Wheat EST resources for functional genomics of abiotic stress

Directory of Open Access Journals (Sweden)

Links Matthew G

2006-06-01

Full Text Available Abstract Background Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS project. Results We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets. Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. Conclusion We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in

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...... knowledge on their structure, function, and implication in cereal processing, agriculture and nutrition. (c) 2006 Society of Chemical Industry...

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......Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass...... to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous...

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (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 establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous 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 perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Genome resource banking of biomedically important laboratory animals.

Science.gov (United States)

Agca, Yuksel

2012-11-01

Genome resource banking is the systematic collection, storage, and redistribution of biomaterials in an organized, logistical, and secure manner. Genome cryobanks usually contain biomaterials and associated genomic information essential for progression of biomedicine, human health, and research. In that regard, appropriate genome cryobanks could provide essential biomaterials for both current and future research projects in the form of various cell types and tissues, including sperm, oocytes, embryos, embryonic or adult stem cells, induced pluripotent stem cells, and gonadal tissues. In addition to cryobanked germplasm, cryobanking of DNA, serum, blood products, and tissues from scientifically, economically, and ecologically important species has become a common practice. For revitalization of the whole organism, cryopreserved germplasm in conjunction with assisted reproductive technologies, offer a powerful approach for research model management, as well as assisting in animal production for agriculture, conservation, and human reproductive medicine. Recently, many developed and developing countries have allocated substantial resources to establish genome resources banks which are responsible for safeguarding scientifically, economically, and ecologically important wild type, mutant, and transgenic plants, fish, and local livestock breeds, as well as wildlife species. This review is dedicated to the memory of Dr. John K. Critser, who has made profound contributions to the science of cryobiology and establishment of genome research and resources centers for mice, rats, and swine. Emphasis will be given to application of genome resource banks to species with substantial contributions to the advancement of biomedicine and human health. Copyright © 2012 Elsevier Inc. All rights reserved.

Harvesting Legume Genomes: Plant Genetic Resources

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Genomics and high through-put phenotyping are ushering in a new era of accessing genetic diversity held in plant genetic resources, the cornerstone of both traditional and genomics-assisted breeding efforts of food legume crops. Acknowledged or not, yield plateaus must be broken given the daunting ...

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

The present paper summarizes the current state of knowledge on cereal phytase that are particular relevant for improving mineral and phosphate bio-availability. Phytases can initiate the hydrolysis of phytate, the main storage form of phosphate in cereals and the major anti-nutritional factor...... 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...... wheat, barley and rye whereas non-Triticeae cereals such as maize and rice have very little MGPA. Recent studies have determined the evolutionary relationships of phytases in Triticeae and non-Triticeae and highlighted the importance of the purple acid phosphatase phytases (PAPhys). In the Triticeae...

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.

Genomic Resource and Genome Guided Comparison of Twenty Type Strains of the Genus Methylobacterium

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Vasvi Chaudhry

2017-12-01

Full Text Available Bacteria of the genus Methylobacterium are widespread in diverse habitats ranging from soil, water and plant (phyllosphere, rhizosphere and endosphere. In the present study, we in house generated genomic data resource of six type strains along with fourteen database genomes of the Methylobacterium genus to carry out phylogenomic, taxonomic, comparative and ecological studies of this genus. Overall, the genus shows high diversity and genetic variation primarily due to its ability to acquire genetic material from diverse sources through horizontal gene transfer. As majority of species identified in this study are plant associated with their genomes equipped with methylotrophy and photosynthesis related gene along with genes for plant probiotic traits. Most of the species genomes are equipped with genes for adaptation and defense for UV radiation, oxidative stress and desiccation. The genus has an open pan-genome and we predicted the role of gain/loss of prophages and CRISPR elements in diversity and evolution. Our genomic resource with annotation and analysis provides a platform for interspecies genomic comparisons in the genus Methylobacterium, and to unravel their natural genome diversity and to study how natural selection shapes their genome with the adaptive mechanisms which allow them to acquire diverse habitat lifestyles. This type strains genomic data display power of Next Generation Sequencing in rapidly creating resource paving the way for studies on phylogeny and taxonomy as well as for basic and applied research for this important genus.

Application of gamma-irradiation to cereals and cereals products

International Nuclear Information System (INIS)

Wootton, M.

1985-01-01

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

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

Science.gov (United States)

Kersey, Paul J; Staines, Daniel M; Lawson, Daniel; Kulesha, Eugene; Derwent, Paul; Humphrey, Jay C; Hughes, Daniel S T; Keenan, Stephan; Kerhornou, Arnaud; Koscielny, Gautier; Langridge, Nicholas; McDowall, Mark D; Megy, Karine; Maheswari, Uma; Nuhn, Michael; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Wilson, Derek; Yates, Andrew; Birney, Ewan

2012-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

Science.gov (United States)

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-04

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Enhancing faba bean (Vicia faba L.) genome resources

NARCIS (Netherlands)

Cooper, James W.; Wilson, Michael H.; Derks, M.F.L.; Smit, Sandra; Kunert, Karl J.; Cullis, Christopher; Foyer, C.H.

2017-01-01

Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

Science.gov (United States)

Sood, Salej; Kumar, Anil; Babu, B. Kalyana; Gaur, Vikram S.; Pandey, Dinesh; Kant, Lakshmi; Pattnayak, Arunava

2016-01-01

The rapid strides in molecular marker technologies followed by genomics, and next generation sequencing advancements in three major crops (rice, maize and wheat) of the world have given opportunities for their use in the orphan, but highly valuable future crops, including finger millet [Eleusine coracana (L.) Gaertn.]. Finger millet has many special agronomic and nutritional characteristics, which make it an indispensable crop in arid, semi-arid, hilly and tribal areas of India and Africa. The crop has proven its adaptability in harsh conditions and has shown resilience to climate change. The adaptability traits of finger millet have shown the advantage over major cereal grains under stress conditions, revealing it as a storehouse of important genomic resources for crop improvement. Although new technologies for genomic studies are now available, progress in identifying and tapping these important alleles or genes is lacking. RAPDs were the default choice for genetic diversity studies in the crop until the last decade, but the subsequent development of SSRs and comparative genomics paved the way for the marker assisted selection in finger millet. Resistance gene homologs from NBS-LRR region of finger millet for blast and sequence variants for nutritional traits from other cereals have been developed and used invariably. Population structure analysis studies exhibit 2–4 sub-populations in the finger millet gene pool with separate grouping of Indian and exotic genotypes. Recently, the omics technologies have been efficiently applied to understand the nutritional variation, drought tolerance and gene mining. Progress has also occurred with respect to transgenics development. This review presents the current biotechnological advancements along with research gaps and future perspective of genomic research in finger millet. PMID:27881984

Prospecting for Microelement Function and Biosafety Assessment of Transgenic Cereal Plants

Directory of Open Access Journals (Sweden)

Xiaofen Yu

2018-03-01

Full Text Available Microelement contents and metabolism are vitally important for cereal plant growth and development as well as end-use properties. While minerals phytotoxicity harms plants, microelement deficiency also affects human health. Genetic engineering provides a promising way to solve these problems. As plants vary in abilities to uptake, transport, and accumulate minerals, and the key enzymes acting on that process is primarily presented in this review. Subsequently, microelement function and biosafety assessment of transgenic cereal plants have become a key issue to be addressed. Progress in genetic engineering of cereal plants has been made with the introduction of quality, high-yield, and resistant genes since the first transgenic rice, corn, and wheat were born in 1988, 1990, and 1992, respectively. As the biosafety issue of transgenic cereal plants has now risen to be a top concern, many studies on transgenic biosafety have been carried out. Transgenic cereal biosafety issues mainly include two subjects, environmental friendliness and end-use safety. Different levels of gene confirmation, genomics, proteomics, metabolomics and nutritiomics, absorption, metabolism, and function have been investigated. Also, the different levels of microelement contents have been measured in transgenic plants. Based on the motivation of the requested biosafety, systematic designs, and analysis of transgenic cereal are also presented in this review paper.

Prospecting for Microelement Function and Biosafety Assessment of Transgenic Cereal Plants.

Science.gov (United States)

Yu, Xiaofen; Luo, Qingchen; Huang, Kaixun; Yang, Guangxiao; He, Guangyuan

2018-01-01

Microelement contents and metabolism are vitally important for cereal plant growth and development as well as end-use properties. While minerals phytotoxicity harms plants, microelement deficiency also affects human health. Genetic engineering provides a promising way to solve these problems. As plants vary in abilities to uptake, transport, and accumulate minerals, and the key enzymes acting on that process is primarily presented in this review. Subsequently, microelement function and biosafety assessment of transgenic cereal plants have become a key issue to be addressed. Progress in genetic engineering of cereal plants has been made with the introduction of quality, high-yield, and resistant genes since the first transgenic rice, corn, and wheat were born in 1988, 1990, and 1992, respectively. As the biosafety issue of transgenic cereal plants has now risen to be a top concern, many studies on transgenic biosafety have been carried out. Transgenic cereal biosafety issues mainly include two subjects, environmental friendliness and end-use safety. Different levels of gene confirmation, genomics, proteomics, metabolomics and nutritiomics, absorption, metabolism, and function have been investigated. Also, the different levels of microelement contents have been measured in transgenic plants. Based on the motivation of the requested biosafety, systematic designs, and analysis of transgenic cereal are also presented in this review paper.

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-01-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (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 establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous 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 perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

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. The...

transPLANT Resources for Triticeae Genomic Data

Directory of Open Access Journals (Sweden)

Manuel Spannagl

2016-03-01

Full Text Available The genome sequences of many important Triticeae species, including bread wheat ( L. and barley ( L., remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT ( is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.

Resources for Functional Genomics Studies in Drosophila melanogaster

Science.gov (United States)

Mohr, Stephanie E.; Hu, Yanhui; Kim, Kevin; Housden, Benjamin E.; Perrimon, Norbert

2014-01-01

Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, “meta” information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally. PMID:24653003

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

Science.gov (United States)

Straub, Shannon C K; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C; Liston, Aaron

2011-05-04

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. 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. 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 and its relatives. This study represents a first

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.

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

Microbial Genome Analysis and Comparisons: Web-based Protocols and Resources

Science.gov (United States)

Fully annotated genome sequences of many microorganisms are publicly available as a resource. However, in-depth analysis of these genomes using specialized tools is required to derive meaningful information. We describe here the utility of three powerful publicly available genome databases and ana...

Mycotoxins in organic and conventional cereals and cereal products grown and marketed in Croatia.

Science.gov (United States)

Pleadin, Jelka; Staver, Mladenka Malenica; Markov, Ksenija; Frece, Jadranka; Zadravec, Manuela; Jaki, Vesna; Krupić, Igor; Vahčić, Nada

2017-08-01

In this study, the levels of aflatoxin B 1 (AFB 1 ), ochratoxin A (OTA), zearalenone (ZEN), deoxynivalenol (DON) and fumonisins (FUM) in unprocessed cereals (n = 189) and cereal-based products (n = 61) were determined using validated ELISA methods. All samples originated from either conventional or organic production corresponded to the 2015 harvest in Croatia. Based on the mean mycotoxin concentrations, the risk for the consumer to exceed the tolerable daily intake (TDI) for these toxins by the consumption of both types of cereals and cereal-based products was assessed. Mycotoxin contamination of organic cereals and organic cereal-based products was not significantly different (p > 0.05). Given that the exposure assessment resulted in a small fraction of the TDI (maximum: DON, 12% of TDI), the levels of the investigated mycotoxins in both types of cereals and cereal-based products from the 2015 harvest did not pose a human health hazard.

Gramene database: Navigating plant comparative genomics resources

Directory of Open Access Journals (Sweden)

Parul Gupta

2016-11-01

Full Text Available Gramene (http://www.gramene.org is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.

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.…

Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya

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Junling Cao

2018-01-01

Full Text Available Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs. Seventy simple sequence repeats (SSRs were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

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…

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…

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Science.gov (United States)

Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W; Taylor, William; Corbett-Detig, Russell B; Stevens, Kristian A; Langley, Charles H; Pool, John E

2015-04-01

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets. Copyright © 2015 by the Genetics Society of America.

Cereal based functional food of Indian subcontinent: a review.

Science.gov (United States)

Das, Arpita; Raychaudhuri, Utpal; Chakraborty, Runu

2012-12-01

Due to constant health awareness and readily available information on usefulness of different diet and their direct link with health, the demand of functional food is increasing day by day. The concept of functional foods includes foods or food ingredients that exert a beneficial effect on host health and/or reduce the risk of chronic disease beyond basic nutritional functions. Increasing awareness of consumer health and interest in functional foods to achieve a healthy lifestyle has resulted in the need for food products with versatile health-benefiting properties. Cereal- and cereal component-based food products offer opportunities to include probiotics, prebiotics, and fibers in the human diet. Various growth studies using probiotic Lactic acid bacteria on cereal-based substrates and utilization of whole grain or components as high-fiber foods in developing novel food products lend support to the idea that cereal-based media may well be good probiotic carriers. It is essential that science and traditional knowledge should go together to find mutually beneficial results. In the Indian subcontinent, making use of fermented food and beverages using local food crops and other biological resources are very common. But the nature of the products and the base material vary from region to region.

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

Science.gov (United States)

Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

2015-12-01

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution.

Science.gov (United States)

Goron, Travis L; Raizada, Manish N

2015-01-01

Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed "orphan cereals." Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.

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. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Investigating Gene Function in Cereal Rust Fungi by Plant-Mediated Virus-Induced Gene Silencing.

Science.gov (United States)

Panwar, Vinay; Bakkeren, Guus

2017-01-01

Cereal rust fungi are destructive pathogens, threatening grain production worldwide. Targeted breeding for resistance utilizing host resistance genes has been effective. However, breakdown of resistance occurs frequently and continued efforts are needed to understand how these fungi overcome resistance and to expand the range of available resistance genes. Whole genome sequencing, transcriptomic and proteomic studies followed by genome-wide computational and comparative analyses have identified large repertoire of genes in rust fungi among which are candidates predicted to code for pathogenicity and virulence factors. Some of these genes represent defence triggering avirulence effectors. However, functions of most genes still needs to be assessed to understand the biology of these obligate biotrophic pathogens. Since genetic manipulations such as gene deletion and genetic transformation are not yet feasible in rust fungi, performing functional gene studies is challenging. Recently, Host-induced gene silencing (HIGS) has emerged as a useful tool to characterize gene function in rust fungi while infecting and growing in host plants. We utilized Barley stripe mosaic virus-mediated virus induced gene silencing (BSMV-VIGS) to induce HIGS of candidate rust fungal genes in the wheat host to determine their role in plant-fungal interactions. Here, we describe the methods for using BSMV-VIGS in wheat for functional genomics study in cereal rust fungi.

Genomic resources for multiple species in the Drosophila ananassae species group.

Science.gov (United States)

Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

2013-01-01

The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa.

Genomics and bioinformatics resources for translational science in Rosaceae.

Science.gov (United States)

Jung, Sook; Main, Dorrie

2014-01-01

Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

Enhancing faba bean (Vicia faba L.) genome resources.

Science.gov (United States)

Cooper, James W; Wilson, Michael H; Derks, Martijn F L; Smit, Sandra; Kunert, Karl J; Cullis, Christopher; Foyer, Christine H

2017-04-01

Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly. Genomic reads were assembled de novo into contigs with a size range of 50-5000 bp. Over 85% of sequences did not align to known genes, of which ~10% could be aligned to known repetitive genetic elements. Over 26 000 of the reference transcriptome unigenes could be aligned to DNA-sequencing (DNA-seq) reads with high confidence. Moreover, this comparison identified 56 668 potential splice points in all identified unigenes. Sequence length data were extended at 461 putative loci through alignment of DNA-seq contigs to full-length, publicly available linkage marker sequences. Reads also yielded coverages of 3466× and 650× for the chloroplast and mitochondrial genomes, respectively. Inter- and intraspecies organelle genome comparisons established core legume organelle gene sets, and revealed polymorphic regions of faba bean organelle genomes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

The impact of domestication and crop improvement on arbuscular mycorrhizal symbiosis in cereals: insights from genetics and genomics.

Science.gov (United States)

Sawers, Ruairidh J H; Ramírez-Flores, M Rosario; Olalde-Portugal, Víctor; Paszkowski, Uta

2018-04-15

Contents Summary I. Introduction II. Recruitment of plant metabolites and hormones as signals in AM symbiosis III. Phytohormones are regulators of AM symbiosis and targets of plant breeding IV. Variations in host response to AM symbiosis V. Outlook Acknowledgements References SUMMARY: Cereals (rice, maize, wheat, sorghum and the millets) provide over 50% of the world's caloric intake, a value that rises to > 80% in developing countries. Since domestication, cereals have been under artificial selection, largely directed towards higher yield. Throughout this process, cereals have maintained their capacity to interact with arbuscular mycorrhizal (AM) fungi, beneficial symbionts that associate with the roots of most terrestrial plants. It has been hypothesized that the shift from the wild to cultivation, and above all the last c. 50 years of intensive breeding for high-input farming systems, has reduced the capacity of the major cereal crops to gain full benefit from AM interactions. Recent studies have shed further light on the molecular basis of establishment and functioning of AM symbiosis in cereals, providing insight into where the breeding process might have had an impact. Classic phytohormones, targets of artificial selection during the generation of Green Revolution semi-dwarf varieties, have emerged as important regulators of AM symbiosis. Although there is still much to be learnt about the mechanistic basis of variation in symbiotic outcome, these advances are providing an insight into the role of arbuscular mycorrhiza in agronomic systems. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

Directory of Open Access Journals (Sweden)

Travis Luc Goron

2015-03-01

Full Text Available Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana, foxtail millet (Setaria italica, kodo millet (Paspalum scrobiculatum, proso millet (Panicum miliaceum, barnyard millet (Echinochloa spp., and little millet (Panicum sumatrense. Local farmers value the small millets for their nutritional and health, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed orphan cereals. Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers (e.g. nutritional quality which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.

A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.

Science.gov (United States)

Yu, Jun; Wong, Gane Ka-Shu; Liu, Siqi; Wang, Jian; Yang, Huanming

2007-06-29

In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not simply a sequencing project targeted to a single rice (Oryza sativa L.) genome, but a full-swing research effort with an ultimate goal of providing inclusive basic genomic information and molecular tools not only to understand biology of the rice, both as an important crop species and a model organism of cereals, but also to focus on a popular superhybrid rice landrace, LYP9. We have completed the first phase of SRGP and provide the rice research community with a finished genome sequence of an indica variety, 93-11 (the paternal cultivar of LYP9), together with ample data on subspecific (between subspecies) polymorphisms, transcriptomes and proteomes, useful for within-species comparative studies. In the second phase, we have acquired the genome sequence of the maternal cultivar, PA64S, together with the detailed catalogues of genes uniquely expressed in the parental cultivars and the hybrid as well as allele-specific markers that distinguish parental alleles. Although SRGP in China is not an open-ended research programme, it has been designed to pave a way for future plant genomics research and application, such as to interrogate fundamentals of plant biology, including genome duplication, polyploidy and hybrid vigour, as well as to provide genetic tools for crop breeding and to carry along a social burden-leading a fight against the world's hunger. It began with genomics, the newly developed and industry-scale research field, and from the world's most populous country. In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops.

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

Science.gov (United States)

Dwivedi, Sangam L.; Scheben, Armin; Edwards, David; Spillane, Charles; Ortiz, Rodomiro

2017-01-01

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

Directory of Open Access Journals (Sweden)

Sangam L. Dwivedi

2017-08-01

Full Text Available There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection

Long-lasting ergot lipids as new biomarkers for assessing the presence of cereals and cereal products in archaeological vessels.

Science.gov (United States)

Lucejko, Jeannette J; La Nasa, Jacopo; Porta, Francesca; Vanzetti, Alessandro; Tanda, Giuseppa; Mangiaracina, Claudio Filippo; Corretti, Alessandro; Colombini, Maria Perla; Ribechini, Erika

2018-03-02

Cereals were very important in ancient diets, however evidence from archaeological sites of the vessels used for processing or storing cereals is comparatively rare. Micro-organisms, as well as chemical-physical effects can easily degrade cereals during the burial period. This can lead to a complete cereal decay and to serious difficulties in estimating the intensity of use of the cereals by ancient populations. Here, we present a novel biomarker approach entailing the detection of secondary lipid metabolites produced by ergot fungi (genus Claviceps), which are common cereal pests. The aim was to identify the original presence of Gramineae and to indirectly establish if vessels were used for cereal storage/processing. The fatty acid and TAG-estolide profiles of the remains from more than 30 archaeological vessels were investigated by gas chromatography/mass spectrometry (GC/MS) and high performance liquid chromatography/high resolution mass spectrometry (HPLC/ESI-Q-ToF). The detection of lipids derived from ergot in archaeological and historic contexts rests on its complex chemistry, providing a unique and relatively recalcitrant chemical signature for cereals. This research demonstrated that the combination of our innovative biomarker approach along with environmental and archaeological evidence can provide unprecedented insights into the incidence of cereals and related processing activities in ancient societies.

