and the vole-mouse comparative cytogenetic map represent the first genome-wide modern genomic resources developed for this

  5. ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes

    OpenAIRE

    Hu, Gang-Qing; Zheng, Xiaobin; Yang, Yi-Fan; Ortet, Philippe; She, Zhen-Su; Zhu, Huaiqiu

    2007-01-01

    Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous gene...

  6. Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms.

    Science.gov (United States)

    Quillery, E; Quenez, O; Peterlongo, P; Plantard, O

    2014-03-01

    Assessing the genetic variability of the tick Ixodes ricinus-an important vector of pathogens in Europe-is an essential step for setting up antitick control methods. Here, we report the first identification of a set of SNPs isolated from the genome of I. ricinus, by applying a reduction in genomic complexity, pyrosequencing and new bioinformatics tools. Almost 1.4 million of reads (average length: 528 nt) were generated with a full Roche 454 GS FLX run on two reduced representation libraries of I. ricinus. A newly developed bioinformatics tool (DiscoSnp), which isolates SNPs without requiring any reference genome, was used to obtain 321 088 putative SNPs. Stringent selection criteria were applied in a bioinformatics pipeline to select 1768 SNPs for the development of specific primers. Among 384 randomly SNPs tested by Fluidigm genotyping technology on 464 individuals ticks, 368 SNPs loci (96%) exhibited the presence of the two expected alleles. Hardy-Weinberg equilibrium tests conducted on six natural populations of ticks have shown that from 26 to 46 of the 384 loci exhibited significant heterozygote deficiency. PMID:24119113

  7. A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

    DEFF Research Database (Denmark)

    Pujolar, J.M.; Jacobsen, M.W.; Frydenberg, J.;

    2013-01-01

    Reduced representation genome sequencing such as restriction-site-associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the Eu...... 425 loci and 376 918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome......Reduced representation genome sequencing such as restriction-site-associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers...

  8. Priority regions for research on dryland cereals and legumes [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Glenn Hyman

    2016-05-01

    Full Text Available Dryland cereals and legumes  are important crops in farming systems across the world.  Yet they are frequently neglected among the priorities for international agricultural research and development, often due to lack of information on their magnitude and extent. Given what we know about the global distribution of dryland cereals and legumes, what regions should be high priority for research and development to improve livelihoods and food security? This research evaluated the geographic dimensions of these crops and the farming systems where they are found worldwide. The study employed geographic information science and data to assess the key farming systems and regions for these crops. Dryland cereal and legume crops should be given high priority in 18 farming systems worldwide, where their cultivated area comprises more than 160 million ha. These regions include the dryer areas of South Asia, West and East Africa, the Middle East and North Africa, Central America and other parts of Asia. These regions are prone to drought and heat stress, have limiting soil constraints, make up half of the global population and account for 60 percent of the global poor and malnourished. The dryland cereal and legume crops and farming systems merit more research and development attention to improve productivity and address development problems. This project developed an open access dataset and information resource that provides the basis for future analysis of the geographic dimensions of dryland cereals and legumes.

  9. Priority regions for research on dryland cereals and legumes [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Glenn Hyman

    2016-07-01

    Full Text Available Dryland cereals and legumes  are important crops in farming systems across the world.  Yet they are frequently neglected among the priorities for international agricultural research and development, often due to lack of information on their magnitude and extent. Given what we know about the global distribution of dryland cereals and legumes, what regions should be high priority for research and development to improve livelihoods and food security? This research evaluated the geographic dimensions of these crops and the farming systems where they are found worldwide. The study employed geographic information science and data to assess the key farming systems and regions for these crops. Dryland cereal and legume crops should be given high priority in 18 farming systems worldwide, where their cultivated area comprises more than 160 million ha. These regions include the dryer areas of South Asia, West and East Africa, the Middle East and North Africa, Central America and other parts of Asia. These regions are prone to drought and heat stress, have limiting soil constraints, make up half of the global population and account for 60 percent of the global poor and malnourished. The dryland cereal and legume crops and farming systems merit more research and development attention to improve productivity and address development problems. This project developed an open access dataset and information resource that provides the basis for future analysis of the geographic dimensions of dryland cereals and legumes.

  10. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.

    Science.gov (United States)

    Yoshida, Catherine E; Kruczkiewicz, Peter; Laing, Chad R; Lingohr, Erika J; Gannon, Victor P J; Nash, John H E; Taboada, Eduardo N

    2016-01-01

    For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub

  11. Current issues in cereal crop biodiversity.

    Science.gov (United States)

    Moreta, Danilo E; Mathur, Prem Narain; van Zonneveld, Maarten; Amaya, Karen; Arango, Jacobo; Selvaraj, Michael Gomez; Dedicova, Beata

    2015-01-01

    The exploration, conservation, and use of agricultural biodiversity are essential components of efficient transdisciplinary research for a sustainable agriculture and food sector. Most recent advances on plant biotechnology and crop genomics must be complemented with a holistic management of plant genetic resources. Plant breeding programs aimed at improving agricultural productivity and food security can benefit from the systematic exploitation and conservation of genetic diversity to meet the demands of a growing population facing climate change. The genetic diversity of staple small grains, including rice, maize, wheat, millets, and more recently quinoa, have been surveyed to encourage utilization and prioritization of areas for germplasm conservation. Geographic information system technologies and spatial analysis are now being used as powerful tools to elucidate genetic and ecological patterns in the distribution of cultivated and wild species to establish coherent programs for the management of plant genetic resources for food and agriculture. PMID:24352706

  12. Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis; FINAL

    International Nuclear Information System (INIS)

    We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year

  13. Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Simon, M. I.; Kim, U.-J.

    2002-02-26

    We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year.

  14. Building A NGS Genomic Resource: Towards Molecular Breeding In L. Perenne

    DEFF Research Database (Denmark)

    Ruttink, Tom; Roldán-Ruiz, Isabel; Asp, Torben;

    To advance the application of molecular breeding in Lolium perenne, we have generated a sequence resource to facilitate gene discovery and SNP marker development. Illumina GAII transcriptome sequencing was performed on meristem-enriched samples of 14 Lolium genotypes. De novo assemblies for indiv...

  15. Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle.

    Science.gov (United States)

    Gompert, Zachariah; Messina, Frank J

    2016-06-01

    Trade-offs have often been invoked to explain the evolution of ecological specialization. Phytophagous insects have been especially well studied, but there has been little evidence that resource-based trade-offs contribute to the evolution of host specialization in this group. Here, we combine experimental evolution and partial genome resequencing of replicate seed beetle selection lines to test the trade-off hypothesis and measure the repeatability of evolution. Bayesian estimates of selection coefficients suggest that rapid adaptation to a poor host (lentil) was mediated by standing genetic variation at multiple genetic loci and involved many of the same variants in replicate lines. Sublines that were then switched back to the ancestral host (mung bean) showed a more gradual and variable (less repeatable) loss of adaptation to lentil. We were able to obtain estimates of variance effective population sizes from genome-wide differences in allele frequencies within and between lines. These estimates were relatively large, which suggests that the contribution of genetic drift to the loss of adaptation following reversion was small. Instead, we find that some alleles that were favored on lentil were selected against during reversion on mung bean, consistent with the genetic trade-off hypothesis. PMID:27130550

  16. Polymorphic microsatellites in the human bloodfluke, Schistosoma japonicum, identified using a genomic resource

    Directory of Open Access Journals (Sweden)

    Spear Robert

    2011-02-01

    Full Text Available Abstract Re-emergence of schistosomiasis in regions of China where control programs have ceased requires development of molecular-genetic tools to track gene flow and assess genetic diversity of Schistosoma populations. We identified many microsatellite loci in the draft genome of Schistosoma japonicum using defined search criteria and selected a subset for further analysis. From an initial panel of 50 loci, 20 new microsatellites were selected for eventual optimization and application to a panel of worms from endemic areas. All but one of the selected microsatellites contain simple tri-nucleotide repeats. Moderate to high levels of polymorphism were detected. Numbers of alleles ranged from 6 to 14 and observed heterozygosity was always >0.6. The loci reported here will facilitate high resolution population-genetic studies on schistosomes in re-emergent foci.

  17. Induced mutants for cereal grain protein improvement

    International Nuclear Information System (INIS)

    Out of 17 papers and one summary presented, six dealing with the genetic improvement of seed protein using ionizing radiations fall within the INIS subject scope. Other topics discussed were non-radiation induced mutants used for cereal grain protein improvement

  18. Predictive Modelling of Mycotoxins in Cereals

    NARCIS (Netherlands)

    Fels, van der H.J.; Liu, C.

    2015-01-01

    In dit artikel worden de samenvattingen van de presentaties tijdens de 30e bijeenkomst van de Werkgroep Fusarium weergegeven. De onderwerpen zijn: Predictive Modelling of Mycotoxins in Cereals.; Microbial degradation of DON.; Exposure to green leaf volatiles primes wheat against FHB but boosts produ

  19. Monitoring the Expression Profiles of Cereal Crops Seedlings by Using Rice cDNA Microarray

    Institute of Scientific and Technical Information of China (English)

    SUNLiang-xian; DONGHai-tao; LIDe-bao

    2004-01-01

    Through exploiting the high homology of cereal crop genes, membranous cDNA microarrays containing 3311 unique rice transcripts (including 1 639 cndosperm-derived transcripts and 1 672 mature stem-derived transcripts) were used for monitoring the expression profiles of l-leaf stage seedlings of 4 cereal crop species: rice, maize, sorghum and barley. After hybridizing with [P] labeled probes, 73.6 % of the arrayed genes generated reliable signals in all of the four cereal crops. Further analysis revealed that among the arrayed genes, a higher percentage of the endosperm-derived transcripts (86.6%) expressed than that of the mature stem-derived genes (60.9 %), indicating that most of the endosperm expressed genes functioned in young seedlings whilc considerable amount of mature stem tissue expressed genes did not express. These results also inferred that some genes might function only at certain developmental stages. By comparing the obtained profdes, 84 genes were identified constantly expressed in all the four cereal crops. Many housekeeping genes, such as polyubiquitin, ubiquitin conjugating enzyme and ribosomal proteins were included in this catalogue. The experiment also identified 14 rice seedling specifically expressed genes, including 3 biotic and abiotic stress induced genes and 1 apoptosis suppressor encoding gene Bax inhibitor-1. This investigation provided invaluable information for comparative genomics of gramineae members.

  20. Monitoring the Expression Profiles of Cereal Crops Seedlings by Using Rice cDNA Microarray

    Institute of Scientific and Technical Information of China (English)

    SUN Liang-xian; DONG Hai-tao; LI De-bao

    2004-01-01

    Through exploiting the high homology of cereal crop genes, membranous cDNA microarrays containing 3 311 unique rice transcripts (including 1 639 endosperm-derived transcripts and 1 672 mature stem-derived transcripts) were used for monitoring the expression profiles of 1-leaf stage seedlings of 4 cereal crop species: rice, maize, sorghum and barley. After hybridizing with [α-33p] labeled probes, 73.6 % of the arrayed genes generated reliable signals in all of the four cereal crops. Further analysis revealed that among the arrayed genes, a higher percentage of the endosperm-derived transcripts (86.6 %) expressed than that of the mature stem-derived genes (60.9 %), indicating that most of the endosperm expressed genes functioned in young seedlings while considerable amount of mature stem tissue expressed genes did not express. These results also inferred that some genes might function only at certain developmental stages. By comparing the obtained profiles, 84 genes were identified constantly expressed in all the four cereal crops. Many housekeeping genes, such as polyubiquitin, ubiquitin conjugating enzyme and ribosomal proteins were included in this catalogue. The experiment also identified 14 rice seedling specifically expressed genes, including 3 biotic and abiotic stress induced genes and 1 apoptosis suppressor encoding gene Bax inhibitor-1. This investigation provided invaluable information for comparative genomics of gramineae members.

  1. A gene expression resource generated by genome-wide lacZ profiling in the mouse

    Directory of Open Access Journals (Sweden)

    Elizabeth Tuck

    2015-11-01

    Full Text Available Knowledge of the expression profile of a gene is a critical piece of information required to build an understanding of the normal and essential functions of that gene and any role it may play in the development or progression of disease. High-throughput, large-scale efforts are on-going internationally to characterise reporter-tagged knockout mouse lines. As part of that effort, we report an open access adult mouse expression resource, in which the expression profile of 424 genes has been assessed in up to 47 different organs, tissues and sub-structures using a lacZ reporter gene. Many specific and informative expression patterns were noted. Expression was most commonly observed in the testis and brain and was most restricted in white adipose tissue and mammary gland. Over half of the assessed genes presented with an absent or localised expression pattern (categorised as 0-10 positive structures. A link between complexity of expression profile and viability of homozygous null animals was observed; inactivation of genes expressed in ≥21 structures was more likely to result in reduced viability by postnatal day 14 compared with more restricted expression profiles. For validation purposes, this mouse expression resource was compared with Bgee, a federated composite of RNA-based expression data sets. Strong agreement was observed, indicating a high degree of specificity in our data. Furthermore, there were 1207 observations of expression of a particular gene in an anatomical structure where Bgee had no data, indicating a large amount of novelty in our data set. Examples of expression data corroborating and extending genotype-phenotype associations and supporting disease gene candidacy are presented to demonstrate the potential of this powerful resource.

  2. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics.

    Science.gov (United States)

    Gallego Romero, Irene; Pavlovic, Bryan J; Hernando-Herraez, Irene; Zhou, Xiang; Ward, Michelle C; Banovich, Nicholas E; Kagan, Courtney L; Burnett, Jonathan E; Huang, Constance H; Mitrano, Amy; Chavarria, Claudia I; Friedrich Ben-Nun, Inbar; Li, Yingchun; Sabatini, Karen; Leonardo, Trevor R; Parast, Mana; Marques-Bonet, Tomas; Laurent, Louise C; Loring, Jeanne F; Gilad, Yoav

    2015-01-01

    Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude. PMID:26102527

  3. Conservation and improvement of native pseudo cereals of Mexico

    International Nuclear Information System (INIS)

    With the purpose of preserving the genetic resources of the local races of pseudo cereals 'red Chia' (Chenopodium berlandieri subspecies nuttalliae), Chia blanca or alegria and Chia negra (belonging to Amaranths hypochondriacus), its were carried out exploration, characterization in situ, collects and conservation activities in the Opopeo and Santa Maria Huiramangaro communities, Michoacan. Field journeys were made and collections were carried out. The morphological typification and of physical and bromatologic characters of the seed were carried out. Parcels for the In situ conservation and the collections have also settled down in two towns of the Toluca Valley for multiplication and ex situ characterization. Seed has been redistributed among the in study area producers to foment the interest of the cultivation. (Author)

  4. Resources.

    Science.gov (United States)

    Stewart, John; MacDonald, Ian

    1980-01-01

    Presents a guide to resources on television drama available to teachers for classroom use in television curriculum. Lists American and British television drama videorecordings of both series and individual presentations and offers a bibliography of "one-off" single fiction plays produced for British television. (JMF)

  5. Changing values of farm animal genomic resources. from historical breeds to the Nagoya Protocol.

    Science.gov (United States)

    Tamminen, Sakari

    2015-01-01

    The paper reviews the history of Animal genetic resources (AnGRs) and claims that over the course of history they have been conceptually transformed from economic, ecologic and scientific life forms into political objects, reflecting in the way in which any valuation of AnGRs is today inherently imbued with national politics and its values enacted by legally binding global conventions. Historically, the first calls to conservation were based on the economic, ecological and scientific values of the AnGR. While the historical arguments are valid and still commonly proposed values for conservation, the AnGR have become highly politicized since the adoption of the Convention of Biological Diversity (CBD), the subsequent Interlaken Declaration, the Global Plan for Action (GPA) and the Nagoya Protocol. The scientific and political definitions of the AnGRs were creatively reshuffled within these documents and the key criteria by which they are now identified and valued today were essentially redefined. The criteria of "in situ condition" has become the necessary starting point for all valuation efforts of AnGRs, effectively transforming their previous nature as natural property and global genetic commons into objects of national concern pertaining to territorially discrete national genetic landscapes, regulated by the sovereign powers of the parties to the global conventions. PMID:26442098

  6. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei.

    Science.gov (United States)

    Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

    2015-10-27

    The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species.

  7. Development of genomic resources for Citrus clementina: Characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences

    Directory of Open Access Journals (Sweden)

    Talon Manuel

    2008-09-01

    Full Text Available Abstract Background Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the characterization of three BAC libraries from Clementine (Citrus clementina, one of the most relevant citrus fresh fruit market cultivars, and the analyses of 46.000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement. Results Three genomic BAC libraries of Citrus clementina were constructed through EcoRI, MboI and HindIII digestions and 56,000 clones, representing an estimated genomic coverage of 19.5 haploid genome-equivalents, were picked. BAC end sequencing (BES of 28,000 clones produced 28.1 Mb of genomic sequence that allowed the identification of the repetitive fraction (12.5% of the genome and estimation of gene content (31,000 genes of this species. BES analyses identified 3,800 SSRs and 6,617 putative SNPs. Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus. Conclusion In this work, we report the characterization of three BAC libraries from C. clementina, and a new set of genomic resources that may be useful for isolation of genes underlying economically important traits, physical mapping and eventually crop improvement in Citrus species. In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has

  8. Genetic erosion of diversity in cereals

    OpenAIRE

    Petrović Sofija; Dimitrijević Miodrag

    2012-01-01

    Cereals play an important role in human nutrition. Consequently, one of the main goals in breeding is to obtain varieties with high genetic potential for yield. Modern agricultural production includes the expansion of intensive varieties over large areas that lead to narrow selection criteria in breeding programs. The consequence is a drastic reduction in the number of species and genotypes (genetic erosion), or harming biological diversity of local populat...

  9. Regulation of aleurone development in cereal grains.

    Science.gov (United States)

    Becraft, Philip W; Yi, Gibum

    2011-03-01

    The aleurone layer of cereal grains is important biologically as well as nutritionally and economically. Here, current knowledge on the regulation of aleurone development is reviewed. Recent reports suggest that the control of aleurone development is more complex than earlier models portrayed. Multiple levels of genetic regulation control aleurone cell fate, differentiation, and organization. The hormones auxin and cytokinin can also influence aleurone development. New technical advances promise to facilitate future progress.

  10. Can genomics boost productivity of orphan crops?

    Science.gov (United States)

    Advances in genomics over the past 20 years have enhanced the precision and efficiency of breeding programs in many temperate cereal crops. One of the first applications of genomics-assisted breeding has been the introgression of loci for resistance to biotic stresses or major quantitative trait loc...

  11. Therapeutic Effect of Cereal Grains: A Review.

    Science.gov (United States)

    Singhal, Poonam; Kaushik, Geetanjali

    2016-04-01

    Over the last few decades, life style changes have resulted in drastic increase in the incidence of diabetes all over the world, especially in the developing countries. Oral hypoglycemic agents and insulin form the main stay in controlling diabetes but they have prominent side effects and fail to significantly alter the course of diabetic complications. Appropriate diet and exercise programs that form a part of lifestyle modifications have proven to be greatly effective in the management of this disease. Dietary therapy is showing a bright future in the prevention and treatment of diabetes. Cereal grains which form the staple diet for humans in most of the countries are increasingly being used to treat diabetes and other associated disorders in view of their anti-diabetic and anti-lipidemic potential. Given this background, this paper reviews the possible mechanisms of lowering blood sugar and cholesterol levels possessed by various commonly consumed cereal grains. It is concluded that cereal grains are not only the potential sources of energy but also possess the therapeutic role in preventing metabolic disorders and decreasing the risk factors for cardiovascular and renal diseases. PMID:25746052

  12. Weed harrowing in organically grown cereal crops avoids yield losses without reducing weed diversity

    OpenAIRE

    Armengot, Laura; José-María, Laura; Chamorro, Lourdes; Sans, Francesc

    2013-01-01

    This report shows that weed harrowing in organic cereal fields is an efficient alternative to herbicides since weed harrowing does not reduce yields compared to weed-free plots. Arable weeds provide resources and habitat to many organisms. However, weeds are the most important constraint to crop production. Indeed, the potential crop losses of the eight major crops due to weed–crop competition amount to about 30 %. New ways of food production are needed due to the current severe biodiversity ...

  13. Efficient Use of Plant Nutrients by Cereal Crops via Optimizing Soil Conditions

    OpenAIRE

    Liu, Guodong; Li, Yuncong; Alva, Ashok

    2009-01-01

    The price of nitrogen (N) fertilizer has increased by 5 fold during the last decade. This has led to a significant decline in net returns. However, the increase in cereal grain price for the same period of time was negligible compared to that of N fertilizer price. Poorly managed N fertilization can cause potential ammonia emission and nitrate contamination of groundwater, in addition to being waste of natural resources. Thus, improving N uptake efficiency in crop production is important to m...

  14. Cereal Production Ratio and NDVI in Spain

    Science.gov (United States)

    Saa-Requejo, Antonio; Recuero, Laura; Palacios, Alicia; Díaz-Ambrona, Carlos G. H.; Tarquis, Ana M.

    2014-05-01

    Droughts are long-term phenomena affecting large regions causing significant damages both in human lives and economic losses. The use of remote sensing has proved to be very important in monitoring the growth of agricultural crops and trying to asses weather impact on crop loss. Several indices has been developed based in remote sensing data being one of them the normalized difference vegetation index (NDVI). In this study we have focus to know the correlation between NDVI data and the looses of rain fed cereal in the Spanish area where this crop is majority. For this propose data from drought damage in cereal come from the pool of agricultural insurance in Spain (AGROSEGURO) including 2007/2008 to 2011/2012 (five agricultural campaigns). This data is given as a ratio between drought party claims against the insured value of production aggregated at the agrarian region level. Medium resolution (500x500 m2) MODIS images were used during the same campaigns to estimate the eight-day composites NDVI at these locations. The NDVI values are accumulated following the normal cycle of the cereal taking in account the sowing date at different sites. At the same time, CORINE Land Cover (2006) was used to classify the pixels belonging to rain fed cereal use including a set of conditions such as pixels showing dry during summer, area in which there has been no change of use. Fallow presence is studied with particular attention as it imposes an inter annual variation between crop and bare soil and causes decreases in greenness in a pixel and mix both situations. This is more complex in the situation in which the avoid fallow and a continuous monoculture is performed. The results shown that around 40% of the area is subject to the regime of fallow while 60% have growing every year. In addition, another variation is detected if the year is humid (decrease of fallow) or dry (increase of fallow). The level of correlation between the drought damage ratios and cumulative NDVI for the

  15. Processing and storage of Indian cereal and cereal products alters its resistant starch content

    OpenAIRE

    Vaidya, Ruchi H.; Sheth, Mini K.

    2010-01-01

    Resistant Starch (RS) is prebiotic in nature and is defined as the sum of starch and products of starch degradation not absorbed in small intestine of healthy individuals but later are fermented by natural microflora of the colon to produce short chain fatty acids. RS acts as a nutraceutical and its consumption leads to many health benefits. The aim of the study is to analyze the RS content in raw and processed cereals and cereal products and determine various processing and storage effects o...

  16. {sup 210}Pb and {sup 210}Po in Finnish cereals

    Energy Technology Data Exchange (ETDEWEB)

    Turtiainen, Tuukka, E-mail: tuukka.turtiainen@stuk.f [STUK, Radiation and Nuclear Safety Authority, P.O. Box 14, 00881 Helsinki (Finland); Kostiainen, Eila, E-mail: eila.kostiainen@stuk.f [STUK, Radiation and Nuclear Safety Authority, P.O. Box 14, 00881 Helsinki (Finland); Hallikainen, Anja, E-mail: anja.hallikainen@evira.f [Finnish Food Safety Authority Evira, Mustialankatu 3, 00790 Helsinki (Finland)

    2011-05-15

    A survey was carried out on the activity concentrations of {sup 210}Pb and {sup 210}Po in cereal grains produced in Finland. The cereal species were wheat (Triticum aestivum), rye (Secale cereale), oats (Avena sativa) and barley (Hordeum vulgare), which account for 90% of the Finnish consumption of cereal products. The survey consisted of 18 flour and 13 unprocessed cereal samples and one hulled grain sample from 22 flour mills. According to the results, the mean {sup 210}Pb/{sup 210}Po concentrations in wheat grains, wheat flour, rye flour, oat grains and barley grains were 0.29, 0.12, 0.29, 0.36 and 0.36 Bq kg{sup -1}, respectively. Combined with the consumption rates of the products, we assess that the mean effective doses from {sup 210}Pb and {sup 210}Po in cereal products for the adult male and female population are 22 and 17 {mu}Sv per year, respectively.

  17. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes [v1; ref status: indexed, http://f1000r.es/445

    Directory of Open Access Journals (Sweden)

    Jennifer Wyffels

    2014-08-01

    Full Text Available Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods and actinoptergii (ray-finned fish including teleosts taxa, but limited for chondrichthyan fishes.  In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate.  SkateBase (http://skatebase.org serves as the skate genome project portal linking data, research tools, and teaching resources.

  18. Organic Cereal Variety and Variety Mixture Trials 1999 - 2003

    OpenAIRE

    Aspray, Claire

    2004-01-01

    The aim of this work was to improve the productivity and stability of organic cereal production by identifying cereal varieties and variety mixtures that are best adapted to organic farming systems. The scientific question and objective was to evaluate the relative performance of cereal mixtures against single varieties in organic systems, in terms of consistency, robustness of yield and quality. The project has run over four years on six sites chosen to represent a range of soil types...

  19. Cereal Structure and Its Relationship to Nutritional Quality

    OpenAIRE

    Yiu, S. H.

    1989-01-01

    Factors that determine the digestibility of carbohydrates and minerals in cereals are examined . Most carbohydrates and minerals in cereals are structurally bound, either surrounded by or associated with cell wall components not easily digested by non-ruminant animals and humans. Treatments such as mechanical grinding and heat improve the digestibility of nutrient s . Further processing and cooking result in structural and physeochemical changes of cereal starch, phytate, and dietary fiber. S...

  20. Intercropping of Cereals and Legumes for Forage Production

    OpenAIRE

    Hamdollah ESKANDARI; Ghanbari, Ahmad; Abdollah JAVANMARD

    2009-01-01

    Cereals are high important in feeding ruminant animals for their high dry matter production and low cost. However, cereals forage is poor in protein content which shows their low quality and nutritive value. Regarding to high feed costs of protein supplementations, legumes can be used in livestock nutrition for their high protein content and, thus, providing cost saving. Since legumes have low dry matter yield, acceptable forage yield and quality can obtained from intercropping of cereals and...

  1. Significance of coarse cereals in health and nutrition: a review

    OpenAIRE

    Kaur, Kiran Deep; Jha, Alok; Sabikhi, Latha; A. K. Singh

    2012-01-01

    This review assesses the nutritional attributes of coarse cereals and also their utilization as food and as formulated foods. These cereals are laden with phytochemicals including phenolic acids, tannins, anthocyanins, phytosterols, avenenathramides and policosanols. They possess high antioxidant properties in vitro than staple cereals and fruits by different purported pathways. There are also some anti-nutritional factors that may be reduced by certain processing treatments. Several epidemio...

  2. Construction of a genome-wide human BAC-Unigene resource. Final progress report, 1989--1996

    Energy Technology Data Exchange (ETDEWEB)

    Lim, C.S.; Xu, R.X.; Wang, M. [and others

    1996-12-31

    Currently, over 30,000 mapped STSs and 27,000 mapped Unigenes (non-redundant, unigene sets of cDNA representing EST clusters) are available for human alone. A total of 44,000 Unigene cDNA clones have been supplied by Research Genetics. Unigenes, or cDNAs are excellent resource for map building for two reasons. Firstly, they exist in two alternative forms -- as both sequence information for PCR primer pairs, and cDNA clones -- thus making library screening by colony hybridization as well as pooled library PCR possible. The authors have developed an efficient and robust procedure to screen genomic libraries with large number of DNA probes. Secondly, the linkage and order of expressed sequences, or genes are highly conserved among human, mouse and other mammalian species. Therefore, mapping with cDNA markers rather than random anonymous STSs will greatly facilitate comparative, evolutionary studies as well as physical map building. They have currently deconvoluted over 10,000 Unigene probes against a 4X coverage human BAC clones from the approved library D by high density colony hybridization method. 10,000 batches of Unigenes are arrayed in an imaginary 100 X 100 matrix from which 100 row pools and 100 column pools are obtained. Library filters are hybridized with pooled probes, thus reducing the number of hybridization required for addressing the positives for each Unigene from 10,000 to 200. Details on the experimental scheme as well as daily progress report is posted on the Web site (http://www.tree.caltech.edu).

  3. Allelic variation at a single gene increases food value in a drought-tolerant staple cereal.

    Science.gov (United States)

    Gilding, Edward K; Frère, Celine H; Cruickshank, Alan; Rada, Anna K; Prentis, Peter J; Mudge, Agnieszka M; Mace, Emma S; Jordan, David R; Godwin, Ian D

    2013-01-01

    The production of adequate agricultural outputs to support the growing human population places great demands on agriculture, especially in light of ever-greater restrictions on input resources. Sorghum is a drought-adapted cereal capable of reliable production where other cereals fail, and thus represents a good candidate to address food security as agricultural inputs of water and arable land grow scarce. A long-standing issue with sorghum grain is that it has an inherently lower digestibility. Here we show that a low-frequency allele type in the starch metabolic gene, pullulanase, is associated with increased digestibility, regardless of genotypic background. We also provide evidence that the beneficial allele type is not associated with deleterious pleiotropic effects in the modern field environment. We argue that increasing the digestibility of an adapted crop is a viable way forward towards addressing food security while maximizing water and land-use efficiency. PMID:23403584

  4. Programmed cell death in cereal aleurone.

    Science.gov (United States)

    Fath, A; Bethke, P; Lonsdale, J; Meza-Romero, R; Jones, R

    2000-10-01

    Progress in understanding programmed cell death (PCD) in the cereal aleurone is described. Cereal aleurone cells are specialized endosperm cells that function to synthesize and secrete hydrolytic enzymes that break down reserves in the starchy endosperm. Unlike the cells of the starchy endosperm, aleurone cells are viable in mature grain but undergo PCD when germination is triggered or when isolated aleurone layers or protoplasts are incubated in gibberellic acid (GA). Abscisic acid (ABA) slows down the process of aleurone cell death and isolated aleurone protoplasts can be kept alive in media containing ABA for up to 6 months. Cell death in barley aleurone occurs only after cells become highly vacuolated and is manifested in an abrupt loss of plasma membrane integrity. Aleurone cell death does not follow the apoptotic pathway found in many animal cells. The hallmarks of apoptosis, including internucleosomal DNA cleavage, plasma membrane and nuclear blebbing and formation of apoptotic bodies, are not observed in dying aleurone cells. PCD in barley aleurone cells is accompanied by the accumulation of a spectrum of nuclease and protease activities and the loss of organelles as a result of cellular autolysis.

  5. Lignan Content in Cereals, Buckwheat and Derived Foods

    Directory of Open Access Journals (Sweden)

    Alessandra Durazzo

    2013-02-01

    Full Text Available Cereal foods are a fundamental part of a balanced diet and several studies have assigned to wholemeal cereal products a protective role in human health, due to their content of bioactive compounds. Within the phytochemicals, lignans are of increasing interest for their potential anticarcinogenic, antioxidant, estrogenic and antiestrogenic activities. The aim of this work is to contribute to the updating of food lignan databases by providing the profile and the amount of lignans in cereals, buckwheat and several cereal based foods commonly consumed in human diets. Values were taken from published papers. Items were divided in different groups, namely grains, brans and flours, bread, cereal staple foods, breakfast cereals and other cereal products, and values for secoisolariciresinol, matairesinol, pinoresinol, lariciresinol are given. For example, the total average values for the mentioned lignans in grains ranged between 23 μg/100 g and 401 μg/100 g dry weight. The contribution of each single lignan molecule to the total value of lignans appears to be different for every cereal species. Lignan content and typology in processed foods depends on the raw materials used, their degree of refinement and on processing conditions.

  6. Concern over ready-to-eat breakfast cereals

    Science.gov (United States)

    The Research and Professional Brief published in the April 2008 issue of the Journal entitled "Examining the Nutritional Quality of Breakfast Cereals Marketed to Children" (1) is of concern. The authors concluded that the "the majority of children's cereals failed to meet national nutrition standard...

  7. Modeling Coupon Values for Ready-To-Eat Breakfast Cereals

    OpenAIRE

    2001-01-01

    A theoretical framework is developed to highlight the significant determinants of coupon values. A fixed effects panel data model is fitted with data from the breakfast cereal industry. The explanatory variables include own retail price, brand loyalty, brand market share, rival coupon redemptions, and firm and product type indicators. Keywords: coupons, ready-to-eat breakfast cereals, panel data model

  8. The relationship between strigolactones and Striga hermonthica infection in cereals

    NARCIS (Netherlands)

    Jamil, M.

    2012-01-01

    Cereal production in Africa is under increasing constraint due to the obligate, out-crossing, hemiparasitic weed Striga hermonthica (Del.) Benth, a member of the Scrophulariaceae family. Striga parasitizes roots of cereals like sorghum, pearl millet, maize and upland rice. It has infested about 40%

  9. INVITRO DIGESTIBILITY OF PROTEIN FROM BARLEY AND OTHER CEREALS

    DEFF Research Database (Denmark)

    Buchmann, N. B.

    1979-01-01

    , the field-grown barleys per se differed too little for the accuracy to be confirmed. The other cereals tested, oats, rye, maize, wheat, and rice, gave unsatisfactory results with pepsin/pancreatin, and also with pepsin, pancreatin, or pronase used separately. The ranking of the cereals according to in vitro...

  10. DEMAND FOR HIGH FIBER AND LOW FIBER CEREALS

    OpenAIRE

    Binkley, James K.; Eales, James S.

    2000-01-01

    Nutritional considerations are of increasing importance in some foods. To address demand for nutrition, we estimate a demand system for cereals of different nutrient types, concentrating on fiber and focussing on five Kellogg's cereals with marked differences in fiber content. Results shed light on the role of price in who demands "healthy" foods.

  11. Population genomics of Fusarium graminearum head blight pathogens in North America

    Science.gov (United States)

    In this study we utilized comparative genomics to identify candidate adaptive alleles in the fungus Fusarium graminearum, the primary pathogen of Fusarium head blight (FHB) in cereal crops. Recent epidemics of FHB have been economically devastating to agriculture, as F. graminearum reduces cereal yi...

  12. Life Cycle Assessment in the Cereal and Derived Products Sector

    DEFF Research Database (Denmark)

    Renzulli, Pietro A.; Bacenetti, Jacopo; Benedetto, Graziella;

    2015-01-01

    This chapter discusses the application of life cycle assessment methodologies to rice, wheat, corn and some of their derived products. Cereal product systems are vital for the production of commodities of worldwide importance that entail particular environmental hot spots originating from...... their widespread use and from their particular nature. It is thus important for tools such as life cycle assessment (LCA) to be tailored to such cereal systems in order to be used as a means of identifying the negative environmental effects of cereal products and highlighting possible pathways to overall...... environmental improvement in such systems. Following a brief introduction to the cereal sector and supply chain, this chapter reviews some of the current cereal-based life cycle thinking literature, with a particular emphasis on LCA. Next, an analysis of the LCA methodological issues emerging from...

  13. MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa

    Science.gov (United States)

    D'Onorio de Meo, Paolo; D'Antonio, Mattia; Griggio, Francesca; Lupi, Renato; Borsani, Massimiliano; Pavesi, Giulio; Castrignanò, Tiziana; Pesole, Graziano; Gissi, Carmela

    2012-01-01

    The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa. PMID:22123747

  14. From amplification to gene in thyroid cancer: A high-resolution mapped bacterial-artificial-chromosome resource for cancer chromosome aberrations guides gene discovery after comparative genome hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Chen, X.N.; Gonsky, R.; Korenberg, J.R. [UCLA School of Medicine, Los Angeles, CA (United States). Cedars-Sinai Research Inst.; Knauf, J.A.; Fagin, J.A. [Univ. of Cincinnati, OH (United States). Div. of Endocrinology/Metabolism; Wang, M.; Lai, E.H. [Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Pharmacology; Chissoe, S. [Washington Univ. School of Medicine, St. Louis, MO (United States). Genome Sequencing

    1998-08-01

    Chromosome rearrangements associated with neoplasms provide a rich resource for definition of the pathways of tumorigenesis. The power of comparative genome hybridization (CGH) to identify novel genes depends on the existence of suitable markers, which are lacking throughout most of the genome. The authors now report a general approach that translates CGH data into higher-resolution genomic-clone data that are then used to define the genes located in aneuploid regions. They used CGH to study 33 thyroid-tumor DNAs and two tumor-cell-line DNAs. The results revealed amplifications of chromosome band 2p21, with less-intense amplification on 2p13, 19q13.1, and 1p36 and with least-intense amplification on 1p34, 1q42, 5q31, 5q33-34, 9q32-34, and 14q32. To define the 2p21 region amplified, a dense array of 373 FISH-mapped chromosome 2 bacterial artificial chromosomes (BACs) was constructed, and 87 of these were hybridized to a tumor-cell line. Four BACs carried genomic DNA that was amplified in these cells. The maximum amplified region was narrowed to 3--6 Mb by multicolor FISH with the flanking BACs, and the minimum amplicon size was defined by a contig of 420 kb. Sequence analysis of the amplified BAC 1D9 revealed a fragment of the gene, encoding protein kinase C epsilon (PKC{epsilon}), that was then shown to be amplified and rearranged in tumor cells. In summary, CGH combined with a dense mapped resource of BACs and large-scale sequencing has led directly to the definition of PKC{epsilon} as a previously unmapped candidate gene involved in thyroid tumorigenesis.

  15. 2004 Cereals reveal an intriguing surprise: the performance of cereals on organic farms

    OpenAIRE

    Wolfe, Martin; Hinchsliffe, Kay

    2005-01-01

    The great variability in the performance of cereals on organic farms that we have highlighted from past research trials has been confirmed in a new and more widely based trial. Participation from 20 producers gives the results a robust character and has enabled us to spot something we had not previously noted. EFRC researchers Prof Martin Wolfe AND Kay Hinchsliffe set out the results. Introduction EFRC is currently working on a Defra-funded project designed to use participatory resear...

  16. Developments in breeding cereals for organic agriculture

    DEFF Research Database (Denmark)

    Wolfe, M.S.; Baresel, J.P.; Desclaux, D.;

    2008-01-01

    The need for increased sustainability of performance in cereal varieties, particularly in organic agriculture (OA), is limited by the lack of varieties adapted to organic conditions. Here, the needs for breeding are reviewed in the context of three major marketing types, global, regional, local......, in European OA. Currently, the effort is determined, partly, by the outcomes from trials that compare varieties under OA and CA (conventional agriculture) conditions. The differences are sufficiently large and important to warrant an increase in appropriate breeding. The wide range of environments within OA...... and between years, underlines the need to try to select for specific adaptation in target environments. The difficulty of doing so can be helped by decentralised breeding with farmer participation and the use of crops buffered by variety mixtures or populations. Varieties for OA need efficient nutrient uptake...

  17. Mercury levels in cereals and vegetables

    International Nuclear Information System (INIS)

    The mercury content of cereals and market vegetables was determined with the flameless Atomic Absorption Spectrophotometry cold vapor method. Except for one sample the values for rye and wheat are below 100 ppb related to plant dry matter. Significant differences in the mercury content during the growth period could not be established. The average Hg-concentration in the kernel was 11 ppb. Vegetables of the Viennese market varied in Hg content between 0.5 and 40.7 ppb (mean values on wet weight basis). Only a few samples of champignons exceeded the permitted 50 ppb Hg tolerance limit, but 89% of the samples showed values of less than or equal to 10 ppb. At per head level of 74 kg vegetables consumed in Austria and an accepted mercury level of 10 ppb the weekly mercury intake is less than 5% of the 300 μg total Hg dosis per week tolerated by the WHO/FAO. (author)

  18. Fusarium head blight of cereals in Denmark

    DEFF Research Database (Denmark)

    Kærgaard Nielsen, Linda; Jensen, Jens Due; Nielsen, Ghita Cordsen;

    2011-01-01

    Quantitative real-time polymerase chain reaction differentiating 10 Fusarium spp. and Microdochium nivale or M. majus was applied to a total of 396 grain samples of wheat, barley, triticale, oat, and rye sampled across Denmark from 2003 to 2007, along with selected samples of wheat and barley from...... 1957 to 2000, to determine incidence and abundance of individual Fusarium spp. The mycotoxins deoxynivalenol (DON), nivalenol, zearalenone, T-2, and HT-2 were quantified using liquid chromatography–double mass spectrometry. Major differences in the Fusarium species complex among the five cereals...... as well as great yearly variation were seen. Fusarium graminearum, F. culmorum, and F. avenaceum were dominant in wheat, with DON as the dominant mycotoxin. F. langsethiae, F. culmorum, and F. avenaceum were dominant in barley and oat, leading to relatively high levels of the mycotoxins T-2 and HT-2. F...

  19. Optimal root arrangement of cereal crops

    Science.gov (United States)

    Jung, Yeonsu; Park, Keunhwan; Kim, Ho-Young

    2015-11-01

    The plant root absorbs water from the soil and supplies it to the rest part of the plant. It consists of a number of root fibers, through whose surfaces water uptake occurs. There is an intriguing observation that for most of cereal crops such as maize and wheat, the volume density of root in the soil declines exponentially as a function of depth. To understand this empirical finding, we construct a theoretical model of root water uptake, where mass transfer into root surface is modeled just as heat flux around a fin. Agreement between the theoretically predicted optimal root distribution in vertical direction and biological data supports the hypothesis that the plant root has evolved to achieve the optimal water uptake in competition with neighbors. This study has practical implication in the agricultural industry as well as optimal design of water transport networks in both micro- and macroscales. Department of Mechanical and Aerospace Engineering, Seoul National University, Seoul 08826, Korea.

  20. A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development.

    Science.gov (United States)

    Mahfooz, Sahil; Singh, Satyendra P; Rakh, Ramraje; Bhattacharya, Arpita; Mishra, Nishtha; Singh, Poonam C; Chauhan, Puneet S; Nautiyal, Chandra S; Mishra, Aradhana

    2016-01-01

    Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ∼38%, whereas hexa-nuceotide repeats were the least (∼10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma. PMID:27199911

  1. A comprehensive characterization of simple sequence repeats in the sequenced Trichoderma genomes provides valuable resources for marker development

    Directory of Open Access Journals (Sweden)

    Sahil eMahfooz

    2016-04-01

    Full Text Available Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in-silico approach to compare the occurrence, relative abundance and density of SSRs in T.atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G+C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ~38%, whereas hexa-nuceotide repeats were the least (~10.2%. Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615. Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma.

  2. Occurrence of Fusarium mycotoxins in Italian cereal and cereal products from organic farming.

    Science.gov (United States)

    Juan, Cristina; Ritieni, Alberto; Mañes, Jordi

    2013-12-01

    In the present study, the occurrence of eighteen mycotoxins, nine trichothecenes (deoxynivalenol, 3-acetyl-deoxynivalenol, 15-acetyl-deoxynivalenol, nivalenol, neosolaniol, diacetoxyscirpenol, fusarenon-X, T-2 toxin and HT-2 toxin), three zearalenones (zearalenone, α-zearalenol and β-zearalenol), and six emergent mycotoxins, beauvericin and five enniatins (A, A1, B, B1 and B4), was monitored in different Italian organic cereals and cereal products by using a liquid chromatography coupled to triple quadrupole mass spectrometry method. A total of 93 organic cereal samples (wheat, barley, rye and oat) were collected from Italy. Limits of quantification ranged from 5 to 15 μg/kg. 80% of analyzed samples contained mycotoxins. The occurrence was 33%, 6.5%, 2%, 27%, 7%, 10% and 43% for deoxynivalenol, HT-2, T-2, nivalenol, zearalenone, beauvericin and enniatins, respectively. The major mycotoxin found was enniatin B4; it was detected in 40% of all analyzed samples and its levels ranged from 5.7 to 284.2 μg/kg. Risk assessment was evaluated by EDI calculations which were lower than TDI for all legislated Fusarium mycotoxins.

  3. Global Information Resources on Rice for Research and Development

    Institute of Scientific and Technical Information of China (English)

    Shri RAM; N.LAXMAN RAO

    2012-01-01

    Various issues concerning the progress of rice research are related to ambiguous germplasm identification,difficulty in tracing pedigree information,and lack of integration between genetic resources,characterization,breeding,evaluation and utilization data.These issues are the constraints in developing knowledge-intensive crop improvement programs.The rapid growth,development and the global spread of modern information and communication technology allow quick adoption in fundamental research.Thus,there is a need to provide an opportunity for the establishment of services which describe the rice information for better accessibility to information resources used by researchers to enhance the competitiveness.This work reviews some of available resources on rice bioinformatics and their roles in elucidating and propagating biological and genomic information in rice research.These reviews will also enable stakeholders to understand and adopt the change in research and development and share knowledge with the global community of agricultural scientists.The establishment like International Rice Information System,Rice Genome Research Project and Integrated Rice Genome Explorer are major initiatives for the improvement of rice.Creation of databases for comparative studies of rice and other cereals are major steps in further improvement of genetic compositions.This paper will also highlight some of the initiatives and organizations working in the field of rice improvement and explore the availability of the various web resources for the purpose of research and development of rice.We are developing a meta web server for integration of online resources such as databases,web servers and journals in the area of bioinformatics.This integrated platform,with acronym /BIRA,is available online at http://ibiranet.in.The resources reviewed here are the excerpts from the resources integrated in /BIRA.

  4. Nitrogen-Use Efficiency, Nitrous Oxide Emissions, and Cereal Production in Brazil: Current Trends and Forecasts.

    Directory of Open Access Journals (Sweden)

    Marcel Viana Pires

    Full Text Available The agriculture sector has historically been a major source of greenhouse gas (GHG emissions into the atmosphere. Although the use of synthetic fertilizers is one of the most common widespread agricultural practices, over-fertilization can lead to negative economic and environmental consequences, such as high production costs, depletion of energy resources, and increased GHG emissions. Here, we provide an analysis to understand the evolution of cereal production and consumption of nitrogen (N fertilizers in Brazil and to correlate N use efficiency (NUE with economic and environmental losses as N2O emissions. Our results show that the increased consumption of N fertilizers is associated with a large decrease in NUE in recent years. The CO2 eq. of N2O emissions originating from N fertilization for cereal production were approximately 12 times higher in 2011 than in 1970, indicating that the inefficient use of N fertilizers is directly related to environmental losses. The projected N fertilizer forecasts are 2.09 and 2.37 million ton for 2015 and 2023, respectively. An increase of 0.02% per year in the projected NUE was predicted for the same time period. However, decreases in the projected CO2 eq. emissions for future years were not predicted. In a hypothetical scenario, a 2.39% increase in cereal NUE would lead to $ 21 million savings in N fertilizer costs. Thus, increases in NUE rates would lead not only to agronomic and environmental benefits but also to economic improvement.

  5. Nitrogen-Use Efficiency, Nitrous Oxide Emissions, and Cereal Production in Brazil: Current Trends and Forecasts.

    Science.gov (United States)

    Pires, Marcel Viana; da Cunha, Dênis Antônio; de Matos Carlos, Sabrina; Costa, Marcos Heil

    2015-01-01

    The agriculture sector has historically been a major source of greenhouse gas (GHG) emissions into the atmosphere. Although the use of synthetic fertilizers is one of the most common widespread agricultural practices, over-fertilization can lead to negative economic and environmental consequences, such as high production costs, depletion of energy resources, and increased GHG emissions. Here, we provide an analysis to understand the evolution of cereal production and consumption of nitrogen (N) fertilizers in Brazil and to correlate N use efficiency (NUE) with economic and environmental losses as N2O emissions. Our results show that the increased consumption of N fertilizers is associated with a large decrease in NUE in recent years. The CO2 eq. of N2O emissions originating from N fertilization for cereal production were approximately 12 times higher in 2011 than in 1970, indicating that the inefficient use of N fertilizers is directly related to environmental losses. The projected N fertilizer forecasts are 2.09 and 2.37 million ton for 2015 and 2023, respectively. An increase of 0.02% per year in the projected NUE was predicted for the same time period. However, decreases in the projected CO2 eq. emissions for future years were not predicted. In a hypothetical scenario, a 2.39% increase in cereal NUE would lead to $ 21 million savings in N fertilizer costs. Thus, increases in NUE rates would lead not only to agronomic and environmental benefits but also to economic improvement. PMID:26252377

  6. Temporal Variation of Mycotoxin Producing Fungi in Norwegian Cereals

    Science.gov (United States)

    Sundheim, Leif; Brodal, Guro; Hofgaard, Inger S.; Rafoss, Trond

    2013-01-01

    Spring barley is grown on about half of the Norwegian cereal area. The rest of the area is equally divided between wheat and oats. Most years the domestic production provides 70%–80% of the domestic market for bread wheat. Barley and oats are mainly grown for animal feed. During the years 2008–2012, severe epidemics of Fusarium head blight have led to increased mycotoxin contamination of cereals. During that period, precipitation was above normal during anthesis and grain maturation. The most important mycotoxin producers have been F. avenaceum, F. culmorum, F. graminearum and F. langsethiae. Increased deoxynivalenol contamination of Norwegian cereals during recent years is due to severe F. graminearum epidemics.

  7. Functional properties of pasta enriched with variable cereal brans

    OpenAIRE

    Kaur, Gurkirat; Sharma, Savita; Nagi, H. P. S.; Dar, Basharat N.

    2011-01-01

    To explore the potentiality of cereal brans for preparation of fiber enriched pasta, various cereal brans (Wheat, Rice, Barley and Oat) were added at 0, 5, 10, 15, 20 and 25 per cent to durum wheat semolina. The effect of cereal bran enrichment on the colour, cooking, sensory quality and shelf life of enriched pasta was assessed at ambient temperature. Pasta prepared with added fiber at 25 per cent level had the highest protein and dietary fiber content as compared to control. Enrichment with...

  8. Production of Drought and Salt Tolerant Transgenic Cereal Plants

    Institute of Scientific and Technical Information of China (English)

    A. Garg; R. Wu

    2007-01-01

    @@ Genetic transformation of cereal plants is a powerful method for producing agronomically useful transgenic plants. Salt and drought stress result in substantial yield losses, which amounts to many billions of dollars each year.

  9. Phytase-mediated mineral solubilization from cereals underin vitrogastric conditions

    DEFF Research Database (Denmark)

    Nielsen, Anne V. F.; Meyer, Anne S.

    2016-01-01

    BACKGROUND Enzymatic dephosphorylation of phytic acid (inositol hexakisphosphate) in cereals may improve mineral bioavailability in humans. This study quantified enzymatic dephosphorylation of phytic acid by measuring inositol tri- to hexakisphosphate (InsP3-6) degradation and iron and zinc release...... cereal phytic acid at similar rates and to similar extents. Microbial phytase-catalysed phytate dephosphorylation was accompanied by increased iron and zinc release from the cereal substrates. For wheat bran at pH 5, the endogenous wheat phytase activity produced mineral release equal to or better than...... simulated gastric conditions. The data infer that acid stable microbial phytases can help improve iron bioavailability from phytate-rich cereal substrates via post-ingestion activity....

  10. How to Stabilize the Cereals Market in a Transition Economy

    OpenAIRE

    Ionel, Iuliana

    2005-01-01

    The Romanian cereals market is in a state of transition, because the grain marketing system is characterized by high risk for market participants. The current situation of grain market is used to estimate the necessity solutions to stabilize the market.

  11. Preparation and Properties of Cereal-Metal Complex Films

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    1 Results Various kinds of biodegradable polymer materials have been researched[1]. In our previous papers,cereals such as wheat,buckwheat,glutinous rice and nonglutinous rice were polycondenced with citric acid and polysilicic acid to prepare copolymer films respectively[2,3].These copolymer fims have relatively good mechanical properties but the water proofness is not so good.Recently,some cereals such as wheat,glutinous rice,nonglutinous rice,kaoliang,millet and maize were reacted with copper chlorid...

  12. The relationship between strigolactones and Striga hermonthica infection in cereals

    OpenAIRE

    Jamil, M

    2012-01-01

    Cereal production in Africa is under increasing constraint due to the obligate, out-crossing, hemiparasitic weed Striga hermonthica (Del.) Benth, a member of the Scrophulariaceae family. Striga parasitizes roots of cereals like sorghum, pearl millet, maize and upland rice. It has infested about 40% of the African agricultural land, resulting in severe yield losses or even complete crop failure worth US billion per annum. The subsistence farmers or approximately 300 million African people lose...

  13. Characteristic of grain contamination with weeds in some cereal varieties

    OpenAIRE

    Franciszek Pawłowski; Marian Wesołowski

    2013-01-01

    Grain contamination with weeds in winter wheat, winter rye, spring barley and seeding oats harvested with combines was examined. A different number of seeds and weed species was found to be present in 1 kg of grain of the cereal varieties compared. Certain similarities were noticed in the botanical composition and in the frequency of occurrence of weed seeds in the examined samples of cereal grains.

  14. Characteristic of grain contamination with weeds in some cereal varieties

    Directory of Open Access Journals (Sweden)

    Franciszek Pawłowski

    2013-12-01

    Full Text Available Grain contamination with weeds in winter wheat, winter rye, spring barley and seeding oats harvested with combines was examined. A different number of seeds and weed species was found to be present in 1 kg of grain of the cereal varieties compared. Certain similarities were noticed in the botanical composition and in the frequency of occurrence of weed seeds in the examined samples of cereal grains.

  15. Modeling Household Preferences for Cereals and Meats in Mexico

    OpenAIRE

    Mejia, Maria; Peel, Derrell S.

    2012-01-01

    Using 2008 household data and a two-step censored model, this article analyzes separability among preferences of the major food groups in Mexico. The main objective of the present paper was to determine if beans and potatoes are not separable from meats and cereals, respectively. Results indicate that beans belong to the protein source demand system and potatoes are not separable from cereals. Another major finding is that corn income elasticity very close to one might indicate a sensitive si...

  16. Determinants of household choice of breakfast cereals: healthy or unhealthy?

    OpenAIRE

    Golub, Alla A.; Binkley, James K.

    2005-01-01

    We studied consumer demand for more and less healthy breakfast cereals. Using ACNielsen Homescan database and USDA food nutrition data, we developed three cereal nutrition indexes for each household in the data. In addition to the standard demographic characteristics of households and prices, we included variables representing differences between private labels and national brands. We found that the structure of the industry, through its effect on the product mix produced, affects consumer ch...

  17. China's projected cereals deficits in a world context

    OpenAIRE

    Alexandratos, Nikos

    1996-01-01

    Lester Brown's recent writings about trends in China's food consumption, production and rapidly rising import requirements and his predictions that the world is running out of potential to increase production of cereals received wide publicity in the press. They increased awareness of the problem among the public, which was stimulated by recent declines in world cereals production per capita, falling stocks and sharp rises in world market prices. This paper is an attempt on my part to extract...

  18. BIOTECHNOLOGY AS A USEFUL TOOL FOR NUTRITIONAL IMPROVEMENT OF CEREAL-BASED MATERIALS ENRICHED WITH POLYUNSATURATED FATTY ACIDS AND PIGMENTS

    Directory of Open Access Journals (Sweden)

    M. Čertík

    2008-09-01

    Full Text Available Cereals represent a major food supply for humanity. Although these sources are rich in proteins and carbohydrates, many of them are deficient in several essential nutrients, such as polyunsaturated fatty acids (PUFAs and carotenoid pigments. One possible approach how to enhance the content of PUFAs or carotenoids in cereal diet is based on biotechnological transformation of cereal materials by solid state fermentations. This technique is powerful tool for effective valorisation of these resources to various types of value-added bioproducts with demanded properties and functions. Selected filamentous Mucorales fungi were applied for conversion of numerous agroindustrial substrates to bioproducts enriched with PUFAs, such as gamma-linolenic acid (GLA, dihomo-gamma-linolenic acid (DGLA, arachidonic acid (AA and eicosapentaenoic acid (EPA. On the other hand, a range of yeast species utilizing agroindustrial substrates were employed for formation of carotenoids, such as β-carotene, torulene, torularhodine and astaxanthin. Such naturally prepared cereal based bioproducts enriched with either PUFAs or carotenoid pigments may be used as an inexpensive food and feed supplement. The work was supported by grant VEGA No. 1/0747/08 from the Grant Agency of Ministry of Education, Slovak Republic.

  19. Spontaneous and divergent hexaploid triticales derived from common wheat × rye by complete elimination of D-genome chromosomes.

    Directory of Open Access Journals (Sweden)

    Hao Li

    Full Text Available Hexaploid triticale could be either synthesized by crossing tetraploid wheat with rye, or developed by crossing hexaploid wheat with a hexaploid triticale or an octoploid triticale.Here two hexaploid triticales with great morphologic divergence derived from common wheat cultivar M8003 (Triticum aestivum L. × Austrian rye (Secale cereale L. were reported, exhibiting high resistance for powdery mildew and stripe rust and potential for wheat improvement. Sequential fluorescence in situ hybridization (FISH and genomic in situ hybridization (GISH karyotyping revealed that D-genome chromosomes were completely eliminated and the whole A-genome, B-genome and R-genome chromosomes were retained in both lines. Furthermore, plentiful alterations of wheat chromosomes including 5A and 7B were detected in both triticales and additionally altered 5B, 7A chromosome and restructured chromosome 2A was assayed in N9116H and N9116M, respectively, even after selfing for several decades. Besides, meiotic asynchrony was displayed and a variety of storage protein variations were assayed, especially in the HMW/LMW-GS region and secalins region in both triticales.This study confirms that whole D-genome chromosomes could be preferentially eliminated in the hybrid of common wheat × rye, "genome shock" was accompanying the allopolyploidization of nascent triticales, and great morphologic divergence might result from the genetic variations. Moreover, new hexaploid triticale lines contributing potential resistance resources for wheat improvement were produced.

  20. Functional genomics strategies with transposons in rice

    NARCIS (Netherlands)

    Greco, R.

    2003-01-01

    Rice is a major staple food crop and a recognizedmonocotylenedousmodel plant from which gene function discovery is projected to contribute to improvements in a variety of cereals like wheat and maize. The recent release of rough drafts of the rice genome sequence for public

  1. Functional properties of pasta enriched with variable cereal brans.

    Science.gov (United States)

    Kaur, Gurkirat; Sharma, Savita; Nagi, H P S; Dar, Basharat N

    2012-08-01

    To explore the potentiality of cereal brans for preparation of fiber enriched pasta, various cereal brans (Wheat, Rice, Barley and Oat) were added at 0, 5, 10, 15, 20 and 25 per cent to durum wheat semolina. The effect of cereal bran enrichment on the colour, cooking, sensory quality and shelf life of enriched pasta was assessed at ambient temperature. Pasta prepared with added fiber at 25 per cent level had the highest protein and dietary fiber content as compared to control. Enrichment with variable fiber sources improved the brightness of pasta, as colour of pasta enhanced significantly. Addition of cereal brans resulted an increase in the water absorption and cooking losses of pasta. This effect was dependent on the level and type of cereal brans. Significant correlation (r = 0.80) was obtained between water absorption and volume expansion in all types of bran enriched pasta. At 25 per cent level of supplementation, maximum solids were leached into cooking water. Bran enriched pasta required less cooking time for complete gelatinization of starch. Increasing level of cereal brans had significantly affected the overall acceptability of enriched pasta. Cooking quality of pasta remained constant during storage. Non significant effect of storage was found on water activity, free fatty acids. Enriched pasta (15 per cent level of wheat, rice and oat bran and 10 per cent barley bran) was highly acceptable upto 4 months of storage with respect to quality.

  2. Distribution patterns of segetal weeds of cereal crops in tajikistan

    International Nuclear Information System (INIS)

    Using the literature data and field research conducted in 2009-2013 the distribution patterns, habitat conditions, phytogeographical characterisation and endangerment of weeds occurring in cereal crops in Tajikistan were analysed. We found out that Tajik weed flora of cereal crops counts 686 taxa. The most species rich families include Asteraceae, Poaceae and Fabaceae. The highest number of cereal weeds were noted in large river valleys of Syr-Daria, Amu-Daria and their tributaries in south-western and northern Tajikistan. This subregions have the warmest climate conditions and extensive arable lands. The greatest weed species richness was observed in submontane and montane elevations between approx. 700 and 1,900 m a.s. Cereal weeds occur frequently outside segetal communities in Tajikistan. They were noted usually in screes, wastelands, xerothermophilous grasslands, river gravel beds and in steppes habitats. The assessment of threat status reveals that ca. 33% of total cereal weed flora in Tajikistan are disappearing or occur very rarely. According to the chorological data we find that in the cereals of Tajikistan, 35 endemic and 14 subendemic species occur. The most numerous chorological elements of threatened weed flora of Tajikistan are Irano-Turanian (55%), pluriregional (16%), cosmopolitan (14,5%), Mediterranean (9%) and Eurosiberian (5%) species. Further research is suggested to explore the distribution patterns of all weed species in Tajikistan as it should be useful for economy and effectiveness of crop production as well as conservation of most valuable species. (author)

  3. Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction.

    Science.gov (United States)

    Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A; Lyons, Russell E; Salin, Krishna R; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B

    2016-05-07

    The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world's most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.

  4. Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii: The Identification of Genes and Markers Associated with Reproduction

    Directory of Open Access Journals (Sweden)

    Hyungtaek Jung

    2016-05-01

    Full Text Available The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.

  5. Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction.

    Science.gov (United States)

    Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A; Lyons, Russell E; Salin, Krishna R; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B

    2016-01-01

    The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world's most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium. PMID:27164098

  6. A potent bidirectional promoter from the monocot cereal Eleusine coracana.

    Science.gov (United States)

    Sen, Saswati; Dutta, Samir Kr

    2016-09-01

    Ragi bifunctional α-amylase-trypsin inhibitor (RBI) of Eleusine coracana (L.) Gaertn. (finger millet) simultaneously inhibits α-amylase and trypsin. In continuation of previous work on the cloning, expression and characterization of RBI, a bidirectional promoter from finger millet was explored on the basis of experimental observations. Two trypsin inhibitors were identified while purifying RBI from a trypsin-Sepharose column eluent. Using an FPLC gel filtration column, these three inhibitors were purified to homogeneity and subjected to MALDI-TOF-TOF-MS/MS analysis and N-terminal sequencing. Both ragi trypsin inhibitors (RTIs) showed the same N-terminal sequence and considerable sequence similarity to RBI, indicating the presence of a multigene protease inhibitor family in finger millet. To gain insight into the evolution of these genes, the upstream region of RBI was explored by Genome Walking. Interestingly, on sequencing, a genome walking product of ∼1 Kb showed presence of an N-terminal RBI specific primer sequence twice but in opposite directions and leaving an intervening region of ∼0.9 Kb. The intervening region was presumed to represent an E. coracana bidirectional promoter (EcBDP), intuitively having a divergent RBI-RTI gene pair at two sides. For assaying the bidirectionality of promoter activity, a dual reporter GUS-GFP vector construct was made for plant expression containing the reporter genes at two ends of EcBDP, which was used to transform Agrobacterium tumefaciens LBA 4404. Transient plant transformation by recombinant Agrobacterium cells was carried out in onion scale epidermal cells and finger millet seedling leaves. Simultaneous expression of GUS and GFP under EcBDP established it as a potent natural bidirectional promoter from monocot origin, thereby potentially having vast application in cereal gene manipulations. In addition, inducibility of the EcBDP by either abscisic acid or cold treatment, as determined by transient

  7. Orthology between genomes of Brachypodium, wheat and rice

    Directory of Open Access Journals (Sweden)

    Balyan Harindra S

    2009-05-01

    Full Text Available Abstract Background In the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, Brachypodium distachyon genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, Brachypodium EST contigs were utilized to resolve orthologous relationships among the genomes of Brachypodium, wheat and rice. Findings Comparative sequence analysis of 3,818 Brachypodium EST (bEST contigs and 3,792 physically mapped wheat EST (wEST contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of Brachypodium, wheat and rice. Conclusion The present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals.

  8. Alternative cereal grains and cereal by-products as sources of energy in poultry diets- A review

    OpenAIRE

    C. I. Medugu,; A. O. Raji,; J. U. Igwebuike; E. Barwa

    2011-01-01

    The increase in the world population, high cost of conventional animal feed ingredients and low protein intake in most developing countries has necessitated animal scientists to search for alternative sources of feed ingredients. This can enhance the production of animals with short generation intervals such as poultry to overcome the protein deficiency. This paper reviews cereal grains and cereal by-products as alternative feed ingredients for formulating poultry diets. Results obtained from...

  9. Development of cereal-based functional food using cereal-mix substrate fermented with probiotic strain - Pichia kudriavzevii OG32.

    Science.gov (United States)

    Ogunremi, Omotade R; Agrawal, Renu; Sanni, Abiodun I

    2015-11-01

    Probiotic strains contribute to the functionality of foods during fermentation. In this present work, cereal-mix was fermented with probiotic Pichia kudriavzevii OG32. Selected fermentation parameters and functional properties of the product were determined. The growth of Pichia kudriavzevii OG32 was supported by the cereal-mix containing 1% salt and 0.2% red chili powder to counts of between 7.46 and 8.22 Log10 cfu/mL within 24 h. Pichia kudriavzevii OG32 increased the viscosity of cereal-mix with the highest inoculum size (1.84x105cfu/ml) giving the highest viscosity of 1793.6 mPa.S. An inoculum size of 1.98 × 10(4) cfu/mL gave the most acceptable product based on the sensory evaluation by the panelist. Forty volatile compounds were identified in the fermented product, while acids (32.21%) and esters (32.37%) accounted for the largest proportions. The cereal-based fermented product scavenged DPPH from 200 μmol/L methanolic solution by 55.71%. Probiotic yeast improved the sensory and some functional properties of cereal-based substrate during fermentation. This is one of the first reports on the volatile composition of cereal-based functional food produced with probiotic yeast. PMID:26788290

  10. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

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

    DEFF Research Database (Denmark)

    Weber, Tilmann; Blin, Kai; Duddela, Srikanth;

    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...... 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...

  12. Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions

    Science.gov (United States)

    Culicoides biting midges (Diptera: Ceratopogonidae) are a major vector group responsible for the biological transmission of a wide variety of globally significant arboviruses, including bluetongue virus (BTV). In this review we examine current biological resources for the study of this genus, with a...

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

    Science.gov (United States)

    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.

  14. Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis: EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

    Directory of Open Access Journals (Sweden)

    Planas Josep V

    2008-10-01

    Full Text Available Abstract Background The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species. Results Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis, larval stages (pre-metamorphosis, metamorphosis, juvenile stages (post-metamorphosis, abnormal fish, and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs. Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34% had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data. Conclusion New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions.

  15. Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

    Science.gov (United States)

    Cerdà, Joan; Mercadé, Jaume; Lozano, Juan José; Manchado, Manuel; Tingaud-Sequeira, Angèle; Astola, Antonio; Infante, Carlos; Halm, Silke; Viñas, Jordi; Castellana, Barbara; Asensio, Esther; Cañavate, Pedro; Martínez-Rodríguez, Gonzalo; Piferrer, Francesc; Planas, Josep V; Prat, Francesc; Yúfera, Manuel; Durany, Olga; Subirada, Francesc; Rosell, Elisabet; Maes, Tamara

    2008-01-01

    Background The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species. Results Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data. Conclusion New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions. PMID:18973667

  16. Storage stability and quality assessment of processed cereal brans.

    Science.gov (United States)

    Sharma, Savita; Kaur, Satinder; Dar, B N; Singh, Baljit

    2014-03-01

    Quality improvement of cereal brans, a health promoting ingredient for functional foods is the emerging research concept due to their low shelf stability and presence of non-nutrient components. A study was conducted to evaluate the storage quality of processed milling industry byproducts so that these can be potentially utilized as a dietary fibre source. Different cereal brans (wheat, rice, barley and oat) were processed by dry, wet, microwave heating, extrusion cooking and chemical methods at variable conditions. Processed brans were stored in high density polyethylene (HDPE) pouches at ambient and refrigeration temperature. Quality assessments (moisture, free fatty acids, water activity and physical quality) of brans were done up to six months, at one month intervals. Free fatty acid content, moisture and water activity of the cereal brans remained stable during the entire storage period. Among treatments, extrusion processing is the most effective for stability. Processing treatments and storage temperature have the positive effect on extending the shelf life of all cereal brans. Therefore, processed cereal brans can be used as a dietary fortificant for the development of value added food products. PMID:24587536

  17. Molecular genetics and evolution of disease resistance in cereals.

    Science.gov (United States)

    Krattinger, Simon G; Keller, Beat

    2016-10-01

    Contents 320 I. 320 II. 321 III. 321 IV. 322 V. 324 VI. 328 VII. 329 330 References 330 SUMMARY: Cereal crops produce a large part of the globally consumed food and feed. Because of the constant presence of devastating pathogens, the molecular characterization of disease resistance is a major research area and highly relevant for breeding. There has been recent and accelerating progress in the understanding of three distinct resistance mechanisms in cereals: resistance conferred by plasma membrane-localized receptor proteins; race-specific resistance conferred by intracellular immune receptors; and quantitative disease resistance. Intracellular immune receptors provide a particularly rich source for evolutionary studies, and have, for example, resulted in the recent discovery of a novel detection mechanism based on integrated decoy domains. Evolutionary studies have also revealed the origins of active resistance genes in both wild progenitors of today's cereals as well as in cultivated forms. In addition, independent evolution of orthologous genes in related cereals has resulted in resistance to different pathogen species. Quantitative resistance genes have been best characterized in wheat. The quantitative resistance genes identified so far in wheat encode transporter proteins or unusual kinase proteins. The recent discoveries in these three different resistance mechanisms have contributed to the basic molecular understanding of cereal immunity against pathogens and have suggested novel applications for resistance breeding.

  18. Salmonella contamination of cereal ingredients for animal feeds.

    Science.gov (United States)

    Davies, R H; Wales, A D

    2013-10-25

    Cereal ingredients for animal feedstuffs may become contaminated by Salmonella on their farms of origin. This is often concentrated in multiple foci, owing to contamination by rodents and other wildlife which may be missed by routine sampling, and may involve serovars of particular public health significance, such as Salmonella Typhimurium (STM). The study examined such contamination in domestically-produced cereal ingredients in the United Kingdom. Cereal-producing farms with associated cattle or pig enterprises (43) and feedmills (6) were investigated, following the isolation of STM from their premises (feedmills) or STM DT104 from their livestock (farms) by routine surveillance. Cereal samples from feedmills yielded two STM isolates from the same premises, of the same phage types as were isolated from wild bird faeces at ingredient intake and product loading areas. Farm investigations identified numerous Salmonella serovars, including STM, on grain harvesting and handling equipment, in grain storage areas, and in wildlife samples. Mice were removed from one pig farm and shed Salmonella Derby and Salmonella Bovismorbificans for 10 months afterwards. Grain stores more than one kilometre away from livestock areas were rarely found to be contaminated with STM. The principal issues with Salmonella contamination of cereals appeared to be the use of livestock areas as temporary grain stores on cattle farms, and access to stored grain by wildlife and domestic animals. PMID:23915993

  19. Salmonella contamination of cereal ingredients for animal feeds.

    Science.gov (United States)

    Davies, R H; Wales, A D

    2013-10-25

    Cereal ingredients for animal feedstuffs may become contaminated by Salmonella on their farms of origin. This is often concentrated in multiple foci, owing to contamination by rodents and other wildlife which may be missed by routine sampling, and may involve serovars of particular public health significance, such as Salmonella Typhimurium (STM). The study examined such contamination in domestically-produced cereal ingredients in the United Kingdom. Cereal-producing farms with associated cattle or pig enterprises (43) and feedmills (6) were investigated, following the isolation of STM from their premises (feedmills) or STM DT104 from their livestock (farms) by routine surveillance. Cereal samples from feedmills yielded two STM isolates from the same premises, of the same phage types as were isolated from wild bird faeces at ingredient intake and product loading areas. Farm investigations identified numerous Salmonella serovars, including STM, on grain harvesting and handling equipment, in grain storage areas, and in wildlife samples. Mice were removed from one pig farm and shed Salmonella Derby and Salmonella Bovismorbificans for 10 months afterwards. Grain stores more than one kilometre away from livestock areas were rarely found to be contaminated with STM. The principal issues with Salmonella contamination of cereals appeared to be the use of livestock areas as temporary grain stores on cattle farms, and access to stored grain by wildlife and domestic animals.