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 .

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

Science.gov (United States)

Bruford, Michael W.; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J.; Amaral, Andreia J.; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F.; Hall, Stephen J. G.; Hanotte, Olivier; Hassan, Faiz-ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A.; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L.; Pompanon, François; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Štambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michèle; Wegmann, Daniel; Zhan, Xiangjiang

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 data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are

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

Science.gov (United States)

Bruford, Michael W; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J; Amaral, Andreia J; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F; Hall, Stephen J G; Hanotte, Olivier; Hassan, Faiz-Ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L; Pompanon, François; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Štambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michèle; Wegmann, Daniel; Zhan, Xiangjiang

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 data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are

Starter cultures for cereal based foods.

Science.gov (United States)

Brandt, Markus J

2014-02-01

Fermented cereals play a significant role in human nutrition in all parts of the world where cereals grow. These fermentations are started spontaneously or there have been traditional techniques developed in order to keep starter cultures for these processes alive. With the growing impact of industrial microbiology during 20th century this traditional starter culture propagation was replaced often, especially in the dairy industry, by the use of pure, frozen or freeze-dried cultures grown on microbial media. In contrast to the production of ethanol from cereals, in sourdough a pasteurization step before inoculation is avoided due to gelatinization of starch and inactivation of endogenous enzymes. Therefore cultures must be competitive to the relatively high microbial load of the cereal raw materials and well adapted to the specific ecology determined by the kind of cereal and the process conditions. Less adapted cultures could be used, but then the process of back-slopping of cultures is limited. Although cereal fermentations take the biggest volume among fermented foods, only for sourdoughs commercial cultures are available. Copyright © 2013 Elsevier Ltd. All rights reserved.

New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits

Directory of Open Access Journals (Sweden)

Feltus Frank A

2011-07-01

Full Text Available Abstract Background Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps for switchgrass will accelerate mapping of value added traits useful to breeding programs and to isolate important target genes using map based cloning. The reported polyploidy series in switchgrass ranges from diploid (2X = 18 to duodecaploid (12X = 108. Like in other large, repeat-rich plant genomes, this genomic complexity will hinder whole genome sequencing efforts. An extensive physical map providing enough information to resolve the homoeologous genomes would provide the necessary framework for accurate assembly of the switchgrass genome. Results A switchgrass BAC library constructed by partial digestion of nuclear DNA with EcoRI contains 147,456 clones covering the effective genome approximately 10 times based on a genome size of 3.2 Gigabases (~1.6 Gb effective. Restriction digestion and PFGE analysis of 234 randomly chosen BACs indicated that 95% of the clones contained inserts, ranging from 60 to 180 kb with an average of 120 kb. Comparative sequence analysis of two homoeologous genomic regions harboring orthologs of the rice OsBRI1 locus, a low-copy gene encoding a putative protein kinase and associated with biomass, revealed that orthologous clones from homoeologous chromosomes can be unambiguously distinguished from each other and correctly assembled to respective fingerprint contigs. Thus, the data obtained not only provide genomic resources for further analysis of switchgrass genome, but also improve efforts for an accurate genome sequencing strategy. Conclusions The construction of the first switchgrass BAC library and comparative analysis of

Collection and hauling of cereal grain chaff

Energy Technology Data Exchange (ETDEWEB)

Reding, B.; Leduc, P. [Prairie Agricultural Machinery Institute, Humboldt, Saskatchewan (Canada); Stumborg, M. [Agriculture Canada, Ottawa, Ontario (Canada)

1993-12-31

Cereal grain chaff has been identified by Energy Mines and Resources, Canada, and Agriculture Canada, as a suitable feedstock for ethanol production. Canada produces 13,300,000 t (14,600,000 ton) of cereal grain chaff annually; mainly in the prairie region. Work conducted at the Prairie Agricultural Machinery Institute (PAMI), Humboldt, Saskatchewan, has determined that the collection of chaff for centralized processing is a problem due to low bulk density in its natural state. This problem can be overcome by densification using either compression or size reduction. Either method will be economical in a chaff shed radius of 140 km (87 mi) when chaff is densified to 160 kg/m{sup 3} (10 lb/ft{sup 3}). The size reduction method of densification may be economical to hauling distances exceeding 166 km (103 mi), particularly if size reduction is a required part of ethanol processing. Further work is under way to develop the required equipment modifications to allow existing farm equipment to be used for this purpose.

[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

Dietary guidelines indicate that to get a proper nutrition is recommended eating 3 or more servings per day of whole grain. However, the recommendation is little known in the Spanish population, and almost the entire population doesn't fulfill it. Therefore, the aim of this review is to analyze the nutritional and health benefits associated with the consumption of whole grain cereals and the potential benefits related to the meeting of this guideline. Literature search regarding the topic. Whole grain cereals are rich in carbohydrates, fiber, vitamins and minerals, and its contribution to the average diet helps to achieve current recommended intakes and nutritional goals, so its consumption in the recommended amount supposes a nutritional benefit. Moreover, several studies indicate that increased consumption of whole grain cereal is associated with protection against various chronic degenerative diseases (cardiovascular, diabetes, cancer and metabolic syndrome), assisting in the maintenance of digestive health and body weight. These results may be due to the contribution of nutrients, fiber and phytochemicals of these foods, as well as the displacement of the diet of other products with a less desirable nutritional profile, taking into account the composition of the average Spanish diet. In fact, the consumption of whole grain cereals has been linked with a possible improvement in the intestinal microbiota and antioxidant protection. In spite of these advantages, cereal consumption is looked with suspicion by many individuals, especially those concerned about weight control and additional benefits associated to consumption of whole grain cereals are not known. Whole grain cereals should be daily consumed in amounts of 3 or more servings/day, to achieve the nutritional and health benefits described in numerous investigations. More outreach is needed to ensure that the guideline is known and it's applied. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA

GPSR: A Resource for Genomics Proteomics and Systems Biology

Indian Academy of Sciences (India)

First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. Small programs as building unit. Why PERL? Why not BioPerl? Why not PERL modules? Advantage of independent programs. Language independent; Can be run independently.

Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum

NARCIS (Netherlands)

Schmidt, R.L.; Durling, M.; de Jager, V.C.L.; Menezes, R. C.; Nordkvist, E.; Svatos, A.; Dubey, Mohit; Lauterbach, L.; Dikschat, J.S.; Karlsson, M.; Garbeva, P.V.

2018-01-01

Fusarium culmorum is one of the most important fungal plant pathogens that causes diseases on a wide diversity of cereal and non-cereal crops. We report herein for the first time the genome sequence of F. culmorum strain PV and its associated secondary metabolome that plays a role in the interaction

Stress, breakfast cereal consumption and cortisol.

Science.gov (United States)

Smith, A P

2002-04-01

Recent research has shown that regular consumption of breakfast cereal is associated with lower stress levels and reports of better physical and mental health. The present study examined this issue using an objective indicator of stress, salivary cortisol. The results showed that stress was associated with higher cortisol levels and daily consumption of breakfast cereal was associated with lower cortisol levels. Although it was not possible to rule out all the alternative explanations of the association between breakfast cereal consumption and cortisol, analyses did show that the effect could not be accounted for by general health or nutritional status. The effects of breakfast cereal consumption and stress were also independent, which shows that the effects of breakfast found here cannot be due to stress buffering. Further research manipulating the nutrient content of the breakfast cereal is now required to provide further information about the mechanisms underlying this effect.

Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

Energy Technology Data Exchange (ETDEWEB)

Reeve, Wayne [Murdoch University

2013-03-01

Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Carotenoids in staple cereals: Metabolism, regulation, and genetic manipulation

Directory of Open Access Journals (Sweden)

shengnan zhai

2016-08-01

Full Text Available 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 grain. 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 DXS (1-deoxyxylulose-5-phosphate synthase influencing isoprenoid precursor supply, PSY (phytoene synthase, LCYB (β-cyclase and LCYE (ε-cyclase controlling biosynthesis, HYDB (1-hydroxy-2-methyl-2-(E-butenyl 4-diphosphate reductase and CCDs (carotenoid cleavage dioxygenases responsible for degradation, and OR (orange conditioning sequestration sink; (2 pro-vitamin A-biofortified crops, such as rice and maize, were developed by either metabolic engineering or marker-assisted breeding; (3 QTLs for carotenoid content on chromosomes 3B, 7A, and 7B were consistently identified, eight carotenogenes including 23 loci were detected, and ten 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 benefitical in improving our precision in improving carotenoid contents. Genomic selection and gene editing are emerging as transformative technologies for vitamin A biofortification.

Global Information Resources on Rice for Research and Development

Directory of Open Access Journals (Sweden)

Shri RAM

2012-12-01

Full Text Available 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 iBIRA, is available online at ibiranet.in. The resources reviewed here are the excerpts from the resources integrated in iBIRA.

GPSR: A Resource for Genomics Proteomics and Systems Biology

Indian Academy of Sciences (India)

First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. A journey from simple computer programs to drug/vaccine informatics. Limitations of existing web services. History repeats (Web to Standalone); Graphics vs command mode. General purpose ...

Vegetable and cereal protein exploitation for fish feed

CSIR Research Space (South Africa)

Erasmus, C

2009-01-01

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

Technologies for enhancement of bioactive components and potential health benefits of cereal and cereal-based foods: Research advances and application challenges.

Science.gov (United States)

Saleh, Ahmed S M; Wang, Peng; Wang, Na; Yang, Shu; Xiao, Zhigang

2017-08-28

Cereal grains are a major source of human food and their production has steadily been increased during the last several decades to meet the demand of our increasing world population. The modernized society and the expansion of the cereal food industry created a need for highly efficient processing technologies, especially flour production. Earlier scientific research efforts have led to the invention of the modern steel roller mill, and the refined flour of wheat has become a basic component in most of cereal-based foods such as breads and pastries because of the unique functionality of wheat protein. On the other hand, epidemiological studies have found that consumption of whole cereal grains was health beneficial. The health benefit of whole cereal grain is attributed to the combined effects of micronutrients, phytochemicals, and dietary fibre, which are mainly located in the outer bran layer and the germ. However, the removal of bran and germ from cereal grains during polishing and milling results in refined flour and food products with lower bioactive compounds and dietary fibre contents than those from whole grain. Also, the level of bioactive compounds in cereal food is influenced by other food preparation procedures such as baking, cooking, extrusion, and puffing. Therefore, food scientists and nutritionists are searching for strategies and processing technologies to enhance the content and bioavailability of nutrients, bioactive compounds, and dietary fibre of cereal foods. The objective of this article was to review the research advances on technologies for the enhancement of bioactive compounds and dietary fibre contents of cereal and cereal-based foods. Bioactivities or biological effects of enhanced cereal and cereal-based foods are presented. Challenges facing the application of the proposed technologies in the food industry are also discussed.

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.

Genome resources for climate-resilient cowpea, an essential crop for food security.

Science.gov (United States)

Muñoz-Amatriaín, María; Mirebrahim, Hamid; Xu, Pei; Wanamaker, Steve I; Luo, MingCheng; Alhakami, Hind; Alpert, Matthew; Atokple, Ibrahim; Batieno, Benoit J; Boukar, Ousmane; Bozdag, Serdar; Cisse, Ndiaga; Drabo, Issa; Ehlers, Jeffrey D; Farmer, Andrew; Fatokun, Christian; Gu, Yong Q; Guo, Yi-Ning; Huynh, Bao-Lam; Jackson, Scott A; Kusi, Francis; Lawley, Cynthia T; Lucas, Mitchell R; Ma, Yaqin; Timko, Michael P; Wu, Jiajie; You, Frank; Barkley, Noelle A; Roberts, Philip A; Lonardi, Stefano; Close, Timothy J

2017-03-01

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

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.

GPSR: A Resource for Genomics Proteomics and Systems Biology

Indian Academy of Sciences (India)

GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

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,

Ukrainian cereals and oilseeds trade

Directory of Open Access Journals (Sweden)

Б. В. Духницький

2016-07-01

Full Text Available Purpose. To analyze peculiarities of Ukrainian cereals and oilseeds trade, the situation on the world market, and determine future prospects of its development. Methods. Analysis and synthesis, comparative evaluation, graphic procedure. Results. The role and place of Ukraine in a total grain supply to the world market was determined. Ukraine is a world’s top ten grain producer. Among domestic agricultural products, cereals, oilseeds and sunflower oil are in the highest demand in the world. In recent years, our state has reinforced its status as one of the leading exporters of cereals. The commodity pattern of cereals and oilseeds export was analyzed with specifying most in-demand positions and the main countries purchasing these pro­ducts. According to the results of 2015, Ukraine obtained the highest foreign currency revenue from export of corn, wheat and barley (in grain structure including soybeans and rapeseed (among oil crops. Key domestic and multinational operators are the main exporters of cereals and oilseeds in Ukraine and still hold their leading position. It was found a significant excess of import price of seeds as compared with export price of crops grown in Ukraine. Assortment of maize and sunflower seeds offered by major companies-producers in Ukraine was studied. Main trends of the world grain market development are considered. Conclusions. It was established that Ukraine is one of the major exporters of cereals and oilseeds. However, volatility of their prices significantly affects the export revenue that was decreasing even with increasing export quantities in kind. The dependence of domestic grain industry development on high-quality imported seed of maize and sunflower hybrids was recorded. It is expected that in the years to come Ukraine will maintain its strong positions in the world’s grain market.

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

OpenAIRE

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

Breakfast Cereals: The Extreme Food Industry

OpenAIRE

John M. Connor

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...

Updates to the Cool Season Food Legume Genome Database: Resources for pea, lentil, faba bean and chickpea genetics, genomics and breeding

Science.gov (United States)

The Cool Season Food Legume Genome database (CSFL, www.coolseasonfoodlegume.org) is an online resource for genomics, genetics, and breeding research for chickpea, lentil,pea, and faba bean. The user-friendly and curated website allows for all publicly available map,marker,trait, gene,transcript, ger...

Combining genetical genomics and bulked segregant analysis differential expression: an approach to gene localization

NARCIS (Netherlands)

Chen, Xinwei; Hedley, P.E.; Morris, J.; Liu, Hui; Niks, R.E.; Waugh, R.

2011-01-01

Positional gene isolation in unsequenced species generally requires either a reference genome sequence or an inference of gene content based on conservation of synteny with a genomic model. In the large unsequenced genomes of the Triticeae cereals the latter, i.e. conservation of synteny with the

Genomic resources in mungbean for future breeding programs

Directory of Open Access Journals (Sweden)

Sue K Kim

2015-08-01

Full Text Available Among the legume family, mungbean (Vigna radiata has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement.

Radiation disinfestation of stored cereals

International Nuclear Information System (INIS)

Boisseau, P.

1988-01-01

Post-harvest grain losses range world-wide between 5 and 10 percent and even 40 percent in some tropical areas where environmental conditions are favourable to cereal degradation. The grain losses during storage are of various origins: insects, microorganisms, rodents, birds. Their consequences on human health and cereal processing are of quantitative and qualitative nature [fr

The cereal starch endosperm development and its relationship with other endosperm tissues and embryo.

Science.gov (United States)

Zheng, Yankun; Wang, Zhong

2015-01-01

The cereal starch endosperm is the central part of endosperm, and it is rich in starch and protein which are the important resources for human food. The starch and protein are separately accumulated in starch granules and protein bodies. Content and configuration of starch granules and protein bodies affect the quality of the starch endosperm. The development of starch endosperm is mediated by genes, enzymes, and hormones, and it also has a close relationship with other endosperm tissues and embryo. This paper reviews the latest investigations on the starch endosperm and will provide some useful information for the future researches on the development of cereal endosperm.

Cereal fungal infection, mycotoxins, and lactic acid bacteria mediated bioprotection: from crop farming to cereal products.

Science.gov (United States)

Oliveira, Pedro M; Zannini, Emanuele; Arendt, Elke K

2014-02-01

Lactic acid bacteria (LAB) metabolites are a reliable alternative for reducing fungal infections pre-/post-harvest with additional advantages for cereal-base products which convene the food market's trend. Grain industrial use is in expansion owing to its applicability in generating functional food. The food market is directed towards functional natural food with clear health benefits for the consumer in detriment to chemical additives. The food market chain is becoming broader and more complex, which presents an ever-growing fungal threat. Toxigenic and spoilage fungi are responsible for numerous diseases and economic losses. Cereal infections may occur in the field or post-processing, along the food chain. Consequently, the investigation of LAB metabolites with antifungal activity has gained prominence in the scientific research community. LAB bioprotection retards the development of fungal diseases in the field and inhibit pathogens and spoilage fungi in food products. In addition to the health safety improvement, LAB metabolites also enhance shelf-life, organoleptic and texture qualities of cereal-base foods. This review presents an overview of the fungal impact through the cereal food chain leading to investigation on LAB antifungal compounds. Applicability of LAB in plant protection and cereal industry is discussed. Specific case studies include Fusarium head blight, malting and baking. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cereals for the semi-arid tropics

International Nuclear Information System (INIS)

De Wet, J.M.J.

1989-01-01

The region of semi-arid tropics is the most famine prone area of the world. This region with nearly one billion people extends across some 20 million square kilometres. Major domesticated cereals adapted to semi-arid regions are sorghum (Sorghum bicolor (L.) Moench), foxtail millet (Setaria italica (L.) P. Beauv.) and pearl millet (Pennisetum glaucum (L.) R. Br.). Several minor cereals are grown as speciality crops, or harvested in the wild in times of severe drought and scarcity. Important in the African Sahel are the fonios Digitaria iburua Stapf, D. exilis (Kapist) Stapf and Brachiaria deflexa (Schumach). C.E. Hubbard. These species are aggressive colonizers and are commonly encouraged as weeds in cultivated fields. Sown genotypes differ from their close wild relatives primarily in the lack of efficient natural seed dispersal. The fonios lend themselves to rapid domestication. Several wild cereals extend well beyond the limits of agriculture into the Sahara. Commonly harvested are the perennial Stipagrostis pungens and Panicum turgidum, and the annual Cenchrus biflorus (kram-kram). Kram-kram yields well under extreme heat and drought stress, and holds promise as a domesticated cereal. Sauwi millet (Panicum sonorum) is promising cereal in arid northwestern Mexico. (author). 31 refs

210Pb and 210Po in Finnish cereals

International Nuclear Information System (INIS)

Turtiainen, Tuukka; Kostiainen, Eila; Hallikainen, Anja

2011-01-01

A survey was carried out on the activity concentrations of 210 Pb and 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 210 Pb/ 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 -1 , respectively. Combined with the consumption rates of the products, we assess that the mean effective doses from 210 Pb and 210 Po in cereal products for the adult male and female population are 22 and 17 μSv per year, respectively.

Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse.

Science.gov (United States)

Eppig, Janan T

2017-07-01

The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided. © The Author 2017. Published by Oxford University Press.

Perancangan Interior Nestlé's Cereal World Di Surabaya

OpenAIRE

Mariana Wibowo, Linda Gunawan

2014-01-01

Nestlé's Cereal World is a new facility in foodservice industry, which people can explore and obtain a new experience about cereal through 4 main facilities: attraction, discover, dining, and shopping. Nestlé's Cereal World design will use Nestlé's interior branding, which the tangible and intangible design will represent the Nestlé's Cereal identity.

Increased plasma homocyst(e)ine after withdrawal of ready-to-eat breakfast cereal from the diet: prevention by breakfast cereal providing 200 microg folic acid.

Science.gov (United States)

Malinow, M R; Duell, P B; Irvin-Jones, A; Upson, B M; Graf, E E

2000-08-01

We tested the hypothesis that cessation of habitual ingestion of breakfast cereals would be associated with elevated plasma homocyst(e)ine concentrations. We anticipated that those subjects who reported consuming breakfast cereals containing 100 to 400 ,microg of folic acid per serving before entering the study would achieve higher plasma homocyst(e)ine concentrations if, in addition to their regular diet, they began ingesting a daily serving of breakfast cereal that contained less than 10 microg of folic acid per serving. Seventy-nine subjects consumed a daily serving of breakfast cereal containing either ine elevation. Breakfast cereal containing 200 microg folic acid per day was sufficient to maintain the homocyst(e)ine lowering effects of commercial cereals. Habitual consumption of commercially available fortified breakfast cereals, usually containing 100 to 400 microg folic acid per serving, had significant homocyst(e)ine lowering effects as shown by the homocyst(e)ine increase after cessation of habitual intake of commercial breakfast cereal. Substitution of breakfast cereal containing only 200 microg folic acid per day was sufficient to maintain the homocyst(e)inelowering effects of commercial cereals.