  20. Nitrogen and phosphorus economy of a legume tree-cereal intercropping system under controlled conditions

    International Nuclear Information System (INIS)

    Considerable amounts of nitrogen (N) and phosphorus (P) fertilizers have been mis-used in agroecosystems, with profound alteration to the biogeochemical cycles of these two major nutrients. To reduce excess fertilizer use, plant-mediated nutrient supply through N2-fixation, transfer of fixed N and mobilization of soil P may be important processes for the nutrient economy of low-input tree-based intercropping systems. In this study, we quantified plant performance, P acquisition and belowground N transfer from the N2-fixing tree to the cereal crop under varying root contact intensity and P supplies. We cultivated Acacia senegal var senegal in pot-culture containing 90% sand and 10% vermiculite under 3 levels of exponentially supplied P. Acacia plants were then intercropped with durum wheat (Triticum turgidum durum) in the same pots with variable levels of adsorbed P or transplanted and intercropped with durum wheat in rhizoboxes excluding direct root contact on P-poor red Mediterranean soils. In pot-culture, wheat biomass and P content increased in relation to the P gradient. Strong isotopic evidence of belowground N transfer, based on the isotopic signature (δ15N) of tree foliage and wheat shoots, was systematically found under high P in pot-culture, with an average N transfer value of 14.0% of wheat total N after 21 days of contact between the two species. In the rhizoboxes, we observed limitations on growth and P uptake of intercropped wheat due to competitive effects on soil resources and minimal evidence of belowground N transfer of N from acacia to wheat. In this intercrop, specifically in pot-culture, facilitation for N transfer from the legume tree to the crop showed to be effective especially when crop N uptake was increased (or stimulated) as occurred under high P conditions and when competition was low. Understanding these processes is important to the nutrient economy and appropriate management of legume-based agroforestry systems. -- Highlights:

  1. Nitrogen and phosphorus economy of a legume tree-cereal intercropping system under controlled conditions

    Energy Technology Data Exchange (ETDEWEB)

    Isaac, M.E., E-mail: marney.isaac@utoronto.ca [CIRAD, UMR Eco and Sols, 34060 Montpellier (France); University of Toronto, Department of Physical and Environmental Sciences, 1265 Military Trail, Toronto, Canada M1C 1A4 (Canada); Hinsinger, P. [INRA, UMR Eco and Sols, 34060 Montpellier (France); Harmand, J.M. [CIRAD, UMR Eco and Sols, 34060 Montpellier (France)

    2012-09-15

    Considerable amounts of nitrogen (N) and phosphorus (P) fertilizers have been mis-used in agroecosystems, with profound alteration to the biogeochemical cycles of these two major nutrients. To reduce excess fertilizer use, plant-mediated nutrient supply through N{sub 2}-fixation, transfer of fixed N and mobilization of soil P may be important processes for the nutrient economy of low-input tree-based intercropping systems. In this study, we quantified plant performance, P acquisition and belowground N transfer from the N{sub 2}-fixing tree to the cereal crop under varying root contact intensity and P supplies. We cultivated Acacia senegal var senegal in pot-culture containing 90% sand and 10% vermiculite under 3 levels of exponentially supplied P. Acacia plants were then intercropped with durum wheat (Triticum turgidum durum) in the same pots with variable levels of adsorbed P or transplanted and intercropped with durum wheat in rhizoboxes excluding direct root contact on P-poor red Mediterranean soils. In pot-culture, wheat biomass and P content increased in relation to the P gradient. Strong isotopic evidence of belowground N transfer, based on the isotopic signature ({delta}{sup 15}N) of tree foliage and wheat shoots, was systematically found under high P in pot-culture, with an average N transfer value of 14.0% of wheat total N after 21 days of contact between the two species. In the rhizoboxes, we observed limitations on growth and P uptake of intercropped wheat due to competitive effects on soil resources and minimal evidence of belowground N transfer of N from acacia to wheat. In this intercrop, specifically in pot-culture, facilitation for N transfer from the legume tree to the crop showed to be effective especially when crop N uptake was increased (or stimulated) as occurred under high P conditions and when competition was low. Understanding these processes is important to the nutrient economy and appropriate management of legume-based agroforestry systems

  2. Two ancient rounds of polyploidy in rice genome

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yang; XU Guo-hua; GUO Xing-yi; FAN Long-jiang

    2005-01-01

    An ancient genome duplication (PPP 1) that predates divergence ofthe cereals has recently been recognihere another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.

  3. Temporal Variation of Mycotoxin Producing Fungi in Norwegian Cereals

    Directory of Open Access Journals (Sweden)

    Leif Sundheim

    2013-12-01

    Full Text Available Spring barley is grown on about half of the Norwegian cereal area. The rest of the area is equally divided between wheat and oats. Most years the domestic production provides 70%–80% of the domestic market for bread wheat. Barley and oats are mainly grown for animal feed. During the years 2008–2012, severe epidemics of Fusarium head blight have led to increased mycotoxin contamination of cereals. During that period, precipitation was above normal during anthesis and grain maturation. The most important mycotoxin producers have been F. avenaceum, F. culmorum, F. graminearum and F. langsethiae. Increased deoxynivalenol contamination of Norwegian cereals during recent years is due to severe F. graminearum epidemics.

  4. Natural variation in grain composition of wheat and related cereals.

    Science.gov (United States)

    Shewry, Peter R; Hawkesford, Malcolm J; Piironen, Vieno; Lampi, Ann-Maija; Gebruers, Kurt; Boros, Danuta; Andersson, Annica A M; Åman, Per; Rakszegi, Mariann; Bedo, Zoltan; Ward, Jane L

    2013-09-01

    The wheat grain comprises three groups of major components, starch, protein, and cell wall polysaccharides (dietary fiber), and a range of minor components that may confer benefits to human health. Detailed analyses of dietary fiber and other bioactive components were carried out under the EU FP6 HEALTHGRAIN program on 150 bread wheat lines grown on a single site, 50 lines of other wheat species and other cereals grown on the same site, and 23-26 bread wheat lines grown in six environments. Principal component analysis allowed the 150 bread wheat lines to be classified on the basis of differences in their contents of bioactive components and wheat species (bread, durum, spelt, emmer, and einkorn wheats) to be clearly separated from related cereals (barley, rye, and oats). Such multivariate analyses could be used to define substantial equivalence when novel (including transgenic) cereals are considered.

  5. Polycyclic aromatic hydrocarbons in cereal products on the Turkish market.

    Science.gov (United States)

    Kacmaz, Sibel

    2016-09-01

    The contamination level of four EU marker polycyclic aromatic hydrocarbons (PAHs) in some cereal-derived products was surveyed in this study. Thirty-eight samples, 20 bread and 18 breakfast cereals, were purchased from retail shops and local markets of East Black sea region in Turkey. The samples were analysed for four EU marker PAHs, using ultrasonic extraction, solid-phase extraction (SPE) clean up and stable-isotope dilution gas chromatography with mass-spectrometric (GC/MS) detection. The method was validated with the parameters linearity, accuracy, precision, limit of detection (LOD), limit of quantitation (LOQ) and uncertainty. Total content of the four PAHs in bread varied from 0.19 to 0.46 µg kg(-1) and in breakfast cereals from 0.10 to 0.87 µg kg(-1). PMID:26986946

  6. Effects of processing on mycotoxin stability in cereals.

    Science.gov (United States)

    Milani, Jafar; Maleki, Gisoo

    2014-09-01

    The mycotoxins that generally occur in cereals and other products are not completely destroyed during food-processing operations and can contaminate finished processed foods. The mycotoxins most usually associated with cereal grains are aflatoxins, ochratoxins, deoxynivalenol, zearalenone and fumonisins. The various food processes that may have effects on mycotoxins include cleaning, milling, brewing, cooking, baking, frying, roasting, flaking, alkaline cooking, nixtamalization, and extrusion. Most of the food processes have variable effects on mycotoxins, with those that utilize high temperatures having the greatest effects. In general, the processes reduce mycotoxin concentrations significantly, but do not eliminate them completely. This review focuses on the effects of various thermal treatments on mycotoxins. PMID:24497303

  7. A comprehensive BAC resource

    OpenAIRE

    Zhao, Shaying

    2001-01-01

    The Human Genome Project has generated extensive map and sequence data for a large number of Bacterial Artificial Chromosome (BAC) clones. In order to maximize the efficient use of the data and to minimize the redundant work for the research community, The Institute for Genomic Research (TIGR) comprehensive BAC resource (cBACr) (http://www.tigr.org/tdb/BacResource/BAC_resource_intro.html) was built as an expansion of the TIGR human BAC ends database. This resource coll...

  8. Molecular genetics of heat tolerance and heat shock proteins in cereals.

    Science.gov (United States)

    Maestri, Elena; Klueva, Natalya; Perrotta, Carla; Gulli, Mariolina; Nguyen, Henry T; Marmiroli, Nelson

    2002-01-01

    Heat stress is common in most cereal-growing areas of the world. In this paper, we summarize the current knowledge on the molecular and genetic basis of thermotolerance in vegetative and reproductive tissues of cereals. Significance of heat stress response and expression of heat shock proteins (HSPs) in thermotolerance of cereal yield and quality is discussed. Major avenues for increasing thermotolerance in cereals via conventional breeding or genetic modification are outlined. PMID:11999842

  9. Major Cereal Grain Fibers and Psyllium in Relation to Cardiovascular Health

    OpenAIRE

    Roizen, Michael F; Mladen Golubic; Kristin Kirkpatrick; Bernstein, Adam M.; Brigid Titgemeier

    2013-01-01

    Numerous studies reveal the cardiovascular benefits of consuming dietary fiber and, especially, cereal fiber. Cereal fiber is associated with cardiovascular risk reduction through multiple mechanisms and consuming a variety of cereal fiber sources offers health benefits specific to the source. Certain cereal fibers have been studied more extensively than others and provide greater support for their incorporation into a healthful diet. β-glucan from oats or barley, or a combination of whole oa...

  10. Projecting Meat and Cereals Demand for China Based on a Meta-Analysis of Income Elasticities

    OpenAIRE

    Zhou; Yu, Xiaohua; Abler, David; Chen, Danhong

    2014-01-01

    There are many projections for China's food demand, and the projection results differ significantly from each other. Different values for income elasticities could be a major reason. This study projects meat and cereals demand for China based on a meta-analysis of the income elasticity estimates using a collection of 143 and 240 income elasticity estimates for cereals and meat products, respectively, from 36 primary studies. We find that income elasticities for most cereals (general cereals, ...

  11. Drought impacts on cereal yields in Iberia

    Science.gov (United States)

    Gouveia, Célia; Liberato, Margarida L. R.; Russo, Ana; Montero, Irene

    2014-05-01

    In the present context of climate change, land degradation and desertification it becomes crucial to assess the impact of droughts to determine the environmental consequences of a potential change of climate. Large drought episodes in Iberian Peninsula have widespread ecological and environmental impacts, namely in vegetation dynamics, resulting in significant crop yield losses. During the hydrological years of 2004/2005 and 2011/2012 Iberia was affected by two extreme drought episodes (Garcia-Herrera et al., 2007; Trigo et al., 2013). This work aims to analyze the spatial and temporal behavior of climatic droughts at different time scales using spatially distributed time series of drought indicators, such as the Standardized Precipitation Evapotranspiration Index (SPEI) (Vicente-Serrano et al., 2010). This climatic drought index is based on the simultaneous use of precipitation and temperature. We have used CRU TS3 dataset to compute SPEI and the Standardized Precipitation Index (SPI). Results will be analyzed in terms of the mechanisms that are responsible by these drought events and will also be used to assess the impact of droughts in crops. Accordingly an analysis is performed to evaluate the large-scale conditions required for a particular extreme anomaly of long-range transport of water vapor from the subtropics. We have used the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA Interim reanalyses, namely, the geopotential height fields, temperature, wind, divergence data and the specific humidity at all pressure levels and mean sea level pressure (MSLP) and total column water vapor (TCWV) for the Euro-Atlantic sector (100°W to 50°E, 0°N-70°N) at full temporal (six hourly) and spatial (T255; interpolated to 0.75° regular horizontal grid) resolutions available to analyse the large-scale conditions associated with the drought onset. Our analysis revealed severe impacts on cereals crop productions and yield (namely wheat) for Portugal and

  12. 40 CFR 406.90 - Applicability; description of the ready-to-eat cereal subcategory.

    Science.gov (United States)

    2010-07-01

    ...-to-eat cereal subcategory. 406.90 Section 406.90 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS GRAIN MILLS POINT SOURCE CATEGORY Ready-to-Eat Cereal Subcategory § 406.90 Applicability; description of the ready-to-eat cereal subcategory....

  13. AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies

    Directory of Open Access Journals (Sweden)

    Shankavaram Uma

    2006-04-01

    Full Text Available Abstract Background Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. Description AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60 and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different

  14. Genome-wide QTL mapping for three traits related to teat number in a White Duroc × Erhualian pig resource population

    Directory of Open Access Journals (Sweden)

    Ai Huashui

    2009-02-01

    Full Text Available Abstract Background Teat number is an important fertility trait for pig production, reflecting the mothering ability of sows. It is also a discrete and often canalized trait presenting bilateral symmetry with minor differences between the two sides, providing a potential power to evaluate fluctuating asymmetry and developmental instability. The knowledge of its genetic control is still limited. In this study, a genome-wide scan was performed with 183 microsatellites covering the pig genome to identify quantitative trait loci (QTL for three traits related to teat number including the total teat number (TTN, the teat number at the left (LTN and right (RTN sides in a large scale White Duroc × Erhualian resource population. Results A sex-average linkage map with a total length of 2350.3 cM and an average marker interval of 12.84 cM was constructed. Eleven genome-wide significant QTL for TTN were detected on 8 autosomes including pig chromosomes (SSC 1, 3, 4, 5, 6, 7, 8 and 12. Six suggestive QTL for this trait were detected on SSC6, 9, 13, 14 and 16. Eight chromosomal regions each on SSC1, 3, 4, 5, 6, 7, 8 and 12 showed significant associations with LTN. These regions were also evidenced as significant QTL for RTN except for those on SSC6 and SSC8. The most significant QTL for the 3 traits were all located on SSC7. Erhualian alleles at most of the identified QTL had positive additive effects except for three QTL on SSC1 and SSC7, at which White Duroc alleles increased teat numbers. On SSC1, 6, 9, 13 and 16, significant dominance effects were observed on TTN, and predominant imprinting effect on TTN was only detected on SSC12. Conclusion The results not only confirmed the QTL regions from previous experiments, but also identified five new QTL for the total teat number in swine. Minor differences between the QTL regions responsible for LTN and RTN were validated. Further fine mapping should be focused on consistently identified regions with small

  15. Coral life history and symbiosis: Functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata

    Directory of Open Access Journals (Sweden)

    Szmant Alina M

    2008-02-01

    -scleractinian cnidarians Nematostella vectensis and Hydra magnipapillata. Conclusion Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

  16. Overview of vectors of cereal viruses in Finland

    OpenAIRE

    Huusela-Veistola, Erja

    2007-01-01

    Barley yellow dwarf virus (BYDV), Oat sterile dwarf virus (OSDV) and Wheat dwarf virus (WDV) are the most serious virus diseases of cereals in Finland. BYDV is transmitted by aphids, mainly by bird cherry oat aphid, Rhopalosiphum padi. OSDV and WDV are leafhopper transmitted viruses.

  17. Analysing lodging of the panicle bearing cereal teff (Eragrostis tef)

    NARCIS (Netherlands)

    Delden, van S.H.; Vos, J.; Ennos, A.R.; Stomph, T.J.

    2010-01-01

    •Lodging, the permanent displacement of crop plants from their vertical because of root or shoot failure, is a major yield constraint of the gluten free, panicle bearing cereal teff. The objective of this paper was to analyse the causes of lodging of teff by using, modifying and validating conventio

  18. Prevention of ochratoxin A in cereals in Europe

    DEFF Research Database (Denmark)

    Olsen, Monica; Jonsson, Nils; Magan, Naresh;

    2006-01-01

    This paper describes objectives and activities of a major European Community project (OTA PREV) aimed at understanding sources of contamination of ochratoxin A in European cereals and related food-stuffs, and the development of strategies to minimise ochratoxin A in the food supply. The project ran...

  19. POTENTIAL OF CEREALS AND PSEUDOCEREALS FOR LACTIC ACID FERMENTATIONS

    Directory of Open Access Journals (Sweden)

    Ľubomír Valík

    2011-04-01

    Full Text Available Cereals and pseudocereals play a significant role in human nutrition. They are source of specific carbohydrates, proteins, lipids, fibre and wide spectrum of vitamins and minerals. Moreover, pseudocereals have a higher content of essential amino acids, e.g. lysine and tryptophan. Cereals and pseudocereals may also contain some antinutrition factors, such as phytic acid, polyphenols, trypsin inhibitors and inhibitors of α-amylase. These are responsible for reducing of protein and carbohydrate digestibility and decreasing accessibility of minerals due to complex formation. This review assesses the applications of cereals and pseudocereals in fermentation technology including the effects of lactic acid bacteria on nutrition, sensory quality and shelf-life. This work is focusing also on fermentation process of cereal matrice leading in degradation of antinutritional factors increase of nutritional value and availability of minerals, proteins and carbohydrates. Lactic acid bacteria produce many aromatic compounds that are beneficial to organoleptic atributes of the products. However, a few questions have been not answered in experiments, yet. For eample, is there any space for evaluation of their suitability to act as carriers of probiotics? Could such the attempts lead in development some special formulae suitable for consumers with food allergies or deficiencies?doi:10.5219/127

  20. Sourdough and cereal fermentation in a nutritional perspective.

    Science.gov (United States)

    Poutanen, Kaisa; Flander, Laura; Katina, Kati

    2009-10-01

    Use of sourdough is of expanding interest for improvement of flavour, structure and stability of baked goods. Cereal fermentations also show significant potential in improvement and design of the nutritional quality and health effects of foods and ingredients. In addition to improving the sensory quality of whole grain, fibre-rich or gluten-free products, sourdough can also actively retard starch digestibility leading to low glycemic responses, modulate levels and bioaccessibility of bioactive compounds, and improve mineral bioavailability. Cereal fermentation may produce non-digestible polysaccharides, or modify accessibility of the grain fibre complex to gut microbiota. It has also been suggested that degradation of gluten may render bread better suitable for celiac persons. The changes in cereal matrix potentially leading to improved nutritional quality are numerous. They include acid production, suggested to retard starch digestibility, and to adjust pH to a range which favours the action of certain endogenous enzymes, thus changing the bioavailability pattern of minerals and phytochemicals. This is especially beneficial in products rich in bran to deliver minerals and potentially protective compounds in the blood circulation. The action of enzymes during fermentation also causes hydrolysis and solubilisation of grain macromolecules, such as proteins and cell wall polysaccharides. This changes product texture, which may affect nutrient and non-nutrient absorption. New bioactive compounds, such as prebiotic oligosaccharides or other metabolites, may also be formed in cereal fermentations.

  1. Zinc biofortification of cereals: rice differs from wheat and barley

    NARCIS (Netherlands)

    Stomph, T.J.; Jiang, W.; Struik, P.C.

    2009-01-01

    In their review, mainly focused on bread wheat (Triticum aestivum), durum wheat (Triticum durum) and barley (Hordeum vulgare), Palmgren et al. 1 M.G. Palmgren et al., Zinc biofortification of cereals: problems and solutions, Trends Plant Sci. 13 (2008), pp. 464–473. Article | PDF (905 K) | View Reco

  2. Algorithms for in-season nutrient management in cereals

    Science.gov (United States)

    The demand for improved decision making products for cereal production systems has placed added emphasis on using plant sensors in-season, and that incorporate real-time, site specific, growing environments. The objective of this work was to describe validated in-season sensor based algorithms prese...

  3. Polyphenols and antioxidant capacity: Rice versus other common cereal grains

    Science.gov (United States)

    The consumption of whole cereal grains has been strongly recommended by many governmental and non-profit health organizations based on epidemiological studies associating whole-grain consumption with reduced incidences of chronic diseases. Bioactive phytochemicals, such as polyphenolic compounds, ri...

  4. Factors Influencing Deoxynivalenol Accumulation in Small Grain Cereals

    Directory of Open Access Journals (Sweden)

    Stephen N. Wegulo

    2012-11-01

    Full Text Available Deoxynivalenol (DON is a mycotoxin produced by the plant pathogenic fungi Fusarium graminearum and F. culmorum. These and other closely related fungi cause a disease known as Fusarium head blight (FHB in small grain cereals. Other mycotoxins produced by FHB-causing fungi include nivalenol, T-2 toxin, and zearalenone. Ingestion of mycotoxin-contaminated food and feed can lead to toxicosis in humans and animals, respectively. DON is the predominant and most economically important of these mycotoxins in the majority of small grain-producing regions of the world. This review examines the factors that influence DON accumulation in small grain cereals from an agricultural perspective. The occurrence and economic importance of FHB and DON in small grain cereals, epidemiological factors and cereal production practices that favor FHB development and DON accumulation in grain under field conditions, and regulatory/advisory standards for DON in food and feed are discussed. This information can be used to develop strategies that reduce DON accumulation in grain before harvest and to mitigate the human and animal health risks associated with DON contamination of food and feed.

  5. Cecil Cereal's Supermarket Search. Teacher's Guide [and] Student Materials.

    Science.gov (United States)

    Estes, Cynthia

    The document presents objectives, teaching methods, activities, and work sheets for a unit on choosing breakfast cereal. The unit is intended to be used as an integral part of the fifth grade health program. Activities take place in a classroom learning center and can be completed in approximately four to six hours of classroom time. Objectives…

  6. Modeling Coupon Values for Ready-To-Eat Breakfast Cereals

    OpenAIRE

    Price, Gregory K.; Connor, John M.; Fulton, Joan R.

    2001-01-01

    A theoretical framework is developed to highlight the significant determinants of coupon values. A fixed effects panel data model is fitted with data from the breakfast cereal industry. The explanatory variables include own retail price, brand loyalty, brand market share, rival coupon redemptions, and firm and product type indicators.

  7. Variety Recommended Lists of Organic Cereals in Emilia-Romagna

    OpenAIRE

    C. Piazza; Foutry, H.; Reggiani, R.; Poli, M.; Bolognesi, S

    2008-01-01

    In order to meet the needs of Emilia-Romagna’s technicians and farmers, specific trials on cereals (soft wheat, hard wheat, barley, corn) for organic production have been carried out since 1995. These trials helped draw up specific Variety Recommended Lists.

  8. Manuring and stable nitrogen isotope ratios in cereals and pulses

    DEFF Research Database (Denmark)

    Fraser, Rebecca A; Bogaard, Amy; Heaton, Tim;

    2011-01-01

    experiments and areas where ‘traditional’ farming is practised. Our aim is to ground-truth interpretation of δ15N values in archaeobotanical crop remains as evidence of past growing conditions and husbandry practices. The results confirm the potentially radical impact of manuring on δ15N values in cereals...

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

    Directory of Open Access Journals (Sweden)

    Tae-Sung Kim

    2015-11-01

    Full Text Available 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.

  10. Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences

    Directory of Open Access Journals (Sweden)

    Zhu Chuanrang

    2010-06-01

    Full Text Available Abstract Background With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies. Results Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs generated in this study. Conclusion Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.

  11. Cereal and nonfat milk support muscle recovery following exercise

    Directory of Open Access Journals (Sweden)

    Liao Yi-Hung

    2009-05-01

    Full Text Available Abstract Background This study compared the effects of ingesting cereal and nonfat milk (Cereal and a carbohydrate-electrolyte sports drink (Drink immediately following endurance exercise on muscle glycogen synthesis and the phosphorylation state of proteins controlling protein synthesis: Akt, mTOR, rpS6 and eIF4E. Methods Trained cyclists or triathletes (8 male: 28.0 ± 1.6 yrs, 1.8 ± 0.0 m, 75.4 ± 3.2 kg, 61.0 ± 1.6 ml O2•kg-1•min-1; 4 female: 25.3 ± 1.7 yrs, 1.7 ± 0.0 m, 66.9 ± 4.6 kg, 46.4 ± 1.2 mlO2•kg-1•min-1 completed two randomly-ordered trials serving as their own controls. After 2 hours of cycling at 60–65% VO2MAX, a biopsy from the vastus lateralis was obtained (Post0, then subjects consumed either Drink (78.5 g carbohydrate or Cereal (77 g carbohydrate, 19.5 g protein and 2.7 g fat. Blood was drawn before and at the end of exercise, and at 15, 30 and 60 minutes after treatment. A second biopsy was taken 60 minutes after supplementation (Post60. Differences within and between treatments were tested using repeated measures ANOVA. Results At Post60, blood glucose was similar between treatments (Drink 6.1 ± 0.3, Cereal 5.6 ± 0.2 mmol/L, p Conclusion These results suggest that Cereal is as good as a commercially-available sports drink in initiating post-exercise muscle recovery.

  12. Involvement of Disperse Repetitive Sequences in Wheat/Rye Genome Adjustment

    OpenAIRE

    Manuela Silva; Miguel Bento; Diana Tomás; Wanda Viegas

    2012-01-01

    The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat and rye, constitutes an excellent model to study polyploidization functional implications. We intend to attain a deeper knowledge of dispersed repetitive sequence involvement in parental genome reshuffle ...

  13. Phytotoxicity and Benzoxazinone Concentration in Field Grown Cereal Rye (Secale cereale L.

    Directory of Open Access Journals (Sweden)

    C. La Hovary

    2016-01-01

    Full Text Available Winter rye (Secale cereale L. is used as a cover crop because of the weed suppression potential of its mulch. To gain insight into the more effective use of rye as a cover crop we assessed changes in benzoxazinone (BX levels in rye shoot tissue over the growing season. Four rye varieties were planted in the fall and samples harvested at intervals the following spring. Two different measures of phytotoxic compound content were taken. Seed germination bioassays were used as an estimate of total phytotoxic potential. Dilutions of shoot extracts were tested using two indicator species to compare the relative toxicity of tissue. In addition, BX (DIBOA, DIBOA-glycoside, and BOA levels were directly determined using gas chromatography. Results showed that rye tissue harvested in March was the most toxic to indicator species, with toxicity decreasing thereafter. Likewise the BX concentration in rye shoot tissue increased early in the season and then decreased over time. Thus, phytotoxicity measured by bioassay and BX levels measured by GC have a similar but not identical temporal profile. The observed decrease in phytotoxic potential and plant BX levels in rye later in the season appears to correlate with the transition from vegetative to reproductive growth.

  14. Alternative cereal grains and cereal by-products as sources of energy in poultry diets- A review

    Directory of Open Access Journals (Sweden)

    C. I. Medugu,

    2011-08-01

    Full Text Available The increase in the world population, high cost of conventional animal feed ingredients and low protein intake in most developing countries has necessitated animal scientists to search for alternative sources of feed ingredients. This can enhance the production of animals with short generation intervals such as poultry to overcome the protein deficiency. This paper reviews cereal grains and cereal by-products as alternative feed ingredients for formulating poultry diets. Results obtained from various sources indicate that diets formulated with alternative cereal grains and cereal by-products had no adverse effects on body weight gain, feed intake, feed conversion ratio and carcass quality of broiler chickens, cockerels and egg quality of laying hens. Inclusion of different levels of brewers’ dried grain, maize offal, rice bran and broken rice are quite acceptable in poultry diets. Therefore, sorghum, millet, maize offal, rice bran and wheat offal, millet bran, spent sorghum grain and broken rice could be recommended as alternative sources of feed ingredients in poultry diets.

  15. Novel Approach for the Analysis and the Optimization of the Cereal Stock Mobility

    Directory of Open Access Journals (Sweden)

    LAKHOUA Mohamed Najeh

    2013-10-01

    Full Text Available After a presentation of the process of thecereals mixture, we present a methodology for theoptimization problem and we validate it through apractical case of the cereals stock mobility process. Infact, the cereal transaction in Tunisia is conditioned bythe quality of the cereals determining the price of thetransaction (purchase or sale. With regards to theimportance of the cereal stock mobility, we werecommitted to study the way to optimize the process ofthe cereals mixture and to reduce disparity in deliveredcereal quality through the use of blinding techniquesand optimization methods.

  16. Effect of gamma irradiation on viscosity reduction of cereal porridges for improving energy density

    Science.gov (United States)

    Lee, Ju-Woon; Kim, Jae-Hun; Oh, Sang-Hee; Byun, Eui-Hong; Yook, Hong-Sun; Kim, Mee-Ree; Kim, Kwan-Soo; Byun, Myung-Woo

    2008-03-01

    Cereal porridges have low energy and nutrient density because of its viscosity. The objective of the present study was to evaluate the effect of irradiation on the reduction of viscosity and on the increasing solid content of cereal porridge. Four cereals, wheat, rice, maize (the normal starchy type) and waxy rice, were used in this study. The porridge with 3000 cP was individually prepared from cereal flour, gamma-irradiated at 20 kGy and tested. Gamma irradiation of 20 kGy was allowed that the high viscous and rigid cereal porridges turned into semi-liquid consistencies. The solid contents of all porridges could increase by irradiation, compared with non-irradiated ones. No significant differences of starch digestibility were observed in all cereal porridge samples. The results indicated that gamma irradiation might be helpful for improving energy density of cereal porridge with acceptable consistency.

  17. Effect of gamma irradiation on viscosity reduction of cereal porridges for improving energy density

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ju-Woon [Radiation Application Research Division, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of)], E-mail: sjwlee@kaeri.re.kr; Kim, Jae-Hun; Oh, Sang-Hee; Byun, Eui-Hong [Radiation Application Research Division, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of); Yook, Hong-Sun; Kim, Mee-Ree [Department of Food and Nutrition, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Kim, Kwan-Soo [Research and Development Department, Greenpia Technology, Yeoju 469-811 (Korea, Republic of); Byun, Myung-Woo [Radiation Application Research Division, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of)], E-mail: mwbyun@kaeri.re.kr

    2008-03-15

    Cereal porridges have low energy and nutrient density because of its viscosity. The objective of the present study was to evaluate the effect of irradiation on the reduction of viscosity and on the increasing solid content of cereal porridge. Four cereals, wheat, rice, maize (the normal starchy type) and waxy rice, were used in this study. The porridge with 3000 cP was individually prepared from cereal flour, gamma-irradiated at 20 kGy and tested. Gamma irradiation of 20 kGy was allowed that the high viscous and rigid cereal porridges turned into semi-liquid consistencies. The solid contents of all porridges could increase by irradiation, compared with non-irradiated ones. No significant differences of starch digestibility were observed in all cereal porridge samples. The results indicated that gamma irradiation might be helpful for improving energy density of cereal porridge with acceptable consistency.

  18. The International Barley Sequencing Consortium — At the Threshold of Efficient Access to the Barley Genome

    Science.gov (United States)

    Sequencing the genome of barley, an agriculturally and industrially important cereal crop and a useful diploid model for bread wheat, has become a realistic undertaking. Important steps have been initiated to improve genomics tools, build and anchor a physical map, develop a high-density genetic ma...

  19. De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae.

    Directory of Open Access Journals (Sweden)

    Mukesh Kumar

    Full Text Available The cereal cyst nematode (CCN, Heterodera avenae is a major pest of wheat (Triticum spp that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy revealed fewer glycoside hydrolases (GHs but more glycosyl transferases (GTs and carbohydrate esterases (CEs when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.

  20. Proteinaceous inhibitors of carbohydrate-active enzymes in cereals: implication in agriculture, cereal processing and nutrition

    DEFF Research Database (Denmark)

    Juge, N.; Svensson, Birte

    2006-01-01

    Enzymes that degrade, modify, or create glycosidic bonds are involved in carbohydrate biosynthesis and remodelling. Microbial carbohydrate-active enzymes form the basis of current green technology in the food, feed, starch, paper and pulp industries and the revolution in genomics may offer long...

  1. Proteomic profiling of 16 cereal grains and the application of targeted proteomics to detect wheat contamination.

    Science.gov (United States)

    Colgrave, Michelle L; Goswami, Hareshwar; Byrne, Keren; Blundell, Malcolm; Howitt, Crispin A; Tanner, Gregory J

    2015-06-01

    Global proteomic analysis utilizing SDS-PAGE, Western blotting and LC-MS/MS of total protein and gluten-enriched extracts derived from 16 economically important cereals was undertaken, providing a foundation for the development of MS-based quantitative methodologies that would enable the detection of wheat contamination in foods. The number of proteins identified in each grain correlated with the number of entries in publicly available databases, highlighting the importance of continued advances in genome sequencing to facilitate accurate protein identification. Subsequently, candidate wheat-specific peptide markers were evaluated by multiple-reaction monitoring MS. The selected markers were unique to wheat, yet present in a wide range of wheat varieties that represent up to 80% of the bread wheat genome. The final analytical method was rapid (15 min) and robust (CV 0.98) spanning over 3 orders of magnitude, and was highly selective and sensitive with detection down to 15 mg/kg in intentionally contaminated soy flour. Furthermore, application of this technology revealed wheat contamination in commercially sourced flours, including rye, millet, oats, sorghum, buckwheat and three varieties of soy.

  2. Comparative analysis of multiple disease resistance in ryegrass and cereal crops.

    Science.gov (United States)

    Jo, Young-Ki; Barker, Reed; Pfender, William; Warnke, Scott; Sim, Sung-Chur; Jung, Geunhwa

    2008-08-01

    Ryegrass (Lolium spp.) is among the most important forage crops in Europe and Australia and is also a popular turfgrass in North America. Previous genetic analysis based on a three-generation interspecific (L. perennexL. multiflorum) ryegrass population identified four quantitative trait loci (QTLs) for resistance to gray leaf spot (Magneporthe grisea) and four QTLs for resistance to crown rust (Puccinia coronata). The current analysis based on the same mapping population detected seven QTLs for resistance to leaf spot (Bipolaris sorokiniana) and one QTL for resistance to stem rust (Puccinia graminis) in ryegrass for the first time. Three QTLs for leaf spot resistance on linkage groups (LGs) 2 and 4 were in regions of conserved synteny to the positions of resistance to net blotch (Drechslera teres) in barley (Hordeum vulgare). One ryegrass genomic region spanning 19 cM on LG 4, which contained three QTLs for resistance to leaf spot, gray leaf spot, and stem rust, had a syntenic relationship with a segment of rice chromosome 3, which contained QTLs for resistance to multiple diseases. However, at the genome-wide comparison based on 72 common RFLP markers between ryegrass and cereals, coincidence of QTLs for disease resistance to similar fungal pathogens was not statistically significant.

  3. Prediction of cereal feed value using spectroscopy and chemometrics

    DEFF Research Database (Denmark)

    Jørgensen, Johannes Ravn; Gislum, René

    2009-01-01

    Feed value in form of FEsv (Feed unit / kg dry matter, for piglets) and FEso (Feed unit / kg dry matter, for sows), EDOM (Enzyme Degradable Organic Matter) and EDOMi (Enzyme Degradable Organic Matter, Ileum) is used in the feed evaluation system for pigs. Analysis of feed value have highlighted...... of EDOM, EDOMi, FEso and FEsv. The outcome of a successful NIRS calibration will be a relatively cheap tool to monitor, diversify and evaluate the quality of cereals for animal feed, a possible tool to assess the feed value of new varieties in the variety testing and a useful, cheap and rapid tool...... for cereal breeders. A collection of 1213 grain samples of wheat, triticale, barley and rye, and related chemical reference analyses to describe the feed value have been established. The samples originate from available field trials over a three-year period. The chemical reference analyses are dry matter...

  4. Glycemic index of cereals and tubers produced in China

    Institute of Scientific and Technical Information of China (English)

    Yue-Xin Yang; Hong-Wei Wang; Hong-Mei Cui; Yan Wang; Lian-Da Yu; Shi-Xue Xiang; Shui-Ying Zhou

    2006-01-01

    AIM: To determine the GI of some cereals and tubers produced in China in an effort to establish the database of glycemic index (GI) of Chinese food.METHODS: Food containing 50 g carbohydrate was consumed by 8-12 healthy adults after they have been fasted for 10 h and blood glucose was monitored for 2 h.Glucose was used as reference food. GI of food was calculated according to a standard method.RESULTS: GI of 9 types of sugar and 60 kinds of food were determined.CONCLUSION: Food GI is mainly determined by nature of carbohydrate and procession. Most of cereals and tubers produced in China have similar GI with their counterparts produced in other countries.

  5. Cereal Grains: Their Impacts on Health and Food Safety

    Institute of Scientific and Technical Information of China (English)

    P Rayas-Duarte; J Uriyapongson

    2006-01-01

    Cereal grains can contribute to maintain health and prevent chronic diseases by supplying biologically active components. The exact mechanism of action of these components is not completely understood, but extensive evidence suggests the antioxidants that are present in the grains are the likely source of benefits. These activities or properties might protect against coronary heart disease and diabetes. The relationships of complex carbohydrates, whole grain products and the prevention of diseases, including type2 diabetes mellitus and coronary heart disease continue to challenge the scientific community. Though cereal grains contribute to a healthy diet there are some people that can not tolerate the proteins present in the grain. This can lead to food allergies and when severe can be diagnosed as celiac disease.

  6. Genetics of cereal adaptation to the man-made habitat

    International Nuclear Information System (INIS)

    The wild progenitor species of all cereals are known with various degrees of certainty. Wild and cultivated taxa of the same species cross and their hybrids are generally fertile. This allows for a study of the genetics of domestication. A survey of the literature, however, reveals few such studies. The adaptation to disturbed habitats is genetically complex, and colonizing ability seems to have been a prerequisite for successful domestication. Natural seed dispersal is controlled by one to several linked genes, and behaves genetically as an overall dominant over loss of efficient seed dispersal mechanisms. Apical dominance, synchronized tillering, and increase in fecundity are complex, recessive genetic traits associated with cereal domestication. Racial evolution resulted from conscious selection by man and involves numerous loci. (author). 43 refs, 4 figs, 1 tab

  7. [Polycyclic aromatic hydrocarbons (PAH) in cereal breakfast products].

    Science.gov (United States)

    Ciemniak, Artur; Chrachol, Lucyna

    2008-01-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants formed by incomplete combustion (pyrolysis) of several organic materials. PAHs occur as complex mixtures, never as individual components. They are chemically stable and highly lipophilic in nature and occur as contaminants in different food categories: vegetables, fruit, cereals, oils and fats, especially barbecued and smoked food. The present study was carried out to determine 16 PAHs in cereal products: musli, corn, oats and barley flakes, and crunchy. The analytical procedure was based on alkaline digestion, extraction with n-hexane and cleaned up in a florisil cartridge. Chromatographic separation was performed using gas chromatography (HP 6890) coupled to mass spectrometry (HP 5973). The levels of PAHs in most samples were generally low and excepting one sample of bred varied between 4.2 to 169 microg/kg. Benzo[a]pyrene, was detected in all samples, at level 0.02 microg/kg to 16 microg/kg. PMID:19143427

  8. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  9. Multiple Adoption of Pest Management Technologies in UK cereal Farming

    OpenAIRE

    Fraser, Iain; Sharma, Abhijit; Bailey, Alastair

    2011-01-01

    In this paper we consider the adoption of pest management technologies by farmers in UK cereal crop systems. While for the majority of UK farmers chemical control of pest outbreaks remains important, there are a range of non-chemical approaches and management practices that can be used to control pest populations. However, few of these alternatives produce levels of control that compare with chemical use in isolation. In this paper we consider the determinants of adoption of different combina...

  10. Starch bioengineering affects cereal grain germination and seedling establishment

    OpenAIRE

    Shaik, Shahnoor Sultana; Carciofi, Massimiliano; Martens, Helle Juel; Hebelstrup, Kim; Blennow, Andreas

    2014-01-01

    Cereal grain germination is central for plant early development, and efficient germination has a major role in crop propagation and malting. Endosperm starch is the prime energy reserve in germination and seedling establishment. In this study, it was hypothesized that optimized starch granule structure, and not only the endosperm starch content per se, is important for germination and seedling establishment. For that purpose, wild-type (WT), and specifically engineered degradable hyperphospho...

  11. Quantitative estimation of sampling uncertainties for mycotoxins in cereal shipments

    OpenAIRE

    Bourgeois, Florent; Lyman, Geoffrey

    2012-01-01

    Many countries receive shipments of bulk cereals from primary producers. There is a volume of work that is ongoing that seeks to arrive at appropriate standards for the quality of the shipments and the means to assess the shipments as they are out-loaded. Of concern are mycotoxin and heavy metal levels, pesticide and herbicide residue levels, and contamination by genetically modified organisms (GMOs). As the ability to quantify these contaminants improves through improved analytical technique...

  12. Impacts of cereal ergot in food animal production

    Directory of Open Access Journals (Sweden)

    Stephanie eCoufal-Majewski

    2016-02-01

    Full Text Available The negative impacts of ergot contamination of grain on the health of humans and animals were first documented during the 5th century AD. Although ergotism is now rare in humans, cleaning contaminated grain concentrates ergot bodies in screenings which are used as livestock feed. Ergot is found worldwide, with even low concentrations of alkaloids in the diet (<100 ppb total reducing the growth efficiency of livestock. Extended periods of increased moisture and cold during flowering promote the development of ergot in cereal crops. Furthermore, the unpredictability of climate change may have detrimental impacts to important cereal crops such as wheat, barley and rye, favouring ergot production. Allowable limits for ergot in livestock feed are confusing as they may be determined by proportions of ergot bodies or by total levels of alkaloids, measurements which may differ widely in their estimation of toxicity. The proportion of individual alkaloids including ergotamine, ergocristine, ergosine, ergocornine and ergocryptine is extremely variable within ergot bodies and the relative toxicity of these alkaloids has yet to be determined. This raises concerns that current recommendations on safe levels of ergot in feeds may be unreliable. Furthermore, the total ergot alkaloid content is greatly dependent on the geographic region, harvest year, cereal species, variety and genotype. Considerable animal to animal variation in the ability of the liver to detoxify ergot alkaloids also exists and the impacts of factors such as pelleting of feeds or use of binders to reduce bioavailability of alkaloids require study. Accordingly, unknowns greatly outnumber the knowns for cereal ergot and further study to help better define allowable limits for livestock would be welcome.

  13. SOME STUDIES ABOUT CEREALS BEHAVIOR DURING FREEZE DRYING PROCESS

    OpenAIRE

    GABRIELA-VICTORIA MNERIE; D. MNERIE; D. ŢUCU

    2013-01-01

    The paper presents some special method and equipment and the principal advantages of freeze-dried food. The freeze drying is a good method of freeze-drying for make some experiments with many kind of cereals, for the improvement that in food production. It is necessary and is possible to study the corn oil extract, wheat flour, the maltodextrin from corn, modified cornstarch, spice extracts, soy sauce, hydrolyzed wheat gluten, partially hydrogenated soybean and cottonseed oil etc. That is ver...

  14. A cross-cultural study of cereal foods' quality perception

    DEFF Research Database (Denmark)

    Krutulyte, Rasa; Grunert, Klaus G.; Costa, Ana I. A.

    information and price were the most important for Danes. The cues and dimensions Portuguese found relevant were fairly different and more category-dependent. Cues like store type for bread, brand for breakfast cereals, pasta and vodka, country-of-origin for vodka, and price for cookies, pasta and vodka were...... more often assessed by the Portuguese as relevant for decision-making at the point-of-purchase. This highlights the need for further cross-cultural research on food quality perception....

  15. Zinc and iron speciation in the cereal grain

    OpenAIRE

    Schjoerring, Jan K.; Persson, Daniel P.; Hansen, Thomas H.; Laursen, Kristian H; Husted, Søren

    2009-01-01

    Phytic acid and proteins are believed to be important for the distribution and bio-availability of zinc and iron in the cereal grain, but little quantitative information is available on the relative importance of different organic ligands. We have used several chromatographic techniques including size exclusion chromatography (SEC) hyphenated to ICP-MS to analyse the molecular speciation of Fe and Zn in tissues of barley and rice seeds. The majority of Fe in barley embryos co-eluted with P as...

  16. Prospects for India's cereal supply and demand to 2020:

    OpenAIRE

    Bhalla, G. S.; Hazell, P. B. R.; John M. Kerr

    1999-01-01

    The possibility of an emerging cereal gap of serious proportions by the year 2020, is a useful illustration of the kind of constructive dialogue IFPRI hopes to encourage. It responds to several quite recent developments, notably the rapid expansion of India's industrial and service sectors since the 1991 structural reforms, the improved prospects for continued growth over the next few decades, and the likelihood of rising per capita incomes that could generate substantially increased demand f...

  17. Supply and demand for cereals in Pakistan 2010-2030:

    OpenAIRE

    Nazli, Hina; Haider, Syed Hamza; Tariq, Asjad

    2012-01-01

    This paper presents the projections of future demand and supply for these two main cereals for 2010, 2015, 2020, 2025, and 2030. For projecting household demand, the Almost Ideal Demand System (LA-AIDS) is estimated for eight food items using the data of nationally representative household survey. The results are used to project the household demand under three different scenarios. These scenarios are: a business-as-usual situation (per capita income is assumed to grow at a rate of 3 percent ...

  18. Application of roasted rice bran in cereal bars

    Directory of Open Access Journals (Sweden)

    Marina Costa Garcia

    2012-12-01

    Full Text Available The objective of this study was to evaluate the viability of using microwave-roasted rice bran as an ingredient in high-fiber cereal bars to obtain a product with good acceptability. The influence of the rice flakes, corn flakes, and roasted rice bran levels on the physical and chemical characteristics of the cereal bars was studied. The overall acceptability of three selected formulations was also evaluated. An increase in the roasted rice bran level in the formulation reduced the force of rupture and water activity, resulted in intermediate density, and caused darkening of the bars. The contents of lipid and total dietary fiber were higher in the formulation with the highest rice bran content, which was therefore classified as functional food. The formulation containing 0.34; 0.32; and 0.34 roasted rice bran, rice flakes, and corn flakes, respectively, seemed to be the best outcome. Cereal bars with roasted rice bran levels between 10 and 20% were accepted by consumers.

  19. Assessment of aflatoxins, ochratoxin A and zearalenone in breakfast cereals.

    Science.gov (United States)

    Iqbal, Shahzad Zafar; Rabbani, Tehmeena; Asi, Muhammad Rafique; Jinap, S

    2014-08-15

    Aflatoxins (AFs), ochratoxin A (OTA) and zearalenone (ZEN) were analysed in 237 breakfast cereal samples collected from central areas of Punjab, Pakistan. According to the results, 41% of the samples were found contaminated with AFs, out of which 16% and 8% samples were found to be above the European Union (EU) maximum content for AFB1 and total AFs, respectively. About 48% samples were found contaminated with OTA and 30% samples were found to be above the EU maximum content. The results have shown that 53% samples of breakfast cereals were found contaminated with ZEN and 8% samples were found to be above the permissible limit of EU. The highest mean level of AFB1 and total AFs were found in semolina i.e. 3.60 and 4.55 μg/kg, respectively. Similarly, semolina was the highest contaminated breakfast cereal for OTA (3.90 μg/kg), while cornflakes (brand B) was found highest contaminated with ZEN (13.45 μg/kg).

  20. Phenolic Compounds of Cereals and Their Antioxidant Capacity.

    Science.gov (United States)

    Van Hung, Pham

    2016-01-01

    Phenolic compounds play an important role in health benefits because of their highly antioxidant capacity. In this review, total phenolic contents (TPCs), phenolic acid profile and antioxidant capacity of the extracted from wheat, corn, rice, barley, sorghum, rye, oat, and millet, which have been recently reported, are summarized. The review shows clearly that cereals contain a number of phytochemicals including phenolics, flavonoids, anthocyanins, etc. The phytochemicals of cereals significantly exhibit antioxidant activity as measured by trolox equivalent antioxidant capacity (TEAC), 2,2-diphenyl-1-picrylhydrazyl radical scavenging, reducing power, oxygen radical absorbance capacity (ORAC), inhibition of oxidation of human low-density lipoprotein (LDL) cholesterol and DNA, Rancimat, inhibition of photochemilumenescence (PCL), and iron(II) chelation activity. Thus, the consumption of whole grains is considered to have significantly health benefits in prevention from chronic diseases such as cardiovascular disease, diabetes, and cancer because of the contribution of phenolic compounds existed. In addition, the extracts from cereal brans are considered to be used as a source of natural antioxidants. PMID:25075608

  1. Gamma irradiation treatment of cereal grains for chick diets

    International Nuclear Information System (INIS)

    Wheat (W), triticale (T), hulled barley (HB), hull-less barley (HLB), hulled oats (HO), and hull-less oats (HLO) were gamma irradiated (60Co) at 0, 3, 6 and 9 Mrad to study the effect of irradiation on the nutritional value of cereal grains for chicks. A significant curvilinear relationship between radiation dose and 3-wk body weight of chicks fed irradiated cereals was noted for T, HB, HLB, HO and HLO. Chicks fed W or T showed no effect or lower body weight, respectively, while body weights of chicks fed barley or oat samples were higher with irradiation. The improvement tended to be maximal at the 6 Mrad level. Irradiation significantly improved the gain-to-feed ratio for chicks fed either HO or HLO. Apparent fat retention and tibia ash were higher in chicks fed irradiated HLO than in those fed untreated HLO. In a second experiment chick body weight, apparent amino acid and fat retention, tibia ash, and gain-to-feed ratios were lower in chicks fed autoclaved (121 degrees C for 20 min) barley than in those fed untreated barley. Irradiation (6 Mrad) subsequent to autoclaving barley samples eliminated these effects. Irradiation appears to benefit cereals containing soluble or mucilagenous fiber types as typified by beta-glucan of barley and oats. These fibers appear prone to irradiation-induced depolymerization, as suggested by increased beta-glucan solubility and reduced extract viscosity for irradiated barley and oat samples

  2. Genomics for Weed Science

    Science.gov (United States)

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and ...

  3. Lentil genetic and genomic resources

    Science.gov (United States)

    Lentil (Lens culinaris spp. culinaris) has a long history associated with the early civilizations 11,000 BP in southwestern Asia. The progenitor taxon is Lens culinaris spp. orientalis. The primary source of germplasm for lentil crop improvement is from the International Center for Agricultural Rese...

  4. Development of Combined Drought Indicator in Cereals to use its predictive value in the Agricultural Insurances: CDI_Cereal

    Science.gov (United States)

    Jimenez-Donaire, Pilar; Tarquis, Ana M.; Giráldez, Juan V.

    2015-04-01

    The agrometeorological or agricultural drought is one of the most severe problems of agriculture. Drought damage is defined in terms of harvest loss due to precipitation shortage that limits soil moisture availability for the crops, substantially reducing crop yield. A method is proposed to identify the rain fed cereal agricultural drought in several Andalusian regions, based on the combination of three indices or anomalies: (i) standard precipitation index (SPI-3) based on Mishra and Desai (2005), (ii) soil moisture described with a water balance model based on the hydrological model by Brocca et al., 2008, and (iii) the normalized difference vegetation index (NDVI) based on Kogan (1995). Coupling the three anomalies, a Combined Drought Indicator -for rain fed cereals- (CDI) has been obtained. This indicator characterizes different warning levels of agricultural drought, which has been successfully assessed with the data of the period 2003-2013 (Jiménez-Donaire, 2014). The final aim of the proposed CDI is to design a warning system based on its components' combination to forecast the drought risk helping both farmers and agricultural insurance agencies. Keywords: drought, SPI, soil moisture, NDVI. References Brocca, L., Melone, F., Moramarco, T.(2008) On the estimation of antecedent wetness conditions in rainfall-runoff modelling. Hydrol. Process. 22, 629-642. Jiménez-Donaire, M.P. (2014) Indicador combinado de sequía para cereales y su valor predictivo en los seguros agrarios: ICS_CEREAL. Master thesis, UCO (In Spanish). Kogan, F.N., 1995. Droughts of the Late 1980s in the United States as Derived from NOAA Polar-Orbiting Satellite Data. Bull. Am. Meteorol. Soc. 76, 655-668. Mishra, A.K., Desai, V.R., 2005. Drought forecasting using stochastic models. Stoch. Environ. Res. Risk Assess. 19, 326-339. Acknowledgements First author acknowledges the Research Grant obtained from CEIGRAM in 2014

  5. On the current status of Phakopsora pachyrhizi genome sequencing

    Directory of Open Access Journals (Sweden)

    Marco eLoehrer

    2014-08-01

    Full Text Available Recent advances in the field of sequencing technologies and bioinformatics allow a more rapid access to genomes of non-model organisms at sinking costs. Accordingly, draft genomes of several economically important cereal rust fungi have been released in the last three years. Aside from the very recent flax rust and poplar rust draft assemblies there are no genomic data available for other dicot-infecting rust fungi. In this article we outline rust fungus sequencing efforts and comment on the current status of Phakopsora pachyrhizi (Asian soybean rust genome sequencing.

  6. STUDY ON POWDERY MILDEW RESISTANCE TRANSFER FROM S. CEREALE L.cv. WEILING RYE INTO WHEAT%威岭栽培黑麦抗白粉病特性导入小麦的研究

    Institute of Scientific and Technical Information of China (English)

    张怀渝; 任正隆

    2007-01-01

    Weiling rye (S. cereale L.cv.),a Chinese dwarf rye,confers high powdery mildew(Erysiphe gramininis f.sp.tritici) in China. My8443,a wheat cultivars infecting seriously powdery mildew disease,was used as the female parent and Weiling rye was used as the donor of powdery mildew resistance in the study. A new wheat-rye translocation line,named No.147,was developed from BC2F6 progenies of wheat cultivars My8443 and Weiling rye to transfer the resistance from Weiling rye to common wheat. The powdery mildew resistance of No.147 and its parents were investigated in seedling and adult stages by artificially inoculating the mixture of advanced pathogenic races in room and field and the single pathogenic race in room. Improved Giemsa Cbanding technique and genomic in situ hybridization (GISH,Genomic in situ hybridization) were used to identify wheat and rye chromosomes. Acid polyacylamide gel electrophoresis(APAGE) separation of endosperm gliadin and simple sequence repeat(SSR) PCR amplification of 11 SCM-Se-cale cereale markers also were employed for 1RS confirmation in the study. The results showed that No.147 was a new 1BL/1RS wheat-rye chromosome translocation with high powdery mildew resistance derived from Weiling rye. The reason on the formation of the new wheat-rye chromosome translocation was analyzed. The utilizations of resistance gene resource derived from Chinese Weiling rye and the new 1BL/1RS translocation line in wheat genetics and breeding improvement were discussed in the paper.%威岭黑麦(Weiling rye)是一个高抗白粉病(Erysiphe gramininis,f.sp.tritici)的中国矮杆栽培黑麦.以Weiling rye作为白粉病抗源,高感白粉病小麦栽培品种My8443为母本,从Weiling rye与小麦My8443远缘杂交的BC2F6后代中鉴定出一个新的小麦-黑麦易位系No.147,以实现威岭黑麦白粉病抗性向普通栽培小麦的转移.No.147及其亲本的抗白粉病特性通过苗期和成株期优势生理小种混合接种和室内单生理小

  7. The Effect of Retail Grocery Coupons for Breakfast Cereals on Household Purchasing Behavior

    OpenAIRE

    Joshua P. Berning; Zheng, Hualu

    2011-01-01

    We examine the affect of retail and manufacturer coupons on the nutritional quality of breakfast cereal purchases made by households. Using household level purchase data we find that coupon usage has a significant impact on the nutritional quality of cereals purchased by households. Specifically, we find that the average sugar content decreases and the fiber content increases. This suggests that coupons have a positive impact on the nutritional quality of cereals purchased by households, hold...

  8. How will conversion to organic cereal production affect carbon stocks in Swedish agricultural soils?

    OpenAIRE

    Andrén, Olof; Kätterer, Thomas; Kirchmann, Holger

    2008-01-01

    Soil carbon changes were modelled over 30 years with the focus on cereal crops, since leys are often managed similarly in organic and conventional agriculture. Other crops were not considered due to difficulties in large-scale cropping of oilseed rape and potatoes organically because of pest problems. Four scenarios were used: 0%, 8% (current), 20% and 100% organic cereal production. Conversion to organic cereal crop production was found to reduce the amount of carbon stored as organic matter...

  9. Yield and nutritive value for ruminants of organic Winter cereals-bard vetch intercrops

    OpenAIRE

    Díaz, A.; Carro Travieso, María Dolores; Palacios, Carlos; Saro, C.; Mateos, I; Tejido, M. L.; Ranilla, M.J.

    2015-01-01

    Organic livestock in the European Union must be fed with organic feed, and forage should be at least 60% of the diet of herbivorous animals. However, the productivity of crops in organic farming is frequently lower than that in conventional farming, and organic cultivation of winter cereals often reduces forage CP content. Intercropping of winter cereals with legumes can provide both higher forage yield and quality compared with winter cereal monocultures, but the results may differ with ...

  10. MRI texture analysis as means for addressing rehydration and milk diffusion of cereals

    OpenAIRE

    Melado Herreros, Angela; Barreiro Elorza, Pilar; Rodríguez Sinobas, Leonor; Fernandez Valle, M. Encarnacion; Ruiz Cabello Osuna, Jesus Maria; Chassagne-Berces, Sophie; Chanvrier, Helene

    2011-01-01

    Cereals microstructure is one of the primary quality attributes of cereals. Cereals rehydration and milk diffusion depends on such microstructure and thus, the crispiness and the texture, which will make it more palatable for the final consumer. Magnetic Resonance Imaging (MRI) is a very powerful topographic tool since acquisition parameter leads to a wide possibility for identifying textures, structures and liquids mobility. It is suited for non-invasive imaging of water and fats. Rehydratio...

  11. MRI texture analysis as means for addressing rehydration and milk diffusion in cereals

    OpenAIRE

    Melado Herreros, Angela; Barreiro Elorza, Pilar; Rodríguez Sinobas, Leonor; Fernandez Valle, M. Encarnacion; Ruiz Cabello Osuna, Jesus Maria; Chassagne-Berces, Sophie; Chanvrier, Helene

    2011-01-01

    Cereals microstructure is one of the primary quality attributes of cereals. Cereals rehydration and milk diffusion depends on such microstructure and thus, the crispiness and the texture, which will make it more palatable for the final consumer. Magnetic Resonance Imaging (MRI) is a very powerful tomographic tool since acquisition parameter leads to a wide possibility for identifying textures, structures and liquids mobility. It is suited for noninvasive imaging of water and fats. Rehydration...

  12. The nutritional and physiological impact of cereal products in human nutrition.

    Science.gov (United States)

    Lorenz, K; Lee, V A

    1977-03-01

    There is a need for reeducation of the population, especially in developed countries, as to the value of cereals in the diet. Cereals provide calories and important nutrients to the diet. Refined cereal products and unrefined cereals have certain advantages and disadvantages. With refinement, some nutrients and fiber are removed, but the body is better able to make use of certain nutrients. Essential nutrients are being replaced through fortification to compensate for losses in processing. The high fiber content of unrefined cereal products is believed to aid in the prevention of certain diseases. Special dietary bakery products have been introduced for the treatment of conditions generally exacerbated by standard food items. The increased consumption of cereal products appears warranted as a means of decreasing the saturated fat and cholesterol consumption. Cereals and cereal products have been mentioned in connection with allergies, celiac disease, schizophrenia, obesity, dental caries, cancer, atherosclerosis, goiter, and diverticulosis. This review discusses the possible role of cereals in the prevention or cause of these health problems. PMID:338251

  13. Brachypodium distachyon-Cochliobolus sativus Pathosystem is a New Model for Studying Plant-Fungal Interactions in Cereal Crops.

    Science.gov (United States)

    Zhong, Shaobin; Ali, Shaukat; Leng, Yueqiang; Wang, Rui; Garvin, David F

    2015-04-01

    Cochliobolus sativus (anamorph: Bipolaris sorokiniana) causes spot blotch, common root rot, and kernel blight or black point in barley and wheat. However, little is known about the molecular mechanisms underlying the pathogenicity of C. sativus or the molecular basis of resistance and susceptibility in the hosts. This study aims to establish the model grass Brachypodium distachyon as a new model for studying plant-fungus interactions in cereal crops. Six B. distachyon lines were inoculated with five C. sativus isolates. The results indicated that all six B. distachyon lines were infected by the C. sativus isolates, with their levels of resistance varying depending on the fungal isolates used. Responses ranging from hypersensitive response-mediated resistance to complete susceptibility were observed in a large collection of B. distachyon (2n=2x=10) and B. hybridum (2n=4x=30) accessions inoculated with four of the C. sativus isolates. Evaluation of an F2 population derived from the cross between two of the B. distachyon lines, Bd1-1 and Bd3-1, with isolate Cs07-47-1 showed quantitative and transgressive segregation for resistance to C. sativus, suggesting that the resistance may be governed by quantitative trait loci from both parents. The availability of whole-genome sequences of both the host (B. distachyon) and the pathogen (C. sativus) makes this pathosystem an attractive model for studying this important disease of cereal crops.

  14. The UCSC Archaeal Genome Browser: 2012 update

    OpenAIRE

    Chan, Patricia P.; Holmes, Andrew D.; Smith, Andrew M.; Tran, Danny; Lowe, Todd M.

    2011-01-01

    The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of ...

  15. The UCSC Genome Browser database: 2015 update

    OpenAIRE

    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

    2014-01-01

    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 al...

  16. ANALYSIS OF FREE AND BOUND CHLOROPHENOXY ACIDS IN CEREALS

    DEFF Research Database (Denmark)

    Løkke, Hans

    1975-01-01

    Extraction of the chlorophenoxy acids 2,4-D and dichlorprop in cereals has been examined by analyzing barley from spraying experiments. A procedure has been set up by combination of acid hydrolysis and enzymatic degradation followed by extraction and clean up on either silica gel or basic aluminum...... oxide. The final determination is based on reaction with diazomethane and subsequently GLC with ECD. This procedure was compared with two different extraction procedures previously described in the literature. The one comparative procedure uses a mixture of 50% diethyl ether/hexane in presence...

  17. SOME STUDIES ABOUT CEREALS BEHAVIOR DURING FREEZE DRYING PROCESS

    Directory of Open Access Journals (Sweden)

    GABRIELA-VICTORIA MNERIE

    2013-07-01

    Full Text Available The paper presents some special method and equipment and the principal advantages of freeze-dried food. The freeze drying is a good method of freeze-drying for make some experiments with many kind of cereals, for the improvement that in food production. It is necessary and is possible to study the corn oil extract, wheat flour, the maltodextrin from corn, modified cornstarch, spice extracts, soy sauce, hydrolyzed wheat gluten, partially hydrogenated soybean and cottonseed oil etc. That is very porous, since it occupies the same volume as the original and so rehydrates rapidly. There is less loss of flavour and texture than with most other methods of drying.

  18. Fusarium head blight of winter rye (Secale cereale L.

    Directory of Open Access Journals (Sweden)

    Irena Kiecana

    2012-12-01

    Full Text Available Investigations on Fusarium head blight of rye were carried out in the years 2005-2007 on 10 production fields in the Lublin region. The percentage of heads showing the fusariosis symptoms in the years 2005-2007 ranged from 0 to 7%. Mycological analysis of kernels and chaff obtained from heads with Fusarium blight (scab symptoms showed that Fusarium avenaceum, Fusarium culmorum and Fusarium sporotrichioides were the largest threat to heads of this cereal. The species of Fusarium poae and Fusarium crookwellense were also isolated from infected rye heads. The dominance of particular species in infecting rye heads was determined by weather conditions.

  19. A cross-cultural study of cereal food quality perception

    DEFF Research Database (Denmark)

    Krutulyte, Rasa; Costa, Ana I. A.; Grunert, Klaus G.

    2009-01-01

    information and price were the most important for Danes. The cues and dimensions Portuguese found relevant were fairly different and more category-dependent. Cues like store type for bread, brand for breakfast cereals, pasta and vodka, country-of-origin (CoO) for vodka, and price for cookies, pasta and vodka...... were more often assessed by the Portuguese as relevant for decision-making at the point-of-purchase. This highlights the need for further cross-cultural research on food quality perception....

  20. DEMAND FOR BREAKFAST CEREALS: WHOLE GRAINS GUIDANCE AND FOOD CHOICE

    OpenAIRE

    Ishdorj, Ariun; Jensen, Helen H.

    2010-01-01

    When using household-level data to examine consumer demand it is common to find that consumers purchase only a subset of the available goods, setting the demand for the remaining goods to zero. Ignoring such censoring of the dependent variables can lead to estimators with poor statistical properties and estimates that lead to poor policy decisions. In this paper we investigate household demand for four types of breakfast cereals, such as whole grain ready-to-eat, non-whole grain ready-to-eat,...

  1. Development of genomic resources for Citrus clementina: Characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences

    OpenAIRE

    Talon Manuel; Ollitrault Patrick; Naranjo M Angel; Terol Javier

    2008-01-01

    Abstract Background Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the char...

  2. The PlaNet Consortium: A Network of European Plant Databases Connecting Plant Genome Data in an Integrated Biological Knowledge Resource

    OpenAIRE

    Schoof, H.; Ernst, R; Mayer, K.F.X.

    2004-01-01

    The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort amo...

  3. Integration of root phenes revealed by intensive phenotyping of root system architecture, anatomy, and physiology in cereals

    Science.gov (United States)

    York, Larry

    2015-04-01

    Food insecurity is among the greatest challenges humanity will face in the 21st century. Agricultural production in much of the world is constrained by the natural infertility of soil which restrains crops from reaching their yield potential. In developed nations, fertilizer inputs pollute air and water and contribute to climate change and environmental degradation. In poor nations low soil fertility is a primary constraint to food security and economic development. Water is almost always limiting crop growth in any system. Increasing the acquisition efficiency of soil resources is one method by which crop yields could be increased without the use of more fertilizers or irrigation. Cereals are the most widely grown crops, both in terms of land area and in yield, so optimizing uptake efficiency of cereals is an important goal. Roots are the primary interface between plant and soil and are responsible for the uptake of soil resources. The deployment of roots in space and time comprises root system architecture (RSA). Cereal RSA is a complex phenotype that aggregates many elemental phenes (elemental units of phenotype). Integration of root phenes will be determined by interactions through their effects on soil foraging and plant metabolism. Many architectural, metabolic, and physiological root phenes have been identified in maize, including: nodal root number, nodal root growth angle, lateral root density, lateral root length, aerenchyma, cortical cell size and number, and nitrate uptake kinetics. The utility of these phenes needs confirmation in maize and in other cereals. The maize root system is composed of an embryonic root system and nodal roots that emerge in successive whorls as the plant develops, and is similar to other cereals. Current phenotyping platforms often ignore the inner whorls and instead focus on the most visible outer whorls after excavating a maize root crown from soil. Here, an intensive phenotyping platform evaluating phenes of all nodal root

  4. Biospecimen Core Resource - TCGA

    Science.gov (United States)

    The Cancer Genome Atlas (TCGA) Biospecimen Core Resource centralized laboratory reviews and processes blood and tissue samples and their associated data using optimized standard operating procedures for the entire TCGA Research Network.

  5. State of cat genomics.

    Science.gov (United States)

    O'Brien, Stephen J; Johnson, Warren; Driscoll, Carlos; Pontius, Joan; Pecon-Slattery, Jill; Menotti-Raymond, Marilyn

    2008-06-01

    Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

  6. Improving feeding systems for sheep in a Mediterranean rain-fed cereals/livestock area of Morocco.

    Science.gov (United States)

    Guessous, F; Rihani, N; Kabbali, A; Johnson, W L

    1989-11-01

    In rain-fed cereal-producing areas of Morocco, stubble and straw from barley and wheat and forage grazed from fallow lands are important feeds for sheep. Supplementation to maintain BW of ewes pregnant while grazing stubble, methods to improve utilization of straw, annual forage legumes to complement grazing of fallow land, and by-product feeds in diets for weaned lambs have been tested in collaborative research trials. Pregnant ewes grazing cereal stubble for 10 to 12 wk at a modest stocking rate and unsupplemented, or at a heavier stocking rate and supplemented after 5 wk, gained about 3 kg; most of the gain occurred in wk 1 to 4 due to intake of residual scattered grain. Following the stubble-grazing period (coincident with late gestation), straw plus an energy supplement alone resulted in low lamb birth weight and survivability. Urea treatment increased N content of straw and holds potential. After the onset of winter rains, self-reseeding annual legume (Medicago spp.) pastures allowed lactating Timahdit ewes to gain 4 kg during 90 d postpartum. Their suckling lambs gained 260 g/d, thus doubling the weight of lamb weaned per ewe compared with those grazing unimproved fallow. Confined growing lambs fed diets with 40% sugarbeet pulp or 20% carob meal gained more than 200 g/d, reducing the time needed to reach market weight. These results demonstrate that marked improvements in performance and efficiency of sheep in Mediterranean rain-fed cereal/livestock systems are possible using locally available resources. PMID:2687218

  7. Seed protein improvement in cereals and grain legumes

    International Nuclear Information System (INIS)

    Plant breeders, molecular biologists, analytical chemists and nutritionists report on progress and achievements to date. High-lysine genotypes of maize, barley and sorghum have been produced. One high-protein variety of wheat is reported available for commercial use. Grain legumes already have high seed protein content but, compared to cereals, less of the total biological yield is available as seed, and intensive efforts are being made to produce genotypes with higher seed yield. Genetic variability is available from world germplasm collections and from induced-mutation programmes. In the basic sciences considerable advances are reported. Putative structural genes determining protein quality and quantity have been located on various chromosomes. In vitro synthesis of legume and cereal storage proteins and the isolation of some mRNA and the preparation and cloning of cDNA have been reported. Uptake and incorporation of N into amino acids, their synthesis into proteins, and interaction between protein and carbohydrate biosynthesis during seed development are discussed. Future prospects are considered including potential selection at the cellular rather than the whole plant level. In only a minority of the 64 papers is the use of nuclear techniques indicated specifically enough to justify individual entries in INIS

  8. Quantification of sugars in breakfast cereals using capillary electrophoresis.

    Science.gov (United States)

    Toutounji, Michelle R; Van Leeuwen, Matthew P; Oliver, James D; Shrestha, Ashok K; Castignolles, Patrice; Gaborieau, Marianne

    2015-05-18

    About 80% of the Australian population consumes breakfast cereal (BC) at least five days a week. With high prevalence rates of obesity and other diet-related diseases, improved methods for monitoring sugar levels in breakfast cereals would be useful in nutrition research. The heterogeneity of the complex matrix of BCs can make carbohydrate analysis challenging or necessitate tedious sample preparation leading to potential sugar loss or starch degradation into sugars. A recently established, simple and robust free solution capillary electrophoresis (CE) method was used in a new application to 13 BCs (in Australia) and compared with several established methods for quantification of carbohydrates. Carbohydrates identified in BCs by CE included sucrose, maltose, glucose and fructose. The CE method is simple requiring no sample preparation or derivatization and carbohydrates are detected by direct UV detection. CE was shown to be a more robust and accurate method for measuring carbohydrates than Fehling method, DNS (3,5-dinitrosalicylic acid) assay and HPLC (high performance liquid chromatography).

  9. CEREALS AS BASIS OF PREVENTING NUTRITION AGAINST OBESITY

    Directory of Open Access Journals (Sweden)

    Ernest Šturdík

    2010-11-01

    Full Text Available Still more alarming obesity studies show in fact that it is largely due to incorrect diet and lifestyle. For suitable alternative for prevention of this disease are now considered cereal foods, mainly based on increased fiber content. The importance of dietary fiber for human organism consist primarily in its protective function before civilization diseases. It has beneficial effects on digestive physiology and it is therefore an important factor in the prevention of obesity, but also other diseases. Fiber consumption in developed countries is low and it is below the lower limit of the recommended dose. Slovaks per day take only 10-12 g of fiber, which represents only 47% of the recommended dose. Recent large-scale epidemiological studies have shown that regular consumption of wholegrain cereals can reduce the risk of heart disease and certain cancers by 30 percent. One of the factors that increase the functionality of foods is the so-called indigestible resistant starch. For its the positive impact on the physiology of digestion is referred to as prebiotics new generation of dietary fiber. The increasing availability of tasty, whole grain products rich in fiber could be health benefits. doi:10.5219/76

  10. Manufacturing cereal bars with high nutritional value through experimental design

    Directory of Open Access Journals (Sweden)

    Roberta Covino

    2015-01-01

    Full Text Available Organizations responsible for public health throughout the world have been increasingly worrying about how to feed populations encouraging a nutritious and balanced diet in order to decrease the occurrence of chronic diseases, which are constantly related to an inadequate diet. Still, due to matters of modern lifestyle consumers are increasingly seeking convenient products. This being so, cereal bars have been an option when the matter is low calorie fast food which is also source of fiber. This study aimed at developing a cereal bar with high dietary fiber, iron, vitamins A and vitamin E, in order to easily enable adult population achieve the daily recommendation for such nutrients. Eight formulations plus the focal point were conducted through experimental planning; sensory analysis with 110 tasters for each block and texture. Afterwards, we conducted centesimal analysis for all three formulations presenting the best sensory results. After statistical analysis and comparison to the means for products available in the market, it was possible to conclude that the product developed presented great acceptance and fiber level more than twice as much as the means for commercial products.

  11. Reduced fungicide doses in cereals: Which parameters to consider?

    DEFF Research Database (Denmark)

    Jørgensen, Lise Nistrup

    2015-01-01

    Abstract:A long tradition for using reduced fungicides rates in cereals have been exploited successfully in Denmark for more than 20 years and a similar trend has also been seen in other Northern European countries. The use of reduced and appropriate dose rates have been driven by field trials wi...... that reduced fungicide rates select less for fungicide resistance and can help to delay development of resistance.......Abstract:A long tradition for using reduced fungicides rates in cereals have been exploited successfully in Denmark for more than 20 years and a similar trend has also been seen in other Northern European countries. The use of reduced and appropriate dose rates have been driven by field trials...... to be controlled successfully at rates down to quarter rates. Fungicides, in general, show highly variable dose responses for specific diseases, which is important to know when specific advice is given. Preventive treatments generally require less input compared with treatments during the latent period or later...

  12. A comparison of methods to quantify prolamin contents in cereals

    Directory of Open Access Journals (Sweden)

    Gianluca Giuberti

    2011-02-01

    Full Text Available Hydrophobic prolamins are endosperm storage proteins accounting for about 40% of the total protein in most cereals seeds. Despite the absence of a reference method, several procedures have been periodically published to quantify prolamins in cereals. The aim of this study was to compare a conventional fractionation assay (LND vs three other methods: one based on sequential extractions (HAM and two rapid turbidimetric procedures (L&H and DRO. Prolamins were extracted in duplicate on barley, corn and wheat samples. For the turbidimetric prolamin evaluation in barley and wheat, a universally available purified gliadin, as alternative to purified zein, was also tested as standard reference material (SRM. The extraction prolamin values were different among grain types (P0.05. LND agreed sufficiently well both with HAM and with L&H methods (R2=0.664 and R2=0.703, respectively, P0.05, whereas a higher prolamin quantification was obtained using HAM (P<0.05. Overall, DRO did not provide similar comparison and performance parameters with respect to other method comparisons. The effect of changing purified zein with purified gliadin was noteworthy only for L&H, both for wheat and barley samples (P<0.01. Considering the increasing attention of animal nutritionists on prolamins, our results could get useful information for routine laboratories analysis.