Formation of the texture of fermented milk and cereal product by varying the particle size distribution of cereal compositions

Directory of Open Access Journals (Sweden)

Pas'ko O. V.

2016-09-01

Full Text Available Combining animal and plant components is a promising direction of creating specialized foods of high biological and nutritional value. In this regard, research aimed at developing a fermented product technology based on combination of raw milk and grain products is relevant. In researches a set of generally accepted standard methods including physical-chemical, microbiological, biochemical, rheological, and mathematical methods of statistical processing of research results and development of mathematical models has been applied. The paper presents the results of research aimed at developing the technology of fermented milk – cereal product. In the first phase of research to substantiate product composition the systematic approach has been applied considering components of the product, changes of their status and properties as the current biotechnological systems (BPS. Selection of the grains' optimum ratio in the composition has been carried out on the basis of a set of indicators: the chemical composition and energy value, the content of B vitamins and dietary fibers, the indicator of biological value, organoleptic characteristics. Analysis of the combined results allows choose cereal flakes composition ratio of 1 : 1 : 1 (Oatmeal : Barley : Rye for further studies. As the main source of carbohydrate honey is used, it also improves the organoleptic properties of the product. Nutritional supplement glycine is used as a modifier of taste and smell. It has been found that introduction of glycine at 0.1 % in the BPS "milk – cereal composition" naturally decreases the intensity of taste and smell of cereal composition. The effect of particle size distribution of cereal composition on properties of the biotechnological system of milky cereal product has been established as well. For technology of the developed product the fraction selected cereal composition (Oatmeal : Barley : Rye as a 1 : 1 : 1 with a particle size of 670–1 000 microns has

Vitamin B2 (riboflavin content in cereal products

Directory of Open Access Journals (Sweden)

Soňa Škrovánková

2010-01-01

Full Text Available Vitamin B2 (riboflavin is a water-soluble essential vitamin. Nowadays an increased risk for riboflavin deficiency may be seen in people on special diets (diabetes mellitus, smokers or heavy alcohol drinkers. In the Czech diet the main sources of the vitamin intake are milk and dairy products followed by cereals and meat. Cereals are good source of this vitamin as it is widely and regularly consumed in different forms. Analyses of the vitamin B2 content in different types of cereal products (flours, breads, pastries, breakfast cereals, cooked pasta of Czech origin using HPLC with reversed phase and UV detection were done. The vitamin B2 content of chosen cereal products decreased in this progression: enriched wholemeal breakfast cereals (the best source of the vitamin, enriched wheat flours, breads – rye and wholemeal wheat breads, whole wheat and spelt flours, wheat bread, cooked whole wheat and rye spaghetti, wheat and multigrain pastries and finally scoured wheat flours.

210Pb and 210Po in Finnish cereals.

Science.gov (United States)

Turtiainen, Tuukka; Kostiainen, Eila; Hallikainen, Anja

2011-05-01

A survey was carried out on the activity concentrations of (210)Pb and (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 (210)Pb/(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(-1), respectively. Combined with the consumption rates of the products, we assess that the mean effective doses from (210)Pb and (210)Po in cereal products for the adult male and female population are 22 and 17 μSv per year, respectively. Copyright © 2010 Elsevier Ltd. All rights reserved.

Human Ageing Genomic Resources: new and updated databases

Science.gov (United States)

Tacutu, Robi; Thornton, Daniel; Johnson, Emily; Budovsky, Arie; Barardo, Diogo; Craig, Thomas; Diana, Eugene; Lehmann, Gilad; Toren, Dmitri; Wang, Jingwei; Fraifeld, Vadim E

2018-01-01

Abstract In spite of a growing body of research and data, human ageing remains a poorly understood process. Over 10 years ago we developed the Human Ageing Genomic Resources (HAGR), a collection of databases and tools for studying the biology and genetics of ageing. Here, we present HAGR’s main functionalities, highlighting new additions and improvements. HAGR consists of six core databases: (i) the GenAge database of ageing-related genes, in turn composed of a dataset of >300 human ageing-related genes and a dataset with >2000 genes associated with ageing or longevity in model organisms; (ii) the AnAge database of animal ageing and longevity, featuring >4000 species; (iii) the GenDR database with >200 genes associated with the life-extending effects of dietary restriction; (iv) the LongevityMap database of human genetic association studies of longevity with >500 entries; (v) the DrugAge database with >400 ageing or longevity-associated drugs or compounds; (vi) the CellAge database with >200 genes associated with cell senescence. All our databases are manually curated by experts and regularly updated to ensure a high quality data. Cross-links across our databases and to external resources help researchers locate and integrate relevant information. HAGR is freely available online (http://genomics.senescence.info/). PMID:29121237

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

MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.

Science.gov (United States)

Iquebal, M A; Jaiswal, Sarika; Mahato, Ajay Kumar; Jayaswal, Pawan K; Angadi, U B; Kumar, Neeraj; Sharma, Nimisha; Singh, Anand K; Srivastav, Manish; Prakash, Jai; Singh, S K; Khan, Kasim; Mishra, Rupesh K; Rajan, Shailendra; Bajpai, Anju; Sandhya, B S; Nischita, Puttaraju; Ravishankar, K V; Dinesh, M R; Rai, Anil; Kumar, Dinesh; Sharma, Tilak R; Singh, Nagendra K

2017-11-02

Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.

Impacts of climate change and inter-annual variability on cereal crops in China from 1980 to 2008.

Science.gov (United States)

Zhang, Tianyi; Huang, Yao

2012-06-01

Negative climate impacts on crop yield increase pressures on food security in China. In this study, climatic impacts on cereal yields (rice, wheat and maize) were investigated by analyzing climate-yield relationships from 1980 to 2008. Results indicated that warming was significant, but trends in precipitation and solar radiation were not statistically significant in most of China. In general, maize is particularly sensitive to warming. However, increase in temperature was correlated with both lower and higher yield of rice and wheat, which is inconsistent with the current view that warming results in decline in yields. Of the three cereal crops, further analysis suggested that reduction in yields with higher temperature is accompanied by lower precipitation, which mainly occurred in northern parts of China, suggesting droughts reduced yield due to lack of water resources. Similarly, a positive correlation between temperature and yield can be alternatively explained by the effect of solar radiation, mainly in the southern part of China where water resources are abundant. Overall, our study suggests that it is inter-annual variations in precipitation and solar radiation that have driven change in cereal yields in China over the last three decades. Copyright © 2011 Society of Chemical Industry.

Competitiveness of organically grown cereals

Directory of Open Access Journals (Sweden)

Jaroslav Jánský

2007-01-01

Full Text Available The contribution is aimed at the assessment of recommended crop management practices of chosen cereals for organic farming. To increase competitiveness, these practices are modified depending on soil and climatic conditions, and on a way of production use. Furthermore, impacts of the recommended crop management practices on economics of growing chosen cereals are evaluated and compared with economic results obtained under conventional farming. It is assumed that achieved results will contribute to the increase in proportion of arable crops in the Czech Republic where organic production offer does not meet current demands.When evaluating results of growing individual cereal species in a selective set of organic farms, triticale, spelt and spring barley (in this ranking can be considered as profitable crops. Moreover, triticale and spelt have even higher gross margin under organic farming than under conventional farming (by 62 % in triticale. Oat brings losses, however, it is important for livestock production. Winter wheat seems to be also unprofitable since less grain is produced at lower imputs per hectare and only part of it is produced in quality “bio”, i.e. marketed for higher prices. Rye also brings losses under organic farming, particularly due to lower yields, similarly to the other mentioned cereals. Special cereal species that are still neglected in organic farming systems are of potential use. Durum wheat has vitreous kernels with a high content of quality gluten which is used for pasta production. It can be grown in the maize production area on fertile soils only.

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.

Using an online genome resource to identify myostatin variation in U.S. sheep

Science.gov (United States)

We created a public, searchable DNA sequence resource for sheep that contained approximately 14x whole genome sequence of 96 rams. The animals represent 10 popular U.S. breeds and share minimal pedigree relationships, making the resource suitable for viewing gene variants in the user-friendly Integ...

Ensembl Genomes 2016: more genomes, more complexity.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

2016-01-04

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Validation of rice genome sequence by optical mapping

Directory of Open Access Journals (Sweden)

Pape Louise

2007-08-01

Full Text Available Abstract Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project and TIGR (The Institute for Genomic Research genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of

A need for determination of arsenic species at low levels in cereal-based food and infant cereals. Validation of a method by IC-ICPMS.

Science.gov (United States)

Llorente-Mirandes, Toni; Calderón, Josep; Centrich, Francesc; Rubio, Roser; López-Sánchez, José Fermín

2014-03-15

The present study arose from the need to determine inorganic arsenic (iAs) at low levels in cereal-based food. Validated methods with a low limit of detection (LOD) are required to analyse these kinds of food. An analytical method for the determination of iAs, methylarsonic acid (MA) and dimethylarsinic acid (DMA) in cereal-based food and infant cereals is reported. The method was optimised and validated to achieve low LODs. Ion chromatography-inductively coupled plasma mass spectrometry (IC-ICPMS) was used for arsenic speciation. The main quality parameters were established. To expand the applicability of the method, different cereal products were analysed: bread, biscuits, breakfast cereals, wheat flour, corn snacks, pasta and infant cereals. The total and inorganic arsenic content of 29 cereal-based food samples ranged between 3.7-35.6 and 3.1-26.0 μg As kg(-1), respectively. The present method could be considered a valuable tool for assessing inorganic arsenic contents in cereal-based foods. Copyright © 2013 Elsevier Ltd. All rights reserved.

Aflatoxin contamination of locallyprocessed cereal-based ...

African Journals Online (AJOL)

Feeding children with cereal-based foods has potential to expose them to aflatoxins (AFs).This study was conducted to determine the occurrence and levels of aflatoxins (AFB1, AFB2, AFG1 and AFG2) in 64 commercial locally produced cereal-based complementary foods obtained from producers and popular markets in ...

Effect of date of termination of a winter cereal rye cover crop (Secale cereale) on corn seedling disease

Science.gov (United States)

Cover cropping is an expanding conservation practice that offers substantial benefits to soil protection, soil health, water quality, and potentially crop yields. Presently, winter cereals are the most widely used cover crops in the upper Midwest. However, winter cereal cover crops preceding corn, ...

A Reference Genome for US Rice

Science.gov (United States)

The development of reference genomes for rice has served as means for understanding the allelic diversity and genetic structure of a cereal grain that feeds half of the world. It has long been understood that Oryza sativa diverged into two major sub-populations Indica and Japonica, over 400 K years ...

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.

Science.gov (United States)

Richardson, Mark F; Sequeira, Fernando; Selechnik, Daniel; Carneiro, Miguel; Vallinoto, Marcelo; Reid, Jack G; West, Andrea J; Crossland, Michael R; Shine, Richard; Rollins, Lee A

2018-01-01

Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range. Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available. This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers. © The Authors 2017. Published by Oxford University Press.

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

Directory of Open Access Journals (Sweden)

Wenning Zheng

Full Text Available 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.

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.

Brachypodium distachyon. A New Model System for Functional Genomics in Grasses1

Science.gov (United States)

Draper, John; Mur, Luis A.J.; Jenkins, Glyn; Ghosh-Biswas, Gadab C.; Bablak, Pauline; Hasterok, Robert; Routledge, Andrew P.M.

2001-01-01

A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of “core pooid” genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n = 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals. PMID:11743099

Dietary fibers and associated phytochemicals in cereal

DEFF Research Database (Denmark)

Knudsen, Knud Erik Bach

2016-01-01

Epidemiological studies have linked whole-grain cereal consumption to a reduced risk of developing several chronic diseases – coronary heart disease, arteriosclerosis, type-2 diabetes and colonic and breast cancer. The underlying physiological mechanisms behind the protective effects of whole......-grains, however, are unclear but is most likely assigned to a concerted action of dietary fiber (DF) and a wide variety of phytochemicals. The DF fraction of cereals consists of non-starch polysaccharides (NSP), resistant starch, oligosaccharides (mostly fructans) and the non-carbohydrate polyphenolic ether...... lignin. The main NSP in cereals are arabinoxylan (AX), mixed linkages β(1-3; 1-4)-glucan (β-glucan) and cellulose, which vary significantly according to the cereal species but also between different tissues of the grains. Rye, triticale, wheat and corn are rich in AX, whereas barley and oats contain...

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. © 2016 WILEY PERIODICALS, INC.

The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species.

Science.gov (United States)

Gilchrist, Anthony Stuart; Shearman, Deborah C A; Frommer, Marianne; Raphael, Kathryn A; Deshpande, Nandan P; Wilkins, Marc R; Sherwin, William B; Sved, John A

2014-12-20

The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations. We produced a draft de novo genome assembly of Australia's major tephritid pest species, Bactrocera tryoni. The male genome (650-700 Mbp) includes approximately 150 Mb of interspersed repetitive DNA sequences and 60 Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions. This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA

Cereal production, high status and climate in Medieval Iceland

Science.gov (United States)

Erlendsson, Egill; Riddell, Scott

2017-04-01

At Hrísbrú (formerly the medieval Mosfell estate) in the Mosfell Valley, southwest Iceland, archaeologists have excavated a medieval skáli (hall) proposed to be the high status residence of a chieftain. This is indicated by the size of the skáli, artefacts (foreign goods), archaeofaunal (cattle/sheep bone) ratios and macrobotanical remains (cereal grain). The analysis of pollen from nearby natural contexts suggests that cereals were grown locally. Using multiple profile palynological approach, this paper examines if the apparent cereal production is representative of high status in the Icelandic context. First as a correlate by confirming that cereals were grown in association with the archaeological features characteristic of high status; secondly, as an indicator in its own right through comparison with other palynological datasets from inferred lower status farms. The presence or absence of cereal-type pollen (cf. barley) and other arable correlates was examined for each site. The results suggest that medieval cereal cultivation in the Mosfell Valley was confined to the landholding of the medieval Mosfell estate. This feature is seen as an attribute of the locale's greater status in relation to the other farms in Mosfell Valley. The abandonment of cereal cultivation at the Mosfell estate around AD 1200 is probably associated with interactions between changes in the nation's social power structure and how marginal cereal production in Iceland was (and is) in terms of climate.

DRDB: An Online Date Palm Genomic Resource Database

Directory of Open Access Journals (Sweden)

Zilong He

2017-11-01

comprehensive genomic resource database of date palm. It can serve as a bioinformatics platform for date palm genomics, genetics, and molecular breeding. DRDB is freely available at http://drdb.big.ac.cn/home.

Effects of serving high-sugar cereals on children's breakfast-eating behavior.

Science.gov (United States)

Harris, Jennifer L; Schwartz, Marlene B; Ustjanauskas, Amy; Ohri-Vachaspati, Punam; Brownell, Kelly D

2011-01-01

To test (1) whether children will consume low-sugar ready-to-eat (RTE) cereals and (2) the effects of serving high- versus low-sugar cereals on the consumption of cereal, refined sugar, fresh fruit, and milk. Using an experimental design, we randomly assigned children (n = 91) who were attending summer day camp to receive a breakfast that included either the choice of 1 of 3 high-sugar cereals (high-sugar condition) or low-sugar cereals (low-sugar condition), as well as low-fat milk, orange juice, bananas, strawberries, and sugar packets. Participants served themselves and completed a background questionnaire after eating. Researchers measured the amount and calories consumed of each food. In both conditions, children reported "liking" or "loving" the cereal they chose. Children in the low-sugar cereal condition consumed, on average, slightly more than 1 serving of cereal (35 g), whereas children in the high-sugar condition consumed significantly more (61 g) and almost twice the amount of refined sugar in total (24.4 vs 12.5 g). Milk and total calories consumed did not differ significantly between conditions, but children in the low-sugar condition were more likely to put fruit on their cereal (54% vs 8%) and consumed a greater portion of total calories from fresh fruit (20% vs 13%). Compared with serving low-sugar cereals, high-sugar cereals increase children's total sugar consumption and reduce the overall nutritional quality of their breakfast. Children will consume low-sugar cereals when offered, and they provide a superior breakfast option.

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

Nutritional quality and child-oriented marketing of breakfast cereals in Guatemala.

Science.gov (United States)

Soo, J; Letona, P; Chacon, V; Barnoya, J; Roberto, C A

2016-01-01

Food marketing has been implicated as an important driver of obesity. However, few studies have examined food marketing in low- and middle-income countries (LMICs). This study documents the prevalence of advertising on cereal boxes in Guatemala and examines associations between various marketing strategies and nutritional quality. One box from all available cereals was purchased from a supermarket located in an urban area in Guatemala City, Guatemala. A content analysis was performed to document child-oriented marketing practices, product claims and health-evoking images. The Nutrient Profile Model (NPM) was used to calculate an overall nutrition score for each cereal (the higher the score, the lower the nutritional quality). In all, 106 cereals were purchased, and half of the cereals featured child-oriented marketing (54, 50.9%). Cereals had a mean (±s.d.) of 5.10±2.83 product claims per cereal, and most cereals (102, 96.2%) contained health-evoking images. Child-oriented cereals had, on average, higher NPM scores (13.0±0.55 versus 7.90±0.74, Ptargeting children were generally of poor nutritional quality. Cereals displaying health claims were also not healthier than those without such claims. Our findings support the need for regulations restricting the use of child-oriented marketing and health claims for certain products.

DFAST and DAGA: web-based integrated genome annotation tools and resources.

Science.gov (United States)

Tanizawa, Yasuhiro; Fujisawa, Takatomo; Kaminuma, Eli; Nakamura, Yasukazu; Arita, Masanori

2016-01-01

Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus , obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii , whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.

Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).

Science.gov (United States)

Spriggs, Andrew; Henderson, Steven T; Hand, Melanie L; Johnson, Susan D; Taylor, Jennifer M; Koltunow, Anna

2018-02-09

Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata  v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. Access to this resource provided here is supported by raw and assembled data downloads.

Counties performance evaluation of cereal production in Albania

OpenAIRE

Silvana Mustafaj; Elfrida Dishmema; Albina Basholli; Brunilda Baraku

2017-01-01

Agriculture is one of the most important sectors of the Albanian economy. Agricultural production occupies for about 1/5 of the country's GDP. Agricultural production includes all realized production in all counties of the country. Cereal constitutes a significant part in agricultural production, which are grown all over the country. The main cereals cultivated in the country are wheat, maize, rye, barley and oats. The highest level of cereal production in Albania is reached in low and coasta...

Dynamics of Major Cereals Productivity in Nepal

Directory of Open Access Journals (Sweden)

Samaya Gairhe

2018-05-01

Full Text Available Cereal crops have played major roles in addressing food security issues in Nepal. In recent years there have been fluctuations in crop production and demands situations due to various reasons. Thus, the present study aims to analyze the dynamics of major cereals productivity in Nepal from 1995 to 2014. Focus group discussions were done in mid-hills and tarai of Nepal in 2015. Percentage change, compound growth rate, annual rate of change, coefficient of variation, instability index were calculated to analyze results. The result shows that the area, production and productivity of major cereals had an increasing trend over the study period. The major factors contributing on productivity increase in cereal crops were irrigation facilities, use of improved and hybrid seeds, chemical fertilizer and better technical knowhow among the farmers. For effective adoption of research outputs to improve the productivity emphasis should also be given on promotion of public private partnership (PPP in research and development.

Current and Future Technologies for Microbiological Decontamination of Cereal Grains.

Science.gov (United States)

Los, Agata; Ziuzina, Dana; Bourke, Paula

2018-06-01

Cereal grains are the most important staple foods for mankind worldwide. The constantly increasing annual production and yield is matched by demand for cereals, which is expected to increase drastically along with the global population growth. A critical food safety and quality issue is to minimize the microbiological contamination of grains as it affects cereals both quantitatively and qualitatively. Microorganisms present in cereals can affect the safety, quality, and functional properties of grains. Some molds have the potential to produce harmful mycotoxins and pose a serious health risk for consumers. Therefore, it is essential to reduce cereal grain contamination to the minimum to ensure safety both for human and animal consumption. Current production of cereals relies heavily on pesticides input, however, numerous harmful effects on human health and on the environment highlight the need for more sustainable pest management and agricultural methods. This review evaluates microbiological risks, as well as currently used and potential technologies for microbiological decontamination of cereal grains. © 2018 Institute of Food Technologists®.

Application of gamma-irradiation to cereals and stockfeeds

International Nuclear Information System (INIS)

Wootton, M.