  13. Impacts of Cereal Ergot in Food Animal Production.

    Science.gov (United States)

    Coufal-Majewski, Stephanie; Stanford, Kim; McAllister, Tim; Blakley, Barry; McKinnon, John; Chaves, Alexandre Vieira; Wang, Yuxi

    2016-01-01

    The negative impacts of ergot contamination of grain on the health of humans and animals were first documented during the fifth century AD. Although ergotism is now rare in humans, cleaning contaminated grain concentrates ergot bodies in screenings which are used as livestock feed. Ergot is found worldwide, with even low concentrations of alkaloids in the diet (ergotamine, ergocristine, ergosine, ergocornine, and ergocryptine is extremely variable within ergot bodies and the relative toxicity of these alkaloids has yet to be determined. This raises concerns that current recommendations on safe levels of ergot in feeds may be unreliable. Furthermore, the total ergot alkaloid content is greatly dependent on the geographic region, harvest year, cereal species, variety, and genotype. Considerable animal-to-animal variation in the ability of the liver to detoxify ergot alkaloids also exists and the impacts of factors, such as pelleting of feeds or use of binders to reduce bioavailability of alkaloids require study. Accordingly, unknowns greatly outnumber the knowns for cereal ergot and further study to help better define allowable limits for livestock would be welcome. PMID:26942186

  14. Simple and efficient methodology to determine mycotoxins in cereal syrups.

    Science.gov (United States)

    Arroyo-Manzanares, Natalia; Huertas-Pérez, José F; Gámiz-Gracia, Laura; García-Campaña, Ana M

    2015-06-15

    Consumption of cereal syrups is increasing nowadays. Mycotoxins may be found in syrups resulting from the use of contaminated raw material or invading microorganisms in the final manufactured product. However, these matrices have been scarcely explored regarding their mycotoxin content. A sensitive, simple and rapid method for the determination of ten mycotoxins (ochratoxin A, fumonisin B1, fumonisin B2, deoxynivalenol, fusarenon-X, T-2 and HT-2 toxin, citrinin, sterigmatocystin and zearalenone) in cereal syrups (rice, wheat and barley) has been developed and characterised using ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) and a sample treatment based on QuEChERS procedure. Matrix-matched calibration curves were established and limits of quantification were below the limits usually established by current legislation in different foodstuff. The relative standard deviation of the whole analytical method was lower than 12% in all cases, while recoveries ranged from 70.2% to 100.6%, therefore fulfilling the current requirements for mycotoxins analysis.

  15. 40 CFR 406.80 - Applicability; description of the hot cereal subcategory.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 28 2010-07-01 2010-07-01 true Applicability; description of the hot cereal subcategory. 406.80 Section 406.80 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS GRAIN MILLS POINT SOURCE CATEGORY Hot Cereal Subcategory §...

  16. Changes in time of sowing, flowering and maturity of cereals in Europe under climate change

    NARCIS (Netherlands)

    Olesen, J.E.; Borgesen, C.D.; Elsgaard, L.; Palosuo, T.; Rötter, R.P.; Skjelväg, A.O.; Peltonen-Sainio, P.; Bórjesson, T.; Trnka, M.; Ewert, F.; Siebert, S.; Brisson, N.; Eitzinger, J.; Asselt, van E.D.; Oberforster, M.; Fels-Klerx, van der H.J.

    2012-01-01

    The phenological development of cereal crops from emergence through flowering to maturity is largely controlled by temperature, but also affected by day length and potential physiological stresses. Responses may vary between species and varieties. Climate change will affect the timing of cereal crop

  17. Effect of infant cereals on zinc and copper absorption during weaning

    International Nuclear Information System (INIS)

    Zinc and copper absorption from five infant cereal products mixed with water, human milk, or cow's milk was measured using an in vivo absorption model (rat pup) involving gastric intubation of extrinsically radiolabeled diets. Whole-body copper 64 uptake, nine hours after intubation, ranged from 14% to 31% of the dose given for the different cereal combinations. The resultant bioavailability of copper from human milk-cereal combinations (23% to 26%) was significantly lower than that from human milk alone (38%). Whole-body zinc 65 uptake, nine hours after intubation, ranged from 13% to 54% of the dose given for the different cereal combinations. These values were significantly lower than the whole-body zinc 65 uptake from milk alone (61%). Zinc availability was lower (13% to 25%) from dry cereal combinations that contained phytic acid (oatmeal and high-protein varieties) compared with the ready-to-serve cereal-fruit combinations (24% to 54%). The highest zinc uptake (37% to 54%) was from rice-fruit combinations that do not contain phytic acid. We estimated the amounts of zinc and copper that would be absorbed from these cereal products and speculated on the potential impact of these foods on the weaning infant's zinc and copper nutriture. Depending on the feeding practices employed during the weaning period, it is apparent that infant cereals may compromise utilization of zinc and copper from milk diets during weaning

  18. ORIGIN AND EVOLUTION OF CEREALS AND METHODS OF STUDYING THEIR BIOMORPHOLOGY

    OpenAIRE

    Belyuchenko I. S.

    2014-01-01

    In the article, the main issues of development of perennial cereals (morphology, phenology, formation of buds, physiology, biochemistry and research methods) are discussed. Peculiarities of regulation of development and the character of their evolution are considered. Problems of evolution of the cereals with widespread use of the data of Russian and foreign authors are discussed

  19. Effect of infant cereals on zinc and copper absorption during weaning

    Energy Technology Data Exchange (ETDEWEB)

    Bell, J.G.; Keen, C.L.; Loennerdal, B.

    1987-10-01

    Zinc and copper absorption from five infant cereal products mixed with water, human milk, or cow's milk was measured using an in vivo absorption model (rat pup) involving gastric intubation of extrinsically radiolabeled diets. Whole-body copper 64 uptake, nine hours after intubation, ranged from 14% to 31% of the dose given for the different cereal combinations. The resultant bioavailability of copper from human milk-cereal combinations (23% to 26%) was significantly lower than that from human milk alone (38%). Whole-body zinc 65 uptake, nine hours after intubation, ranged from 13% to 54% of the dose given for the different cereal combinations. These values were significantly lower than the whole-body zinc 65 uptake from milk alone (61%). Zinc availability was lower (13% to 25%) from dry cereal combinations that contained phytic acid (oatmeal and high-protein varieties) compared with the ready-to-serve cereal-fruit combinations (24% to 54%). The highest zinc uptake (37% to 54%) was from rice-fruit combinations that do not contain phytic acid. We estimated the amounts of zinc and copper that would be absorbed from these cereal products and speculated on the potential impact of these foods on the weaning infant's zinc and copper nutriture. Depending on the feeding practices employed during the weaning period, it is apparent that infant cereals may compromise utilization of zinc and copper from milk diets during weaning.

  20. Exploring the Boundaries of N2-Fixation in Cereals and Grasses: A Hypothetical and Experimental Framework

    NARCIS (Netherlands)

    Giller, K.E.; Merckx, R.

    2003-01-01

    Despite more than 40 years of research on free-living and endophytic bacteria associated with cereals and grasses, conclusive examples of impacts of non-symbiotic N2-fixation in agriculture are lacking. All available methods for measurement of N2-fixation associated with cereals and grasses have bee

  1. Cereal area and nitrogen use efficiency are drivers of future nitrogen fertilizer consumption.

    Science.gov (United States)

    Dobermann, Achim; Cassman, Kenneth G

    2005-12-01

    At a global scale, cereal yields and fertilizer N consumption have increased in a near-linear fashion during the past 40 years and are highly correlated with one another. However, large differences exist in historical trends of N fertilizer usage and nitrogen use efficiency (NUE) among regions, countries, and crops. The reasons for these differences must be understood to estimate future N fertilizer requirements. Global nitrogen needs will depend on: (i) changes in cropped cereal area and the associated yield increases required to meet increasing cereal demand from population and income growth, and (ii) changes in NUE at the farm level. Our analysis indicates that the anticipated 38% increase in global cereal demand by 2025 can be met by a 30% increase in N use on cereals, provided that the steady decline in cereal harvest area is halted and the yield response to applied N can be increased by 20%. If losses of cereal cropping area continue at the rate of the past 20 years (-0.33% per year) and NUE cannot be increased substantially, a 60% increase in global N use on cereals would be required to meet cereal demand. Interventions to increase NUE and reduce N losses to the environment must be accomplished at the farm- or field-scale through a combination of improved technologies and carefully crafted local policies that contribute to the adoption of improved N management; uniform regional or national directives are unlikey to be effective at both sustaining yield increases and improving NUE. Examples from several countries show that increases in NUE at rates of 1% per year or more can be achieved if adequate investments are made in research and extension. Failure to arrest the decrease in cereal crop area and to improve NUE in the world's most important agricultural systems will likely cause severe damage to environmental services at local, regional, and global scales due to a large increase in reactive N load in the environment.

  2. Cereal area and nitrogen use efficiency are drivers of future nitrogen fertilizer consumption

    Institute of Scientific and Technical Information of China (English)

    Achim; Dobermann; Kenneth; G.; Cassman

    2005-01-01

    At a global scale, cereal yields and fertilizer N consumption have increased in a near-linear fashion during the past 40 years and are highly correlated with one another. However,large differences exist in historical trends of N fertilizer usage and nitrogen use efficiency (NUE)among regions, countries, and crops. The reasons for these differences must be understood to estimate future N fertilizer requirements. Global nitrogen needs will depend on: (i) changes in cropped cereal area and the associated yield increases required to meet increasing cereal demand from population and income growth, and (ii) changes in NUE at the farm level. Our analysis indicates that the anticipated 38% increase in global cereal demand by 2025 can be met by a 30% increase in N use on cereals, provided that the steady decline in cereal harvest area is halted and the yield response to applied N can be increased by 20%. If losses of cereal cropping area continue at the rate of the past 20 years (-0.33% per year) and NUE cannot be increased substantially, a 60% increase in global N use on cereals would be required to meet cereal demand. Interventions to increase NUE and reduce N losses to the environment must be accomplished at the farm- or field-scale through a combination of improved technologies and carefully crafted local policies that contribute to the adoption of improved N management; uniform regional or national directives are unlikey to be effective at both sustaining yield increases and improving NUE. Examples from several countries show that increases in NUE at rates of 1% per year or more can be achieved if adequate investments are made in research and extension. Failure to arrest the decrease in cereal crop area and to improve NUE in the world's most important agricultural systems will likely cause severe damage to environmental services at local, regional, and global scales due to a large increase in reactive N load in the environment.

  3. Structural and functional analysis of rice genome

    Indian Academy of Sciences (India)

    Akhilesh K. Tyagi; Jitendra P. Khurana; Paramjit Khurana; Saurabh Raghuvanshi; Anupama Gaur; Anita Kapur; Vikrant Gupta; Dibyendu Kumar; V. Ravi; Shubha Vij; Parul Khurana; Sulabha Sharma

    2004-04-01

    Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4–6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at > 50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macro- and micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.

  4. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes

    Directory of Open Access Journals (Sweden)

    Anderson Olin D

    2008-07-01

    Full Text Available Abstract Background Wheat, barley, and rye, of tribe Triticeae in the Poaceae, are among the most important crops worldwide but they present many challenges to genomics-aided crop improvement. Brachypodium distachyon, a close relative of those cereals has recently emerged as a model for grass functional genomics. Sequencing of the nuclear and organelle genomes of Brachypodium is one of the first steps towards making this species available as a tool for researchers interested in cereals biology. Findings The chloroplast genome of Brachypodium distachyon was sequenced by a combinational approach using BAC end and shotgun sequences derived from a selected BAC containing the entire chloroplast genome. Comparative analysis indicated that the chloroplast genome is conserved in gene number and organization with respect to those of other cereals. However, several Brachypodium genes evolve at a faster rate than those in other grasses. Sequence analysis reveals that rice and wheat have a ~2.1 kb deletion in their plastid genomes and this deletion must have occurred independently in both species. Conclusion We demonstrate that BAC libraries can be used to sequence plastid, and likely other organellar, genomes. As expected, the Brachypodium chloroplast genome is very similar to those of other sequenced grasses. The phylogenetic analyses and the pattern of insertions and deletions in the chloroplast genome confirmed that Brachypodium is a close relative of the tribe Triticeae. Nevertheless, we show that some large indels can arise multiple times and may confound phylogenetic reconstruction.

  5. Starch bioengineering affects cereal grain germination and seedling establishment

    DEFF Research Database (Denmark)

    Shaik, Shahnoor Sultana; Carciofi, Massimiliano; Martens, Helle Juel;

    2014-01-01

    -amylase was generally suppressed in both HP and AO lines throughout germination. As further supported by scanning electron microscopy and histochemical analyses on grain and seedlings, it was concluded that inadequate starch granule deposition in combination with the suppressed hydrolase activity leads to temporal......Cereal grain germination is central for plant early development, and efficient germination has a major role in crop propagation and malting. Endosperm starch is the prime energy reserve in germination and seedling establishment. In this study, it was hypothesized that optimized starch granule...... structure, and not only the endosperm starch content per se, is important for germination and seedling establishment. For that purpose, wild-type (WT), and specifically engineered degradable hyperphosphorylated (HP) starch and more resistant amylose-only (AO) starch barley lines were used. The transgenics...

  6. DETERMINATION OF PRIMARY METABOLITES IN CEREAL MILLING FRACTIONS

    Directory of Open Access Journals (Sweden)

    Eva Ivanišová

    2013-10-01

    Full Text Available The aim of this study was to determine of primary metabolites (content of starch, total dietary fibre, reducing sugars, proteins and amino acids in four milling fractions of selected cereals (barley, wheat, oat, spelt, rye, triticale grew in the year 2009. It was found that flour fractions (break flour and reduction flour showed the lower content of primary metabolites than bran fractions (fine bran and coarse bran. The aim of this study was also to mention the potential use of bran parts of grain - substances from these parts can be isolated and after treatment, which causes their efficiently usable for human body, they can be used for fortification of wide range of food products.

  7. Variability in nutrient composition of cereal grains from different origins.

    Science.gov (United States)

    Lee, Jinyoung; Nam, Doo Seok; Kong, Changsu

    2016-01-01

    Nutrient composition of individual feed ingredient in mixed feed is important for accurate formulation of animal feeds. However, each feed ingredient can be different depending on its origin. Therefore, this study was conducted to investigate the variability in nutrient compositions of corn, wheat, and barley grains from different origins. Cereal grains used in this study were from 5 countries for 432 corn samples, 5 countries for 65 wheat samples, and 3 countries for 60 barley samples. They were imported to Korea between 2006 and 2015. These grain samples were subjected to analysis for moisture, crude protein (CP), ether extract (EE), crude fiber (CF), ash, calcium (Ca), phosphorus (P), and gross energy (GE). The concentrations of moisture, CP, EE, CF, ash, Ca, P, and GE of corn differed (P formulating animal feeds.

  8. Fusarium mycotoxins in cereals harvested from Hungarian fields.

    Science.gov (United States)

    Tima, Helga; Brückner, Andrea; Mohácsi-Farkas, Csilla; Kiskó, Gabriella

    2016-06-01

    The Fusarium mycotoxins deoxynivalenol (DON), zearalenone (ZEN) and T-2 frequently contaminate grain crops in Middle and Eastern Europe. In this survey, 116 cereal samples (maize, wheat, barley and oat) were examined for DON, ZEN and T-2 mycotoxins. Samples were collected from different areas in two Hungarian regions (North and South Transdanubia). The method of analysis was indirect competitive ELISA. Maize was the most contaminated grain regarding DON (86%), ZEN (41%) and T-2 (55%) toxins. The average results of the deoxynivalenol and zearalenone tests of maize proved to be significantly higher than those of barley or oat. DON was the most represented Fusarium mycotoxin followed by T-2 and ZEN. The examination of these mycotoxins would be necessary at a larger scale as to re-evaluate permissible levels, so increase of the monitoring programme would be advisable for the future. PMID:26892197

  9. Parallel Domestication of the Heading Date 1 Gene in Cereals.

    Science.gov (United States)

    Liu, Huanhuan; Liu, Hangqin; Zhou, Leina; Zhang, Zhihai; Zhang, Xuan; Wang, Mingli; Li, Haixia; Lin, Zhongwei

    2015-10-01

    Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 (HD1), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.

  10. Sugar as part of a balanced breakfast? What cereal advertisements teach children about healthy eating.

    Science.gov (United States)

    LoDolce, Megan E; Harris, Jennifer L; Schwartz, Marlene B

    2013-01-01

    Marketing that targets children with energy-dense, nutrient-poor foods is a likely contributor to the childhood obesity crisis. High-sugar ready-to-eat cereals are the packaged food most frequently promoted in child-targeted food advertising on television. The authors combined content analysis of product nutritional quality and messages presented in cereal television advertisements with syndicated data on exposure to those ads. The analysis quantifies children's exposure to specific products and messages that appear in advertisements and compares it with adult exposure. Children viewed 1.7 ads per day for ready-to-eat cereals, and 87% of those ads promoted high-sugar products; adults viewed half as many ads, and ads viewed were equally likely to promote high- and low-sugar cereals. In addition, the messages presented in high-sugar ads viewed by children were significantly more likely to convey unrealistic and contradictory messages about cereal attributes and healthy eating. For example, 91% of high-sugar cereal ads viewed by children ascribed extraordinary powers to these products, and 67% portrayed healthy and unhealthy eating behaviors. Given children's vulnerability to the influence of advertising, the emotional and mixed messages used to promote high-sugar cereals are confusing and potentially misleading. PMID:24175878

  11. Identification of aroma active compounds of cereal coffee brew and its roasted ingredients.

    Science.gov (United States)

    Majcher, Małgorzata A; Klensporf-Pawlik, Dorota; Dziadas, Mariusz; Jeleń, Henryk H

    2013-03-20

    Cereal coffee is a coffee substitute made mainly from roasted cereals such as barley and rye (60-70%), chicory (15-20%), and sugar beets (6-10%). It is perceived by consumers as a healthy, caffeine free, non-irritating beverage suitable for those who cannot drink regular coffee made from coffee beans. In presented studies, typical Polish cereal coffee brew has been subjected to the key odorants analysis with the application of gas chromatography-olfactometry (GC-O) and aroma extract dilution analysis (AEDA). In the analyzed cereal coffee extract, 30 aroma-active volatiles have been identified with FD factors ranging from 16 to 4096. This approach was also used for characterization of key odorants in ingredients used for the cereal coffee production. Comparing the main odors detected in GC-O analysis of roasted cereals brew to the odor notes of cereal coffee brew, it was evident that the aroma of cereal coffee brew is mainly influenced by roasted barley. Flavor compound identification and quantitation has been performed with application of comprehensive multidimentional gas chromatography and time-of-flight mass spectrometry (GCxGC-ToFMS). The results of the quantitative measurements followed by calculation of the odor activity values (OAV) revealed 17 aroma active compounds of the cereal coffee brew with OAV ranging from 12.5 and 2000. The most potent odorant was 2-furfurylthiol followed by the 3-mercapto-3-methylbutyl formate, 3-isobutyl-2-methoxypyrazine and 2-ethyl-3,5-dimethylpyrazine, 2-thenylthiol, 2,3-butanedione, 2-methoxy phenol and 2-methoxy-4-vinyl phenol, 3(sec-butyl)-2-methoxypyrazine, 2-acetyl-1-pyrroline, 3-(methylthio)-propanal, 2,3-pentanedione, 4-hydroxy-2,5-dimethyl-3-(2H)-furanone, (E,E)-2,4-decadienal, (Z)-4-heptenal, phenylacetaldehyde, and 1-octen-3-one. PMID:23414530

  12. The Cereal Pollen Sensitivity and Effect of the Asthma Clinics in Sanliurfa

    Directory of Open Access Journals (Sweden)

    Erkan Ceylan

    2012-07-01

    Full Text Available Aim: Our aim in this study was to detect the kinds of cereal that cause cereal pollens sensitivity, and to investigate the effects of cereal pollen sensitivity on the asthma clinic. Material and Method: In this study 140 cases from Sanliurfa with asthma (83 women, 57 men, with the mean age of 26.3-7.9 year and sensitivity against cereal pollen demonstrated by skin prick test, who applied to OSM Ortadogu Hospital Chest Diseases Outpatient Clinic in the period of March-June were evaluated prospectively. The patients’ peak expiratory flow (PEF values measured in the morning and evening, changes in PEF, asthma symptom score and the symptom-relieving therapy used during the 16-weeks study period were recorded and evaluated in the clinic with FEV1 results at the beginning, month 1, 2, 3 and 4. Results: Of the patients with sensitivity against cereals pollens, 25.4% had allergy against Hordeum vulgare, 23.6% against Secale cereale, 20.7% against Triticum sativum, 19,3% against Zea mays and 18.6% against Avena sativa. Prior to the study and at the end of follow up period, morning and evening PEF values, asthma scores and symptom relieving drug usage were same cereals pollens sensitivity (p>0.05. Discussion: Accordance to the vegetation of Sanliurfa region, important ratio of the sensitivities were detected with prick test against Hordeum vulgare, Secale cereale, Triticum sativum, Zea mays and Avena sativa pollens. The effects of cereals pollens were similar rates of asthma clinics.

  13. The benefits of breakfast cereal consumption: a systematic review of the evidence base.

    Science.gov (United States)

    Williams, Peter G

    2014-09-01

    There have been no comprehensive reviews of the relation of breakfast cereal consumption to nutrition and health. This systematic review of all articles on breakfast cereals to October 2013 in the Scopus and Medline databases identified 232 articles with outcomes related to nutrient intake, weight, diabetes, cardiovascular disease, hypertension, digestive health, dental and mental health, and cognition. Sufficient evidence was available to develop 21 summary evidence statements, ranked from A (can be trusted to guide practice) to D (weak and must be applied with caution). Breakfast cereal consumption is associated with diets higher in vitamins and minerals and lower in fat (grade B) but is not associated with increased intakes of total energy or sodium (grade C) or risk of dental caries (grade B). Most studies on the nutritional impact are cross-sectional, with very few intervention studies, so breakfast cereal consumption may be a marker of an overall healthy lifestyle. Oat-, barley-, or psyllium-based cereals can help lower cholesterol concentrations (grade A), and high-fiber, wheat-based cereals can improve bowel function (grade A). Regular breakfast cereal consumption is associated with a lower body mass index and less risk of being overweight or obese (grade B). Presweetened breakfast cereals do not increase the risk of overweight and obesity in children (grade C). Whole-grain or high-fiber breakfast cereals are associated with a lower risk of diabetes (grade B) and cardiovascular disease (grade C). There is emerging evidence of associations with feelings of greater well-being and a lower risk of hypertension (grade D), but more research is required. PMID:25225349

  14. Influence of host and geographic locale on the distribution of Colletotrichum cereale lineages.

    Directory of Open Access Journals (Sweden)

    Lisa A Beirn

    Full Text Available Colletotrichum cereale is an ascomycete inhabitant of cool-season Pooideae grasses. The fungus has increased in frequency over the past decade as a destructive pathogen of Poa annua and Agrostis stolonifera turfgrass. Colletotrichum cereale exists as two lineages, designated clades A and B, but little is known about the distribution of these clades in natural environments, or what role these subdivisions may play in the trajectory of disease outbreaks. In this study, our objective was to determine the frequency of C. cereale clades A and B. To rapidly discriminate between the two C. cereale clades, a real-time PCR assay was developed based on the Apn2 gene. A collection of 700 C. cereale pathogens and endophytes from twenty Pooideae grass genera were genotyped. 87% of the collection was identifed as part of clade A, 11.7% as part of clade B, and 1.3% was a mixture. Colletotrichum cereale from turfgrass hosts in North America were most commonly members of clade A (78%. The overabundance of clade A in turfgrass isolates was directly attributable to the dominance of this lineage from southern sampling sites, irrespective of host. In contrast, 111 C. cereale turfgrass isolates collected from northern sampling sites were evenly distributed between clades A and B. Only 28% of C. cereale from A. stolonifera at northern sampling sites were part of clade A. These data show that environmental factors such as geographic location and host identity likely played a role in the distribution of the major C. cereale clades in North American turfgrass.

  15. Sequence composition and gene content of the short arm of rye (Secale cereale chromosome 1.

    Directory of Open Access Journals (Sweden)

    Silvia Fluch

    Full Text Available BACKGROUND: The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. METHODOLOGY/PRINCIPAL FINDINGS: Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3% being the most abundant. More than four thousand simple sequence repeat (SSR sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice. CONCLUSIONS: The present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye.

  16. THE USE OF PSEUDO-CEREALS FLOURS IN BAKERY / UTILISATION DE FARINES DES PSEUDO-CEREALES DANS LA BOULANGERIE

    Directory of Open Access Journals (Sweden)

    ROMULUS MARIAN BURLUC

    2012-06-01

    Full Text Available Nowadays, a special attention should be given to the nutritional properties of foods. In the bakery industry there is a tendency to develop innovative range of bakery products by using the therapeutic role of cereals that are not used at their true potential (buckwheat, millet, rice, oats. Among bioactive components present in the pseudocereal flours, flavones group is highlighted, in particular rutine, the most important ramnoglicosid with multiple beneficial effects on health. The aims of this study were the obtention of different bakery products (bread, biscuits from raw materials with high therapeutic potential (fiber, antioxidant capacity, minerals, the optimization of process parameters and recipes, and the characterization of finished products in terms of sensory and physico-chemical properties. The results confirm that the use of unusual raw materials for the Romanian market led to obtaining high quality finished products with special therapeutic features.

  17. The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers.

    Science.gov (United States)

    Overby, Casey Lynnette; Tarczy-Hornoch, Peter; Demner-Fushman, Dina

    2009-01-01

    Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to therapy. These scientific discoveries need to be translated into practical applications to optimize patient care. Translating research into practice can be facilitated by supplying clinicians with research evidence. We assessed the role of existing tools in extracting answers to translational research questions in the area of genomic medicine. We: evaluate the coverage of translational research terms in the Unified Medical Language Systems (UMLS) Metathesaurus; determine where answers are most often found in full-text articles; and determine common answer patterns. Findings suggest that we will be able to leverage the UMLS in development of natural language processing algorithms for automated extraction of answers to translational research questions from biomedical text in the area of genomic medicine. PMID:19761578

  18. Assessment of mixtures of mycotoxins in cereal based foods available in Portuguese market

    OpenAIRE

    Martins, Carla; Assunção, Ricardo; Cunha, S.; Jager, A.; Alvito, Paula

    2015-01-01

    Mycotoxins are secondary metabolites of fungi that cause toxic and carcinogenic outcomes in humans exposed to them1. Mycotoxins affect several commodities including cereal grains and their finished products, infant formula and baby foods2. This study aimed to determine the incidence and levels of 20 mycotoxins and metabolites (AFB1, AFB2, AFG1, AFG2, AFM1, OTA, NIV, NEO, DAS, FUS-X, DON, 15-AC-DON, 3-AC-DON, HT-2, T-2, VER, T-2 TETROL, T-2 TRIOL), in breakfast cereals and cereal based baby fo...

  19. Semi-dwarf cereal mutants and their use in cross-breeding III

    International Nuclear Information System (INIS)

    A Co-ordinated Research Programme on the ''Evaluation of semi-dwarf mutants as cross-breeding material in cereals'' was initiated in 1980, with the main objective to provide cereal breeders with new, alternative sources of genes for semi-dwarf, lodging resistant plant types. The present publication includes papers presented at the final Research Co-ordination Meeting. Papers presented by participants in the Co-ordinated Research Programme demonstrate that these objectives were successfully achieved. As an additional result of this programme more improved genotypes of cereals with other desirable characters as earliness, better harvest index and improved plant architecture have become available for practical breeding. Refs, figs, tabs

  20. Distribution of carotenoids in endosperm, germ, and aleurone fractions of cereal grain kernels.

    Science.gov (United States)

    Ndolo, Victoria U; Beta, Trust

    2013-08-15

    To compare the distribution of carotenoids across the grain, non-corn and corn cereals were hand dissected into endosperm, germ and aleurone fractions. Total carotenoid content (TCC) and carotenoid composition were analysed using spectrophotometry and HPLC. Cereal carotenoid composition was similar; however, concentrations varied significantly (paleurone layer had zeaxanthin levels 2- to 5-fold higher than lutein among the cereals. Positive significant correlations (paleurone layer. Our findings suggest that the aleurone of wheat, oat, corn and germ of barley have significantly enhanced carotenoid levels.

  1. Using fuzzy logic for automatic control: Case study of a problem of cereals samples classification

    Directory of Open Access Journals (Sweden)

    Lakhoua Najeh Mohamed

    2009-01-01

    Full Text Available The aim of this paper is to present the use of fuzzy logic for automatic control of industrial systems particularly the way to approach a problem of classification. We present a case study of a grading system of cereals that allows us to determine the price of transactions of cereals in Tunisia. Our contribution in this work consists in proposing not only an application of the fuzzy logic on the grading system of cereals but also a methodology enabling the proposing of a new grading system based on the concept of 'Grade' while using the fuzzy logic techniques. .

  2. The Nipponbare genome and the next-generation of rice genomics research in Japan.

    Science.gov (United States)

    Matsumoto, Takashi; Wu, Jianzhong; Itoh, Takeshi; Numa, Hisataka; Antonio, Baltazar; Sasaki, Takuji

    2016-12-01

    The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits. PMID:27447712

  3. First Draft Genome Sequence of a UK Strain (UK99) of Fusarium culmorum.

    Science.gov (United States)

    Urban, Martin; King, Robert; Andongabo, Ambrose; Maheswari, Uma; Pedro, Helder; Kersey, Paul; Hammond-Kosack, Kim

    2016-01-01

    Fusarium culmorum is a soilborne fungal plant pathogen that causes foot and root rot and Fusarium head blight on small-grain cereals, in particular on wheat and barley. We report herein the draft genome sequence of a 1998 field strain called FcUK99 adapted to the temperate climate found in England. PMID:27634986

  4. First Draft Genome Sequence of a UK Strain (UK99) of Fusarium culmorum

    Science.gov (United States)

    King, Robert; Andongabo, Ambrose; Maheswari, Uma; Pedro, Helder; Kersey, Paul

    2016-01-01

    Fusarium culmorum is a soilborne fungal plant pathogen that causes foot and root rot and Fusarium head blight on small-grain cereals, in particular on wheat and barley. We report herein the draft genome sequence of a 1998 field strain called FcUK99 adapted to the temperate climate found in England. PMID:27634986

  5. Conservation and improvement of native pseudo cereals of Mexico; Conservacion y mejoramiento de pseudocereales nativos de Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Garcia A, J.M.; Cruz T, E. [ININ, Departamento de Biologia, 52750 La Marquesa, Estado de Mexico (Mexico); Mapes S, C. [Instituto de Biologia, UNAM, 04510 Mexico D.F. (Mexico); Laguna C, A. [Universidad Autonoma del Estado de Mexico, Toluca (Mexico)

    2007-07-01

    With the purpose of preserving the genetic resources of the local races of pseudo cereals 'red Chia' (Chenopodium berlandieri subspecies nuttalliae), Chia blanca or alegria and Chia negra (belonging to Amaranths hypochondriacus), its were carried out exploration, characterization in situ, collects and conservation activities in the Opopeo and Santa Maria Huiramangaro communities, Michoacan. Field journeys were made and collections were carried out. The morphological typification and of physical and bromatologic characters of the seed were carried out. Parcels for the In situ conservation and the collections have also settled down in two towns of the Toluca Valley for multiplication and ex situ characterization. Seed has been redistributed among the in study area producers to foment the interest of the cultivation. (Author)

  6. Teff, an Orphan Cereal in the Chloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses

    Science.gov (United States)

    Xu, Jianhong; Bennetzen, Jeffrey L.; Messing, Joachim

    2016-01-01

    Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragrostis tef) has been sequenced. We find gene duplications, deletions, and rapid mutations in protein-coding sequences. The main SSPs in teff, like other grasses, are prolamins, here called eragrostins. Teff has γ- and δ-prolamins, but has no β-prolamins. One δ-type prolamin (δ1) in teff has higher methionine (33%) levels than in maize (23–25%). The other δ-type prolamin (δ2) has reduced methionine residues (<10%) and is phylogenetically closer to α prolamins. Prolamin δ2 in teff represents an intermediate between δ and α types that appears to have been lost in maize and other Panicoideae, and was replaced by the expansion of α-prolamins. Teff also has considerably larger numbers of α-prolamin genes, which we further divide into five sub-groups, where α2 and α5 represent the most abundant α-prolamins both in number and in expression. In addition, indolines that determine kernel softness are present in teff and the panicoid cereal called foxtail millet (Setaria italica) but not in sorghum or maize, indicating that these genes were only recently lost in some members of the Panicoideae. Moreover, this study provides not only information on the evolution of SSPs in the grass family but also the importance of α-globulins in protein aggregation and germplasm divergence. PMID:27190000

  7. Relative severity of aflatoxin contamination of cereal crops in West Africa.

    Science.gov (United States)

    Bandyopadhyay, Ranajit; Kumar, Manjula; Leslie, John F

    2007-10-01

    Aflatoxins are a common contaminant of cereals that can cause cancer, liver disease, immune suppression, retarded growth and development, and death, depending on the level and duration of exposure. Maize is an introduced crop to Africa and there have been efforts over the last 20 years or so to replace traditional cereal crops, such as sorghum (Sorghum bicolor) and pearl millet (Pennisetum glaucum), with maize. We found that maize was significantly more heavily colonized by aflatoxin-producing Aspergillus spp. than either sorghum or millet, with overall aflatoxin levels being correspondingly higher. On average, Nigerians consume 138 kg cereals annually. If the primary cereal is sorghum instead of maize, then the risk of aflatoxin-related problems is reduced 4-fold; if it is pearl millet, then the risks are reduced 8-fold. Development programs and other ventures to increase maize production in marginal cropping areas of Africa should be reconsidered and, instead, efforts to improve/maintain traditional crops encouraged.

  8. Rich nutrition from the poorest - Cereal fermentations in Africa and Asia

    NARCIS (Netherlands)

    Nout, M.J.R.

    2009-01-01

    Cereal fermentations in Africa and Asia involve mainly the processing of maize, rice, sorghum and the millets. Lactic acid bacteria (Lactobacillus, Pediococcus), Enterobacter spp., yeasts (Candida, Debaryomyces, Endomycopsis, Hansenula, Pichia, Saccharomyces and Trichosporon spp.) and filamentous fu

  9. The prevalence and distribution of Fusarium species in Norwegian cereals: a survey

    DEFF Research Database (Denmark)

    Kosiak, B.; Torp, M.; Skjerve, E.;

    2003-01-01

    In the period 1994-1996 a post-harvest survey was conducted in wheat, barley and oats to assess the occurrence and geographic distribution of Fusarium species in Norwegian cereals. The number of samples investigated was adjusted proportionally to the production of each cereal species within...... the regions. A total of 695 grain samples were analysed. The amount of Fusarium infection varied with cereal species and region of origin. The most frequently isolated Fusarium spp. from all samples were F. avenaceum, F. poae, F. tricinctum and F. culmorum. Other important toxigenic Fusarium spp. were F...... and F. culmorum demonstrated in this study , corresponded to previously reported DON-distribution, although DON seems to be produced by different species in different regions. Distribution of the isolated Fusarium species and comparison between cereals and locations are discussed....

  10. Comparative Evaluation of Functional Properties of Some Commonly Used Cereal and Legume Flours and Their Blends

    Directory of Open Access Journals (Sweden)

    Haq Nawaz

    2015-12-01

    Full Text Available Functional properties such as protein solubility, swelling capacity, water holding capacity, gelling ability, bulk density and foaming capacity of flours of some commonly used cereals and legume (wheat, refined wheat, maize and chickpea and their blends were studied. Blends of flours were prepared by mixing equal proportions of selected floors. Statistically significant difference  in studied functional properties except bulk density was observed among cereal flours and their blends. Chickpea flour was found to possess comparatively high water holding capacity, protein solubility index and swelling capacity. The functional properties of maize and wheat flours were found to be improved when blended with chickpea. Chickpea flour and its blends with cereal flours were found to possess good functional score and suggested as favorable candidates for use in the preparation of viscous foods and bakery products. The data provide guidelines regarding the improvement in functional properties of economically favorable cereal flours.

  11. Ochratoxin A and ochratoxin-producing fungi on cereal grain in China: a review.

    Science.gov (United States)

    Zhihong, Liang; Kunlun, Huang; Yunbo, Luo

    2015-01-01

    The mycotoxin ochratoxin A (OTA) is known to be the main contaminant of cereal grain and has become increasingly important in recent years. Therefore, a survey of ochratoxigenic fungi and OTA contamination in China is a special challenge. This paper summarises data on cereals and moulds (Aspergillus niger, Penicillium verrucosum, Aspergillus ochraceus, for example) and on grain and OTA from 1973 by searching Chinese information databases (NCKI, VIP, DuXiu etc.), calculating the OTA-producing mould detection rate, referring to sampling locations, latitude and temperature, and also combining six grain-producing areas of ochratoxigenic fungi and OTA positive rate through a comprehensive analysis. It is concluded that in China rice (excluding shell rice) has less OTA contamination than wheat or maize. The contamination of cereal grains with Aspergillus section Nigri (formerly of the A. niger group) is a serious problem in China, and these fungi may be the main ochratoxigenic fungi on cereals.

  12. Ochratoxin A and ochratoxin-producing fungi on cereal grain in China: a review.

    Science.gov (United States)

    Zhihong, Liang; Kunlun, Huang; Yunbo, Luo

    2015-01-01

    The mycotoxin ochratoxin A (OTA) is known to be the main contaminant of cereal grain and has become increasingly important in recent years. Therefore, a survey of ochratoxigenic fungi and OTA contamination in China is a special challenge. This paper summarises data on cereals and moulds (Aspergillus niger, Penicillium verrucosum, Aspergillus ochraceus, for example) and on grain and OTA from 1973 by searching Chinese information databases (NCKI, VIP, DuXiu etc.), calculating the OTA-producing mould detection rate, referring to sampling locations, latitude and temperature, and also combining six grain-producing areas of ochratoxigenic fungi and OTA positive rate through a comprehensive analysis. It is concluded that in China rice (excluding shell rice) has less OTA contamination than wheat or maize. The contamination of cereal grains with Aspergillus section Nigri (formerly of the A. niger group) is a serious problem in China, and these fungi may be the main ochratoxigenic fungi on cereals. PMID:25571918

  13. Evaluation of Antioxidant Properties in Cereals: Study of Some Traditional Italian Wheats

    Directory of Open Access Journals (Sweden)

    Alessandra Durazzo

    2015-09-01

    Full Text Available Whole grain cereals contain a wide range of phytochemicals and it is often difficult to ascribe protective effects on metabolic health to any one particular constituent. The interactions among bioactive components, which contribute highly to the total antioxidant capacity of cereals, represent the first step in the evaluation of food potential health benefits. This research focused on the determination of antioxidant properties in grains and whole flours of some traditional Italian wheats. Results showed that hydrolysable polyphenols in grains are 85% of total polyphenols and contribute 95% of the total antioxidant properties, which indicates that hydrolysable polyphenols represent an important fraction of polyphenols in cereals. The distinction between extractable and non-extractable antioxidants was shown to be of paramount importance for an adequate determination of antioxidant capacity in cereals and represents a key element in the definition of potential nutritional value of the food matrix under consideration.

  14. 10 Reasons to be Tantalized by the B73 Maize Genome

    OpenAIRE

    Fusheng Wei; Jianwei Zhang; Shiguo Zhou; Ruifeng He; Mary Schaeffer; Kristi Collura; David Kudrna; Faga, Ben P.; Marina Wissotski; Wolfgang Golser; Rock, Susan M.; Graves, Tina A.; Fulton, Robert S.; Ed Coe; Patrick S Schnable

    2009-01-01

    Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize geno...

  15. Genome-wide association study for rib eye muscle area in a Large White×Minzhu F2 pig resource population

    Institute of Scientific and Technical Information of China (English)

    GUO Yun-yan; ZHANG Long-chao; WANG Li-xian; LIU Wen-zhong

    2015-01-01

    Rib eye muscle area (REMA) is an economicaly important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study (GWAS), the Ilumina PorcineSNP60 BeadChip containing 62163 single nucleotide polymorphisms (SNPs) was used to genotype 557 pigs from a porcine Large White×Minzhu intercross population. The REMA (at the 5th–6th, 10th–11th and the last ribs) was measured after slaughtered at the age of (240±7) d for each animal. Association tests between REMA trait and SNPs were performedvia the Genome-Wide Rapid Asso-ciation using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. From the Ensembl porcine database, SNP annotation was implemented usingSus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed signiifcant association with REMA at the last rib at the chromosome-wide signiifcance level. None of the SNPs of REMA at the 5th–6th rib and only a few numbers of the SNPs of REMA at the 10th–11th ribs were found in this study. The Haploview V3.31 program and the Haplo.Stats R package were used to detect and visualize haplotype blocks and to analyze the association of the detected haplotype blocks with REMA at the last rib. A linkage analysis revealed that 4 haplotype blocks contained 4, 4, 2, and 4 SNPs, respectively. Annotations from pig reference genome suggested 2 genes (NOS2,NLK) in block 1 (266 kb), one gene (TMIGD1) in block 2 (348 kb), and one gene (MAP2K4) in block 3 (453 kb). A functional analysis indicated thatMYH3andMYH13 genes are the potential genes controling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred thatNOS2 and NLK genes maybe the main genes of REMA at the last ribs.

  16. Preference Heterogeneity and Habit Persistence: The Case of Breakfast Cereal Consumption

    OpenAIRE

    Thunström, Linda

    2008-01-01

    This paper estimates the strength and heterogeneity across households in state dependence associated with breakfast cereal consumption, where positive state dependence implies habit persistence and negative state dependence implies variety-seeking in consumption. The analysis relies on a discrete choice model and finds that breakfast cereal consumption is generally highly habitual, but the degree of habit persistence exhibits heterogeneity across households. In addition, some households can b...

  17. U.S. READY-TO-EAT BREAKFAST CEREALS' EXPANSION IN CHINA

    OpenAIRE

    Zhang, Fang

    1999-01-01

    US ready-to-eat breakfast cereals entered the Chinese market in the mid-1990s. In the past years, this all-American food has been generating business losses. Such underperformance calls for prompt strategic modification by the cereal investors. This study focuses on foreign entry strategy and product strategy, and characterizes a combination of literature review and case study. Literature review seeks appropriate theories and frameworks, and therefore renders a sound conceptual foundation for...

  18. Material wear and failure mode analysis of breakfast cereal extruder barrels and screw elements

    Science.gov (United States)

    Mastio, Michael Joseph, Jr.

    2005-11-01

    Nearly seventy-five years ago, the single screw extruder was introduced as a means to produce metal products. Shortly after that, the extruder found its way into the plastics industry. Today much of the world's polymer industry utilizes extruders to produce items such as soda bottles, PVC piping, and toy figurines. Given the significant economical advantages of extruders over conventional batch flow systems, extruders have also migrated into the food industry. Food applications include the meat, pet food, and cereal industries to name just a few. Cereal manufacturers utilize extruders to produce various forms of Ready-to-Eat (RTE) cereals. These cereals are made from grains such as rice, oats, wheat, and corn. The food industry has been incorrectly viewed as an extruder application requiring only minimal energy control and performance capability. This misconception has resulted in very little research in the area of material wear and failure mode analysis of breakfast cereal extruders. Breakfast cereal extruder barrels and individual screw elements are subjected to the extreme pressures and temperatures required to shear and cook the cereal ingredients, resulting in excessive material wear and catastrophic failure of these components. Therefore, this project focuses on the material wear and failure mode analysis of breakfast cereal extruder barrels and screw elements, modeled as a Discrete Time Markov Chain (DTMC) process in which historical data is used to predict future failures. Such predictive analysis will yield cost savings opportunities by providing insight into extruder maintenance scheduling and interchangeability of screw elements. In this DTMC wear analysis, four states of wear are defined and a probability transition matrix is determined based upon 24,041 hours of operational data. This probability transition matrix is used to predict when an extruder component will move to the next state of wear and/or failure. This information can be used to determine

  19. Simultaneous determination of nitrogen and phosphorus in cereals using 14 MeV Neutron Activation Analysis

    International Nuclear Information System (INIS)

    A method using 14 MeV neutron activation analysis was developed form non-destructive simultaneous determination of N and P in cereals. The samples were irradiated 5 min. after 0,5 min. decay time. The induced activities were measured using gamma spectrometry with Nal(Tl) well type detector. The accuracy, precision and detection limits obtained are discussed as well as the analytical results for different types of cereals. (Author) 10 refs., 8 tab., 1 fig

  20. Spatiotemporal Dynamics of Oligofructan Metabolism and Suggested Functions in Developing Cereal Grains

    OpenAIRE

    Manuela ePeukert; Johannes eThiel; Hans-Peter eMock; Doris eMarko; Winfriede eWeschke; Andrea eMatros

    2016-01-01

    Oligofructans represent one of the most important groups of sucrose-derived water–soluble carbohydrates in the plant kingdom. In cereals, oligofructans accumulate in above ground parts of the plants (stems, leaves, seeds) and their biosynthesis leads to the formation of both types of glycosidic linkages (ß(2,1); ß(2,6)-fructans) or mixed patterns. In recent studies, tissue- and development- specific distribution patterns of the various oligofructan types in cereal grains have been shown, whic...

  1. Spatiotemporal Dynamics of Oligofructan Metabolism and Suggested Functions in Developing Cereal Grains

    OpenAIRE

    Peukert, Manuela; Thiel, Johannes; Mock, Hans-Peter; Marko, Doris; Weschke, Winfriede; Matros, Andrea

    2016-01-01

    Oligofructans represent one of the most important groups of sucrose-derived water–soluble carbohydrates in the plant kingdom. In cereals, oligofructans accumulate in above ground parts of the plants (stems, leaves, seeds) and their biosynthesis leads to the formation of both types of glycosidic linkages [β(2,1); β(2,6)-fructans] or mixed patterns. In recent studies, tissue- and development- specific distribution patterns of the various oligofructan types in cereal grains have been shown, whic...

  2. Impact of selected antagonistic fungi on Fusarium species – toxigenic cereal pathogens

    OpenAIRE

    Delfina Popiel; Hanna Kwaśny; Jerzy Chełkowski; Łukasz Stępień; Magdalena Laskowska

    2013-01-01

    Fusarium-ear blight is a destructive disease in various cereal-growing regions and leads to significant yield and quality losses for farmers and to contamination of cereal grains with mycotoxins, mainly deoxynivalenol and derivatives, zearalenone and moniliformin. Fusarium pathogens grow well and produce significant inoculum on crop resiudues. Reduction of mycotoxins production and pathogen sporulation may be influenced by saprophytic fungi, exhibiting antagonistic effect. Dual culture bioass...

  3. Suitability of cereal porridges as substrate for probiotic strain Lactobacillus rhamnosus GG

    OpenAIRE

    Ľubomír Valík; Monika Kocková

    2013-01-01

    The aim of this work was to find new substrates suitable for growth and metabolism of probiotic strain Lactobacillus rhamnosus GG, which would be interesting for development of new functional food. The growth and metabolic activity of Lb. rhamnosus GG in cereal (rye, barley, oat and millet) porridges were monitored during fermentation process. Cereal and porridges, were inoculated with this strain at two initial levels to obtain approximately 5 or 6 log colony form units per gram of suspensio...

  4. Ochratoxin A producing Penicillium verrucosum isolates from cereals reveal large AFLP fingerprinting variability

    OpenAIRE

    Frisvad, J C; Lund, F; Elmholt, S.

    2005-01-01

    Aims: To examine if molecular amplified fragment length polymorphism (AFLP) fingerprinting of the only ochratoxin A-producing species in European cereals, Penicillium verrucosum, can be used as a method in hazard analysis using critical control points (HACCP). Methods and Results: A total of 321 isolates of P. verrucosum were isolated from ochratoxin A contaminated cereals from Denmark (oats), UK (wheat and barley) and Sweden (wheat). Of these, 236 produced ochratoxin A as determined by t...

  5. Catch crops as universal and effective method for reducing nitrogen leaching loss in spring cereal production: A meta-analysis.

    Science.gov (United States)

    Valkama, Elena; Lemola, Riitta; Känkänen, Hannu; Turtola, Eila

    2016-04-01

    Sustainable farms produce adequate amounts of a high-quality product, protect their resources and are both environmentally friendly and economically profitable. Nitrogen (N) fertilization decisively influences the cereal yields as well as increases soil N balance (N input in fertilizer - N output in harvested yield), thereby leading to N losses to the environment. However, while N input reduction affects soil N balance, such approach would markedly reduce N leaching loss only in case of abnormally high N balances. As an alternative approach, the growing of catch crops aims to prevent nutrient leaching in autumn after harvest and during the following winter, but due to competition, catch crops may also reduce yields of the main crop. Although studies have explored the environmental effects of catch crops in cereal production in the Nordic countries (Denmark, Sweden, Finland and Norway) during the past 40 years, none has yet carried out a meta-analysis. We quantitatively summarized 35 studies on the effect of catch crops (non-legume and legume) undersown in spring cereals on N leaching loss or its risk as estimated by the content of soil nitrate N or its sum with ammonium in late autumn. The meta-analysis also included the grain yield and N content of spring cereals. To identify sources of variation, we studied the effects of soil texture and management (ploughing time, the amount of N applied, fertilizer type), as well as climatic (annual precipitation) and experimental conditions (duration of experiments, lysimeter vs. field experiments). Finally, we examined whether the results differed between the countries or over the decades. Compared to control groups with no catch crops, non-legume catch crops, mainly ryegrass species, reduced N leaching loss by 50% on average, and soil nitrate N or inorganic N by 35% in autumn. Italian ryegrass depleted soil N more effectively (by 60%) than did perennial ryegrass or Westerwolds ryegrass (by 25%). In contrast, legumes (white

  6. Development of a Genomic Resource and Quantitative Trait Loci Mapping of Male Calling Traits in the Lesser Wax Moth, Achroia grisella.

    Directory of Open Access Journals (Sweden)

    Jennifer M Gleason

    Full Text Available In the study of sexual selection among insects, the Lesser Waxmoth, Achroia grisella (Lepidoptera: Pyralidae, has been one of the more intensively studied species over the past 20 years. Studies have focused on how the male calling song functions in pair formation and on the quantitative genetics of male song characters and female preference for the song. Recent QTL studies have attempted to elucidate the genetic architecture of male song and female preference traits using AFLP markers. We continued these QTL studies using SNP markers derived from an EST library that allowed us to measure both DNA sequence variation and map loci with respect to the lepidopteran genome. We report that the level of sequence variation within A. grisella is typical among other Lepidoptera that have been examined, and that comparison with the Bombyx mori genome shows that macrosynteny is conserved. Our QTL map shows that a QTL for a male song trait, pulse-pair rate, is situated on the Z chromosome, a prediction for sexually selected traits in Lepidoptera. Our findings will be useful for future studies of genetic architecture of this model species and may help identify the genetics associated with the evolution of its novel acoustic communication.

  7. GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes.

    Science.gov (United States)

    Kim, Mara; Cooper, Brian A; Venkat, Rohit; Phillips, Julie B; Eidem, Haley R; Hirbo, Jibril; Nutakki, Sashank; Williams, Scott M; Muglia, Louis J; Capra, J Anthony; Petren, Kenneth; Abbot, Patrick; Rokas, Antonis; McGary, Kriston L

    2016-01-01

    Mammalian gestation and pregnancy are fast evolving processes that involve the interaction of the fetal, maternal and paternal genomes. Version 1.0 of the GEneSTATION database (http://genestation.org) integrates diverse types of omics data across mammals to advance understanding of the genetic basis of gestation and pregnancy-associated phenotypes and to accelerate the translation of discoveries from model organisms to humans. GEneSTATION is built using tools from the Generic Model Organism Database project, including the biology-aware database CHADO, new tools for rapid data integration, and algorithms that streamline synthesis and user access. GEneSTATION contains curated life history information on pregnancy and reproduction from 23 high-quality mammalian genomes. For every human gene, GEneSTATION contains diverse evolutionary (e.g. gene age, population genetic and molecular evolutionary statistics), organismal (e.g. tissue-specific gene and protein expression, differential gene expression, disease phenotype), and molecular data types (e.g. Gene Ontology Annotation, protein interactions), as well as links to many general (e.g. Entrez, PubMed) and pregnancy disease-specific (e.g. PTBgene, dbPTB) databases. By facilitating the synthesis of diverse functional and evolutionary data in pregnancy-associated tissues and phenotypes and enabling their quick, intuitive, accurate and customized meta-analysis, GEneSTATION provides a novel platform for comprehensive investigation of the function and evolution of mammalian pregnancy. PMID:26567549

  8. EFFECTS GENERATED BY THE ACCESSION TO THE EUROPEAN UNION IN THE FIELD OF TRADING CEREAL PRODUCTS

    Directory of Open Access Journals (Sweden)

    Ion DONA

    2012-01-01

    Full Text Available The European consumer exigencies, the mechanisms of the Common Agricultural Policy, the European norms and standards, the ecological productions are as many challenges to which the producers, processors, traders and decision makers in the agro food field, and specifically for our research, in the cereals field, must face in order for the Romanian products to be present on an external market, as well as on an internal market that are increasingly competitive.In this paper we have concluded a brief analysis of the cereals market nationally and on a European level, and of the common support policies in this sector, of the common market organizations, as well as of the implications of the accession over the trade of cereal products. Also, we have made several recommendations within this paper targeting the specific sectorial aspects of the cereals sector: in order to fully profit from the possibilities offered by the Common Agricultural Policy instruments and from the demand and prices growth its necessary that Romanian producers organize and make, together, major investments in cereals conditioning and storage systems; the majority of Romanian producers sell the cereals immediately after harvest, when prices are at their lowest level; storage in good conditions of the harvest could allow a substantial increase of profit.

  9. Sensorial analysis evaluation in cereal bars preserved by ionizing radiation processing

    Science.gov (United States)

    Villavicencio, A. L. C. H.; Araújo, M. M.; Fanaro, G. B.; Rela, P. R.; Mancini-Filho, J.

    2007-11-01

    Gamma-rays utilized as a food-processing treatment to eliminate insect contamination is well established in food industries. Recent troubles in Brazilian cereal bars commercialization require a special consumer's attention because some products were contaminated by insects. To solve the problem, food-irradiation treatment was utilized as a safe and effective solution. The final product was free of insect contamination. The aim of this study was to determine the best radiation dose processing utilized to disinfestations and detect some change on sensorial characteristic by sensorial analysis in cereal bars. In this study, three different kinds of cereal bars were purchased in São Paulo (Brazil) in supermarkets and irradiated with 1.0, 2.0 and 3.0 kGy at "Instituto de Pesquisas Energéticas e Nucleares" (IPEN-CNEN/SP). The samples were treated with ionizing radiation using a 60Co gamma-ray facility (Gammacell 220, A.E.C.L.). That radiation doses were used successfully as an anti-insect treatment in the cereal bars, since in some food industries doses up to 3.0 kGy are used to guarantee at least a dose of 1.0 kGy in internal cereal bars package. Sensorial analysis was necessary since cereal bars contain ingredients very sensitive to ionizing radiation process.

  10. Sensorial analysis evaluation in cereal bars preserved by ionizing radiation processing

    International Nuclear Information System (INIS)

    Gamma-rays utilized as a food-processing treatment to eliminate insect contamination is well established in food industries. Recent troubles in Brazilian cereal bars commercialization require a special consumer's attention because some products were contaminated by insects. To solve the problem, food-irradiation treatment was utilized as a safe and effective solution. The final product was free of insect contamination. The aim of this study was to determine the best radiation dose processing utilized to disinfestations and detect some change on sensorial characteristic by sensorial analysis in cereal bars. In this study, three different kinds of cereal bars were purchased in Sao Paulo (Brazil) in supermarkets and irradiated with 1.0, 2.0 and 3.0 kGy at 'Instituto de Pesquisas Energeticas e Nucleares' (IPEN-CNEN/SP). The samples were treated with ionizing radiation using a 60Co gamma-ray facility (Gammacell 220, A.E.C.L.). That radiation doses were used successfully as an anti-insect treatment in the cereal bars, since in some food industries doses up to 3.0 kGy are used to guarantee at least a dose of 1.0 kGy in internal cereal bars package. Sensorial analysis was necessary since cereal bars contain ingredients very sensitive to ionizing radiation process

  11. APPLICATION OF WESTERN BLOT ANALYSIS FOR DETECTION OF PROLAMIN PROTEINS IN CEREAL GRAINS AND BREAD

    Directory of Open Access Journals (Sweden)

    Ewa Cieślik

    2011-02-01

    Full Text Available Celiac disease is an inflammatory condition of the small intestine in genetically susceptible individuals caused by ingestion of wheat gluten and corresponding proteins from barley and rye. Cereal storage proteins (prolamins are responsible for immunological response of patients with celiac disease. Prolamins are alcohol soluble fractions, namely gliadins (wheat, hordeins (barley and secalins (rye. The main triggering factor is wheat fraction with low molecular weight (20-30 kDa called α-gliadins. Immunochemical detection of celiac active proteins is based on reactivity of gluten-detecting antibodies with prolamins extracted from cereals. In our study, we used Western blot analysis for detection of prolamin complex in cereal grains and processed foods (breads. Western blot was carried out by polyclonal antibody raised against wheat gluten. Reaction was positive for all kind of cereal grains. The samples of wheat and spelt wheat show much more positive affinity to antibody than rye and oat. As well as for cereal grains, all samples of bread showed positive immunological reaction with used antibody. Western blot analysis with gluten polyclonal antibody is suitable method for qualitative detection of prolamin complex in cereal grains and processed foods.doi:10.5219/115

  12. The gluten-free diet: testing alternative cereals tolerated by celiac patients.

    Science.gov (United States)

    Comino, Isabel; Moreno, María de Lourdes; Real, Ana; Rodríguez-Herrera, Alfonso; Barro, Francisco; Sousa, Carolina

    2013-10-01

    A strict gluten-free diet (GFD) is the only currently available therapeutic treatment for patients with celiac disease, an autoimmune disorder of the small intestine associated with a permanent intolerance to gluten proteins. The complete elimination of gluten proteins contained in cereals from the diet is the key to celiac disease management. However, this generates numerous social and economic repercussions due to the ubiquity of gluten in foods. The research presented in this review focuses on the current status of alternative cereals and pseudocereals and their derivatives obtained by natural selection, breeding programs and transgenic or enzymatic technology, potential tolerated by celiac people. Finally, we describe several strategies for detoxification of dietary gluten. These included enzymatic cleavage of gliadin fragment by Prolyl endopeptidases (PEPs) from different organisms, degradation of toxic peptides by germinating cereal enzymes and transamidation of cereal flours. This information can be used to search for and develop cereals with the baking and nutritional qualities of toxic cereals, but which do not exacerbate this condition. PMID:24152755

  13. Sensorial analysis evaluation in cereal bars preserved by ionizing radiation processing

    Energy Technology Data Exchange (ETDEWEB)

    Villavicencio, A.L.C.H. [Instituto de Pesquisas Energeticas e Nucleares-IPEN-CNEN/SP, Centro de Tecnologia das Radiacoes, Lab. de Deteccao de Alimentos Irradiados, Travessa R. No. 400, Cidade Universitaria, CEP 05508-910, Sao Paulo (Brazil)], E-mail: villavic@ipen.br; Araujo, M.M.; Fanaro, G.B.; Rela, P.R. [Instituto de Pesquisas Energeticas e Nucleares-IPEN-CNEN/SP, Centro de Tecnologia das Radiacoes, Lab. de Deteccao de Alimentos Irradiados, Travessa R. No. 400, Cidade Universitaria, CEP 05508-910, Sao Paulo (Brazil); Mancini-Filho, J. [Faculdade de Ciencias Farmaceuticas-FCF/USP, Departamento de Alimentos e Nutricao Experimental, Lab. de Lipides, Sao Paulo (Brazil)], E-mail: jmancini@usp.br

    2007-11-15

    Gamma-rays utilized as a food-processing treatment to eliminate insect contamination is well established in food industries. Recent troubles in Brazilian cereal bars commercialization require a special consumer's attention because some products were contaminated by insects. To solve the problem, food-irradiation treatment was utilized as a safe and effective solution. The final product was free of insect contamination. The aim of this study was to determine the best radiation dose processing utilized to disinfestations and detect some change on sensorial characteristic by sensorial analysis in cereal bars. In this study, three different kinds of cereal bars were purchased in Sao Paulo (Brazil) in supermarkets and irradiated with 1.0, 2.0 and 3.0 kGy at 'Instituto de Pesquisas Energeticas e Nucleares' (IPEN-CNEN/SP). The samples were treated with ionizing radiation using a {sup 60}Co gamma-ray facility (Gammacell 220, A.E.C.L.). That radiation doses were used successfully as an anti-insect treatment in the cereal bars, since in some food industries doses up to 3.0 kGy are used to guarantee at least a dose of 1.0 kGy in internal cereal bars package. Sensorial analysis was necessary since cereal bars contain ingredients very sensitive to ionizing radiation process.

  14. The Gluten-Free Diet: Testing Alternative Cereals Tolerated by Celiac Patients

    Directory of Open Access Journals (Sweden)

    Carolina Sousa

    2013-10-01

    Full Text Available A strict gluten-free diet (GFD is the only currently available therapeutic treatment for patients with celiac disease, an autoimmune disorder of the small intestine associated with a permanent intolerance to gluten proteins. The complete elimination of gluten proteins contained in cereals from the diet is the key to celiac disease management. However, this generates numerous social and economic repercussions due to the ubiquity of gluten in foods. The research presented in this review focuses on the current status of alternative cereals and pseudocereals and their derivatives obtained by natural selection, breeding programs and transgenic or enzymatic technology, potential tolerated by celiac people. Finally, we describe several strategies for detoxification of dietary gluten. These included enzymatic cleavage of gliadin fragment by Prolyl endopeptidases (PEPs from different organisms, degradation of toxic peptides by germinating cereal enzymes and transamidation of cereal flours. This information can be used to search for and develop cereals with the baking and nutritional qualities of toxic cereals, but which do not exacerbate this condition.

  15. From the concept of totipotency to biofortified cereals.

    Science.gov (United States)

    Potrykus, Ingo

    2015-01-01

    I was a college teacher when opportunity opened a path into academia. A fascination with totipotency channeled me into research on tissue culture. As I was more interested in contributions to food security than in scientific novelty, I turned my attention to the development of genetic modification technology for cereals. From my cell culture experience, I had reasons not to trust Agrobacterium for that purpose, and I developed direct gene transfer instead. In the early 1990s, I became aware of the problem of micronutrient deficiency, particularly vitamin A deficiency in rice-eating populations. Golden Rice, which contains increased amounts of provitamin A, was probably instrumental for the concept of biofortification to take off. I realized that this rice would remain an academic exercise if product development and product registration were not addressed, and this is what I focused on after my retirement. Although progress is slowly being made, had I known what this pursuit would entail, perhaps I would not have started. Hopefully Golden Rice will reach the needy during my lifetime. PMID:25423078

  16. A tradeoff frontier for global nitrogen use and cereal production

    International Nuclear Information System (INIS)

    Nitrogen fertilizer use across the world’s croplands enables high-yielding agricultural production, but does so at considerable environmental cost. Imbalances between nitrogen applied and nitrogen used by crops contributes to excess nitrogen in the environment, with negative consequences for water quality, air quality, and climate change. Here we utilize crop input-yield models to investigate how to minimize nitrogen application while achieving crop production targets. We construct a tradeoff frontier that estimates the minimum nitrogen fertilizer needed to produce a range of maize, wheat, and rice production levels. Additionally, we explore potential environmental consequences by calculating excess nitrogen along the frontier using a soil surface nitrogen balance model. We find considerable opportunity to achieve greater production and decrease both nitrogen application and post-harvest excess nitrogen. Our results suggest that current (circa 2000) levels of cereal production could be achieved with ∼50% less nitrogen application and ∼60% less excess nitrogen. If current global nitrogen application were held constant but spatially redistributed, production could increase ∼30%. If current excess nitrogen were held constant, production could increase ∼40%. Efficient spatial patterns of nitrogen use on the frontier involve substantial reductions in many high-use areas and moderate increases in many low-use areas. Such changes may be difficult to achieve in practice due to infrastructure, economic, or political constraints. Increases in agronomic efficiency would expand the frontier to allow greater production and environmental gains

  17. Seed protein improvement in cereals and grain legumes

    International Nuclear Information System (INIS)

    Based upon the recommendations of a panel of experts in 1968, the Joint FAO/IAEA Division of Atomic Energy in Food and Agriculture established an international programme to improve the protein content and quality in seed crops of importance to developing countries. Reports of previous meetings held under this programme have been published by the IAEA. The meeting on Seed Protein Improvement in Cereals and Grain Legumes, held in September 1978, marked the formal end of the FAO/IAEA/GSF Co-ordinated Research Programme on Seed Protein Improvement. It reviewed the progress achieved. Volume I covers 27 papers. Following a review of the world protein and nutritional situation, the contributions are grouped under the main headings of the need for and use of variability in protein characteristics; genetics, biochemistry and physiology of seed storage proteins; analytical and nutritional techniques; and coordinated research programmes under a joint FAO/IAEA/GSF programme on grain protein improvement. Individual papers of direct relevance are cited as separate entries in INIS

  18. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals.

    Science.gov (United States)

    Singh, Amit Kumar; Singh, Rakesh; Subramani, Rajkumar; Kumar, Rajesh; Wankhede, Dhammaprakash P

    2016-06-01

    Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains. PMID:27252585

  19. Irradiation on cereal bars incorporated with pineapple skin

    International Nuclear Information System (INIS)

    One of the major current concerns to the food industry is the management of residues generated in its production processes. Thus, several studies have been developed, seeking alternative uses for these residues, in order to minimize environmental impacts and add value to products previously discarded. Combining this idea with the increasingly search for healthy and practical products, by consumers, this study aimed the characterization of cereal bars irradiated with doses of 0 kGy, 1 kGy, and 2 kGy, incorporated with dried pineapple skin. The following analyses were carried out: moisture, proteins, lipids, ashes, carbohydrates, energetic value, antioxidant potential, phenolic content, organic acids, and fatty acids profile. The results observed for the centesimal composition did not vary as a function of the radiation doses used, reducing only the levels of antioxidants, phenolic compounds, and organic acids. The product showed potential for becoming an effective way of reusing a food industry residue and the irradiation interfered on the nutritional characteristics of the final product. (author)

  20. A tradeoff frontier for global nitrogen use and cereal production

    Science.gov (United States)

    Mueller, Nathaniel D.; West, Paul C.; Gerber, James S.; MacDonald, Graham K.; Polasky, Stephen; Foley, Jonathan A.

    2014-05-01

    Nitrogen fertilizer use across the world’s croplands enables high-yielding agricultural production, but does so at considerable environmental cost. Imbalances between nitrogen applied and nitrogen used by crops contributes to excess nitrogen in the environment, with negative consequences for water quality, air quality, and climate change. Here we utilize crop input-yield models to investigate how to minimize nitrogen application while achieving crop production targets. We construct a tradeoff frontier that estimates the minimum nitrogen fertilizer needed to produce a range of maize, wheat, and rice production levels. Additionally, we explore potential environmental consequences by calculating excess nitrogen along the frontier using a soil surface nitrogen balance model. We find considerable opportunity to achieve greater production and decrease both nitrogen application and post-harvest excess nitrogen. Our results suggest that current (circa 2000) levels of cereal production could be achieved with ˜50% less nitrogen application and ˜60% less excess nitrogen. If current global nitrogen application were held constant but spatially redistributed, production could increase ˜30%. If current excess nitrogen were held constant, production could increase ˜40%. Efficient spatial patterns of nitrogen use on the frontier involve substantial reductions in many high-use areas and moderate increases in many low-use areas. Such changes may be difficult to achieve in practice due to infrastructure, economic, or political constraints. Increases in agronomic efficiency would expand the frontier to allow greater production and environmental gains.

  1. Where do Protein Bodies of Cereal Seeds Come From?

    Science.gov (United States)

    Pedrazzini, Emanuela; Mainieri, Davide; Marrano, Claudia A.; Vitale, Alessandro

    2016-01-01

    Protein bodies of cereal seeds consist of ordered, largely insoluble heteropolymers formed by prolamin storage proteins within the endoplasmic reticulum (ER) of developing endosperm cells. Often these structures are permanently unable to traffic along the secretory pathway, thus representing a unique example for the use of the ER as a protein storage compartment. In recent years, marked progress has been made in understanding what is needed to make a protein body and in formulating hypotheses on how protein body formation might have evolved as an efficient mechanism to store large amounts of protein during seed development, as opposed to the much more common system of seed storage protein accumulation in vacuoles. The major key evolutionary events that have generated prolamins appear to have been insertions or deletions that have disrupted the conformation of the eight-cysteine motif, a protein folding motif common to many proteins with different functions and locations along the secretory pathway, and, alternatively, the fusion between the eight-cysteine motif and domains containing additional cysteine residues. PMID:27540384

  2. Genome re-annotation: a wiki solution?

    OpenAIRE

    Salzberg, Steven L.

    2007-01-01

    The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution.

  3. Ensembl variation resources

    Directory of Open Access Journals (Sweden)

    Marin-Garcia Pablo

    2010-05-01

    Full Text Available Abstract Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

  4. The barley genome sequence assembly reveals three additional members of the CslF (1,3;1,4-β-glucan synthase gene family.

    Directory of Open Access Journals (Sweden)

    Miriam Schreiber

    Full Text Available An important component of barley cell walls, particularly in the endosperm, is (1,3;1,4-β-glucan, a polymer that has proven health benefits in humans and that influences processability in the brewing industry. Genes of the cellulose synthase-like (Csl F gene family have been shown to be involved in (1,3;1,4-β-glucan synthesis but many aspects of the biosynthesis are still unclear. Examination of the sequence assembly of the barley genome has revealed the presence of an additional three HvCslF genes (HvCslF11, HvCslF12 and HvCslF13 which may be involved in (1,3;1,4-β-glucan synthesis. Transcripts of HvCslF11 and HvCslF12 mRNA were found in roots and young leaves, respectively. Transient expression of these genes in Nicotiana benthamiana resulted in phenotypic changes in the infiltrated leaves, although no authentic (1,3;1,4-β-glucan was detected. Comparisons of the CslF gene families in cereals revealed evidence of intergenic recombination, gene duplications and translocation events. This significant divergence within the gene family might be related to multiple functions of (1,3;1,4-β-glucans in the Poaceae. Emerging genomic and global expression data for barley and other cereals is a powerful resource for characterising the evolution and dynamics of complete gene families. In the case of the CslF gene family, the results will contribute to a more thorough understanding of carbohydrate metabolism in grass cell walls.

  5. Effects of cereal bars for breakfast and mid-morning snacks on mood and memory.

    Science.gov (United States)

    Smith, Andrew P; Wilds, Amanda

    2009-01-01

    The aim of the present study was to examine the effects of consuming cereal bars, given either for breakfast or a mid-morning snack, on mood and memory. Thirty-two volunteers (16 males, 16 females; mean age, 20 years 9 months) were randomly assigned to one of four groups formed by combining breakfast (cereal bar versus no breakfast) and snack (cereal bar versus no snack) conditions. A baseline session was completed at 08:30 h followed by breakfast at 9:00 h, another test at 10:00 h, followed by a mid-morning snack and then a final test at 12:00 h. In each session, volunteers rated their mood and carried out four memory tasks: free recall; recognition memory; a verbal reasoning task; and a semantic processing task. The results showed that volunteers who consumed a cereal bar for breakfast felt more alert, happy and sociable and less anxious. In addition, they also recalled more words in a free recall task. When the cereal bar was consumed as a mid-morning snack, alertness and hedonic tone increased, especially in the group who received no breakfast. The group who had no breakfast reported reduced anxiety after consumption of the snack. Recall was also improved after the snack. These findings show that consuming cereal bars in the early and mid-morning leads to beneficial behavioural effects. The results confirm earlier research on effects of breakfast and extend our knowledge of effects of snacks. Consumption of cereal bars may have important practical applications especially in situations where preparation of breakfast is difficult.

  6. Prehistoric cereal foods from Greece and Bulgaria: investigation of starch microstructure in experimental and archaeological charred remains

    OpenAIRE

    Valamoti, Soultana-Maria; Samuel, Delwen; Bayram, Mustafa; Elena MARINOVA

    2008-01-01

    Abstract In order to investigate ancient cereal cooking practices, the microstructure of preserved starch in charred ground cereal remains recovered from prehistoric sites in Greece and Bulgaria has been analysed. A comparative modern set of cooked and subsequently charred cereals was produced. By scanning electron microscopy it is demonstrated that, under some conditions, distinctive cooked starch structure survives the charring process. Charring alone can occasionall...

  7. Investigation of lactic acid bacteria mediated bioprotection with applications in cereal industry. Case-study: malting process

    OpenAIRE

    Oliveira, Pedro Miguel Rodrigues

    2014-01-01

    Antifungal compounds produced by Lactic acid bacteria (LAB) metabolites can be natural and reliable alternative for reducing fungal infections pre- and post-harvest with a multitude of additional advantages for cereal-base products. Toxigenic and spoilage fungi are responsible for numerous diseases and economic losses. This thesis includes an overview of the impact fungi have on aspects of the cereal food chain. The applicability of LAB in plant protection and cereal industry is discussed in ...

  8. Active oxygen and cell death in cereal aleurone cells.

    Science.gov (United States)

    Fath, Angelika; Bethke, Paul; Beligni, Veronica; Jones, Russell

    2002-05-01

    The cereal aleurone layer is a secretory tissue whose function is regulated by gibberellic acid (GA) and abscisic acid (ABA). Aleurone cells lack functional chloroplasts, thus excluding photosynthesis as a source of active oxygen species (AOS) in cell death. Incubation of barley aleurone layers or protoplasts in GA initiated the cell death programme, but incubation in ABA delays programmed cell death (PCD). Light, especially blue and UV-A light, and H(2)O(2) accelerate PCD of GA-treated aleurone cells, but ABA-treated aleurone cells are refractory to light and H(2)O(2) and are not killed. It was shown that light elevated intracellular H(2)O(2), and that the rise in H(2)O(2) was greater in GA-treated cells compared to cells in ABA. Experiments with antioxidants show that PCD in aleurone is probably regulated by AOS. The sensitivity of GA-treated aleurone to light and H(2)O(2) is a result of lowered amounts of enzymes that metabolize AOS. mRNAs encoding catalase, ascorbate peroxidase and superoxide dismutase are all reduced during 6-18 h of incubation in GA, but these mRNAs were present in higher amounts in cells incubated in ABA. The amounts of protein and enzyme activities encoded by these mRNAs were also dramatically reduced in GA-treated cells. Aleurone cells store and metabolize neutral lipids via the glyoxylate cycle in response to GA, and glyoxysomes are one potential source of AOS in the GA-treated cells. Mitochondria are another potential source of AOS in GA-treated cells. AOS generated by these organelles bring about membrane rupture and cell death.