1983-01-01

Gamma-radiation may be used on cereals and stockfeeds to control insect infestation and, at higher dose rates, microbiological problems such as mould growth, aflatoxin production, pathogens, rope producing bacteria and total plate count. Major problems arise only at relatively high dose levels and affect functionality of cereals in terms of germination, dough properties, starch behaviour and cake and noodle quality. Chemical and physical changes to starch have the greatest impact on the properties of cereals and their products as a consequence of gamma-radiation

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

Science.gov (United States)

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

2015-01-01

The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. © The Author(s) 2015. Published by Oxford University Press.

Detection genetic variability of secale cereale L. by scot markers

Directory of Open Access Journals (Sweden)

Lenka Petrovičová

2017-01-01

Full Text Available Rye (Secale cereale L. is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI, probability of identity (PI and polymorphic information content (PIC. The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b. Subscluster 2a included only genotype Valtické (CSK. In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars. Normal 0 21 false false false EN-GB X-NONE X-NONE

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

Science.gov (United States)

Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

2013-01-01

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest. PMID:23193269

The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species.

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Marc Tollis

Full Text Available Agassiz's desert tortoise (Gopherus agassizii is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1 that turtles are among the slowest-evolving genome-enabled reptiles, (2 amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3 fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

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....

From protein catalogues towards targeted proteomics approaches in cereal grains

DEFF Research Database (Denmark)

Finnie, Christine; Sultan, Abida; Grasser, Klaus D.

2011-01-01

Due to their importance for human nutrition, the protein content of cereal grains has been a subject of intense study for over a century and cereal grains were not surprisingly one of the earliest subjects for 2D-gel-based proteome analysis. Over the last two decades, countless cereal grain prote...

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

Science.gov (United States)

Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Lajus, Aurélie; Josso, Adrien; Mercier, Jonathan; Renaux, Alexandre; Rollin, Johan; Rouy, Zoe; Roche, David; Scarpelli, Claude; Médigue, Claudine

2017-01-04

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The healthfulness and prominence of sugar in child-targeted breakfast cereals in Canada.

Science.gov (United States)

Potvin Kent, Monique; Cameron, Cher; Philippe, Sarah

2017-09-01

The objective of this study was to compare the nutritional content and healthfulness of child-targeted and "not child-targeted" breakfast cereals and to assess the predominance of added sugar in these products. We collected data on the nutritional content of 262 unique breakfast cereals found in the five largest grocery store chains in Ottawa (Ontario) and Gatineau (Quebec). We noted the first five ingredients and the number of added sugars present in each cereal from the ingredients list. The various cereal brands were then classified as either "healthier" or "less healthy" using the UK Nutrient Profile Model. We assessed each cereal to determine if it was child-targeted or not, based on set criteria. Statistical comparisons were made between child and not child-targeted cereals. 19.8% of all breakfast cereals were child-targeted, and these were significantly lower in total and saturated fat. Child-targeted cereals were significantly higher in sodium and sugar and lower in fibre and protein, and were three times more likely to be classified as "less healthy" compared to not child-targeted cereals. No child-targeted cereals were sugar-free, and sugar was the second most common ingredient in 75% of cereals. Six breakfast cereal companies had child-targeted product lines that consisted entirely of "less healthy" cereals. There is a need for regulations that restrict food marketing to children and youth under the age of 17 on packaging to reduce their appeal to this age group. Children's breakfast cereals also need to be reformulated through government-set targets, or through regulation should compliance be deemed unacceptable.

Species of Heterodera cysts in cereal fields in Flanders.

Science.gov (United States)

Yilmaz, Zeliha Colak; Deeren, Anne-Marie; De Sutter, Nancy; Viaene, Nicole

2009-01-01

Heterodera is a genus of cyst-forming nematodes, including the cereal cysts which can provoke yield reductions in grain crops. As little is known about the occurrence of these cysts in Belgian grain fields, a survey was organized, starting in Flanders. Soil samples were taken from 50 fields where cereals are grown in rotation with mainly beet, potato and vegetables. Cysts were extracted from the 112 samples and 10 individuals per sample were identified up to species level by morphometrical and morphological observations. The beet cyst nematode, Heterodera schachtii, was found in 34 fields (56%) at infestation levels varying from 0.6 to 1322 cysts/kg soil. Other Heterodera species (e.g. H. trifolii, H. mani) were found in low numbers and sometimes in mixtures with H. schachtii, but no cereal cysts were detected. This survey confirms that beet cyst nematodes are a problem in Flanders. The few cereal cysts that might be present were perhaps not detected due to the few individuals that were identified. For this reason, molecular identification tools which allow fast and accurate identification of Heterodera species would be very useful. It could be interesting to find out why cereal cysts are suppressed in our regions and to expand the survey to the Walloon region where more cereals are grown.

East African governments' responses to high cereal prices

NARCIS (Netherlands)

Meijerink, G.W.; Roza, P.; Berkum, van S.

2009-01-01

This study analyses the responses of governments in four East African countries (Kenya, Tanzania, Uganda and Ethiopia) with respect to price formation and price transmission in the cereal sector. All four countries were confronted with high cereal prices in 2008. Government policies applied largely

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.

Life Cycle Assessment in the Cereal and Derived Products Sector

DEFF Research Database (Denmark)

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

2015-01-01

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......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...

Characterization of bioactive compounds from monascus purpureus fermented different cereal substrates

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Eva Ivanišová

2017-01-01

Full Text Available Solid-state fermenting of cereals by Monascus is interesting strategy to produce cereals with more beneficial components.  The objective of this study was to determine selected primary and secondary metabolites in cereals (rice, wheat, barley, sorghum, corn, buckwheat fermented by Monascus purpreus and subsequently compare amount of these compounds with control sample (cereals without Monascus. In fermented cereals was determined higher protein, fat, reducing sugars, crude fiber and ash content with compare to non-fermented cereals. The antioxidant activity measured by DPPH assay, ABTS assay as well as reducing power assay was also higher in fermented Monascus cereals with the best results in rice (3.09 ±0.02; 62.9 ±2.24; 43.19 ±2.07 mg TEAC per g of dry weight. Sample of fermented rice contained the highest level of total polyphenols (15.31 ±3.62 mg GAE per g of dry weight, total flavonoids (1.65 mg QE per g of dry weight and total phenolic acids (9.47 ±0.56 mg CAE per g of dry weight. In fermented cereals was also determined higher contact of reducing sugars (highest value in rice 246.97 ±7.96 mg GE per g, proteins (highest value in buckwheat 28.47 ±1.24%, ash (highest value in sorghum 2.74 ±0.08% and fat (highest value in corn 4.89 ±0.03% with compare to non-fermented samples. Results of crude fiber content of both - fermented and non-fermented cereals were balanced with similar values. Results of this study shown that Monascus purpureus fermented cereal substrates might be a potential sources of several bioactive compounds in food products.

Less healthy breakfast cereals are promoted more frequently in large supermarket chains in Canada

Directory of Open Access Journals (Sweden)

Monique Potvin Kent

2017-11-01

Full Text Available Abstract Background The majority of food expenditures are made in supermarkets and this environment influences our purchasing and food intake. Breakfast cereals are frequently marketed as healthy food choices. The objective of this study was to examine the frequency of in–store promotions for cold breakfast cereals in Canadian supermarkets and to determine whether healthier or less healthy breakfast cereals are promoted more frequently. Methods Data was collected once per week over a four-week period from a convenience sample of the five largest Canadian supermarkets in the Ottawa/Gatineau area. Data collection included the number of shelf facings, promotional displays, and the cost of cereals/100 g. The UK Nutrient Profiling Model was used to determine the healthfulness of each breakfast cereal. Results 29.8% (n = 67 of the 225 unique cereals were classified as healthier and 70.2% (n = 158 were classified as less healthy. Less healthy cereals were displayed at eye level, in the profitable middle shelves, 2.9 times more frequently than healthier cereals. There were 5.3 times more breakfast cereal shelf facings, 4.2 more end cap displays, 1.7 more mid-aisle displays and 3.3 more special pricing signage for less healthy cereals compared to healthier cereals. Less healthy cereals had a significantly higher average total number of shelf facings compared to healthier cereals (t = −4.28 (280.8, p < .001. Conclusions Breakfast cereal manufacturers need to consider reformulation of their breakfast cereals to improve their healthfulness and supermarkets need to increase the marketing of healthy breakfast cereals within their stores.

Effect of infant cereals on zinc and copper absorption during weaning

International Nuclear Information System (INIS)

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

1987-01-01

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

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

Science.gov (United States)

2010-07-01

... produce various breakfast cereals normally available for human consumption without cooking. ...-to-eat cereal subcategory. 406.90 Section 406.90 Protection of Environment ENVIRONMENTAL PROTECTION... Cereal Subcategory § 406.90 Applicability; description of the ready-to-eat cereal subcategory. The...

Less healthy breakfast cereals are promoted more frequently in large supermarket chains in Canada.

Science.gov (United States)

Potvin Kent, Monique; Rudnicki, Erika; Usher, Crystal

2017-11-13

The majority of food expenditures are made in supermarkets and this environment influences our purchasing and food intake. Breakfast cereals are frequently marketed as healthy food choices. The objective of this study was to examine the frequency of in-store promotions for cold breakfast cereals in Canadian supermarkets and to determine whether healthier or less healthy breakfast cereals are promoted more frequently. Data was collected once per week over a four-week period from a convenience sample of the five largest Canadian supermarkets in the Ottawa/Gatineau area. Data collection included the number of shelf facings, promotional displays, and the cost of cereals/100 g. The UK Nutrient Profiling Model was used to determine the healthfulness of each breakfast cereal. 29.8% (n = 67) of the 225 unique cereals were classified as healthier and 70.2% (n = 158) were classified as less healthy. Less healthy cereals were displayed at eye level, in the profitable middle shelves, 2.9 times more frequently than healthier cereals. There were 5.3 times more breakfast cereal shelf facings, 4.2 more end cap displays, 1.7 more mid-aisle displays and 3.3 more special pricing signage for less healthy cereals compared to healthier cereals. Less healthy cereals had a significantly higher average total number of shelf facings compared to healthier cereals (t = -4.28 (280.8), p supermarkets need to increase the marketing of healthy breakfast cereals within their stores.

Phytase-mediated mineral solubilization from cereals underin vitrogastric conditions

DEFF Research Database (Denmark)

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

2016-01-01

that of the microbial phytases. No increases in soluble cadmium, lead or arsenic were observed with microbial phytase-catalyzed phytate dephosphorylation. CONCLUSION Microbial phytase treatment abated phytate chelation hence enhanced the release of iron and zinc from the phytate-rich cereals at the simulated gastric......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...

Cadmium contamination in cereal-based diets and diet ingredients

International Nuclear Information System (INIS)

Siitonen, P.H.; Thompson, H.C. Jr.

1990-01-01

Cereal-based diet and/or diet ingredient cadmium levels were determined by graphite furnace AAS. Cadmium contamination was 88.3 and 447 ppb in two cereal-based diets, 44.6 and 48.9 ppb in two purified diets, and ranged from less than 1.1 to 22,900 ppb in the ingredients of one cereal-based diet. The major source of cadmium contamination was attributed to the calcium supplement used for diet formulation. Comparative analyses of two purified diet samples and one cereal-based diet by the National Institute of Standards and Technology (NIST, formerly the National Bureau of Standards) and the National Center for Toxicological Research (NCTR) gave virtually identical results for Cd. A comparative study of Cd levels determined by flame and furnace AAS was also made by the NCTR and the NIST

Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.

Science.gov (United States)

Wang, Chao; Shi, Xue; Liu, Lin; Li, Haiyan; Ammiraju, Jetty S S; Kudrna, David A; Xiong, Wentao; Wang, Hao; Dai, Zhaozhao; Zheng, Yonglian; Lai, Jinsheng; Jin, Weiwei; Messing, Joachim; Bennetzen, Jeffrey L; Wing, Rod A; Luo, Meizhong

2013-11-01

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.

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

Directory of Open Access Journals (Sweden)

Zhang Qifa

2008-11-01

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

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.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

Directory of Open Access Journals (Sweden)

Wenning Zheng

2016-03-01

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

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

NARCIS (Netherlands)

Yuen, Ryan K C; Merico, Daniele; Bookman, Matt; Howe, Jennifer L.; Thiruvahindrapuram, Bhooma; Patel, Rohan V.; Whitney, Joe; Deflaux, Nicole; Bingham, Jonathan; Wang, Zhuozhi; Pellecchia, Giovanna; Buchanan, Janet A.; Walker, Susan; Marshall, Christian R.; Uddin, Mohammed; Zarrei, Mehdi; Deneault, Eric; D'Abate, Lia; Chan, Ada J S; Koyanagi, Stephanie; Paton, Tara; Pereira, Sergio L.; Hoang, Ny; Engchuan, Worrawat; Higginbotham, Edward J.; Ho, Karen; Lamoureux, Sylvia; Li, Weili; MacDonald, Jeffrey R.; Nalpathamkalam, Thomas; Sung, Wilson W L; Tsoi, Fiona J.; Wei, John; Xu, Lizhen; Tasse, Anne Marie; Kirby, Emily; Van Etten, William; Twigger, Simon; Roberts, Wendy; Drmic, Irene; Jilderda, Sanne; Modi, Bonnie Mackinnon; Kellam, Barbara; Szego, Michael; Cytrynbaum, Cheryl; Weksberg, Rosanna; Zwaigenbaum, Lonnie; Woodbury-Smith, Marc; Brian, Jessica; Senman, Lili; Iaboni, Alana; Doyle-Thomas, Krissy; Thompson, Ann; Chrysler, Christina; Leef, Jonathan; Savion-Lemieux, Tal; Smith, Isabel M.; Liu, Xudong; Nicolson, Rob; Seifer, Vicki; Fedele, Angie; Cook, Edwin H.; Dager, Stephen; Estes, Annette; Gallagher, Louise; Malow, Beth A.; Parr, Jeremy R.; Spence, Sarah J.; Vorstman, Jacob; Frey, Brendan J.; Robinson, James T.; Strug, Lisa J.; Fernandez, Bridget A.; Elsabbagh, Mayada; Carter, Melissa T.; Hallmayer, Joachim; Knoppers, Bartha M.; Anagnostou, Evdokia; Szatmari, Peter; Ring, Robert H.; Glazer, David; Pletcher, Mathew T.; Scherer, Stephen W.

2017-01-01

We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information,

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

NARCIS (Netherlands)

Bruford, M.W.; Ginja, Catarina; Hoffmann, Irene; Megens, Hendrik Jan

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).

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

NARCIS (Netherlands)

Bruford, Michael W; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J; Amaral, Andreia J; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F; Hall, Stephen J G; Hanotte, Olivier; Hassan, Faiz-Ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L; Pompanon, François; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Štambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michèle; Wegmann, Daniel; Zhan, Xiangjiang

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,

Hyperphosphorylation of cereal starch

DEFF Research Database (Denmark)

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

2011-01-01

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...... 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......-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...

Resource allocation for maximizing prediction accuracy and genetic gain of genomic selection in plant breeding: a simulation experiment.

Science.gov (United States)

Lorenz, Aaron J

2013-03-01

Allocating resources between population size and replication affects both genetic gain through phenotypic selection and quantitative trait loci detection power and effect estimation accuracy for marker-assisted selection (MAS). It is well known that because alleles are replicated across individuals in quantitative trait loci mapping and MAS, more resources should be allocated to increasing population size compared with phenotypic selection. Genomic selection is a form of MAS using all marker information simultaneously to predict individual genetic values for complex traits and has widely been found superior to MAS. No studies have explicitly investigated how resource allocation decisions affect success of genomic selection. My objective was to study the effect of resource allocation on response to MAS and genomic selection in a single biparental population of doubled haploid lines by using computer simulation. Simulation results were compared with previously derived formulas for the calculation of prediction accuracy under different levels of heritability and population size. Response of prediction accuracy to resource allocation strategies differed between genomic selection models (ridge regression best linear unbiased prediction [RR-BLUP], BayesCπ) and multiple linear regression using ordinary least-squares estimation (OLS), leading to different optimal resource allocation choices between OLS and RR-BLUP. For OLS, it was always advantageous to maximize population size at the expense of replication, but a high degree of flexibility was observed for RR-BLUP. Prediction accuracy of doubled haploid lines included in the training set was much greater than of those excluded from the training set, so there was little benefit to phenotyping only a subset of the lines genotyped. Finally, observed prediction accuracies in the simulation compared well to calculated prediction accuracies, indicating these theoretical formulas are useful for making resource allocation

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

Science.gov (United States)

Talukder, Shyamal K.; Saha, Malay C.

2017-01-01

Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder. PMID:28798766

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

Directory of Open Access Journals (Sweden)

Shyamal K. Talukder

2017-07-01

Full Text Available Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs. Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.

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.

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome

Science.gov (United States)

Schoof, Heiko; Zaccaria, Paolo; Gundlach, Heidrun; Lemcke, Kai; Rudd, Stephen; Kolesov, Grigory; Arnold, Roland; Mewes, H. W.; Mayer, Klaus F. X.

2002-01-01

Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published. Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence. Besides completing the list of genes, we need to discover their cellular roles, their regulation and their interactions in order to understand the workings of the whole plant. The MIPS Arabidopsis thaliana Database (MAtDB; http://mips.gsf.de/proj/thal/db) started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project and the Arabidopsis Genome Initiative. Our aim is to transform MAtDB into an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities and by creating a comprehensive resource for Arabidopsis as a reference model for other species, including crop plants. PMID:11752263

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.

Exploiting Genomic Resources for Efficient Conservation and Use of Chickpea, Groundnut, and Pigeonpea Collections for Crop Improvement

Directory of Open Access Journals (Sweden)

C. L. Laxmipathi Gowda

2013-11-01

Full Text Available Both chickpea ( L. and pigeonpea [ (L. Millsp.] are important dietary source of protein while groundnut ( L. is one of the major oil crops. Globally, approximately 1.1 million grain legume accessions are conserved in genebanks, of which the ICRISAT genebank holds 49,485 accessions of cultivated species and wild relatives of chickpea, pigeonpea, and groundnut from 133 countries. These genetic resources are reservoirs of many useful genes for present and future crop improvement programs. Representative subsets in the form of core and mini core collections have been used to identify trait-specific genetically diverse germplasm for use in breeding and genomic studies in these crops. Chickpea, groundnut, and pigeonpea have moved from “orphan” to “genomic resources rich crops.” The chickpea and pigeonpea genomes have been decoded, and the sequences of groundnut genome will soon be available. With the availability of these genomic resources, the germplasm curators, breeders, and molecular biologists will have abundant opportunities to enhance the efficiency of genebank operations, mine allelic variations in germplasm collection, identify genetically diverse germplasm with beneficial traits, broaden the cultigen’s genepool, and accelerate the cultivar development to address new challenges to production, particularly with respect to climate change and variability. Marker-assisted breeding approaches have already been initiated for some traits in chickpea and groundnut, which should lead to enhanced efficiency and efficacy of crop improvement. Resistance to some pests and diseases has been successfully transferred from wild relatives to cultivated species.

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/.

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

Science.gov (United States)

Jung, Sook; Jesudurai, Christopher; Staton, Margaret; Du, Zhidian; Ficklin, Stephen; Cho, Ilhyung; Abbott, Albert; Tomkins, Jeffrey; Main, Dorrie

2004-09-09

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. 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. 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/.

Draft genome of the medaka fish: a comprehensive resource for medaka developmental genetics and vertebrate evolutionary biology.

Science.gov (United States)

Takeda, Hiroyuki

2008-06-01

The medaka Oryzias latipes is a small egg-laying freshwater teleost, and has become an excellent model system for developmental genetics and evolutionary biology. The medaka genome is relatively small in size, approximately 800 Mb, and the genome sequencing project was recently completed by Japanese research groups, providing a high-quality draft genome sequence of the inbred Hd-rR strain of medaka. In this review, I present an overview of the medaka genome project including genome resources, followed by specific findings obtained with the medaka draft genome. In particular, I focus on the analysis that was done by taking advantage of the medaka system, such as the sex chromosome differentiation and the regional history of medaka species using single nucleotide polymorphisms as genomic markers.

Characterization of Breakfast Cereals Available in the Mexican Market: Sodium and Sugar Content.