  9. Progress of cereal transformation technology mediated by Agrobacterium tumefaciens

    Directory of Open Access Journals (Sweden)

    Yukoh eHiei

    2014-11-01

    Full Text Available Monocotyledonous plants were believed to be not transformable by the soil bacterium Agrobacterium tumefaciens until two decades ago, although convenient protocols for infection of leaf disks and subsequent regeneration of transgenic plants had been well established in a number of dicotyledonous species by then. This belief was reinforced by the fact that monocotyledons are mostly outside the host range of crown gall disease caused by the bacterium and by the failures in trials in monocotyledons to mimic the transformation protocols for dicotyledons. However, a key reason for the failure could have been the lack of active cell divisions at the wound sites, which are the basis of tissue culture and transformation in dicotyledons, in monocotyledons. The complexity and narrow optimal windows of critical factors, such as genotypes of plants, conditions of the plants from which explants are prepared, tissue culture methods and culture media, pre-treatments of explants, strains of A. tumefaciens, inducers of virulence genes, transformation vectors, selection marker genes and selective agents, kept technical hurdles high. Eventually it was determined that rice and maize could be transformed by co-cultivating cells of callus cultures or immature embryos, which are actively dividing or about to divide, with A. tumefaciens. Subsequently, these initial difficulties were resolved one by one by many research groups, and the major cereals are now transformed quite efficiently. As many as 15 independent transgenic events may be regenerated from a single piece of immature embryo of rice. Maize transformation protocols are well established, and almost all transgenic events deregulated for commercialization after 2003 were generated by Agrobacterium-mediated transformation. Wheat, barley and sorghum are also among those plants that can be efficiently transformed by A. tumefaciens.

  10. Nitrogen and phosphorus economy of a legume tree-cereal intercropping system under controlled conditions.

    Science.gov (United States)

    Isaac, M E; Hinsinger, P; Harmand, J M

    2012-09-15

    Considerable amounts of nitrogen (N) and phosphorus (P) fertilizers have been mis-used in agroecosystems, with profound alteration to the biogeochemical cycles of these two major nutrients. To reduce excess fertilizer use, plant-mediated nutrient supply through N(2)-fixation, transfer of fixed N and mobilization of soil P may be important processes for the nutrient economy of low-input tree-based intercropping systems. In this study, we quantified plant performance, P acquisition and belowground N transfer from the N(2)-fixing tree to the cereal crop under varying root contact intensity and P supplies. We cultivated Acacia senegal var senegal in pot-culture containing 90% sand and 10% vermiculite under 3 levels of exponentially supplied P. Acacia plants were then intercropped with durum wheat (Triticum turgidum durum) in the same pots with variable levels of adsorbed P or transplanted and intercropped with durum wheat in rhizoboxes excluding direct root contact on P-poor red Mediterranean soils. In pot-culture, wheat biomass and P content increased in relation to the P gradient. Strong isotopic evidence of belowground N transfer, based on the isotopic signature (δ(15)N) of tree foliage and wheat shoots, was systematically found under high P in pot-culture, with an average N transfer value of 14.0% of wheat total N after 21 days of contact between the two species. In the rhizoboxes, we observed limitations on growth and P uptake of intercropped wheat due to competitive effects on soil resources and minimal evidence of belowground N transfer of N from acacia to wheat. In this intercrop, specifically in pot-culture, facilitation for N transfer from the legume tree to the crop showed to be effective especially when crop N uptake was increased (or stimulated) as occurred under high P conditions and when competition was low. Understanding these processes is important to the nutrient economy and appropriate management of legume-based agroforestry systems.

  11. Cereal Feeding in Fishes Nutrition for Fishery in Fresh Water from Banat Region

    Directory of Open Access Journals (Sweden)

    Dumitru Mnerie

    2010-10-01

    Full Text Available Fisheries have traditionally been managed by direct restrictions, including seasonal and area closures, minimum mesh size, and access limitations. In recent years, licensing and an individual quota system were introduced as effortcontrol measures, in order to bring fishing effort more in line with the available resources. The overall responsibility for fisheries policy in Romania falls under auspices of the Ministry of Agriculture, Forests and Rural Development through its Directorate of Fisheries. The major objectives of Romanian fisheries are to bring the national fisheries legislation closer to the European Union (EU Common Fisheries Policy (CFP and to set up the administrative capacity and institutional building needed to cope with EU accession in 2007. In June 2001, Romania completed negotiations with EU in the area of fisheries, accepting the entire acquis communautaire without requesting any derogation or transition periods. The European Fisheries Fund will support Romania as a new EU Member State to develop a competitive, modern and dynamic fisheries sector, based on sustainable fishing and aquaculture activities, while also taking account of other important aspects such as environmental protection, the demands of the consumers and the food industry. The program is also expected to increase the competitiveness of the fisheries sector, encourage job creation and promote the growth of the aquaculture industry. The paper shows some aspects about Romanian fishery policy, an important opportunity for development research in fishery in fresh water from Banat region. Also, it is presents some research results about using the cereal feeding as fish’s nutrition, in special for common carp.

  12. Exploiting phytochemicals for developing a 'push-pull' crop protection strategy for cereal farmers in Africa.

    Science.gov (United States)

    Khan, Zeyaur R; Midega, Charles A O; Bruce, Toby J A; Hooper, Antony M; Pickett, John A

    2010-10-01

    Lepidopteran stemborers and parasitic weeds in the genus Striga are major constraints to efficient production of cereals, the most important staple food crops in Africa. Smallholder farmers are resource constrained and unable to afford expensive chemicals for crop protection. Development of a push-pull approach for integrated pest and weed management is reviewed here. Appropriate plants were discovered that naturally emit signalling chemicals (semiochemicals). Plants highly attractive for egg laying by stemborer pests were selected and employed as trap crops (pull), to draw pests away from the main crop. Of these, Napier grass, Pennisetum purpureum (Schumach), despite its attractiveness, supported minimal survival of the pests' immature stages. Plants that repelled stemborer pests, notably molasses grass, Melinis minutiflora P. Beauv., and forage legumes in the genus Desmodium, were selected as intercrops (push). Desmodium intercrops suppress Striga hermonthica (Del.) Benth. through an allelopathic mechanism. Their root exudates contain novel flavonoid compounds, which stimulate suicidal germination of S. hermonthica seeds and dramatically inhibit its attachment to host roots. The companion crops provide valuable forage for farm animals while the leguminous intercrops also improve soil fertility and moisture retention. The system is appropriate as it is based on locally available plants, not expensive external inputs, and fits well with traditional mixed cropping systems in Africa. To date it has been adopted by more than 30,000 smallholder farmers in East Africa where maize yields have increased from ∼1 t ha(-1) to 3.5 t ha(-1). Future directions for semiochemical delivery by plants including biotechnological opportunities are discussed.

  13. Exploiting phytochemicals for developing a 'push-pull' crop protection strategy for cereal farmers in Africa.

    Science.gov (United States)

    Khan, Zeyaur R; Midega, Charles A O; Bruce, Toby J A; Hooper, Antony M; Pickett, John A

    2010-10-01

    Lepidopteran stemborers and parasitic weeds in the genus Striga are major constraints to efficient production of cereals, the most important staple food crops in Africa. Smallholder farmers are resource constrained and unable to afford expensive chemicals for crop protection. Development of a push-pull approach for integrated pest and weed management is reviewed here. Appropriate plants were discovered that naturally emit signalling chemicals (semiochemicals). Plants highly attractive for egg laying by stemborer pests were selected and employed as trap crops (pull), to draw pests away from the main crop. Of these, Napier grass, Pennisetum purpureum (Schumach), despite its attractiveness, supported minimal survival of the pests' immature stages. Plants that repelled stemborer pests, notably molasses grass, Melinis minutiflora P. Beauv., and forage legumes in the genus Desmodium, were selected as intercrops (push). Desmodium intercrops suppress Striga hermonthica (Del.) Benth. through an allelopathic mechanism. Their root exudates contain novel flavonoid compounds, which stimulate suicidal germination of S. hermonthica seeds and dramatically inhibit its attachment to host roots. The companion crops provide valuable forage for farm animals while the leguminous intercrops also improve soil fertility and moisture retention. The system is appropriate as it is based on locally available plants, not expensive external inputs, and fits well with traditional mixed cropping systems in Africa. To date it has been adopted by more than 30,000 smallholder farmers in East Africa where maize yields have increased from ∼1 t ha(-1) to 3.5 t ha(-1). Future directions for semiochemical delivery by plants including biotechnological opportunities are discussed. PMID:20670998

  14. Draft genome sequence of Talaromyces islandicus ("Penicillium islandicum") WF-38-12, a neglected mold with significant biotechnological potential.

    Science.gov (United States)

    Schafhauser, Thomas; Wibberg, Daniel; Rückert, Christian; Winkler, Anika; Flor, Liane; van Pée, Karl-Heinz; Fewer, David P; Sivonen, Kaarina; Jahn, Linda; Ludwig-Müller, Jutta; Caradec, Thibault; Jacques, Philippe; Huijbers, Mieke M E; van Berkel, Willem J H; Weber, Tilmann; Wohlleben, Wolfgang; Kalinowski, Jörn

    2015-10-10

    Talaromyces (Penicillium) islandicus is a common mold found in stored rice or cereals. It has a highly versatile metabolism characterized by the secretion of numerous biopolymer degrading enzymes, mycotoxins, and anthraquinones that altogether offer a broad range of potential industrial applications. Here, we report the draft genome sequence of Talaromyces islandicus, which provides the basis of a biotechnological usage of this species. PMID:26197417

  15. Draft genome sequence and chemical profiling of Fusarium langsethiae, an emerging producer of type A trichothecenes

    DEFF Research Database (Denmark)

    Lysøe, Erik; Frandsen, Rasmus John Normand; Divon, Hege H.;

    2016-01-01

    Fusarium langsethiae is a widespread pathogen of small grain cereals, causing problems with T-2 and HT-2 toxin contamination in grains every year. In an effort to better understand the biology of this fungus, we present a draft genome sequence of F. langsethiae Fl201059 isolated from oats in Norway...

  16. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  17. Genomic Aspects of Research Involving Polyploid Plants

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL

    2011-01-01

    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  18. Domestication genomics: evidence from animals.

    Science.gov (United States)

    Wang, Guo-Dong; Xie, Hai-Bing; Peng, Min-Sheng; Irwin, David; Zhang, Ya-Ping

    2014-02-01

    Animal domestication has far-reaching significance for human society. The sequenced genomes of domesticated animals provide critical resources for understanding the genetic basis of domestication. Various genomic analyses have shed a new light on the mechanism of artificial selection and have allowed the mapping of genes involved in important domestication traits. Here, we summarize the published genomes of domesticated animals that have been generated over the past decade, as well as their origins, from a phylogenomic point of view. This review provides a general description of the genomic features encountered under a two-stage domestication process. We also introduce recent findings for domestication traits based on results from genome-wide association studies and selective-sweep scans for artificially selected genomic regions. Particular attention is paid to issues relating to the costs of domestication and the convergent evolution of genes between domesticated animals and humans.

  19. Major Cereal Grain Fibers and Psyllium in Relation to Cardiovascular Health

    Directory of Open Access Journals (Sweden)

    Michael F. Roizen

    2013-04-01

    Full Text Available Numerous studies reveal the cardiovascular benefits of consuming dietary fiber and, especially, cereal fiber. Cereal fiber is associated with cardiovascular risk reduction through multiple mechanisms and consuming a variety of cereal fiber sources offers health benefits specific to the source. Certain cereal fibers have been studied more extensively than others and provide greater support for their incorporation into a healthful diet. β-glucan from oats or barley, or a combination of whole oats and barley, and soluble fiber from psyllium reduces the risk of coronary heart disease; inulin-type fructans added to foods and beverages may modestly decrease serum triacylglycerols; arabinoxylan and resistant starch may improve glycemic control. Individuals with low cereal fiber intake should increase their intake of whole grains in order to receive the benefits of whole grains in addition to fiber. For those adjusting to the texture and palatability of whole grains, turning to added-fiber products rich in β-glucan and psyllium may allow them to reach their fiber goals without increasing caloric intake.

  20. THE SUPPLEMENTARY RELATIONS BETWEEN THE PROTEINS OF MOTTLED GRAM BEAN AND CERTAIN OTHER CEREALS

    Institute of Scientific and Technical Information of China (English)

    罗登义

    2006-01-01

    @@ It has been well understood that a mixture of vegetable and animal proteins is of higher quality than the former alone, and also there are some remarkable instances of effective supplementing between the proteins of certain cereals and certain legume seeds[1]. In practice, it is very valuable for the selection of human diets and farm-animal relations. This question is especially important in China where the protein of the average diet are mainly of vegetable origin, in which about 83 percent are derived from cereals and 11 percent from beans[2]. However, a review of the literature indicates that no work has been done on the supplementary relationships of the protein of mottled gram bean with those of other cereals. The writer purchased, therefore, from the Peiping market some cheaper cereals commonly used in China, namely, yellow corn(黄玉米), red kaoliang(红高粱),oat meal(油麦面),panicled glutinous and non-glutinous millets(黄米及糜子米); and determined the supplementary values between the proteins of mottled gram bean and these cereals. The experimental details are communicated in the present paper.

  1. Effect of flaxseed flour incorporation on the physical properties and consumer acceptability of cereal bars.

    Science.gov (United States)

    Khouryieh, H; Aramouni, F

    2013-12-01

    Extensive research has revealed numerous nutritional and health benefits of flaxseed due primarily to its nutrients content. The objective of this study was to evaluate the effect of flaxseed flour addition on the physical and sensory characteristics of cereal bars. Four formulations of the flaxseed cereal bars were prepared by partially replacing oats with flaxseed flour added at levels of 0 (control), 6%, 12% and 18%. There were no significant differences (p > 0.05) in water activity, moisture and firmness values between the flaxseed bars and control. Flaxseed addition significantly (p bars. There were no significant differences (p > 0.05) between the 12% flax cereal bars and the control with respect to sensory attributes and overall acceptability. The overall acceptability for both 12% flax bars and the control was in between 'like moderately' and 'like slightly' on the 9-point hedonic scale. The overall acceptability was most highly correlated with flavor acceptability for both control (r = 0.80) and 12% flax (r = 0.82) cereal bars. Flaxseed bars provided 12% dietary fiber of the daily recommended value. These results indicated that flaxseed flour incorporation up to 12% substantially enhanced the nutritional qualities of the cereal bars without affecting their sensory and quality properties.

  2. Perspectives for geographically oriented management of fusarium mycotoxins in the cereal supply chain.

    Science.gov (United States)

    van der Fels-Klerx, H J; Booij, C J H

    2010-06-01

    This article provides an overview of available systems for management of Fusarium mycotoxins in the cereal grain supply chain, with an emphasis on the use of predictive mathematical modeling. From the state of the art, it proposes future developments in modeling and management and their challenges. Mycotoxin contamination in cereal grain-based feed and food products is currently managed and controlled by good agricultural practices, good manufacturing practices, hazard analysis critical control points, and by checking and more recently by notification systems and predictive mathematical models. Most of the predictive models for Fusarium mycotoxins in cereal grains focus on deoxynivalenol in wheat and aim to help growers make decisions about the application of fungicides during cultivation. Future developments in managing Fusarium mycotoxins should include the linkage between predictive mathematical models and geographical information systems, resulting into region-specific predictions for mycotoxin occurrence. The envisioned geographically oriented decision support system may incorporate various underlying models for specific users' demands and regions and various related databases to feed the particular models with (geographically oriented) input data. Depending on the user requirements, the system selects the best fitting model and available input information. Future research areas include organizing data management in the cereal grain supply chain, developing predictive models for other stakeholders (taking into account the period up to harvest), other Fusarium mycotoxins, and cereal grain types, and understanding the underlying effects of the regional component in the models.

  3. Macro-Elements and Trace Elements in Cereal Grains Cultivated in Latvia

    Directory of Open Access Journals (Sweden)

    Jākobsone Ida

    2015-09-01

    Full Text Available Cereal-based foods have great importance in the compensation of micro- and trace element deficiency, because 50% of the foods produced worldwide are made up of cereal grains. The aim of the research was to determine the concentration of macro-elements and trace elements in different cereals cultivated in Latvia. Various cereals were used in the research: rye (n = 45, barley (n = 54, spring wheat (n = 27, winter wheat (n = 53, triticale (n = 45 and oats (n = 42. Thirteen macro- and trace elements (Cd, Pb, Ni, Cr, Al, Cu, K, Na, Mn, Fe, Zn, Mg, Ca were determined in cereal grain samples (n = 266. Macro-elements and trace elements varied significantly (p < 0.01 or p < 0.001. The highest concentrations of macro- and trace elements were found in oats and the lowest in rye. The obtained data will expand the opportunity for food and nutrition scientists to evaluate content of the examined elements in grain products, and dietary consumption (bioavailability of the examined macro-elements and trace elements.

  4. Perspectives for geographically oriented management of fusarium mycotoxins in the cereal supply chain.

    Science.gov (United States)

    van der Fels-Klerx, H J; Booij, C J H

    2010-06-01

    This article provides an overview of available systems for management of Fusarium mycotoxins in the cereal grain supply chain, with an emphasis on the use of predictive mathematical modeling. From the state of the art, it proposes future developments in modeling and management and their challenges. Mycotoxin contamination in cereal grain-based feed and food products is currently managed and controlled by good agricultural practices, good manufacturing practices, hazard analysis critical control points, and by checking and more recently by notification systems and predictive mathematical models. Most of the predictive models for Fusarium mycotoxins in cereal grains focus on deoxynivalenol in wheat and aim to help growers make decisions about the application of fungicides during cultivation. Future developments in managing Fusarium mycotoxins should include the linkage between predictive mathematical models and geographical information systems, resulting into region-specific predictions for mycotoxin occurrence. The envisioned geographically oriented decision support system may incorporate various underlying models for specific users' demands and regions and various related databases to feed the particular models with (geographically oriented) input data. Depending on the user requirements, the system selects the best fitting model and available input information. Future research areas include organizing data management in the cereal grain supply chain, developing predictive models for other stakeholders (taking into account the period up to harvest), other Fusarium mycotoxins, and cereal grain types, and understanding the underlying effects of the regional component in the models. PMID:20537276

  5. Major cereal grain fibers and psyllium in relation to cardiovascular health.

    Science.gov (United States)

    Bernstein, Adam M; Titgemeier, Brigid; Kirkpatrick, Kristin; Golubic, Mladen; Roizen, Michael F

    2013-05-01

    Numerous studies reveal the cardiovascular benefits of consuming dietary fiber and, especially, cereal fiber. Cereal fiber is associated with cardiovascular risk reduction through multiple mechanisms and consuming a variety of cereal fiber sources offers health benefits specific to the source. Certain cereal fibers have been studied more extensively than others and provide greater support for their incorporation into a healthful diet. β-glucan from oats or barley, or a combination of whole oats and barley, and soluble fiber from psyllium reduces the risk of coronary heart disease; inulin-type fructans added to foods and beverages may modestly decrease serum triacylglycerols; arabinoxylan and resistant starch may improve glycemic control. Individuals with low cereal fiber intake should increase their intake of whole grains in order to receive the benefits of whole grains in addition to fiber. For those adjusting to the texture and palatability of whole grains, turning to added-fiber products rich in β-glucan and psyllium may allow them to reach their fiber goals without increasing caloric intake.

  6. Significance of Ochratoxin A in Breakfast Cereals from the United States.

    Science.gov (United States)

    Lee, Hyun Jung; Ryu, Dojin

    2015-11-01

    Ochratoxin A (OTA) has been found in all major cereal grains including oat, wheat, and barley worldwide and considered as a potential concern in food safety. A total of 489 samples of corn-, rice-, wheat-, and oat-based breakfast cereal were collected from U.S. retail marketplaces over a two-year period, and OTA was determined by high-performance liquid chromatography. Overall, 205 samples (42%) were contaminated with OTA in the range from 0.10 to 9.30 ng/g. The levels OTA were mostly below of the European Commission Regulation (3 ng/g) except in 16 samples of oat-based cereals. The incidence of OTA was highest in oat-based breakfast cereals (70%, 142/203), followed by wheat-based (32%, 38/117), corn-based (15%, 15/103), and rice-based breakfast cereals (15%, 10/66). On the basis of the incidence and concentration of OTA, oats and oat-based products may need greater attention in further surveillance programs and development of intervention strategies to reduce health risks in consumers.

  7. Characterisation of dietary fibre components in cereals and legumes used in Serbian diet.

    Science.gov (United States)

    Dodevska, Margarita S; Djordjevic, Brizita I; Sobajic, Sladjana S; Miletic, Ivanka D; Djordjevic, Predrag B; Dimitrijevic-Sreckovic, Vesna S

    2013-12-01

    The typical Serbian diet is characterised by high intake of cereal products and also legumes are often used. The content of total fibre as well as certain fibre fractions was determined in cereals, cereal products, and cooked legumes. The content of total fibre in cooked cereals and cereal products ranged from 2.5 to 20.8 g/100 g, and in cooked legumes from 14.0 to 24.5 g/100 g (on dry matter basis). Distribution of analysed fibre fractions and their quantities differed significantly depending on food groups. Fructans and arabinoxylans were the most significant fibre fractions in rye flakes, and β-glucan in oat flakes, cellulose and resistant starch were present in significant amounts in peas and kidney beans. When the size of regular food portions was taken into consideration, the best sources of total dietary fibre were peas and kidney beans (more than 11 g/serving). The same foods were the best sources of cellulose (4.98 and 3.56 g/serving) and resistant starch (3.90 and 2.83 g/serving). High intake of arabinoxylans and fructans could be accomplished with cooked wheat (3.20 g and 1.60 g/serving, respectively). Oat (1.39 g/serving) and barley flakes (1.30 g/serving) can be recommended as the best sources of β-glucan. PMID:23870869

  8. Association and haplotype analysis of candidate genes in five genomic regions linked to sow maternal infanticide in a white Duroc × Erhualian resource population

    Directory of Open Access Journals (Sweden)

    Ding Nengshui

    2011-02-01

    Full Text Available Abstract Background Maternal infanticide is an extreme and failed maternal behavior, which is defined as an active attack on piglets using the jaws, resulting in serious or fatal bite wounds. It brings big economic loss to the pig industry and severe problems to piglets' welfare. But little is known about the genetic background of this behavior. Quantitative trait loci (QTL for maternal infanticide were identified in a White Duroc × Erhualian intercross by a non-parametric linkage analysis (NPL in our previous study. In this study, associations of 194 microsatellite markers used in NPL analysis with maternal infanticide behavior were further analyzed by transmission-disequilibrium test (TDT. On this basis, seven genes (ESR2, EAAT2, BDNF, OXTR, 5-HTR2C, DRD1 and GABRA6 at five genomic regions were selected and further analyzed. Associations of single nucleotide polymorphisms (SNPs and haplotypes in each gene with maternal infanticide behavior were evaluated. Results Microsatellite markers on pig chromosome (SSC 2, 13, 15, and X displayed significance at P ESR2 SNPs had nominal evidence for association (P A at EAAT2 g. 233G > A and allele T at DRD1 g.1013C > G > T also showed evidence of overtransmission to infanticidal sows. In the overall tests of association of haplotypes, candidate genes of ESR2, EAAT2 and DRD1 achieved overall significance level (P ESR2, EAAT2 and DRD1 showed higher frequencies to infanticidal sows (P Conclusions From association tests of SNPs and haplotypes, ESR2, EAAT2 and DRD1 showed significant associations with maternal infanticide. This result supported the existence of QTL for maternal infanticide behavior on SSC1, SSC2 and SSC16.

  9. Proteinaceous inhibitors of carbohydrate-active enzymes in cereals - implication in agriculture, cereal-processing and nutrition

    DEFF Research Database (Denmark)

    Juge, Nathalie; Svensson, Birte

    2006-01-01

    Enzymes that degrade, modify, or create glycosidic bonds are involved in carbohydrate biosynthesis and remodelling. Microbial carbohydrate-active enzymes form the basis of current green technology in the food, feed, starch, paper and pulp industries and the revolution in genomics may offer long...

  10. What Will We Do with a Cotton Genome Sequence?

    Institute of Scientific and Technical Information of China (English)

    BRUBAKER Curt

    2008-01-01

    @@ With the publication of "Toward Sequencing Cotton (Gossypium) Genomes" [Chen et al.PlantPhysiology,2007,145:1303-1310-] a clear consensus emerged from the cotton genomics community not only that cotton genome sequences were a critical resource for research and commercial innovationin cotton genomics,but that there was a logical means of achieving this goal.

  11. OryzaGenome: Genome Diversity Database of Wild Oryza Species.

    Science.gov (United States)

    Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori

    2016-01-01

    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/. PMID:26578696

  12. Legume-Cereal Intercropping Improves Forage Yield, Quality and Degradability.

    Science.gov (United States)

    Zhang, Jie; Yin, Binjie; Xie, Yuhuai; Li, Jing; Yang, Zaibin; Zhang, Guiguo

    2015-01-01

    Intercropping legume with cereal is an extensively applied planting pattern in crop cultivation. However, forage potential and the degradability of harvested mixtures from intercropping system remain unclear. To investigate the feasibility of applying an intercropping system as a forage supply source to ruminants, two consecutive experiments (experiments 1 and 2) involving a field cultivation trial and a subsequent in vivo degradable experiment were conducted to determine the forage production performance and the ruminally degradable characteristics of a harvested mixture from an alfalfa/corn-rye intercropping system. In experiment 1, the intercropping system was established by alternating alfalfa and corn or rye with a row ratio of 5:2. Dry matter (DM) and nutrient yields were determined. In experiment 2, forages harvested from the different treatments were used as feedstuff to identify nutrient degradation kinetics and distribution of components between the rapidly degradable (a), potentially degradable (b) and the degradation rate constant (c) of 'b' fraction by in sacco method in Small-Tail Han wether Sheep. The intercropping system of alfalfa and corn-rye provided higher forage production performance with net increases of 9.52% and 34.81% in DM yield, 42.13% and 16.74% in crude protein (CP) yield, 25.94% and 69.99% in degradable DM yield, and 16.96% and 5.50% in degradable CP yield than rotation and alfalfa sole cropping systems, respectively. In addition, the harvest mixture from intercropping system also had greater 'a' fraction, 'b' fraction, 'c' values, and effective degradability (E value) of DM and CP than corn or rye hay harvested from rotation system. After 48-h exposure to rumen microbes, intercropping harvest materials were degraded to a higher extent than separately degraded crop stems from the sole system as indicated by visual microscopic examination with more tissues disappeared. Thus, the intercropping of alfalfa and corn-rye exhibited a greater

  13. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

    DEFF Research Database (Denmark)

    Lewis, Nathan E; Liu, Xin; Li, Yuxiang;

    2013-01-01

    stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages...

  14. Exploring the potential of symbiotic fungal endophytes in cereal disease suppression

    DEFF Research Database (Denmark)

    O'Hanlon, Karen; Knorr, Kamilla; Jørgensen, Lise Nistrup;

    2012-01-01

    Cereal crops are an essential source of nutrition worldwide. The incidence and severity of fungal diseases, in particular foliar diseases such as leaf spots, mildews and rusts, is a serious challenge to cereal production, and this problem is likely to escalate with the changing global climate......, and environmental and health concerns surrounding the use of chemical treatments. There is currently a demand for new disease control strategies, and one such strategy involves the use of symbiotic fungal endophytes as biological control agents against fungal pathogens in cereals. Despite the fact that biological....... Traditional and current methods for controlling fungal pathogens include the use of fungicides, good farming practices, and increasing plant resistance through conventional breeding. While effective, these strategies also carry limitations, mainly due to fungicide-resistance, breakdown of plant resistance...

  15. Effect of primary processing of cereals and legumes on its nutritional quality: A comprehensive review

    Directory of Open Access Journals (Sweden)

    Morteza Oghbaei

    2016-12-01

    Full Text Available Cereals and legumes are important part of dietaries and contribute substantially to nutrient intake of human beings. They are significant source of energy, protein, dietary fiber, vitamins, minerals, and phytochemicals. Primary processing of cereals and legumes is an essential component of their preparation before use. For some grains, dehusking is an essential step, whereas for others, it could be milling the grain into flour. Grains are subjected to certain processing treatments to impart special characteristics and improve organoleptic properties such as expanded cereals. All these treatments result in alteration of their nutritional quality which could either be reduction in nutrients, phytochemicals and antinutrients or an improvement in digestibility or availability of nutrients. It is important to understand these changes occurring in grain nutritional quality on account of pre-processing treatments to select appropriate techniques to obtain maximum nutritional and health benefits. This review attempts to throw light on nutritional alterations occurring in grains due to pre-processing treatments.

  16. Bound phytophenols from ready-to-eat cereals: comparison with other plant-based foods.

    Science.gov (United States)

    Neacsu, M; McMonagle, J; Fletcher, R J; Scobbie, L; Duncan, G J; Cantlay, L; de Roos, B; Duthie, G G; Russell, W R

    2013-12-01

    Whole-grain diets are linked to reduced risk of several chronic diseases (heart disease, cancer, diabetes, metabolic syndrome) and all-cause mortality. There is increasing evidence that these benefits are associated with the gut microbiota and that release of fibre-related phenolic metabolites in the gut is a contributing factor. Additional sources of these metabolites include fruits and vegetables, but the evidence for their protective effects is less well established. With respect to the availability of bound phytophenols, ready-to-eat cereals are compared with soft fruits (considered rich in antioxidants) and other commonly consumed fruits and vegetables. The results demonstrated that when compared with an equivalent serving of fruits or vegetables, a recommended portion of whole-grain cereals deliver substantially higher amounts of bound phytophenols, which are available for metabolism in the colon. The increased amount of these phenolic metabolites may, in part, explain the evidence for the protective effects of whole-grain cereals.

  17. Archaeobotanical study of ancient food and cereal remains at the Astana Cemeteries, Xinjiang, China.

    Science.gov (United States)

    Chen, Tao; Wu, Yan; Zhang, Yongbing; Wang, Bo; Hu, Yaowu; Wang, Changsui; Jiang, Hongen

    2012-01-01

    Starch grain, phytolith and cereal bran fragments were analyzed in order to identify the food remains including cakes, dumplings, as well as porridge unearthed at the Astana Cemeteries in Turpan of Xinjiang, China. The results suggest that the cakes were made from Triticum aestivum while the dumplings were made from Triticum aestivum, along with Setaria italica. The ingredients of the porridge remains emanated from Panicum miliaceum. Moreover, direct macrobotantical evidence of the utilization of six cereal crops, such as Triticum aestivum, Hordeum vulgare var. coeleste, Panicum miliaceum, Setaria italica, Cannabis sativa, and Oryza sativa in the Turpan region during the Jin and Tang dynasties (about 3(rd) to 9(th) centuries) is also presented. All of these cereal crops not only provided food for the survival of the indigenous people, but also spiced up their daily life.

  18. Ochratoxin A in Danish cereals 1986-1992 and daily intake by the Danish population

    DEFF Research Database (Denmark)

    Jørgensen, Kevin; Rasmussen, Gitte; Thorup, Inger

    1996-01-01

    Ochratoxin A is a common contaminant in Danish cereals, and surveillance of ochratoxin A in cereals has been a part of the Danish monitoring system since 1986. Occurrence of ochratoxin A is highly related to the climatic conditions during harvest. Rye is the crop which is most often contaminated...... and contains the highest levels of ochratoxin A. The result of the survey period from 1986 to 1992 (total of 1431 samples) together with food consumption data is the basis of intake calculations. Especially in years with wet weather during harvest, the daily intake of ochratoxin A for some individuals...... in the Danish population could reach levels which exceed the tolerable daily intake (TDI) for ochratoxin A of 5 ng/kg bw suggested by The Nordic Working Group on Food Toxicology and Risk Evaluation. A maximum limit of 5 mu g ochratoxin A per kg cereal would keep the daily intake below 5 ng/kg bw....

  19. Archaeobotanical study of ancient food and cereal remains at the Astana Cemeteries, Xinjiang, China.

    Directory of Open Access Journals (Sweden)

    Tao Chen

    Full Text Available Starch grain, phytolith and cereal bran fragments were analyzed in order to identify the food remains including cakes, dumplings, as well as porridge unearthed at the Astana Cemeteries in Turpan of Xinjiang, China. The results suggest that the cakes were made from Triticum aestivum while the dumplings were made from Triticum aestivum, along with Setaria italica. The ingredients of the porridge remains emanated from Panicum miliaceum. Moreover, direct macrobotantical evidence of the utilization of six cereal crops, such as Triticum aestivum, Hordeum vulgare var. coeleste, Panicum miliaceum, Setaria italica, Cannabis sativa, and Oryza sativa in the Turpan region during the Jin and Tang dynasties (about 3(rd to 9(th centuries is also presented. All of these cereal crops not only provided food for the survival of the indigenous people, but also spiced up their daily life.

  20. Spatiotemporal Dynamics of Oligofructan Metabolism and Suggested Functions in Developing Cereal Grains

    Directory of Open Access Journals (Sweden)

    Manuela ePeukert

    2016-01-01

    Full Text Available Oligofructans represent one of the most important groups of sucrose-derived water–soluble carbohydrates in the plant kingdom. In cereals, oligofructans accumulate in above ground parts of the plants (stems, leaves, seeds and their biosynthesis leads to the formation of both types of glycosidic linkages (ß(2,1; ß(2,6-fructans or mixed patterns. In recent studies, tissue- and development- specific distribution patterns of the various oligofructan types in cereal grains have been shown, which are possibly related to the different phases of grain development, such as cellular differentiation of grain tissues and storage product accumulation. Here, we summarize the current knowledge about oligofructan biosynthesis and accumulation kinetics in cereal grains. We focus on the spatiotemporal dynamics and regulation of oligofructan biosynthesis and accumulation in developing barley grains (deduced from a combination of metabolite, transcript and proteome analyses. Finally, putative physiological functions of oligofructans in developing grains are discussed.

  1. High resolution melting analysis as a new approach to discriminate gluten-containing cereals.

    Science.gov (United States)

    Martín-Fernández, Begoña; Costa, Joana; de-Los-Santos-Álvarez, Noemí; López-Ruiz, Beatriz; Oliveira, M Beatriz P P; Mafra, Isabel

    2016-11-15

    With this work, it is intended to propose a novel approach based on high resolution melting (HRM) analysis to detect wheat and discriminate it from other gluten-containing cereals. The method consisted of a real-time PCR assay targeting the gene encoding for the germ agglutinin isolectin A protein (Tri a 18 allergen), using the fluorescent Evagreen dye combined with HRM analysis. The results enabled wheat differentiation from other phylogenetically related cereals, namely barley, rye and oat with high level of confidence. Additionally, a quantitative real-time PCR approach was proposed, allowing detecting and quantifying wheat down to 20mg/kg in rice flour and 20pg of wheat DNA (∼1.1 DNA copies). Its application was successfully achieved in the analysis of processed foods to verify labelling compliance, being considered as a cost-effective tool for the specific detection of cereals in gluten-free foods. PMID:27283646

  2. Potential of phytase-mediated iron release from cereal-based foods: a quantitative view

    DEFF Research Database (Denmark)

    Nielsen, Anne Veller Friis; Tetens, Inge; Meyer, Anne S.

    2013-01-01

    The major part of iron present in plant foods such as cereals is largely unavailable for direct absorption in humans due to complexation with the negatively charged phosphate groups of phytate (myo-inositol (1,2,3,4,5,6)-hexakisphosphate). Human biology has not evolved an efficient mechanism...... phytate complexes, and (3) the extent of phytate dephosphorylation required for iron release from inositol phosphates is warranted. Phytase-mediated iron release can improve iron absorption from plant foods. There is a need for development of innovative strategies to obtain better effects....... to naturally release iron from iron phytate complexes. This narrative review will evaluate the quantitative significance of phytase-catalysed iron release from cereal foods. In vivo studies have shown how addition of microbially derived phytases to cereal-based foods has produced increased iron absorption via...

  3. 76 FR 65204 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2011-10-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Genomic Resource...: Rudy O. Pozzatti, Ph.D., Scientific Review Officer, Scientific Review Branch, National Human...