Science.gov (United States)

Nieto, Claudia; Rincon-Gallardo Patiño, Sofia; Tolentino-Mayo, Lizbeth; Carriedo, Angela; Barquera, Simón

2017-08-16

Preschool Mexican children consume 7% of their total energy intake from processed breakfast cereals. This study characterized the nutritional quality and labelling (claims and Guideline Daily Amount (GDA)) of the packaged breakfast cereals available in the Mexican market. Photographs of all breakfast cereals available in the 9 main food retail chains in the country were taken. The nutrition quality of cereals was assessed using the United Kingdom Nutrient Profiling Model (UKNPM). Claims were classified using the International Network for Food and Obesity/non-communicable Diseases Research, Monitoring and Action Support (INFORMAS) taxonomy and the GDA was defined according to the Mexican regulation, NOM-051. Overall, a total of 371 different breakfast cereals were analysed. The nutritional profile showed that 68.7% were classified as "less healthy". GDAs and claims were displayed more frequently on the "less healthy" cereals. Breakfast cereals within the "less healthy" category had significantly higher content of energy, sugar and sodium ( p < 0.001). Most of the claims were displayed in the "less healthy" cereals ( n = 313). This study has shown that there is a lack of consistency between the labelling on the front of the pack and the nutritional quality of breakfast cereals.

Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management

Directory of Open Access Journals (Sweden)

Sarika Jaiswal

2017-11-01

Full Text Available Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database (TaSSRDb is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169 from complex, hexaploid wheat genome (~17 GB along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb and lowest (74.57 SSRs/Mb SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability testing, EDV (Essentially Derived Variety/IV (Initial Variety disputes, seed

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

Science.gov (United States)

Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

2013-11-01

Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in

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.

Genomic tools in pearl millet breeding for drought tolerance: Status and prospects

Directory of Open Access Journals (Sweden)

Desalegn Debelo Serba

2016-11-01

Full Text Available Pearl millet (Penisetum glaucum (L R. Br. is a hardy cereal crop grown in the arid and semiarid tropics where other cereals are likely to fail to produce economic yields due to drought and heat stresses. Adaptive evolution, a form of natural selection shaped the crop to grow and yield satisfactorily with limited moisture supply or under periodic water deficits in the soil. Drought tolerance is a complex polygenic trait that various morphological and physiological responses are controlled by hundreds of genes and significantly influenced by the environment. The development of genomic tools will have enormous potential to improve the efficiency and precision of conventional breeding. The apparent independent domestication events, highly outcrossing nature and traditional cultivation in stressful environments maintained tremendous amount of polymorphism in pearl millet. This high polymorphism of the crop has been revealed by genome mapping that in turn stimulated the mapping and tagging of genomic regions controlling important traits such as drought tolerance. Mapping of a major QTL for terminal drought tolerance in independent populations envisaged the prospect for the development of molecular breeding in pearl millet. To accelerate genetic gains for drought tolerance targeted novel approaches such as establishment of marker-trait associations, genomic selection tools, genome sequence and genotyping-by-sequencing are still limited. Development and application of high throughput genomic tools need to be intensified to improve the breeding efficiency of pearl millet to minimize the impact of climate change on its production.

Genome interplay in the grain transcriptome of hexaploid bread wheat.

Science.gov (United States)

Pfeifer, Matthias; Kugler, Karl G; Sandve, Simen R; Zhan, Bujie; Rudi, Heidi; Hvidsten, Torgeir R; Mayer, Klaus F X; Olsen, Odd-Arne

2014-07-18

Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome. Copyright © 2014, American Association for the Advancement of Science.

Cereal bars produced with banana peel flour: evaluation of acceptability and sensory profile.

Science.gov (United States)

Carvalho, Vania Silva; Conti-Silva, Ana Carolina

2018-01-01

A mixture design was used to investigate the effects of banana peel flour, rice flakes and oat flour on sensory acceptability of cereal bars, with subsequent evaluation of sensory profile of products identified as having high acceptability. Regions of greater response for acceptability of the cereal bars, which are dependent on the three investigated components, were found. Although having good acceptability, sensory profiles of cereal bars were different. A cereal bar with the lowest quantity of banana peel flour was described as having a higher amount of rice flakes, chewiness and crispness, while formulations with intermediate and highest quantities of banana peel flour were described by darker color, higher banana aroma and bitter taste. Contrary to expectations, banana flavor of cereal bar with highest quantity of banana peel flour was lower than cereal bars with intermediate quantities. Cereal bars were not different in terms of hardness and adhesiveness and they also had a similar sweet taste and oat flavor. The use of banana peel flour in production of cereal bars is feasible and, even with different sensory profiles, cereal bars with banana peel flour are acceptable, which may favor the development of new products for different market niches. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

The integrated microbial genome resource of analysis.

Science.gov (United States)

Checcucci, Alice; Mengoni, Alessio

2015-01-01

Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.

Depicted serving size: cereal packaging pictures exaggerate serving sizes and promote overserving.

Science.gov (United States)

Tal, Aner; Niemann, Stina; Wansink, Brian

2017-02-06

Extensive work has focused on the effects of nutrition label information on consumer behavior on the one hand, and on the effects of packaging graphics on the other hand. However, little work has examined how serving suggestion depictions - graphics relating to serving size - influence the quantity consumers serve themselves. The current work examines the prevalence of exaggerated serving size depictions on product packaging (study 1) and its effects on food serving in the context of cereal (study 2). Study 1 was an observational field survey of cereal packaging. Study 2 was a mixed experimental cross-sectional design conducted at a U.S. university, with 51 student participants. Study 1 coded 158 US breakfast cereals and compared the serving sizes depicted on the front of the box with the suggested serving size stated on the nutrition facts panel. Study 2 measured the amount of cereal poured from exaggerated or accurate serving size depictions. Study 1 compared average servings via t-tests. Study 2 used a mixed model with cereal type as the repeated measure and a compound symmetry covariance matrix. Study 1 demonstrated that portion size depictions on the front of 158 cereal boxes were 65.84% larger (221 vs. 134 calories) than the recommended portions on nutrition facts panels of those cereals. Study 2 showed that boxes that depicted exaggerated serving sizes led people to pour 20% more cereal compared to pouring from modified boxes that depicted a single-size portion of cereal matching suggested serving size. This was 45% over the suggested serving size. Biases in depicted serving size depicted on cereal packaging are prevalent in the marketplace. Such biases may lead to overserving, which may consequently lead to overeating. Companies should depict the recommended serving sizes, or otherwise indicate that the depicted portion represents an exaggerated serving size.

Depicted serving size: cereal packaging pictures exaggerate serving sizes and promote overserving

Directory of Open Access Journals (Sweden)

Aner Tal

2017-02-01

Full Text Available Abstract Background Extensive work has focused on the effects of nutrition label information on consumer behavior on the one hand, and on the effects of packaging graphics on the other hand. However, little work has examined how serving suggestion depictions - graphics relating to serving size - influence the quantity consumers serve themselves. The current work examines the prevalence of exaggerated serving size depictions on product packaging (study 1 and its effects on food serving in the context of cereal (study 2. Methods Study 1 was an observational field survey of cereal packaging. Study 2 was a mixed experimental cross-sectional design conducted at a U.S. university, with 51 student participants. Study 1 coded 158 US breakfast cereals and compared the serving sizes depicted on the front of the box with the suggested serving size stated on the nutrition facts panel. Study 2 measured the amount of cereal poured from exaggerated or accurate serving size depictions. Study 1 compared average servings via t-tests. Study 2 used a mixed model with cereal type as the repeated measure and a compound symmetry covariance matrix. Results Study 1 demonstrated that portion size depictions on the front of 158 cereal boxes were 64.7% larger (221 vs. 134 calories than the recommended portions on nutrition facts panels of those cereals. Study 2 showed that boxes that depicted exaggerated serving sizes led people to pour 17.8% more cereal compared to pouring from modified boxes that depicted a single-size portion of cereal matching suggested serving size. This was 42% over the suggested serving size. Conclusions Biases in depicted serving size depicted on cereal packaging are prevalent in the marketplace. Such biases may lead to overserving, which may consequently lead to overeating. Companies should depict the recommended serving sizes, or otherwise indicate that the depicted portion represents an exaggerated serving size.

Breakfast cereal consumption and subjective reports of health.

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Smith, A P

1999-11-01

The aim of the present study was to attempt to replicate and extend a recent result which showed that breakfast cereal consumption was associated with better mental health. The general population sample studied here (262 volunteers aged between 21 and 85 years, mean age: 60.9 years) was older than the sample in the previous study. The results showed that those who consumed breakfast cereal every day reported better mental and physical health than those who consumed it less frequently. This association was still present when demographic factors, indicators of lifestyle, such as smoking, or other aspects of diet were covaried. Further research is now required to elucidate the mechanisms underlying this robust association between daily breakfast cereal consumption and well-being.

Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives.

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Zhang, Yingxiao; Iaffaldano, Brian J; Zhuang, Xiaofeng; Cardina, John; Cornish, Katrina

2017-02-02

Rubber dandelion (Taraxacum kok-saghyz, TK) is being developed as a domestic source of natural rubber to meet increasing global demand. However, the domestication of TK is complicated by its colocation with two weedy dandelion species, Taraxacum brevicorniculatum (TB) and the common dandelion (Taraxacum officinale, TO). TB is often present as a seed contaminant within TK accessions, while TO is a pandemic weed, which may have the potential to hybridize with TK. To discriminate these species at the molecular level, and facilitate gene flow studies between the potential rubber crop, TK, and its weedy relatives, we generated genomic and marker resources for these three dandelion species. Complete chloroplast genome sequences of TK (151,338 bp), TO (151,299 bp), and TB (151,282 bp) were obtained using the Illumina GAII and MiSeq platforms. Chloroplast sequences were analyzed and annotated for all the three species. Phylogenetic analysis within Asteraceae showed that TK has a closer genetic distance to TB than to TO and Taraxacum species were most closely related to lettuce (Lactuca sativa). By sequencing multiple genotypes for each species and testing variants using gel-based methods, four chloroplast Single Nucleotide Polymorphism (SNP) variants were found to be fixed between TK and TO in large populations, and between TB and TO. Additionally, Expressed Sequence Tag (EST) resources developed for TO and TK permitted the identification of five nuclear species-specific SNP markers. The availability of chloroplast genomes of these three dandelion species, as well as chloroplast and nuclear molecular markers, will provide a powerful genetic resource for germplasm differentiation and purification, and the study of potential gene flow among Taraxacum species.

The Palatability of Cereal Based Nutritional Supplements in Cancer Patients

Science.gov (United States)

Baik, Hyun Wook; Lee, Yu Sun; Song, Min-Kyung

2014-01-01

Recently, it is reported that intervention of oral nutritional supplement improves the nutritional status of cancer patients, and the effectiveness is affected by the sensory preference of cancer patients on the oral nutritional supplement. However, the variety of oral nutritional supplement is extremely limited and the number of patient's benefits from using the products are restricted mostly due to sensory dislikes. The objective of this study was to provide sensory preference score of trial manufactured products with different accessory ingredients to maximize the use of oral nutritional supplements. Cancer patients (n = 30) and age, sex-matched healthy volunteers (n = 30) participated in the sensory assessments (taste, flavor, viscosity, color and overall preference) of three types of oral supplements (cereal base, cereal base+herb and cereal base+fruit) and a control supplement product with scorched cereal flavor, a top seller in current Korean market. Results indicate that the cancer patients' overall preference was significantly higher for the control supplement, and fruit added supplement was preferred over plain cereal and herb added products, although the difference was insignificant. However, there was no significant preference difference for the supplements among the control group for all sensory factors. These results suggest that cancer patients are more sensitive to sensory preferences compared to the control group, and the patients prefer the flavor of cooked cereal which is a staple food in Korea. PMID:24527420

Variations in cereal volume affect the amount selected and eaten for breakfast

OpenAIRE

Rolls, Barbara J.; Meengs, Jennifer S.; Roe, Liane S.

2014-01-01

Food volume could influence both the portions that people take and the amount that they eat, but these effects have had little investigation. The influence of food volume was tested by systematically reducing the flake size of a breakfast cereal so that the cereal was more compact and the same weight filled a smaller volume. In a crossover design, 41 adults ate cereal for breakfast once a week for four weeks during 2011-2012. The cereal was either standard wheat flakes or th...

Speciation of chromium in bread and breakfast cereals.

Science.gov (United States)

Mathebula, Mpho Wendy; Mandiwana, Khakhathi; Panichev, Nikolas

2017-02-15

Bread and breakfast cereals are a major constituents of the human diet, yet their Cr(VI) content is not known. Chromium(VI) was determined in these products by high resolution continuum source atomic absorption spectrometer (HR-CS AAS) after leaching Cr(VI) with 0.10molL(-1) Na2CO3. The results showed that 33-73% of total Cr (58.17±5.12μgkg(-1)-156.1±6.66μgkg(-1)) in bread exist as Cr(VI) and the highest total Cr content was found in brown bread. It was shown that Cr(III) is oxidized to Cr(VI) during toasting of bread. Chromium(VI) content in breakfast cereals ranged between 20.4±4μgkg(-1) and 470.4±68μgkg(-1). Therefore, it can be concluded that bread and breakfast cereals contains Cr(VI) which does not exceed maximum acceptable concentration (MAC) of 0.003mgkg(-1)bw(-1)day(-1) through daily consumption of half a bowl (65g) of breakfast cereal and four slices of toasted (122g) or untoasted bread (160g). Copyright © 2016 Elsevier Ltd. All rights reserved.

The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations.

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Keane, Michael; Craig, Thomas; Alföldi, Jessica; Berlin, Aaron M; Johnson, Jeremy; Seluanov, Andrei; Gorbunova, Vera; Di Palma, Federica; Lindblad-Toh, Kerstin; Church, George M; de Magalhães, João Pedro

2014-12-15

The naked mole rat (Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent native to East Africa. Although its genome was previously sequenced, here we report a new assembly sequenced by us with substantially higher N50 values for scaffolds and contigs. We analyzed the annotation of this new improved assembly and identified candidate genomic adaptations which may have contributed to the evolution of the naked mole rat's extraordinary traits, including in regions of p53, and the hyaluronan receptors CD44 and HMMR (RHAMM). Furthermore, we developed a freely available web portal, the Naked Mole Rat Genome Resource (http://www.naked-mole-rat.org), featuring the data and results of our analysis, to assist researchers interested in the genome and genes of the naked mole rat, and also to facilitate further studies on this fascinating species. © The Author 2014. Published by Oxford University Press.

Genomic resources for a unique, low-virulence Babesia taxon from China

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Guiquan Guan

2016-10-01

Full Text Available Abstract Background Babesiosis is a socioeconomically important tick-borne disease of animals (including humans caused by haemoprotozoan parasites. The severity of babesiosis relates to host and parasite factors, particularly virulence/pathogenicity. Although Babesia bovis is a particularly pathogenic species of cattle, there are species of Babesia of ruminants that have limited pathogenicity. For instance, the operational taxonomic unit Babesia sp. Xinjiang (abbreviated here as Bx of sheep from China is substantially less virulent/pathogenic than B. bovis is in cattle. Although the reason for this distinctiveness is presently unknown, it is possible that Bx has a reduced ability to adhere to cells or evade/suppress immune responses, which might relate to particular proteins, such as the variant erythrocyte surface antigens (VESAs. Results We sequenced and annotated the 8.4 Mb nuclear draft genome of Bx and compared it with those of B. bovis and B. bigemina by synteny analysis; we also investigated the genetic relationship of Bx with selected Babesia species and related apicomplexans for which genomic datasets are available, and explored the VESA complement in Bx. Conclusions The availability of the Bx genome now provides unique opportunities to elucidate aspects of the molecular biology, biochemistry and physiology of Bx, and to explore the reason(s for its limited virulence and/or apparent ability to evade immune attack by the host animal. Moreover, the present genomic resource and an in vitro culture system for Bx raises the prospect of establishing a functional genomic platform to explore essential genes as new intervention targets against babesiosis.

Genomic resources for a unique, low-virulence Babesia taxon from China.

Science.gov (United States)

Guan, Guiquan; Korhonen, Pasi K; Young, Neil D; Koehler, Anson V; Wang, Tao; Li, Youquan; Liu, Zhijie; Luo, Jianxun; Yin, Hong; Gasser, Robin B

2016-10-27

Babesiosis is a socioeconomically important tick-borne disease of animals (including humans) caused by haemoprotozoan parasites. The severity of babesiosis relates to host and parasite factors, particularly virulence/pathogenicity. Although Babesia bovis is a particularly pathogenic species of cattle, there are species of Babesia of ruminants that have limited pathogenicity. For instance, the operational taxonomic unit Babesia sp. Xinjiang (abbreviated here as Bx) of sheep from China is substantially less virulent/pathogenic than B. bovis is in cattle. Although the reason for this distinctiveness is presently unknown, it is possible that Bx has a reduced ability to adhere to cells or evade/suppress immune responses, which might relate to particular proteins, such as the variant erythrocyte surface antigens (VESAs). We sequenced and annotated the 8.4 Mb nuclear draft genome of Bx and compared it with those of B. bovis and B. bigemina by synteny analysis; we also investigated the genetic relationship of Bx with selected Babesia species and related apicomplexans for which genomic datasets are available, and explored the VESA complement in Bx. The availability of the Bx genome now provides unique opportunities to elucidate aspects of the molecular biology, biochemistry and physiology of Bx, and to explore the reason(s) for its limited virulence and/or apparent ability to evade immune attack by the host animal. Moreover, the present genomic resource and an in vitro culture system for Bx raises the prospect of establishing a functional genomic platform to explore essential genes as new intervention targets against babesiosis.

Distribution patterns of segetal weeds of cereal crops in tajikistan

International Nuclear Information System (INIS)

Nowak, A.; Nowak, S.

2015-01-01

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)

Sweetpotato- and cereal-based infant foods: protein quality assessment, and effect on body composition using sprague dawley rats as a model.

Science.gov (United States)

Amagloh, Francis Kweku; Chiridza, Tracy; Lemercier, Marie-Eve; Broomfield, Anne; Morel, Patrick C H; Coad, Jane

2015-01-01

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% (Pbody 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.

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

International Nuclear Information System (INIS)

Isaac, M.E.; Hinsinger, P.; Harmand, J.M.

2012-01-01

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. -- Highlights

Conservation and improvement of native pseudo cereals of Mexico

International Nuclear Information System (INIS)

Garcia A, J.M.; Cruz T, E.; Mapes S, C.; Laguna C, A.

2007-01-01

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)

Limited resources of genome sequencing in developing countries: Challenges and solutions

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Mohamed Helmy

2016-06-01

Full Text Available The differences between countries in national income, growth, human development and many other factors are used to classify countries into developed and developing countries. There are several classification systems that use different sets of measures and criteria. The most common classifications are the United Nations (UN and the World Bank (WB systems. The UN classification system uses the UN Human Development Index (HDI, an indicator that uses statistic of life expectancy, education, and income per capita for countries' classification. While the WB system uses gross national income (GNI per capita that is calculated using the World Bank Atlas method. According to the UN and WB classification systems, there are 151 and 134 developing countries, respectively, with 89% overlap between the two systems. Developing countries have limited human development, and limited expenditure in education and research, among several other limitations. The biggest challenge facing genomic researchers and clinicians is limited resources. As a result, genomic tools, specifically genome sequencing technologies, which are rapidly becoming indispensable, are not widely available. In this report, we explore the current status of sequencing technologies in developing countries, describe the associated challenges and emphasize potential solutions.

MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.

Science.gov (United States)

Médigue, Claudine; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Gautreau, Guillaume; Josso, Adrien; Lajus, Aurélie; Langlois, Jordan; Pereira, Hugo; Planel, Rémi; Roche, David; Rollin, Johan; Rouy, Zoe; Vallenet, David

2017-09-12

The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources. © The Author 2017. Published by Oxford University Press.

Multi-scale trade-off analysis of cereal residue use for livestock feeding vs. soil mulching in the Mid-Zambezi Valley, Zimbabwe

NARCIS (Netherlands)

Baudron, F.; Delmotte, S.; Corbeels, M.; Herrera, J.M.; Tittonell, P.A.

2015-01-01

Cereal residues represent a major resource for livestock feeding during the dry season in southern Africa. When kept on the soil surface instead of feeding them to livestock, crop residues can contribute to increasing soil fertility and maintaining crop productivity in the short- and the long-term.

Sensorial analysis evaluation in cereal bars preserved by ionizing radiation processing

International Nuclear Information System (INIS)

Villavicencio, A.L.C.H.; Araujo, M.M.; Fanaro, G.B.; Rela, P.R.; Mancini-Filho, J.

2007-01-01

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 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 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

Extracellular peptidases of the cereal pathogen Fusarium graminearum.

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Rohan George Thomas Lowe

2015-11-01

Full Text Available The plant pathogenic fungus Fusarium graminearum (Fgr creates economic and health risks in cereals agriculture. Fgr causes head blight (or scab of wheat and stalk rot of corn, reducing yield, degrading grain quality and polluting downstream food products with mycotoxins. Fungal plant pathogens must secrete proteases to access nutrition and to breakdown the structural protein component of the plant cell wall. Research into the proteolytic activity of Fgr is hindered by the complex nature of the suite of proteases secreted. We used a systems biology approach comprising genome analysis, transcriptomics and label-free quantitative proteomics to characterise the peptidases deployed by Fgr during growth. A combined analysis of published microarray transcriptome datasets revealed seven transcriptional groupings of peptidases based on in vitro growth, in planta growth, and sporulation behaviours. An orbitrap MS/MS proteomics technique defined the extracellular proteases secreted by Fusarium graminearum. A meta-classification based on sequence characters and transcriptional/translational activity in planta and in vitro provides a platform to develop control strategies that target Fgr peptidases.

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

Temporal Variation of Mycotoxin Producing Fungi in Norwegian Cereals

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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.

[Hydrocyanic acid content in cerals and cereal products].

Science.gov (United States)

Lehmann, G; Zinsmeister, H D; Erb, N; Neunhoeffer, O

1979-03-01

In the above paper for the first time a systematic study of the amount of hydrocyanic acid in grains and cereal products is reported. Among 24 analysed wheat, rye, maize and oats types, the presence of hydrocyanic acid could be identified in 19 cases in their Karyopses. Similar is the result with 28 among 31 analysed cereal products. The content of hydrocyanic acid lies between 0.1 and 45 microgram/100 gr dried mass.

Variations in cereal volume affect the amount selected and eaten for breakfast.

Science.gov (United States)

Rolls, Barbara J; Meengs, Jennifer S; Roe, Liane S

2014-09-01

Food volume could influence both the portions that people take and the amount that they eat, but these effects have had little investigation. The influence of food volume was tested by systematically reducing the flake size of a breakfast cereal so that the cereal was more compact and the same weight filled a smaller volume. In a crossover design, 41 adults ate cereal for breakfast once a week for 4 weeks during 2011 and 2012. The cereal was either standard wheat flakes or the same cereal crushed to reduce the volume to 80%, 60%, or 40% of the standard. A constant weight of cereal was provided in an opaque container and participants poured the amount they wanted into a bowl, added fat-free milk and noncalorie sweetener as desired, and consumed as much as they wanted. Results from a mixed linear model showed that as flake size was reduced, subjects poured a smaller volume of cereal, but still took a greater amount by weight and energy content (both P values breakfast energy intake increased from a mean±standard error of the mean of 286±18 kcal to 358±19 kcal, an increase of a mean±standard error of the mean 34%±7% (Pportion served, which in turn affects energy intake. Copyright © 2014 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Optimizing the allocation of resources for genomic selection in one breeding cycle.

Science.gov (United States)

Riedelsheimer, Christian; Melchinger, Albrecht E

2013-11-01

We developed a universally applicable planning tool for optimizing the allocation of resources for one cycle of genomic selection in a biparental population. The framework combines selection theory with constraint numerical optimization and considers genotype  ×  environment interactions. Genomic selection (GS) is increasingly implemented in plant breeding programs to increase selection gain but little is known how to optimally allocate the resources under a given budget. We investigated this problem with model calculations by combining quantitative genetic selection theory with constraint numerical optimization. We assumed one selection cycle where both the training and prediction sets comprised double haploid (DH) lines from the same biparental population. Grain yield for testcrosses of maize DH lines was used as a model trait but all parameters can be adjusted in a freely available software implementation. An extension of the expected selection accuracy given by Daetwyler et al. (2008) was developed to correctly balance between the number of environments for phenotyping the training set and its population size in the presence of genotype × environment interactions. Under small budget, genotyping costs mainly determine whether GS is superior over phenotypic selection. With increasing budget, flexibility in resource allocation increases greatly but selection gain leveled off quickly requiring balancing the number of populations with the budget spent for each population. The use of an index combining phenotypic and GS predicted values in the training set was especially beneficial under limited resources and large genotype × environment interactions. Once a sufficiently high selection accuracy is achieved in the prediction set, further selection gain can be achieved most efficiently by massively expanding its size. Thus, with increasing budget, reducing the costs for producing a DH line becomes increasingly crucial for successfully exploiting the

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.

Creation of BAC genomic resources for cocoa ( Theobroma cacao L.) for physical mapping of RGA containing BAC clones.

Science.gov (United States)

Clément, D; Lanaud, C; Sabau, X; Fouet, O; Le Cunff, L; Ruiz, E; Risterucci, A M; Glaszmann, J C; Piffanelli, P

2004-05-01

We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

Ensembl Genomes 2013: scaling up access to genome-wide data.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

2014-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Breakfast cereals and risk of hypertension in the Physicians’ Health Study I

Science.gov (United States)

Kochar, Jinesh; Gaziano, J. Michael; Djoussé, Luc

2012-01-01

Summary Background and aims Hypertension is a major public health problem. While many dietary factors affect the risk of developing hypertension, limited data are available on the association between consumption of breakfast cereal and incident hypertension. We examined the association between breakfast cereal consumption and the risk of hypertension. Methods We prospectively analyzed data from 13,368 male participants of the Physicians’ Health Study I. Consumption of breakfast cereals was estimated using an abbreviated food frequency questionnaire and incident hypertension was ascertained through yearly follow-up questionnaires. Results The average age of study participants was 52.4 ±8.9 years (range 39.7-85.9) during the initial assessment of cereal intake (1981-1983). During a mean follow up of 16.3 years, 7,267 cases of hypertension occurred. The crude incidence rates of hypertension were 36.7, 34.0, 31.7, and 29.6 cases/1,000 person-years for people reporting breakfast cereal intake of 0, ≤ 1, 2-6, and ≥ 7 servings/week, respectively. In a Cox regression model adjusting for age, smoking, body mass index, alcohol consumption, fruit and vegetable consumption, physical activity, and history of diabetes mellitus, hazard ratios (95% CI) for hypertension were 1.0 (reference), 0.93 (0.88-0.99), 0.88 (0.83-0.94), and 0.81 (0.75-0.86) from the lowest to the highest category of cereal consumption, respectively (p for trend cereals and was observed in lean as well as overweight or obese participants. Conclusions The results of this longitudinal cohort study suggest that whole grain breakfast cereal consumption confers a lower risk of hypertension in middle-aged adult males PMID:21868140

Impact of sodium chloride on breakfast cereal products

OpenAIRE

Moreau, Lydie

2009-01-01

To reduce the amount of sodium chloride in breakfast cereals without changing their properties, it is necessary to understand the role of this salt. Hence, a model system was developed. This model, composed of native waxy maize starch, glucose and a mixture of amino-acids generated similar colour and residual volatiles after heating compared to commercial breakfast cereals. Systematically designed experiments used this model to study the influence of NaCl concentration (0 % to 5.44 %) on colo...

El cerealémetro

Directory of Open Access Journals (Sweden)

Santos López, Pascual

2006-01-01

Full Text Available "Apparatus for measuring wheat" was the title that Geronimo Salmerón Gómez put his invention patented in 1939. Which calls for defining the quality of wheat is marketed. Salmerón always worried about the price of bread and flour quality came to manufacture his invention usually called "Cerealémetro".

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. © 2014 American Society for Nutrition.

A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases.

Science.gov (United States)

Periwal, Vinita

2017-07-01

Genome editing with engineered nucleases (zinc finger nucleases, TAL effector nucleases s and Clustered regularly inter-spaced short palindromic repeats/CRISPR-associated) has recently been shown to have great promise in a variety of therapeutic and biotechnological applications. However, their exploitation in genetic analysis and clinical settings largely depends on their specificity for the intended genomic target. Large and complex genomes often contain highly homologous/repetitive sequences, which limits the specificity of genome editing tools and could result in off-target activity. Over the past few years, various computational approaches have been developed to assist the design process and predict/reduce the off-target activity of these nucleases. These tools could be efficiently used to guide the design of constructs for engineered nucleases and evaluate results after genome editing. This review provides a comprehensive overview of various databases, tools, web servers and resources for genome editing and compares their features and functionalities. Additionally, it also describes tools that have been developed to analyse post-genome editing results. The article also discusses important design parameters that could be considered while designing these nucleases. This review is intended to be a quick reference guide for experimentalists as well as computational biologists working in the field of genome editing with engineered nucleases. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

Science.gov (United States)

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

2015-01-16

Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity. To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the

Breakfast cereals and risk of hypertension in the Physicians' Health Study I.

Science.gov (United States)

Kochar, Jinesh; Gaziano, J Michael; Djoussé, Luc

2012-02-01

Hypertension is a major public health problem. While many dietary factors affect the risk of developing hypertension, limited data are available on the association between consumption of breakfast cereal and incident hypertension. We examined the association between breakfast cereal consumption and the risk of hypertension. We prospectively analyzed data from 13,368 male participants of the Physicians' Health Study I. Consumption of breakfast cereals was estimated using an abbreviated food frequency questionnaire and incident hypertension was ascertained through yearly follow-up questionnaires. The average age of study participants was 52.4 ± 8.9 years (range 39.7-85.9) during the initial assessment of cereal intake (1981-1983). During a mean follow up of 16.3 years, 7267 cases of hypertension occurred. The crude incidence rates of hypertension were 36.7, 34.0, 31.7, and 29.6 cases/1000 person-years for people reporting breakfast cereal intake of 0, ≤1, 2-6, and ≥7 servings/week, respectively. In a Cox regression model adjusting for age, smoking, body mass index, alcohol consumption, fruit and vegetable consumption, physical activity, and history of diabetes mellitus, hazard ratios (95% CI) for hypertension were 1.0 (reference), 0.93 (0.88-0.99), 0.88 (0.83-0.94), and 0.81 (0.75-0.86) from the lowest to the highest category of cereal consumption, respectively (p for trend cereals and was observed in lean as well as overweight or obese participants. The results of this longitudinal cohort study suggest that whole grain breakfast cereal consumption confers a lower risk of hypertension in middle-aged adult males. Copyright © 2011 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics

Science.gov (United States)

Schoof, Heiko; Ernst, Rebecca; Nazarov, Vladimir; Pfeifer, Lukas; Mewes, Hans-Werner; Mayer, Klaus F. X.

2004-01-01

Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db. PMID:14681437

A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome.

Science.gov (United States)

Cox, Laura A; Glenn, Jeremy P; Spradling, Kimberly D; Nijland, Mark J; Garcia, Roy; Nathanielsz, Peter W; Ford, Stephen P

2012-06-15

The pregnant sheep has provided seminal insights into reproduction related to animal and human development (ovarian function, fertility, implantation, fetal growth, parturition and lactation). Fetal sheep physiology has been extensively studied since 1950, contributing significantly to the basis for our understanding of many aspects of fetal development and behaviour that remain in use in clinical practice today. Understanding mechanisms requires the combination of systems approaches uniquely available in fetal sheep with the power of genomic studies. Absence of the full range of sheep genomic resources has limited the full realization of the power of this model, impeding progress in emerging areas of pregnancy biology such as developmental programming. We have examined the expressed fetal sheep heart transcriptome using high-throughput sequencing technologies. In so doing we identified 36,737 novel transcripts and describe genes, gene variants and pathways relevant to fundamental developmental mechanisms. Genes with the highest expression levels and with novel exons in the fetal heart transcriptome are known to play central roles in muscle development. We show that high-throughput sequencing methods can generate extensive transcriptome information in the absence of an assembled and annotated genome for that species. The gene sequence data obtained provide a unique genomic resource for sheep specific genetic technology development and, combined with the polymorphism data, augment annotation and assembly of the sheep genome. In addition, identification and pathway analysis of novel fetal sheep heart transcriptome splice variants is a first step towards revealing mechanisms of genetic variation and gene environment interactions during fetal heart development.

Evaluation of the protein quality of cereal mutants

International Nuclear Information System (INIS)

Eggum, B.O.

1984-01-01

Protein content, true protein digestibility, biological value, net protein utilization, and utilizable protein in several varieties of barley, wheat and rice were determined in nitrogen-balance trials with rats. It appeared that protein quality varied significantly between these three cereal grains, with the lowest values for wheat. However, the protein content was markedly higher in wheat; consequently, utilizable protein was highest in this cereal grain. The different varieties within barley, wheat and rice varied considerably in protein quality. This demonstrates a large variation in the potential for protein synthesis. The main problem with rice and barley is the low protein concentration, whereas with wheat the biggest problem seems to be the quality of the protein. As the lysine level in all cereal grains, expressed in percentage of the protein, cannot meet the requirements for either man or domestic animals efforts should be made to increase the lysine concentration in these food sources. (author)

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.

The contribution of breakfast cereals to the nutritional intake of the materially deprived UK population.

Science.gov (United States)

Holmes, B A; Kaffa, N; Campbell, K; Sanders, T A B

2012-01-01

Breakfast is an important source of micronutrients in the diet and its consumption has been linked to positive health outcomes. The present analysis investigated the contribution that breakfast cereals make to the nutrient intakes of the materially deprived (low income) UK population. Data for 3728 respondents aged 2 years and over from the UK Low Income Diet and Nutrition Survey (2003-2005) were analysed. Nutrient intakes of consumers and non-consumers of breakfast cereal were compared. Breakfast cereals were consumed by 49% of men, 58% of women, 80% of boys and 80% of girls, and median intakes were: 35, 25, 29 and 21 g/d, respectively. Consumers of breakfast cereals had higher intakes of thiamin, riboflavin, niacin, biotin, folate, vitamin B(6), vitamin B(12), iron and zinc than non-consumers. Breakfast cereal consumption was also related to higher intakes of calcium, attributable to higher milk consumption. The intake of wholegrain and high-fibre breakfast cereals was associated with a higher intake of non-starch polysaccharides. Intakes of niacin, biotin, calcium and zinc were higher but that of vitamin B(6) was lower among consumers of exclusively wholegrain and high-fibre breakfast cereals compared with consumers of other breakfast cereals. There were no significant differences observed in intakes of non-milk extrinsic sugars according to type of breakfast cereal consumed. Breakfast cereals make a significant contribution to the micronutrient intake of the low-income UK population.

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

, 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...... control by symbiotic fungal endophytes has been documented, particularly with respect to clavicipitaceous endophytes in C3 cool-season grasses, this area remains relatively underexplored in cereals. We highlight for the first time the potential in using symbiotic fungal endophytes to control foliar cereal...

Effect of fermentation and malting on some cereal weaning foods ...

African Journals Online (AJOL)

Effect of fermentation and malting on some cereal weaning foods enriched with African locust beans were carried out. Cereals (wheat and millet) were malted for the period of 144 hours and further fermented for 48 hours by natural fermentation. The millet, wheat and locust bean flours were mixed together in the ratio ...

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 ...

Cereal Foods and Health : New results and science-based nutrition guidelines

NARCIS (Netherlands)

Gibson, S.; Ashwell, M.; Kamp, J.W. van der

2013-01-01

Recent epidemiological studies, in populations with higher intakes of whole grain, have extended and confirmed the evidence from previous findings showing an association between whole grain cereal or cereal fibre consumption and prevention of several non-communicable diseases. Although the results

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...

The Benefits of Breakfast Cereal Consumption: A Systematic Review of the Evidence Base1234

Science.gov (United States)

Williams, Peter G.

2014-01-01

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

Brand-Supermarket Demand for Breakfast Cereals and Retail Competition

OpenAIRE

Benaissa Chidmi; Rigoberto A. Lopez

2007-01-01

The Berry, Levinsohn, and Pakes (1995) market equilibrium model is extended to the supermarket chain level to examine consumer choices and retail competition for thirty-seven brands of breakfast cereals in Boston. Estimated taste parameters for product characteristics vary significantly across consumers. Although consumers are price-sensitive with respect to their chosen cereals, they exhibit strong brand and supermarket loyalty. Retail markups increase and marginal costs decrease with grocer...

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

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.

Quality and Safety Aspects of Cereals (Wheat) and Their Products.

Science.gov (United States)

Varzakas, Theo

2016-11-17

Cereals and, most specifically, wheat are described in this chapter highlighting on their safety and quality aspects. Moreover, wheat quality aspects are adequately addressed since they are used to characterize dough properties and baking quality. Determination of dough properties is also mentioned and pasta quality is also described in this chapter. Chemometrics-multivariate analysis is one of the analyses carried out. Regarding production weighing/mixing of flours, kneading, extruded wheat flours, and sodium chloride are important processing steps/raw materials used in the manufacturing of pastry products. Staling of cereal-based products is also taken into account. Finally, safety aspects of cereal-based products are well documented with special emphasis on mycotoxins, acrylamide, and near infrared methodology.

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

Science.gov (United States)

Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

2016-12-01

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

COMPARATIVE EVALUATION OF CHANGE IN SALIVARY pH ON CONSUMPTION OF DRY READY TO EAT CEREALS, CEREALS WITH AND WITHOUT ADDED SUGAR IN MILK- AN IN -VIVO STUDY

OpenAIRE

Mahesh J*, Sapna B, Veeresh DJ, Divya D

2016-01-01

Background: Dry, Ready to Eat Cereals are a combination of refined sugar and starch, most commonly consumed breakfast in the modern human diet. The present study was done to investigate the effects of combination foods on salivary pH. Objective: To assess and compare the salivary pH changes after consumption of Dry Ready to Eat Cereals (REC), Cereals with plain and sugar added milk. Method: Thirty six adults of age 18 to 25 years were assessed for salivary pH at baseline followed by one minut...

OryzaGenome: Genome Diversity Database of Wild Oryza Species

KAUST Repository

Ohyanagi, Hajime

2015-11-18

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 textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited 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/.

The Genome Atlas Resource

DEFF Research Database (Denmark)

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

2010-01-01

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...

Valorization of cereal based biorefinery byproducts: reality and expectations.

Science.gov (United States)

Elmekawy, Ahmed; Diels, Ludo; De Wever, Heleen; Pant, Deepak

2013-08-20

The growth of the biobased economy will lead to an increase in new biorefinery activities. All biorefineries face the regular challenges of efficiently and economically treating their effluent to be compatible with local discharge requirements and to minimize net water consumption. The amount of wastes resulting from biorefineries industry is exponentially growing. The valorization of such wastes has drawn considerable attention with respect to resources with an observable economic and environmental concern. This has been a promising field which shows great prospective toward byproduct usage and increasing value obtained from the biorefinery. However, full-scale realization of biorefinery wastes valorization is not straightforward because several microbiological, technological and economic challenges need to be resolved. In this review we considered valorization options for cereals based biorefineries wastes while identifying their challenges and exploring the opportunities for future process.

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

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......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...... 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....

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives.

Science.gov (United States)

Crossa, José; Pérez-Rodríguez, Paulino; Cuevas, Jaime; Montesinos-López, Osval; Jarquín, Diego; de Los Campos, Gustavo; Burgueño, Juan; González-Camacho, Juan M; Pérez-Elizalde, Sergio; Beyene, Yoseph; Dreisigacker, Susanne; Singh, Ravi; Zhang, Xuecai; Gowda, Manje; Roorkiwal, Manish; Rutkoski, Jessica; Varshney, Rajeev K

2017-11-01

Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding. Copyright © 2017 Elsevier Ltd. All rights reserved.

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. PMID:23193293

Use of Red Cactus Pear (Opuntia ficus-indica Encapsulated Powder to Pigment Extruded Cereal

Directory of Open Access Journals (Sweden)

Martha G. Ruiz-Gutiérrez

2017-01-01

Full Text Available Encapsulated powder of the red cactus pear is a potential natural dye for the food industry and a known antioxidant. Although the use of this powder is possible, it is not clear how it alters food properties, thus ensuing commercial acceptability. The aim of this study was to evaluate the effect of encapsulated powder of the red cactus pear on the physicochemical properties of extruded cereals. The powder was mixed (2.5, 5.0, and 7.5% w/w with maize grits and extruded (mix moisture 22%, temperature 100°C, and screw speed 325 rpm. The physical, chemical, and sensory characteristics of the extruded cereal were evaluated; extruded cereal without encapsulated powder was used as a control. All cereal extrudates pigmented with the encapsulated powder showed statistically significant differences (P<0.05 in expansion, water absorption, color, density, and texture compared to the control. The encapsulated powder had a positive effect on expansion and water absorption indices, as well as color parameters, but a negative effect on density and texture. Extruded cereal properties were significantly (P<0.05 correlated. Sensorially, consumers accepted the extruded cereal with a lower red cactus pear powder content (2.5% w/w, because this presented characteristics similar to extruded cereal lacking pigment.