  4. De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode

    Directory of Open Access Journals (Sweden)

    Xu De-Lin

    2012-04-01

    Full Text Available Abstract Background Aegilops variabilis No.1 is highly resistant to cereal cyst nematode (CCN. However, a lack of genomic information has restricted studies on CCN resistance genes in Ae. variabilis and has limited genetic applications in wheat breeding. Results Using RNA-Seq technology, we generated a root transcriptome at a sequencing depth of 4.69 gigabases of Ae. variabilis No. 1 from a pooled RNA sample. The sample contained equal amounts of RNA extracted from CCN-infected and untreated control plants at three time-points. Using the Trinity method, nearly 52,081,238 high-quality trimmed reads were assembled into a non-redundant set of 118,064 unigenes with an average length of 500 bp and an N50 of 599 bp. The total assembly was 59.09 Mb of unique transcriptome sequences with average read-depth coverage of 33.25×. In BLAST searches of our database against public databases, 66.46% (78,467 of the unigenes were annotated with gene descriptions, conserved protein domains, or gene ontology terms. Functional categorization further revealed 7,408 individual unigenes and three pathways related to plant stress resistance. Conclusions We conducted high-resolution transcriptome profiling related to root development and the response to CCN infection in Ae. variabilis No.1. This research facilitates further studies on gene discovery and on the molecular mechanisms related to CCN resistance.

  5. Sweetpotato- and cereal-based infant foods: protein quality assessment, and effect on body composition using sprague dawley rats as a model.

    Directory of Open Access Journals (Sweden)

    Francis Kweku Amagloh

    Full Text Available The Protein Digestibility Corrected Amino Acid Score (PDCAAS of sweetpotato-based complementary foods (OFSP ComFa and CFSP ComFa and cereal-based infant products (Weanimix and Cerelac was assessed using 3 wk-old male Sprague Dawley rats weighing between 53-67 g as a model for human infants. Also, the effect of consumption of the infant formulations on lean mass, bone mass content and fat mass was evaluated by Dual-Energy X-ray Absorptiometry (DEXA using 6 wk-old Sprague Dawley rats (initial weight, 206-229 g. The ComFa products and Weanimix are household-level formulations, and Cerelac is a commercial infant cereal. The true protein digestibility score for Cerelac was 96.27%, and about 1.8% (P<0.0001 higher than that for OFSP ComFa, CFSP ComFa and Weanimix. However, OFSP ComFa had the highest un-truncated PDCAAS by a difference of 4.1%, than CFSP ComFa, and about 20% difference compared with both the Weanimix and Cerelac. All the products investigated had PDCAAS greater than 70%, the minimum protein quality requirement for complementary foods. Among the rats assigned to the four formulations, their bone mass and fat mass composition were not significantly different (P=0.08 and P=0.85, respectively. However, the rats on CFSP ComFa had higher lean mass than those on Cerelac (321.67 vs. 297.19 g; P=0.03. The findings from the PDCAAS and the DEXA-measured body composition studies indicate that complementary foods could be formulated from readily available agricultural resources at the household-level to support growth as would a nutritionally adequate industrial-manufactured infant cereal. Nonetheless, it should be noted that the findings of our studies are based on an animal model.

  6. Barriers and incentives to the production of bioethanol from cereal straw: A farm business perspective

    International Nuclear Information System (INIS)

    The EU renewable energy directive stipulates a requirement for 10% of transport fuels to be derived from renewable sources by 2020. Second generation biofuels offer potential to contribute towards this target with cereal straw representing a potentially large feedstock source. From an on-farm survey of 240 arable farmers, timeliness of crop establishment and benefits of nutrient retention from straw incorporation were cited as reasons for straw incorporation. However, two-thirds (one-third) of farmers would supply wheat (barley) straw for bioenergy. The most popular contract length and continuous length of straw supply was either 1 or 3 years. Contracts stipulating a fixed area of straw supply for a fixed price were the most frequently cited preferences, with £50 t−1 the most frequently cited minimum contract price that farmers would find acceptable. Arable farmers in England would be willing to sell 2.52 Mt of cereal straw for bioenergy purposes nationally and 1.65 Mt in the main cereal growing areas of Eastern England. Cereal straw would be diverted from current markets or on-farm uses and from straw currently incorporated into soil. Policy interventions may be required to incentivise farmers to engage in this market, but food and fuel policies must increasingly be integrated to meet societal goals. - Highlights: • English arable farmer survey to determine potential supply for straw based biofuel. • Two-thirds of farmers would supply wheat straw for bioenergy. • Farmers willing to sell 1.65 Mt of cereal straw from the main cereal producing regions. • Farmer preference for a fixed area of straw supply for a contracted fixed price. • £50 t−1 the most frequently cited minimum contract price farmers find acceptable

  7. Aspects of the selection, design and use of high lysine cereals

    International Nuclear Information System (INIS)

    A discussion of the need for and the considerations involved in the breeding of high lysine cereals is presented. Progress in the discovery and exploitation of genotypes with high lysine characters in maize and barley are briefly reviewed. The role and some of the characteristics of the dye-binding capacity (DBC) methods are evaluated along with the ways in which DBC results should be used in combination with other information. Lastly, the changes in attitudes and procedures associated with the acceptance of a product of a new technology such as nutritionally improved cereals is discussed. (author)

  8. Resistant starch content of conventionally boiled and pressure-cooked cereals, legumes and tubers

    OpenAIRE

    Yadav, B. S.; Sharma, A.; Yadav, R. B.

    2010-01-01

    Resistant starch (RS) content was determined in the conventionally boiled (H1) and pressure-cooked (H2) cereals, legumes and tubers using enzymatic method. Both H1 and H2 legumes contained higher amount of RS as compared to cereals and tubers. H1 and H2 lentils showed highest RS content of 5.0 and 4.9% (dwb), respectively. Higher RS content in legumes can be attributed to the presence of intact tissue/cell structures enclosing starch granules and high level of amylose (26–33%) and high conten...

  9. Content of phenolic acids and ferulic acid dehydrodimers in 17 rye (Secale cereale L.) varieties

    DEFF Research Database (Denmark)

    Andreasen, Mette Findal; Christensen, L P; Meyer, A S;

    2000-01-01

    The contents of pnenolic acids and ferulic acid dehydrodimers were quantified by HPLC analysis after alkaline hydrolysis in kernels of 17 rye (Secale cereale L.) varieties grown in one location in Denmark during 1997 and 1998. Significant variations (P ... of the analyzed components were observed among the different rye varieties and also between different harvest years. However, the content of phenolic acids in the analyzed rye varieties was narrow compared to cereals such as wheat and barley. The concentration of ferulic acid, the most abundant phenolic acid...

  10. Organic dairy production based on rapeseed, rapeseed cake or cereals as supplement to silage ad libitum

    OpenAIRE

    Mogensen, Lisbeth; Ingvartsen, Klaus L; Kristensen, Troels; Seested, Susanne; Thamsborg, Stig M.

    2004-01-01

    This experiment presents the effect of 100% organic feed rations grown at an equal area per cow on milk production performance and metabolic responses. A total of 174 Danish Holstein cows were included in two experiments on two commercial organic dairy farms during the winter 2000/2001. Three types of supplementary feed were examined: 5 kg cereals, 3 kg rapeseed/cereal pellet or 1 kg rapeseed cake fed with a mixture of clover grass silage, whole crop silage and grass pellets ad libitum. The s...

  11. Winter cereal yields as affected by animal manure and green manure in organic arable farming

    DEFF Research Database (Denmark)

    Olesen, Jørgen E; Askegaard, Margrethe; Rasmussen, Ilse Ankjær

    2009-01-01

    The effect of nitrogen (N) supply through animal and green manures on grain yield of winter wheat and winter rye was investigated from 1997 to 2004 in an organic farming crop rotation experiment in Denmark on three different soil types varying from coarse sand to sandy loam. Two experimental...... and applying the material to the cereals in the rotation, possibly after digestion in a biogas reactor. Cereal grain protein content was increased more by the N in the grass-clover than from manure application, probably due to different timing ofN availability. Green-manure crops or manures with a relatively...

  12. Development of cereal and legume based food products for the elderly

    OpenAIRE

    Satusap, Pruet; Chavasit, Visith; Kriengsinyos, Wantanee; Judprasong, Kunchit

    2014-01-01

    Diets for elderly must contain nutritious foods, fit their physiological limitations, and match with their food culture. Cereals and legumes are suggested food choices regardless of their cultures and beliefs. Ready-to-eat products containing suitable macronutrient patterns from cereals and legumes were developed. Energy distributions from carbohydrate (60 kcal/100 kcal), protein (15 kcal/100 kcal), and fat (25 kcal/100 kcal), protein quality, and percent energy from saturated fatty acid and ...

  13. Genome size in Anthurium evaluated in the context of karyotypes and phenotypes

    Science.gov (United States)

    Anthurium is an important horticultural flower crop from family Araceae in order Alismatales, a monocot lineage considered to have diverged from other monocots prior to the divergence of the cereals lineage. Currently there is a virtual lack of molecular-genetic resources that would greatly augment...

  14. A Study on the Stability of Deoxynivalenol during the Production of Selected Flour-Based Foods and Wheat Flake Cereal

    Science.gov (United States)

    Deoxynivalenol (DON) is a mycotoxin that is commonly found in cereals and cereal-based products. Some processing methods reduce its concentrations in the finished products whereas others do not. The concentrations of DON in flour, wheat and a selection of food products prepared from them using co...

  15. 9 CFR 318.15 - Tagging chemicals, preservatives, cereals, spices, etc., “U.S. retained.”

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Tagging chemicals, preservatives...; REINSPECTION AND PREPARATION OF PRODUCTS General § 318.15 Tagging chemicals, preservatives, cereals, spices, etc., “U.S. retained.” When any chemical, preservative, cereal, spice, or other substance is...

  16. High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L. genes involved in frost response

    Directory of Open Access Journals (Sweden)

    Korzun Viktor

    2011-01-01

    Full Text Available Abstract Background Rye (Secale cereale L. is the most frost tolerant cereal species. As an outcrossing species, rye exhibits high levels of intraspecific diversity, which makes it well-suited for allele mining in genes involved in the frost responsive network. For investigating genetic diversity and the extent of linkage disequilibrium (LD we analyzed eleven candidate genes and 37 microsatellite markers in 201 lines from five Eastern and Middle European rye populations. Results A total of 147 single nucleotide polymorphisms (SNPs and nine insertion-deletion polymorphisms were found within 7,639 bp of DNA sequence from eleven candidate genes, resulting in an average SNP frequency of 1 SNP/52 bp. Nucleotide and haplotype diversity of candidate genes were high with average values π = 5.6 × 10-3 and Hd = 0.59, respectively. According to an analysis of molecular variance (AMOVA, most of the genetic variation was found between individuals within populations. Haplotype frequencies varied markedly between the candidate genes. ScCbf14, ScVrn1, and ScDhn1 were dominated by a single haplotype, while the other 8 genes (ScCbf2, ScCbf6, ScCbf9b, ScCbf11, ScCbf12, ScCbf15, ScIce2, and ScDhn3 had a more balanced haplotype frequency distribution. Intra-genic LD decayed rapidly, within approximately 520 bp on average. Genome-wide LD based on microsatellites was low. Conclusions The Middle European population did not differ substantially from the four Eastern European populations in terms of haplotype frequencies or in the level of nucleotide diversity. The low LD in rye compared to self-pollinating species promises a high resolution in genome-wide association mapping. SNPs discovered in the promoters or coding regions, which attribute to non-synonymous substitutions, are suitable candidates for association mapping.

  17. RIKEN mouse genome encyclopedia.

    Science.gov (United States)

    Hayashizaki, Yoshihide

    2003-01-01

    We have been working to establish the comprehensive mouse full-length cDNA collection and sequence database to cover as many genes as we can, named Riken mouse genome encyclopedia. Recently we are constructing higher-level annotation (Functional ANnoTation Of Mouse cDNA; FANTOM) not only with homology search based annotation but also with expression data profile, mapping information and protein-protein database. More than 1,000,000 clones prepared from 163 tissues were end-sequenced to classify into 159,789 clusters and 60,770 representative clones were fully sequenced. As a conclusion, the 60,770 sequences contained 33,409 unique. The next generation of life science is clearly based on all of the genome information and resources. Based on our cDNA clones we developed the additional system to explore gene function. We developed cDNA microarray system to print all of these cDNA clones, protein-protein interaction screening system, protein-DNA interaction screening system and so on. The integrated database of all the information is very useful not only for analysis of gene transcriptional network and for the connection of gene to phenotype to facilitate positional candidate approach. In this talk, the prospect of the application of these genome resourced should be discussed. More information is available at the web page: http://genome.gsc.riken.go.jp/.

  18. COMPUTATIONAL RESOURCES FOR BIOFUEL FEEDSTOCK SPECIES

    Energy Technology Data Exchange (ETDEWEB)

    Buell, Carol Robin [Michigan State University; Childs, Kevin L [Michigan State University

    2013-05-07

    While current production of ethanol as a biofuel relies on starch and sugar inputs, it is anticipated that sustainable production of ethanol for biofuel use will utilize lignocellulosic feedstocks. Candidate plant species to be used for lignocellulosic ethanol production include a large number of species within the Grass, Pine and Birch plant families. For these biofuel feedstock species, there are variable amounts of genome sequence resources available, ranging from complete genome sequences (e.g. sorghum, poplar) to transcriptome data sets (e.g. switchgrass, pine). These data sets are not only dispersed in location but also disparate in content. It will be essential to leverage and improve these genomic data sets for the improvement of biofuel feedstock production. The objectives of this project were to provide computational tools and resources for data-mining genome sequence/annotation and large-scale functional genomic datasets available for biofuel feedstock species. We have created a Bioenergy Feedstock Genomics Resource that provides a web-based portal or clearing house for genomic data for plant species relevant to biofuel feedstock production. Sequence data from a total of 54 plant species are included in the Bioenergy Feedstock Genomics Resource including model plant species that permit leveraging of knowledge across taxa to biofuel feedstock species.We have generated additional computational analyses of these data, including uniform annotation, to facilitate genomic approaches to improved biofuel feedstock production. These data have been centralized in the publicly available Bioenergy Feedstock Genomics Resource (http://bfgr.plantbiology.msu.edu/).

  19. Patterns of Cereal Yield Growth across China from 1980 to 2010 and Their Implications for Food Production and Food Security.

    Science.gov (United States)

    Li, Xiaoyun; Liu, Nianjie; You, Liangzhi; Ke, Xinli; Liu, Haijun; Huang, Malan; Waddington, Stephen R

    2016-01-01

    After a remarkable 86% increase in cereal production from 1980 to 2005, recent crop yield growth in China has been slow. County level crop production data between 1980 and 2010 from eastern and middle China were used to analyze spatial and temporal patterns of rice, wheat and maize yield in five major farming systems that include around 90% of China's cereal production. Site-specific yield trends were assessed in areas where those crops have experienced increasing yield or where yields have stagnated or declined. We find that rice yields have continued to increase on over 12.3 million hectares (m. ha) or 41.8% of the rice area in China between 1980 and 2010. However, yields stagnated on 50% of the rice area (around 14.7 m. ha) over this time period. Wheat yields increased on 13.8 m. ha (58.2% of the total harvest area), but stagnated on around 3.8 m. ha (15.8% of the harvest area). Yields increased on a smaller proportion of the maize area (17.7% of harvest area, 5.3 m. ha), while yields have stagnated on over 54% (16.3 m. ha). Many parts of the lowland rice and upland intensive sub-tropical farming systems were more prone to stagnation with rice, the upland intensive sub-tropical system with wheat, and maize in the temperate mixed system. Large areas where wheat yield continues to rise were found in the lowland rice and temperate mixed systems. Land and water constraints, climate variability, and other environmental limitations undermine increased crop yield and agricultural productivity in these systems and threaten future food security. Technology and policy innovations must be implemented to promote crop yields and the sustainable use of agricultural resources to maintain food security in China. In many production regions it is possible to better match the crop with input resources to raise crop yields and benefits. Investments may be especially useful to intensify production in areas where yields continue to improve. For example, increased support to maize

  20. Patterns of Cereal Yield Growth across China from 1980 to 2010 and Their Implications for Food Production and Food Security

    Science.gov (United States)

    Li, Xiaoyun; Liu, Nianjie; You, Liangzhi; Ke, Xinli; Liu, Haijun; Huang, Malan; Waddington, Stephen R.

    2016-01-01

    After a remarkable 86% increase in cereal production from 1980 to 2005, recent crop yield growth in China has been slow. County level crop production data between 1980 and 2010 from eastern and middle China were used to analyze spatial and temporal patterns of rice, wheat and maize yield in five major farming systems that include around 90% of China's cereal production. Site-specific yield trends were assessed in areas where those crops have experienced increasing yield or where yields have stagnated or declined. We find that rice yields have continued to increase on over 12.3 million hectares (m. ha) or 41.8% of the rice area in China between 1980 and 2010. However, yields stagnated on 50% of the rice area (around 14.7 m. ha) over this time period. Wheat yields increased on 13.8 m. ha (58.2% of the total harvest area), but stagnated on around 3.8 m. ha (15.8% of the harvest area). Yields increased on a smaller proportion of the maize area (17.7% of harvest area, 5.3 m. ha), while yields have stagnated on over 54% (16.3 m. ha). Many parts of the lowland rice and upland intensive sub-tropical farming systems were more prone to stagnation with rice, the upland intensive sub-tropical system with wheat, and maize in the temperate mixed system. Large areas where wheat yield continues to rise were found in the lowland rice and temperate mixed systems. Land and water constraints, climate variability, and other environmental limitations undermine increased crop yield and agricultural productivity in these systems and threaten future food security. Technology and policy innovations must be implemented to promote crop yields and the sustainable use of agricultural resources to maintain food security in China. In many production regions it is possible to better match the crop with input resources to raise crop yields and benefits. Investments may be especially useful to intensify production in areas where yields continue to improve. For example, increased support to maize

  1. Sensitization to cereals and peanut evidenced by skin prick test and specific IgE in food-tolerant, grass pollen allergic patients

    DEFF Research Database (Denmark)

    Martens, Maria; Schnoor, Heidi J; Malling, Hans-Jørgen;

    2011-01-01

    The botanical relation between grass and cereal grains may be relevant when diagnosing food allergy to cereals. The aim was to investigate the diagnostic specificity of skin prick test (SPT) and specific immunoglobulin E (sIgE) tests to cereals and peanut in grass pollen allergic subjects without...

  2. On the fuel quality of cereal grains - Impact of soil composition, cereal species and variety; Braensleegenskaper hos spannmaalskaerna. Betydelsen av jordart, saedesslag och sort

    Energy Technology Data Exchange (ETDEWEB)

    Hadders, G.; Arshadi, M.; Nilsson, Calle; Burvall, J.

    2001-07-01

    105 samples of seven cereal varieties from winter wheat, winter triticale, barley and oats were analysed. The samples were collected from some hundred locations with varying soil composition in southern Sweden (regions of Goetaland and Svealand). The samples were analysed concerning - the content of ashes (all samples) - the main components in the ashes (all samples) - the heat value (21 samples) - the melting behaviour of the ashes (21 samples). The results from the laboratory has been statistically analysed using multivariate data analysis. Multivariate data analysis is based on advanced mathematical and statistical calculations to gain information from large amounts of data. The models used try to describe data, not by analysing one variable at a time, but by simultaneously take into consideration all variables and also interactions between these, which usually leads to a considerable increase in the amount of relevant information from measured chemical data. The soil composition at the growing site seem to be of little importance for the fuel quality of cereal grains, in contradiction to what is reported for Reed Canary Grass (Phalaris arundinacea) and straw from cereal grains. Relatively large differences in fuel quality between the cereal species studied were found. The differences were particularly large comparing wheat and oats. This was mainly true for the composition of the ashes and its melting behaviour, but to some extent also for the heat value. Most striking is that oats differs from the other species by having considerably higher contents of silica, and lower content of potassium and phosphorus. These circumstances have in other corresponding contexts been of positive impact on the melting behaviour of the ashes. The result also shows that it is possible to predict several parameters by multivariate data analysis. It is possible to some extent to predict the content of ashes in the fuel and the contents of the four main metal oxides in the ashes (K

  3. New Local, National and Regional Cereal Price Indices for Improved Identification of Food Insecurity

    Science.gov (United States)

    Brown, Molly E.; Tondel, Fabien; Thorne, Jennifer A.; Essam, Timothy; Mann, Bristol F.; Stabler, Blake; Eilerts, Gary

    2011-01-01

    Large price increases over a short time period can be indicative of a deteriorating food security situation. Food price indices developed by the United Nations Food and Agriculture Organization (FAO) are used to monitor food price trends at a global level, but largely reflect supply and demand conditions in export markets. However, reporting by the United States Agency for International Development (USAID)'s Famine Early Warning Systems Network (FEWS NET) indicates that staple cereal prices in many markets of the developing world, especially in surplus-producing areas, often have a delayed and variable response to international export market price trends. Here we present new price indices compiled for improved food security monitoring and assessment, and specifically for monitoring conditions of food access across diverse food insecure regions. We found that cereal price indices constructed using market prices within a food insecure region showed significant differences from the international cereals price, and had a variable price dispersion across markets within each marketshed. Using satellite-derived remote sensing information that estimates local production and the FAO Cereals Index as predictors, we were able to forecast movements of the local or national price indices in the remote, arid and semi-arid countries of the 38 countries examined. This work supports the need for improved decision-making about targeted aid and humanitarian relief, by providing earlier early warning of food security crises.

  4. The effect of perennials as green manure on cereal productivity and disease incidence

    Energy Technology Data Exchange (ETDEWEB)

    Skuodiene, R.; Nekrosiene, R.

    2012-11-01

    Field experiments were conducted at the Vezaiciai Branch of the Lithuanian Research Centre for Agriculture and Forestry during the period 2002-2007. They were designed to ascertain the effects of phytomass of different perennial pre-crops used for green manure on the productivity and on the occurrence of foliar fungal diseases of cereal agrocenoses. Plant residues and phytomass ploughed down as green manures positively affected cereal indices of crop productivity not only for the first but for the second year as well. It influenced the productivity of cereal segments. The largest amount of metabolizable energy was in the yield of cereal sequence under white clover (Trifolium repens L.) 83.23-84.76% GJ ha{sup 1}. The potential accumulated by perennials of the second year of development was more efficiently utilised by winter triticale (Triticosecale Wittm.) cv. Tevo, and that of perennials of the third year of development was more efficiently utilised by spring barley (Hordeum vulgare L.) cv. Ula. Perennials had a significant effect on the spread of foliar diseases in winter triticale (Triticosecale Wittm.) and spring barley (Hordeum vulgare L.) agrocenoses. The severity of the disease was 1.1-1.3 times higher in the winter triticale (Triticosecale Wittm.) treatments with white clover (Trifolium repens L.) pre-crops. Foliar disease incidence and severity was 1.1-1.2 times higher in the agrocenoses of spring barley (Hordeum vulgare L.) after legumes of the third year of development, especially after lucerne (Medicago sativa L.). (Author) 28 refs.

  5. The Effect of Plant Proteins Derived from Cereals and Legumes on Heme Iron Absorption

    Directory of Open Access Journals (Sweden)

    Valerie Weinborn

    2015-10-01

    Full Text Available The aim of this study is to determine the effect of proteins from cereals and legumes on heme iron (Fe absorption. The absorption of heme Fe without its native globin was measured. Thirty adult females participated in two experimental studies (15 per study. Study I focused on the effects of cereal proteins (zein, gliadin and glutelin and study II on the effects of legume proteins (soy, pea and lentil on heme Fe absorption. When heme was given alone (as a control, study I and II yielded 6.2% and 11.0% heme absorption (p > 0.05. In study I, heme Fe absorption was 7.2%, 7.5% and 5.9% when zein, gliadin and glutelin were added, respectively. From this, it was concluded that cereal proteins did not affect heme Fe absorption. In study II, heme Fe absorption was 7.3%, 8.1% and 9.1% with the addition of soy, pea and lentil proteins, respectively. Only soy proteins decreased heme Fe absorption (p < 0.05. These results suggest that with the exception of soy proteins, which decreased absorption, proteins derived from cereals and legumes do not affect heme Fe absorption.

  6. Barriers and incentives to the production of bioethanol from cereal straw: A farm business perspective.

    Science.gov (United States)

    Glithero, N J; Ramsden, S J; Wilson, P

    2013-08-01

    The EU renewable energy directive stipulates a requirement for 10% of transport fuels to be derived from renewable sources by 2020. Second generation biofuels offer potential to contribute towards this target with cereal straw representing a potentially large feedstock source. From an on-farm survey of 240 arable farmers, timeliness of crop establishment and benefits of nutrient retention from straw incorporation were cited as reasons for straw incorporation. However, two-thirds (one-third) of farmers would supply wheat (barley) straw for bioenergy. The most popular contract length and continuous length of straw supply was either 1 or 3 years. Contracts stipulating a fixed area of straw supply for a fixed price were the most frequently cited preferences, with £50 t(-1) the most frequently cited minimum contract price that farmers would find acceptable. Arable farmers in England would be willing to sell 2.52 Mt of cereal straw for bioenergy purposes nationally and 1.65 Mt in the main cereal growing areas of Eastern England. Cereal straw would be diverted from current markets or on-farm uses and from straw currently incorporated into soil. Policy interventions may be required to incentivise farmers to engage in this market, but food and fuel policies must increasingly be integrated to meet societal goals. PMID:24926116

  7. Occurrence of free and conjugated Fusarium mycotoxins in cereal based food

    OpenAIRE

    Vendl, O.; Crews, C.; MacDonald, S; R. Krska; Berthiller, F.

    2010-01-01

    Abstract A collection of 84 cereal based food products in 25 composites, including beer, was screened for the presence of deoxynivalenol, zearalenone and their respective metabolites deoxynivalenol-3-glucopyranoside, 3-acetyl-deoxynivalenol, zearalenol-4-glucopyranoside, ?-zearalenol, ?-zearalenol, ?-zearalenol-4-glucopyranoside, ?-zearalenol-4-glucopyranoside and zearalenone-4-sulfate. The most abundant analyte was zearalenone-4-sulfate, which was found in 13 composites, albeit in...

  8. Cereal bar with added chayote peel flour: physico-chemical and sensory characteristics among children

    Directory of Open Access Journals (Sweden)

    Tatiane Wendler de Cristo

    2015-12-01

    Full Text Available The study aimed to verify the sensory acceptability of traditional cereal bars and cereal bars added with chayote peel flour, and determine the physico-chemical compositions of their formulations. Five cereal bars formulas were prepared and analyzed as follows: F1: standard (0% and with the addition of chayote peel flour in the proportions of 6.75% (F2; 13.5% (F3; 20.25% (F4 and 27% (F5. Sixty tasters, aged 7-10 took part in the sensorial analysis. There was no significant difference (p> 0.05 regarding appearance, aroma, texture and color among formulations. For the attributes taste, overall acceptance and purchase intention, higher scores were given towards the standard sample when compared to F5, but no differences were observed among the other sample scores. There was no statistical difference (p>0.05 for moisture, protein, fat and calories between F1 and F4 formulations. However, higher levels of ash and dietary fiber and lower level of carbohydrates were observed in F4 compared to F1. The formulas preparation demonstrated that a level of addition of up to 20.25% of chayote peel flour in cereal bars was well accepted by the panel, with a sensory acceptance similar to the standard product and good trading expectation.

  9. Innovaciones Tecnológicas y Tendencias de Desarrollo en las cosechadoras de Cereales

    OpenAIRE

    Moya Gonzalez, Adolfo; Valero Ubierna, Constantino

    2012-01-01

    Revisamos en este artículo los temas en los que ingenieros y científicos están trabajando para aportar innovaciones a la cosecha de cereal. Además se revisa el mercado español y las últimas novedades comerciales presentadas por los fabricantes.

  10. Sourdough lactic acid bacteria: exploration of non-wheat cereal-based fermentation.

    Science.gov (United States)

    Coda, Rossana; Cagno, Raffaella Di; Gobbetti, Marco; Rizzello, Carlo Giuseppe

    2014-02-01

    Cereal-based foods represent a very important source of biological as well as of cultural diversity, as testified by the wide range of derived fermented products. A trend that is increasingly attracting bakery industries as well as consumers is the use of non-conventional flours for the production of novel products, characterised by peculiar flavour and better nutritional value. Lactic acid bacteria microbiota of several non-wheat cereals and pseudo-cereals has been recently deeply investigated with the aim of studying the biodiversity and finding starter cultures for sourdough fermentation. Currently, the use of ancient or ethnic grains is mainly limited to traditional typical foods and the bread making process is not well standardised with consequent negative effects on the final properties. The challenge in fermenting such grains is represented by the necessity to combine good technology and sensory properties with nutritional/health benefits. The choice of the starter cultures has a critical impact on the final quality of cereal-based products, and strains that dominate and outcompete contaminants should be applied for specific sourdough fermentations. In this sense, screening and characterisation of the lactic acid bacteria microbiota is very useful in the improvement of a peculiar flour, from both a nutritional and technological point of view.

  11. Cereal crops as viable production and storage systems for pharmaceutical scFv antibodies.

    Science.gov (United States)

    Stöger, E; Vaquero, C; Torres, E; Sack, M; Nicholson, L; Drossard, J; Williams, S; Keen, D; Perrin, Y; Christou, P; Fischer, R

    2000-03-01

    This report describes the stable expression of a medically important antibody in the staple cereal crops rice and wheat. We successfully expressed a single-chain Fv antibody (ScFvT84.66) against carcinoembryonic antigen (CEA), a well characterized tumor-associated marker antigen. scFv constructs were engineered for recombinant antibody targeting to the plant cell apoplast and ER. Up to 30 microg/g of functional recombinant antibody was detected in the leaves and seeds of wheat and rice. We confirmed that transgenic dry seeds could be stored for at least five months at room temperature, without significant loss of the amount or activity of scFvT84.66. Our results represent the first transition from model plant expression systems, such as tobacco and Arabidopsis, to widely cultivated cereal crops, such as rice and wheat, for expression of an antibody molecule that has already shown efficacy in clinical applications. Thus, we have established that molecular pharming in cereals can be a viable production system for such high-value pharmaceutical macromolecules. Our findings provide a strong foundation for exploiting alternative uses of cereal crops both in industrialized and developing countries.

  12. NITROGEN AND PHOSPHORUS LIMITED PRODUCTION OF CEREALS AND SEMINATURAL ANNUAL-TYPE PASTURES IN SW SPAIN

    NARCIS (Netherlands)

    Esselink, Peter; VANGILS, H

    1994-01-01

    Nutrient limited primary production of semi-natural pastures dominated by annuals and of cereals grown in rotation with grazing was surveyed in Extremadura (Spain), using the N and P concentration and the P/N ratio of plant tissue. The N concentration varied between 2.0-3.2 % in pasture legumes and

  13. The Profile and Bioaccessibility of Phenolic Compounds in Cereals Influenced by Improved Extrusion Cooking Treatment.

    Science.gov (United States)

    Zeng, Zicong; Liu, Chengmei; Luo, Shunjing; Chen, Jun; Gong, Ersheng

    2016-01-01

    The aim of this study was to investigate the effect of Improved Extrusion Cooking Treatment (IECT) on the phenolics and its bioaccessibility in cereals, represented by brown rice, wheat, and oat. Data showed that total phenolic content and total antioxidant activity in free form were significantly decreased, while the bound form was increased after IECT. After IECT, the total free phenolic acids of brown rice and wheat were significantly decreased by 5.88% and 45.66%, respectively, while the total bound phenolic acids of brown rice, wheat, and oat were significantly increased by 6.45%, 8.78%, and 9.10%, respectively. Brown rice provided the most bioaccessible phenolics and antioxidant compounds, followed by oat and wheat. IECT significantly decreased the bioaccessible phenolics of brown rice and oat by 31.09% and 30.95%, while it had minimal effect on the bioaccessible phenolics of wheat. These results showed that IECT greatly affected the phenolics and its bioaccessibiltiy of cereals, with the effect depending on cereal matrix and the sensitivity of free and bound phenolics. Furthermore, bioaccessible phenolic acids of raw and processed cereals were considerably low, and it slightly contributed to the bioaccessible phenolics. PMID:27513581

  14. Development and Life History of Sitophilus zeamais (Coleoptera: Curculionidae on Cereal Crops

    Directory of Open Access Journals (Sweden)

    James Adebayo Ojo

    2016-01-01

    Full Text Available The maize weevil, Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae, is one of the most destructive pests of stored cereals. Knowledge of the life history and biology is important to the development of an integrated pest management program. Investigation was carried out on developmental biology of S. zeamais on four main cereal crops, maize, rice, sorghum, and millet, under laboratory conditions. Egg incubation, oviposition periods, and larval instar development were not different significantly among the food hosts. Number of eggs laid varied significantly among the cereal grains; mean fecundity was highest on maize (67.2±3.16 and lowest on millet (53.8±0.17. Number of immature (larva and pupa and adult stages varied significantly among the cereal grains. There exist four larval instars with a varied mean head capsule width, with a mean total instar larval developmental period of 23.1, 22.2, 22.2, and 21.6 d on maize, rice, sorghum, and millet, respectively. There was linear relationship and significant correlation between the stages of larval development and head capsule width. The mean developmental period from egg to adult varied, being highest on maize (34.7 d and lowest on sorghum (33.5 d.

  15. Identification of secreted proteins of Aspergillus oryzae associated with growth on solid cereal substrates

    NARCIS (Netherlands)

    Biesebeke, R. te; Boussier, A.; Biezen, N. van; Hondel, C.A.M.J.J. van den; Punt, P.J.

    2006-01-01

    Filamentous growth of Aspergillus oryzae on solid cereal substrates involves secretion of substrate converting enzymes and a solid substrate specific polarised hyphal growth phenotype. To identify proteins produced under these specific conditions, the extracts of A. oryzae grown on wheat-based media

  16. Breakfast Eating Pattern and Ready-to-Eat Cereals Consumption among Schoolchildren in Kuala Lumpur

    OpenAIRE

    KOO, Hui-Chin; ABDUL JALIL, Siti Nurain; Ruzita, ABD TALIB

    2015-01-01

    Background: Studies from the West have demonstrated that ready-to-eat cereals (RTECs) are a common form of breakfast and more likely to be consumed by children. This study aimed to investigate the breakfast eating pattern and RTECs consumption among schoolchildren in Kuala Lumpur.

  17. The Effect of Plant Proteins Derived from Cereals and Legumes on Heme Iron Absorption.

    Science.gov (United States)

    Weinborn, Valerie; Pizarro, Fernando; Olivares, Manuel; Brito, Alex; Arredondo, Miguel; Flores, Sebastián; Valenzuela, Carolina

    2015-11-01

    The aim of this study is to determine the effect of proteins from cereals and legumes on heme iron (Fe) absorption. The absorption of heme Fe without its native globin was measured. Thirty adult females participated in two experimental studies (15 per study). Study I focused on the effects of cereal proteins (zein, gliadin and glutelin) and study II on the effects of legume proteins (soy, pea and lentil) on heme Fe absorption. When heme was given alone (as a control), study I and II yielded 6.2% and 11.0% heme absorption (p > 0.05). In study I, heme Fe absorption was 7.2%, 7.5% and 5.9% when zein, gliadin and glutelin were added, respectively. From this, it was concluded that cereal proteins did not affect heme Fe absorption. In study II, heme Fe absorption was 7.3%, 8.1% and 9.1% with the addition of soy, pea and lentil proteins, respectively. Only soy proteins decreased heme Fe absorption (p < 0.05). These results suggest that with the exception of soy proteins, which decreased absorption, proteins derived from cereals and legumes do not affect heme Fe absorption. PMID:26529009

  18. Legume N2 fixation - An efficient source of nitrogen for cereal production

    International Nuclear Information System (INIS)

    Nitrogen deficiency is a major factor limiting yields of cereals. With wheat, the most commonly-grown cereal in rain-fed agriculture, the soil must supply 30-40 kg N/ha in a plant-available form (usually as nitrate) for each tonne of grain produced. In some of the developed countries and energy-rich LDC's, N is supplied in sufficient amounts as fertilizers. In the majority of countries, however, this is not possible principally because of the high cost. Research has shown that the soil following an annual crop legume often contains 30-60 kg N/ha more than after a cereal crop and that this increased plant-available N is converted into increased cereal grain yield. The N benefits are due to the legume's capacity to fix atmospheric N2. Amounts fixed by the annual crop legumes range from zero to more than 400 kg/ha. There is, however, scope to manage legume N2 fixation for maximum benefit, through practices that optimize crop growth and minimize the suppressive effects of soil nitrate. One possible aid to management may come through the development and use of simple mathematical functions (models) that will allow farmers to estimate amounts of N2 fixed by a legume crop and the potential net N benefit resulting from that crop. (author). 42 refs, 6 figs, 5 tabs

  19. In situ ruminal crude protein degradability of by-products from cereals, oilseeds and animal origin

    NARCIS (Netherlands)

    Habib, G.; Khan, N.A.; Ali, M.; Bezabih, M.

    2013-01-01

    The aim of this study was to establish a database on in situ ruminal crude protein (CP) degradability characteristics of by-products from cereal grains, oilseeds and animal origin commonly fed to ruminants in Pakistan and South Asian Countries. The oilseed by-products were soybean meal, sunflower me

  20. Understanding mechanisms of host resistance against greenbug in cereal crops - an interdisciplinary, collaborative approach

    Science.gov (United States)

    At Texas AgriLife Research - Amarillo, we have an ongoing research program focusing on elucidating the mechanisms of interactions between the phloem-feeding aphid pests and cereal crop hosts using the wheat-greenbug as a model system. During this workshop, recent results from our research on the fo...