Prediction of cereal feed value using spectroscopy and chemometrics

DEFF Research Database (Denmark)

Jørgensen, Johannes Ravn; Gislum, René

2009-01-01

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...... value, the prediction error has to be compared with the error in the chemical analysis. Prediction error by NIRS prediction of feed value is above the error of the chemical measurement. The conclusion is that it is possible to predict the feed value in cereals with NIRS quickly and cheaply...

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

Presence of aflatoxins in cereals from Serbia

Directory of Open Access Journals (Sweden)

Kos Jovana J.

2014-01-01

Full Text Available Aflatoxins (AFs, one of the most toxic and the strongest natural carcinogens can be found in a variety of food commodities, including cereals. For that purpose, the aim of this study was to investigate occurrence of AFs (AFB1, AFG1, AFB2 and AFG2 in 130 cereal samples. AFs content was determined by direct competitive Enzyme Linked Immunosorbent Assay (ELISA method. Samples with AFs content higher than 1 μg/kg were analyzed again with confirmatory High Performance Liquid Chromatography with fluorescence detection (HPLC-FLD. Analyses showed that none of the analyzed wheat (30, barley (20, oats (20 and rye (20 samples was contaminated with AFs. On the other hand, among 40 analyzed maize samples 24 of them (60% were contaminated in the following way: 6 (25% samples had AFs concentration between 1 and 10 μg/kg, 14 (58% samples between 10 and 50 μg/kg and 4 (17% between 50 and 70.3 μg/kg. The most predominant aflatoxin was AFB1 which was detected in all contaminated maize samples. AFG1, AFB2 and AFG2 were found in 12, 5 and 1 sample, respectively. This study represents the first investigation of the occurrence of AFs in five different cereals from Serbia.

Determination of Trace Elements in Thai Cereal

International Nuclear Information System (INIS)

Permnamtip, Vorapot; Busamongkol, Arporn; Laoharojanaphand, Sirinart; Chaiyasith, Suwan

2007-08-01

Full text: Trace elements were analyzed in Thai cereal, e.g. rice and bean, by using neutron activation analysis (NAA). The selected cereals are major food items for Thai population. The data obtained from this work will be useful for nutrition and safety consumption of Thai cereal. Trace elements verified include Al, As, Br, Ca, Cd, Cl, Cr, Cu, Fe, I, K, Mg, Mn, Mo, Se, Sn, V and Zn. It was found that Al, As, Br, Cl, Cu, Fe, Mn, Zn, Ca, K and Mg are presented in the range of 2.2 to 35.7, 0.15 to 0.21, 0.44 to 13.5, 55.6 to 640.3, 16.3 to 16.5, 158.9 to 161.1, 12.2 to 55.7, 8.2 to 58.1 (g/g (ppm) , 0.02 to 0.28, 0.09 to 1.99 and 0.03 to 0.26 %, respectively. For Cd, Cr, I, Mo, Se, Sn and V were not found in sample because the concentrations were lower than detection limit. Precision and accuracy were determined by analyzing standard reference materials: NIST 1568a, NIST 8704, ACSP DORM-1, NIES No.9 and NMIJ 7302 to a

Alternative futures for world cereal and meat consumption.

Science.gov (United States)

Rosegrant, M W; Leach, N; Gerpacio, R V

1999-05-01

Fundamental changes in the global structure of food demand will lead to an extraordinary increase in the importance of developing countries in global food markets. Economic growth in developing countries is changing consumption patterns, with slower growth (and in many countries actual declines) in per capita food consumption of grains and rapidly growing per capita and total meat consumption, combined with induced growth in cereal feed consumption. The present paper examines the hypothesis, suggested by some researchers, that high-meat diets in developed countries limit improvement in food security in developing countries. These analysts argue that reduced meat consumption in developed countries would release cereals from livestock feed to food for poorer populations, thus improving food security in developing countries. Using the International Food Policy Research Institute (Washington, DC, USA) global food projections model, the international model for policy analysis of agricultural commodities and trade (see Rosegrant et al. 1995), we first analyse the implications for future global cereal and meat supply and demand resulting from changes in global income, population growth and other structural changes, then simulate alternative scenarios to examine the effect of large reductions in meat consumption in developed countries on food consumption and food security in developing countries. The paper shows that while the long-term prospects for food supply, demand and trade indicate a strengthening of world cereal and livestock markets, the improvement in food security in the developing world will be slow, and changes in the dietary patterns in developed countries are not an effective route to improvement in food security in developing countries.

Study on fluorescence of Maillard reaction compounds in breakfast cereals.

Science.gov (United States)

Delgado-Andrade, Cristina; Rufián-Henares, José A; Morales, Francisco J

2006-09-01

During the advanced stage of the Maillard reaction (MR) in food processing and cooking, Amadori rearrangement products undergo dehydration and fission and fluorescent substances are formed. Free and total (free + linked to the protein backbone) fluorescence (FIC) due to Maillard compounds in 60 commercial breakfast cereals was evaluated. Pronase was used for efficient release of linked fluorescent Maillard compounds from the protein backbone. Results were correlated with some heat-induced markers of the extent of the MR or sugar caramelisation during cereal processing, such as hydroxymethylfurfural, furfural, glucosilisomaltol and furosine. The effect of sample composition (dietary-fibre added, protein, etc.) on levels of FIC, expressed as fluorescence intensity (FI) per milligram of sample, is discussed. FIC is significantly correlated to the protein content of the sample and fluorescent Maillard compounds are mainly linked to the protein backbone. The ratio of total-FIC to free-FIC was 10.4-fold for corn-based, wheat-based and multicereal-based breakfast cereals but significantly higher in rice-based samples. Addition of dietary fibre or honey increased the FIC values. Data support the usefulness of FIC measurement as an unspecific heat-induced marker in breakfast cereals.

diArk – a resource for eukaryotic genome research

Directory of Open Access Journals (Sweden)

Kollmar Martin

2007-04-01

Full Text Available Abstract Background The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interested in single gene analyses (from a phylogenetic, a structural biology or other perspective it is therefore important to have up-to-date knowledge about the various resources providing primary data. Description The database is built around 3 central tables: species, sequencing projects and publications. The species table contains commonly and alternatively used scientific names, common names and the complete taxonomic information. For projects the sequence type and links to species project web-sites and species homepages are stored. All publications are linked to projects. The web-interface provides comprehensive search modules with detailed options and three different views of the selected data. We have especially focused on developing an elaborate taxonomic tree search tool that allows the user to instantaneously identify e.g. the closest relative to the organism of interest. Conclusion We have developed a database, called diArk, to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes. Currently, diArk provides information about 415 eukaryotes, 823 sequencing projects, and 248 publications.

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

International Nuclear Information System (INIS)

1988-03-01

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

Projecting meat and cereals demand for China based on a meta-analysis of income elasticities

OpenAIRE

Zhou, De; 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, ...

Occurrence of Methylmercury in Rice-Based Infant Cereals and Estimation of Daily Dietary Intake of Methylmercury for Infants.

Science.gov (United States)

Cui, Wenbin; Liu, Guangliang; Bezerra, Mayara; Lagos, Danielle A; Li, Yanbin; Cai, Yong

2017-11-08

Recent reports of elevated levels of methylmercury (MeHg) in rice revealed the possible occurrence of MeHg in infant rice cereals, leading to potential MeHg exposure through cereal consumption. Total mercury (THg) and MeHg levels in 119 infant cereal samples commonly marketed in the United States and China and estimated daily intake of MeHg through cereal consumption were determined. Concentrations of THg and MeHg in the tested cereal samples ranged from 0.35 to 15.9 μg/kg and from 0.07 to 13.9 μg/kg with means of 2.86 and 1.61 μg/kg, respectively. Rice-based cereals contained MeHg levels significantly higher than those of nonrice cereals, indicating that MeHg in rice could be source of MeHg in cereals. Cereal consumption could be a potential pathway of MeHg exposure for infants, as the EDI through cereal consumption amounted to 4-122% of the MeHg reference dose, suggesting the necessity of further evaluation of the potential health risk of dietary MeHg exposure to infants.

GenColors-based comparative genome databases for small eukaryotic genomes.

Science.gov (United States)

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Trace Metals in Vegetables and Cereals- A Case Study of Indian Market-2016

Directory of Open Access Journals (Sweden)

Abaidya Nath Singh

2017-03-01

Full Text Available Background & Aims of the Study: Vegetables and Cereals are considered vital for properly-balanced diet given that they deliver vitamins, minerals, nutritional fiber, and phytochemicals. This study aimed to assess the concentration of As, Cu, Cd, Pb, Cr and Hg in common vegetables and cereals in urban open markets in Varanasi district, India Materials & Methods: Total 260 edible portions of vegetable samples of 13 species were collected in March to October, 2016 from predefined market sites. These samples classified into roots, stems, leafy vegetables, fruits, and legumes. These samples (unwashed, acetic acid washed and boiled were assessed using atomic absorption spectrophotometer. The statistical evaluations were carried out using the IBM SPSS 21. Results: The results obtained reveal that unwashed vegetables and cereals as compared to washed and boiled samples contain higher trace metal concentration. The order of heavy metal concentration was observed in Cu>Pb>Cd>As in vegetable and cereals samples. Hg and Cr were not detected in any samples. The mean value of Cu, Cd and Pb in unwashed and washed vegetables and cereals were lower than PFA standard except As, whereas in boiled vegetables and cereals are lower than PFA standard but the mean value of Cd and Pb were many folds higher than the EU standard at all the market site samples. Leafy vegetables were found to contain the highest metals values especially Spinacia oleracea followed by roots vegetable like Brassica rapa, at all the studied sites. The market sites MS3 located in the vicinity of industrial zone and in proximity to national highway showed elevated levels of trace metals concentration in the vegetables and cereals as compared to other market sites. Conclusions: The results showed that, the As, Cu, Cd and Pb concentration were reduced to about 12.5%, 5.87%, 11.36% and 10.42% of the initial concentrations by 2% acetic acid washing and to 25%, 21.87%, 20.45% and 16.67% of the initial

Surgimiento y desarrollo de cosechadoras de cereales. Caso de estudio Cuba

Directory of Open Access Journals (Sweden)

Idalberto Macías Socarrás

2017-05-01

Full Text Available En el presente trabajo se hace una reseña histórica acerca del surgimiento y desarrollo de las cosechadoras de cereales en el mundo, su introducción en Cuba, así como el papel que se ha jugado en el desarrollo de estas máquinas, en este artículo se tratan los equipos empleados para la recolección de cultivos aprovechados por sus granos, fundamentalmente los cereales (trigo, cebada, avena, centeno, maíz, sorgo, arroz, Adicionalmente, se explicarán aspectos de las cosechadoras: la evolución histórica de la recolección de cereales y, finalmente, los elementos básicos que forman parte de estas máquinas, modo de funcionamiento, regulación y pérdidas. Además, de exponer los elementos y componentes más habituales de las cosechadoras, se incluye especialmente las novedades y avances técnicos que se empiezan a implantar en las cosechadoras, como pueden ser los sistemas de trilla forzada, la separación rotativa, los sensores electrónicos de rendimiento.   Abstract In this paper, a historical review is made of the emergence and development of cereal harvesters in the world, their introduction in Cuba, as well as the role played in the development of these machines, this article deals with the equipment (Cereals, wheat, barley, oats, rye, maize, sorghum, rice, aspects of harvesters will also be explained: the historical evolution of cereal harvesting and, finally, The basic elements that are part of these machines, mode of operation, regulation and losses. In addition, to exposing the most common elements and components of combine harvesters, special mention is made of the novelties and technical advances that are beginning to be introduced in harvesters, such as forced threshing systems, rotary separation, and electronic performance sensors.

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.

9 CFR 318.15 - Tagging chemicals, preservatives, cereals, spices, etc., “U.S. retained.”

Science.gov (United States)

2010-01-01

..., cereals, spices, etc., âU.S. retained.â 318.15 Section 318.15 Animals and Animal Products FOOD SAFETY AND...; 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 intended...

Survival and growth of Enterobacter sakazakii in infant cereal as affected by composition, reconstitution liquid, and storage temperature.

Science.gov (United States)

Lin, Li-Chun; Beuchat, Larry R

2007-06-01

Invasive infections caused by Enterobacter sakazakii have occurred predominantly in low-birth-weight neonates and infants younger than 2 months of age. However, infections have also occurred in healthy infants up to 8 months of age and in immunocompromised children up to 4 years of age. The ability of E. sakazakii to survive and grow in infant cereals as affected by composition of the cereal, composition of the reconstitution liquid, and temperature is unknown. A study was done to determine the survival and growth characteristics of E. sakazakii initially at populations of 0.005 and 0.52 CFU/ml of infant rice cereal, oatmeal cereal, or rice with mixed fruit cereal reconstituted with water, milk, or apple juice. Reconstituted cereals were stored at 4, 12, 21, and 30 degrees C, and populations were monitored for up to 72 h. Growth did not occur in reconstituted cereals stored at 4 degrees C or in cereals reconstituted with apple juice and stored at 12 degrees C. Populations (> or =1 CFU/ml) were detected in cereals reconstituted with water or milk and stored at 12, 21, and 30 degres C for 24, 8, and 4 h, respectively. The composition of infant cereals did not markedly affect the survival or growth of E. sakazakii in reconstituted cereals. Populations of E. sakazakii in reconstituted cereal decreased with increases in populations of mesophilic aerobic microflora up to 8 to 9 log CFU/ml, which was concurrent with decreases in pH. E. sakazakii, initially at 2.62 log CFU/ml of rice cereal reconstituted with apple juice (pH 4.32), survived at 40C for at least 14 days. The pathogen grew at 21 and 30 degrees C within 2 days and then decreased to undetectable levels (<1 CFU/10 ml) in cereal stored at 21 degrees C for 5 days or 30'C for 4 days. Initially, at 7.32 log CFU/ml, E. sakazakii was detected in rice cereal stored at 4 degrees C for 50 days. It is recommended that reconstituted infant cereals stored at 21 or 30 degrees C be discarded within 4 h after preparation or

Panthaleus major /Duges/ of cereals in Bulgaria

Directory of Open Access Journals (Sweden)

V. Maneva

2016-12-01

Full Text Available Abstract. Until recently, Penthaleus major (Dugès has not been recognized as an economically significant pest for the cereal crops. After climatic changes, its population began to grow and inflict damages around the world. The aim of this study was to investigate its distribution in Bulgaria and establish whether it presents a danger to the cereal crops. In the autumn of 2015 and the spring of 2016, a monitoring survey was conducted to establish Penthaleus major (Dugès with the cereal crops in Bulgaria. Over 60 sowed fields were investigated from all around the country. Samples were taken to identify the pest. It was established that Penthaleus major (Dugès inflicted harm to the wheat in north-eastern (12-14 mites per stem and south-eastern Bulgaria (6-8 mites per stem. Its density was under the threshold of economic harm. There was not found infestation of barley, rye, oat and triticale. On the field boundaries bordering the areas attacked by the mite were reported the following weeds: Capsella bursa pastoris (L. Medic, Descurania sophia (L. Welb. et Berth, Senecio spp., Sisymbrium orientale Torn., Taraxsacum officinale Weber, Anthemis spp., Bromus arvensis L., Eragrostis pilosa (L. P.B. Lolium temulentum L., which can be habitat for Penthaleus major (Dugès.

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.

Diuraphis noxia (Kurdjumov) - a New Pest of Cereals in Croatia

OpenAIRE

Tanja Gotlin Čuljak; Jasminka Igrc Barčić

2002-01-01

The first finding of the Russian Wheat Aphid (RWA), Diuraphis noxia Kurdjumov in Croatia was registered in 1999. This insect is important pest of cereals (specially in wheat and barley) in USD and South Africa. Information on morphometrie allows a differentiation to other similar-looking species. The distribution of the species is briefly demonstrated. Damage to small grain cereals, range of host plants and possible strategies to control the aphids are presented.

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...

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

of several cues and dimensions in their evaluation of the perceived quality of bread, cookies, breakfast cereals, pasta and vodka. Portuguese and Lithuanians consistently gave a significantly higher average importance to all the cues and quality dimensions considered, for all products, than their Danish...... 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...

A cross-cultural study of cereal foods' quality perception

DEFF Research Database (Denmark)

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

of several cues and dimensions in their evaluation of the perceived quality of bread, cookies, breakfast cereals, pasta and vodka. Portuguese and Lithuanians consistently gave a significantly higher average importance to all the cues and quality dimensions considered, for all products, than their Danish...... 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...

Suitability of cereal porridges as substrate for probiotic strain Lactobacillus rhamnosus GG

Directory of Open Access Journals (Sweden)

Ľubomír Valík

2013-02-01

Full Text Available 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 suspension after sterilization and cooling,. Fermentation was led stationary at 37 °C for 48 hours and viable cell count, pH value, titratable acidity and organic acids were analysed. Metabolic activity of Lb. rhamnosus GG was influenced by inoculation level and by the type of cereal used. The cereals fermented by lactic acid bacteria, especially probiotic strains, might broaden the offer of probiotic products for those suffering from milk allergy.doi:10.5219/242 Normal 0 21 false false false SK X-NONE X-NONE

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

OpenAIRE

La Hovary, C.; Danehower, D. A.; Ma, G.; Reberg-Horton, C.; Williamson, J. D.; Baerson, S. R.; Burton, J. D.

2016-01-01

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 tot...

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

Copper content in cereals grown in the model condition

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Ľuboš Harangozo

2017-01-01

Full Text Available The consumption of cereals in Slovakia but also worldwide is increasing by every year. From 30000 to 50000 tons of mercury circulates thought the biosphere that gets into the atmosphere degassing of the earth's crust and world oceans. Trace element as copper is one of the most efficient antioxidants in the body, often referred to as an element of beauty. It acts as a powerful catalyst for many enzymes and vitamins, through which already small amounts affects many activities in the body (strengthens immunity, reduces levels of histamine. It accumulates in the barley, beans, cucumber, nuts or milk and so on. The aim of our work was the evaluation of transfer of mercury from sludge to edible part of chosen cereals. The objectives were achieved in simulated conditions of growing pot experiment. We used agricultural soil from the location of Výčapy - Opatovce for the realization of the experiment. The sludge, which was added at various doses, was taken from Central Spiš area from locality of Rudňany near the village where minedironore that contains mainly cooper and mercury during last few decades was. We used three types of cereals: barley (Hordeum sativum L. variety PRESTIGE, spring wheat (Triticum aestivum L. variety ISJARISSA and oat (Avena sativa L. variety TATRAN. The length of growing season was 90 days. From the obtained results of two years can be concluded that the accumulation of cooper by seed follows barley ˂ oat ˂ wheat. Even though that the barley is characterized by the highest accumulation of cooper in the seeds, the content did not exceed the maximum level specified by The Codex Alimentarius of the Slovak Republic (CA SR. The results shows that the suitable cultivation of the cereals in localities, which are contaminated with heavy metals, especially by cooper, that the high content of cooper in soil do not pose a risk of accumulation of the metal into the cereal grain.

Developments in breeding cereals for organic agriculture

DEFF Research Database (Denmark)

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

2008-01-01

into the crop can be helped by diversification within the crop, allowing complementation and compensation among plants. Although the problems of breeding cereals for organic farming systems are large, there is encouraging progress. This lies in applications of ecology to organic crop production, innovations......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...

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

2013-09-04

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.

Breakfast cereal industry pledges to self-regulate advertising to youth: will they improve the marketing landscape?

Science.gov (United States)

Schwartz, Marlene B; Ross, Craig; Harris, Jennifer L; Jernigan, David H; Siegel, Michael; Ostroff, Joshua; Brownell, Kelly D

2010-04-01

In 2007, the Council of Better Business Bureaus created the Children's Food and Beverage Advertising Initiative to improve the nutritional profile of products marketed to children in the United States. We provide quantitative baseline data describing (a) the amount of child-directed breakfast cereal advertising in 2007; (b) an assessment of the nutritional value for all cereals advertised on television; and (c) the relationship between nutrition quality and child exposure to television advertising for major cereal brands. In 2007, the average American child viewed 757 cereal ads, and 98 per cent of these ads promoted unhealthy cereals that would be prohibited from advertising to children in the United Kingdom. Healthy cereals were advertised in 2007 in the United States, but adults, not children, were predominantly exposed to these ads. These quantitative methods can be used in the future to evaluate the impact of industry self-regulation efforts to improve the marketing landscape.

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

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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.

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

Science.gov (United States)

Kumar, Mukesh; Gantasala, Nagavara Prasad; Roychowdhury, Tanmoy; Thakur, Prasoon Kumar; Banakar, Prakash; Shukla, Rohit N; Jones, Michael G K; Rao, Uma

2014-01-01

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.

Acrylamide exposure among Turkish toddlers from selected cereal-based baby food samples.

Science.gov (United States)

Cengiz, Mehmet Fatih; Gündüz, Cennet Pelin Boyacı

2013-10-01

In this study, acrylamide exposure from selected cereal-based baby food samples was investigated among toddlers aged 1-3 years in Turkey. The study contained three steps. The first step was collecting food consumption data and toddlers' physical properties, such as gender, age and body weight, using a questionnaire given to parents by a trained interviewer between January and March 2012. The second step was determining the acrylamide levels in food samples that were reported on by the parents in the questionnaire, using a gas chromatography-mass spectrometry (GC-MS) method. The last step was combining the determined acrylamide levels in selected food samples with individual food consumption and body weight data using a deterministic approach to estimate the acrylamide exposure levels. The mean acrylamide levels of baby biscuits, breads, baby bread-rusks, crackers, biscuits, breakfast cereals and powdered cereal-based baby foods were 153, 225, 121, 604, 495, 290 and 36 μg/kg, respectively. The minimum, mean and maximum acrylamide exposures were estimated to be 0.06, 1.43 and 6.41 μg/kg BW per day, respectively. The foods that contributed to acrylamide exposure were aligned from high to low as bread, crackers, biscuits, baby biscuits, powdered cereal-based baby foods, baby bread-rusks and breakfast cereals. Copyright © 2013 Elsevier Ltd. All rights reserved.

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Science.gov (United States)

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Textural characteristics of ready-to-eat breakfast cereals produced from different types of cereal and with varying water addition during extrusion process

Directory of Open Access Journals (Sweden)

Žaneta Ugarčić-Hardi

2010-01-01

Full Text Available Textural characteristics of ready-to-eat breakfast cereals were evaluated in order to determine the influence of wheat, corn and rice flour, as well as a varying water addition during the extrusion process. Extruded breakfast cereal balls were made of wheat semolina in combination with wheat, corn or rice flour. Three different levels of water addition (21 %, 23 % and 27 % were used during the extrusion process. Samples were prepared with and without surface sugar coating. Sensory and instrumental assessments (TA.XT Plus were used to evaluate textural attributes of dry samples and samples during immersion in milk. Weibull equation was used for nonlinear estimation of experimental data obtained for milk absorption and crispiness as a function of time. Crispiness of dry extruded balls without coating was much higher than for samples with coating. The highest values for crispness were observed for wheat extruded balls and the lowest for samples with corn flour addition. Increasing water addition during the extrusion process significantly increased crispness of ready-to-eat breakfast cereals. The rate of milk absorption and loss of crispiness were significantly higher for samples without coating than for samples with coating.

Wholegrain cereals and bread: a duet of the Mediterranean diet for the prevention of chronic diseases.

Science.gov (United States)

Gil, Angel; Ortega, Rosa M; Maldonado, José

2011-12-01

The promotion of healthy lifestyles is one of the major goals of governments and international agencies all over the world. Wholegrain cereals are rich in nutrients and many phytochemical compounds, with recognised benefits for health, including dietary fibre, a number of phenolic compounds, lignans, vitamins and minerals and other bioactive components. The aim of the present work is to review the fundamental studies that support the consumption of wholegrain cereals and bread to prevent chronic diseases. Descriptive review considering human studies. Subjects included in randomised intervention trials and cohort studies from different countries published up to 2010. Several studies show consistently that subjects who ingest three or more portions of foods per day based on wholegrain cereals have a 20-30 % lower risk of CVD than subjects who ingest low quantities of cereals. This level of protection is not observed with the ingestion of refined cereals, these being even higher than with the intake of fruit and vegetables. Likewise, high intake of wholegrain cereals and their products, such as whole-wheat bread, is associated with a 20-30 % reduction in the risk of type 2 diabetes. Finally, protection against the risk of colorectal cancer and polyps, other cancers of the digestive tract, cancers related to hormones and pancreatic cancer has been associated with the regular consumption of wholegrain cereals and derived products. The regular intake of wholegrain cereals can contribute to reduction of risk factors related to non-communicable chronic diseases.

Dietary fibre fractions in cereal foods measured by a new integrated AOAC method.

Science.gov (United States)

Hollmann, Juergen; Themeier, Heinz; Neese, Ursula; Lindhauer, Meinolf G

2013-10-01

The reliable determination of soluble, insoluble and total dietary fibre in baked goods and cereal flours is an important issue for research, nutritional labelling and marketing. We compared total dietary fibre (TDF) contents of selected cereal based foods determined by AOAC Method 991.43 and the new AOAC Method 2009.01. Fifteen bread and bakery products were included in the study. Our results showed that TDF values of cereal products determined by AOAC Method 2009.01 were always significantly higher than those determined by AOAC Method 991.43. This was explained by the inclusion of low molecular weight soluble fibre fractions and resistant starch fractions in the TDF measurement by AOAC 2009.01. This documents that nutritional labelling of cereal products poses the challenge how to update TDF data in nutrient databases in a reasonable time with an acceptable expenditure. Copyright © 2013. Published by Elsevier Ltd.

Purchases of ready-to-eat cereals vary across US household sociodemographic categories according to nutritional value and advertising targets.

Science.gov (United States)

Castetbon, Katia; Harris, Jennifer L; Schwartz, Marlene B

2012-08-01

To describe ready-to-eat (RTE) cereal purchases in 2008 in the USA according to cereal nutritional quality and marketing strategy and household sociodemographic characteristics. Cross-sectional study of purchases in one year. Each type of cereal was assigned to one of four nutrition quality categories (based on Nutrient Profile Index, NPI) and one of four advertising categories based on television exposure and analysis of packaging (child-targeted, family-targeted, adult-targeted and no television advertising). Medians and distributions of purchase indicators were calculated for the cereal categories and the distributions were compared across sociodemographic groups. RTE cereals (n 249) with complete label and nutritional content. RTE cereal purchases according to household sociodemographic characteristics obtained from Nielsen Homescan, a nationally representative panel of households. Purchases of RTE cereals were highest in households with one or more child and lowest in African-American and Asian households, as well as those earning advertised products, advertised child-targeted cereals were purchased thirteen times more frequently; family-targeted brand purchases were ten times higher; and adult-targeted cereals were purchased four times more frequently. Our findings suggest that improving the nutritional quality of RTE cereals with advertising targeted to children could also lead to increased consumption of healthier products by young people.

Les Malalties dels cereals

OpenAIRE

Puiggrós i Jové, Josep Maria

1989-01-01

En aquest treball es fa una descripció de les principals malalties dels cereals que han estat trobades a Catalunya. Agrupant-les segons ataquin la fulla i espiga: oïdi, rovells, septòries, Rhynchosporium, Helminthosporium, i virus; al coll i tija: Cercosporella, Ophiobolus, Rhizoctbnia i Fusarium o bé les que vénen de la llavor: carbons, càries i Helminthospbrium. A part de la descripció, hom fa esment de les observacions efectuades els darrers anys en els diferents indrets de...

Evaluation of iron bioavailability in a mixture of cereals, seeds, and grains ("Human Ration"

Directory of Open Access Journals (Sweden)

Bárbara Nery Enes

2014-03-01

Full Text Available Iron bioavailability was evaluated in three mixtures of cereals, seeds, and grains ("Human Ration": light, regular, and homemade provided to rats. The animals received an iron depletion diet for 21 days, followed by a repletion diet containing 12 mg·kg-1 of iron for 14 days. The hemoglobin regeneration efficiency and the relative biological value did not differ between the light mixture and control group. The iron bioavailability of the light mixture of cereals, seeds, and grains and the control group were 99.99±27.62 and 80.02±36.63, respectively, while the regular and homemade mixtures of cereals, seeds, and grains showed lower iron bioavailability, 50.12±35.53 and 66.66±15.44, respectively; the iron content of the diet with light cereal mixture light was statistically similar to that of the control (ferrous sulfate 99.99±27.62. The high content of tannin (202.81±19.53 mg·100-1 in the diet with the regular cereal mixture may have contributed to its low iron bioavailability. The higher intake of soluble fiber by the animals fed the light mixture (21.15±0.92 g was moderately correlated (r=0.5712, p=0.0018 with the concentration of propionate in the caecal bulk (65.49±11.08 µmol/g. The short chain fatty acids produced by soluble fiber fermentation, associated with the low-content of tannin may have improved iron solubility and absorption in the light cereal mixture diet. The iron bioavailability in the light mixture of cereals, seeds, and grains was similar to that of ferrous sulfate.

Induced mutants for cereal grain protein improvement

International Nuclear Information System (INIS)

1982-01-01

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

Involvement of Disperse Repetitive Sequences in Wheat/Rye Genome Adjustment

Directory of Open Access Journals (Sweden)

Manuela Silva

2012-07-01

Full Text Available 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 in triticale and in wheat-rye addition lines that have the entire wheat genome plus each rye chromosome pair. Through Random Amplified Polymorphic DNA (RAPD analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental genomes. Moreover, the sequential nature of those events was revealed by the increased absence of rye-origin bands in wheat-rye addition lines in comparison with triticale. Remodeled band sequencing revealed that both repetitive and coding genome domains are affected in wheat-rye hybrid genotypes. Additionally, the amplification and sequencing of pSc20H internal segments showed that the disappearance of parental bands may result from restricted sequence alterations and unraveled the involvement of wheat/rye related repetitive sequences in genome adjustment needed for hybrid plant stabilization.

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

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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.

A phenome-based functional analysis of transcription factors in the cereal head blight fungus, Fusarium graminearum.

Directory of Open Access Journals (Sweden)

Hokyoung Son

2011-10-01

Full Text Available Fusarium graminearum is an important plant pathogen that causes head blight of major cereal crops. The fungus produces mycotoxins that are harmful to animal and human. In this study, a systematic analysis of 17 phenotypes of the mutants in 657 Fusarium graminearum genes encoding putative transcription factors (TFs resulted in a database of over 11,000 phenotypes (phenome. This database provides comprehensive insights into how this cereal pathogen of global significance regulates traits important for growth, development, stress response, pathogenesis, and toxin production and how transcriptional regulations of these traits are interconnected. In-depth analysis of TFs involved in sexual development revealed that mutations causing defects in perithecia development frequently affect multiple other phenotypes, and the TFs associated with sexual development tend to be highly conserved in the fungal kingdom. Besides providing many new insights into understanding the function of F. graminearum TFs, this mutant library and phenome will be a valuable resource for characterizing the gene expression network in this fungus and serve as a reference for studying how different fungi have evolved to control various cellular processes at the transcriptional level.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

Science.gov (United States)

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Properties of duck meat sausages supplemented with cereal flours.

Science.gov (United States)

Yang, H S; Ali, M S; Jeong, J Y; Moon, S H; Hwang, Y H; Park, G B; Joo, S T

2009-07-01

Duck meat sausages were prepared using 10% beef fat (FDS) and 10% hydrated cereal flours including rice (RDS), wheat, corn, millet, and barley to replace fat. Control duck sausages (DS) were also prepared only with duck meat and duck meat plus 10% beef fat. Results showed that protein and fat contents significantly decreased and total expressible fluid reduced with the addition of cereal flours in duck sausage batters. The FDS had higher fat content and lower pH compared with others. Duck sausages with 10% supplemented wheat flour showed the lowest cooking loss among sausages and had similar redness and chroma values to FDS and DS. Texture analysis indicated that hardness of duck sausage significantly decreased when cereal flours and beef fat were added. In particular, RDS showed the lowest values for all texture measurements compared with others. Result of moisture absorption capacity suggested that the decrease in hardness in RDS was due to higher moisture retention for rice flour treatment. Sensory evaluation indicated that DS had significantly lower overall acceptability than RDS, due to its off-flavor, whereas RDS had higher overall acceptability than DS.

Yield gaps and resource use across farming zones in the central rift valley of Ethiopia

NARCIS (Netherlands)

Getnet, Mezegebu; Ittersum, van Martin; Hengsdijk, Huib; Descheemaeker, Katrien

2016-01-01

In the Central Rift Valley (CRV) of Ethiopia, low productive cereal systems and a declining resource base call for options to increase crop productivity and improve resource use efficiency to meet the growing demand of food. We compiled and analysed a large amount of data from farmers’ fields

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

Science.gov (United States)

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

2012-10-13

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

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

Science.gov (United States)

Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

2018-04-12

The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

Fruit and cereal bioactives: sources, chemistry, and applications

National Research Council Canada - National Science Library

Tokusoglu, Ozlem; Hall, Clifford, III

2011-01-01

"Presenting up-to-date data in an easy-to-use format, this comprehensive overview of the chemistry of bioactive components of fruits and cereals addresses the role of these compounds in determining...

A comparison of the nutritional quality of organic and conventional ready-to-eat breakfast cereals based on NuVal scores.

Science.gov (United States)

Woodbury, Nancy J; George, Valerie A

2014-07-01

To identify whether there were differences in nutritional quality between organic and conventional ready-to-eat breakfast cereals of similar types, based on NuVal scores. The current descriptive study analysed NuVal scores for 829 ready-to-eat breakfast cereals and eighteen different cereal types. ANOVA was used to compare the mean NuVal scores of 723 conventional cereals with those of 106 organic cereals. Ready-to-eat breakfast cereals (n 829) with NuVal scores. Not applicable. There was no significant difference in NuVal scores between conventional (mean 28·4 (sd 13·4)) and organic (mean 30·6 (sd 13·2)) cereal types. Consumers who choose the organic version of a ready-to-eat breakfast cereal believing that nutritional quality is superior may not be making a valid assumption. Public health nutrition educators must help consumers understand that organic cereals are not necessarily more nutritious and their consumption could result in excessive intake of undesirable nutrients, such as fat, sugar and sodium.

Integration of genomic resources to uncover pleiotropic regions associated with age at puberty and reproductive longevity in sows

Science.gov (United States)

Commercial and experimental genetic resources were used to investigate genetic pleiotropic factors that influence age at puberty, litter-size and reproductive longevity. The phenotypes were complemented by high-density genotyping and whole genome and RNA sequencing. The SNPs from Porcine SNP60 BeadA...

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.

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.

Science.gov (United States)

Arnaiz, Olivier; Van Dijk, Erwin; Bétermier, Mireille; Lhuillier-Akakpo, Maoussi; de Vanssay, Augustin; Duharcourt, Sandra; Sallet, Erika; Gouzy, Jérôme; Sperling, Linda

2017-06-26

The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage. We generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource. We have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3' and 5' UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis

The association between consumption of breakfast cereals and BMI in schoolchildren aged 12-17 years: the VYRONAS study.

Science.gov (United States)

Kosti, Rena I; Panagiotakos, Demosthenes B; Zampelas, Antonis; Mihas, Costas; Alevizos, Alevizos; Leonard, Clare; Tountas, Yannis; Mariolis, Anargiros

2008-10-01

To evaluate whether consumption of breakfast cereals is associated with BMI in a sample of Greek adolescents. A cross-sectional health and nutrition survey. During 2004-5, 2008 schoolchildren aged 12-17 years were selected from twelve schools located in Vyronas region (Athens metropolitan area). Height and weight were measured and BMI was calculated. A semiquantitative FFQ was applied and multiple logistic regression analysis was used. Overall, 4.7% of boys and 1.7% of girls were obese, whereas 19.4% of boys and 13.2% of girls were overweight. Only 20.7% of boys and 15.5% of girls reported that they consume cereals as a first choice for breakfast. Consumption of breakfast cereals was associated with lower BMI in boys (P=0.08) and girls(P=0.019), irrespective of age and physical activity status. More prominent results were observed for daily cereal consumption or for more than two daily servings of cereals consumed for breakfast. Consumption of pre-sweetened breakfast cereals was associated with lower BMI compared with non-pre-sweetened or no intake of cereals, in both genders (PConsumption of breakfast cereals was associated with 33% (95% CI 14%, 48%) lower likelihood of overweight/obesity, irrespective of age, sex and physical activity status. Consumption of breakfast cereals was associated with lower BMI levels and a lower likelihood of overweight/obesity in both genders; thus a solid basis for public health professionals could be built when issuing advice on weight management.

Adjustment of Weed Hoeing to Narrowly Spaced Cereals

Directory of Open Access Journals (Sweden)

Jannis Machleb

2018-04-01

Full Text Available Weed hoeing can be successfully performed in wide row crops, such as sugar beet, maize, soybean and wide spaced cereals. However, little experience is available for hoeing in narrow cereal row spaces below 200 mm. Yet, mechanical weed control can pose an alternative to herbicide applications by reducing the herbicide resistant populations present in the field. In this experiment, it was investigated whether hoeing is feasible in cereals with 150 and 125 mm row spacings. The trial was set up at two locations (Ihinger Hof and Kleinhohenheim in southwest Germany. Three different conventional hoeing sweeps, a goosefoot sweep, a no-till sweep and a down-cut side knife were adjusted to the small row widths, and hoeing was performed once with a tractor and a standard hoeing frame which was guided by a second human operator. The average grain yield, crop and weed biomass, and weed control efficacy of each treatment were recorded. The goosefoot and no-till sweep were tested at driving speeds of 4 and 6 km·h−1. The down-cut side knife was applied at 4 km·h−1. The results indicate that hoeing caused no yield decrease in comparison to a conventional herbicide application or manual weeding. The highest yield with a mechanical treatment was recorded for the no-till sweeps at both trial locations. Hoeing was performed successfully in narrowly spaced cereals of 150 and 125 mm, and the weed control efficacy of the mechanical treatments ranged from 50.9% at Kleinhohenheim to 89.1% at Ihinger Hof. Future experiments are going to focus on more distinct driving speeds ranging from 2 to 10 km·h−1 and performing more than one pass with the hoe. Additionally, combining the mechanical weeding tools with a camera-steered hoeing frame could increase accuracy, allow for higher working speeds and substitute the second human operator guiding the hoe.

Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

Science.gov (United States)

Wisniewski-Dyé, Florence; Lozano, Luis; Acosta-Cruz, Erika; Borland, Stéphanie; Drogue, Benoît; Prigent-Combaret, Claire; Rouy, Zoé; Barbe, Valérie; Mendoza Herrera, Alberto; González, Victor; Mavingui, Patrick

2012-01-01

Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation. PMID:24705077

Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

Directory of Open Access Journals (Sweden)

Victor González

2012-09-01

Full Text Available Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510. The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis, and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.

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.

Physicochemical, nutritive and safety evaluation of local cereal ...

African Journals Online (AJOL)

SARAH

2014-11-30

Nov 30, 2014 ... practices and good manufacturing processing should be considered. Such initiatives need to be carried amongst local cereal producers to help minimize food safety risk and ... potential for contamination and deterioration with.

Relative severity of fumonisin contamination of cereal crops in West Africa.

Science.gov (United States)

Vismer, Hester F; Shephard, Gordon S; Rheeder, John P; van der Westhuizen, Liana; Bandyopadhyay, Ranajit

2015-01-01

Traditional and improved varieties of maize, pearl millet and sorghum were planted by small-scale farmers under the direction of the International Institute for Tropical Agriculture in two Nigerian agro-ecological zones: the Sudan Savanna and the Northern Guinea Savanna. Samples were collected for the determination of Fusarium infection and fumonisin (B1, B2 and B3) contamination. A previous paper reported Aspergillus infection and aflatoxin contamination of these samples. Fusarium infection levels, measured by per cent kernels infected, were modest with mean levels for the above cereals of 16% ± 11% (SD), 12% ± 7% and 13% ± 16%, respectively. However, the Fusarium species recovered from maize were predominantly the fumonisin producers F. verticillioides and F. proliferatum, together making an infection rate of 15% ± 10%, whereas these species were present to a limited extent only in the other two cereals, 1% ± 1% for pearl millet and 2% ± 6% for sorghum. Fumonisin contamination was variable but reflected the diversity of Fusarium producers in these three cereals. Mean levels were 228 ± 579 µg kg(-1) (range fumonisins in maize as well as in the traditional African cereals, millet and sorghum (89% co-occurrence across all three cereals). The low fumonisin levels may be ascribed to the use of good agricultural practices. Of the Fusarium species present, those in maize consisted mainly of fumonisin producers, the opposite of what was observed in pearl millet and sorghum. It is concluded that replacement of maize by pearl millet and sorghum could improve food safety with regards to aflatoxin B and fumonisin B exposure.

Pipeline to upgrade the genome annotations

Directory of Open Access Journals (Sweden)

Lijin K. Gopi

2017-12-01

Full Text Available Current era of functional genomics is enriched with good quality draft genomes and annotations for many thousands of species and varieties with the support of the advancements in the next generation sequencing technologies (NGS. Around 25,250 genomes, of the organisms from various kingdoms, are submitted in the NCBI genome resource till date. Each of these genomes was annotated using various tools and knowledge-bases that were available during the period of the annotation. It is obvious that these annotations will be improved if the same genome is annotated using improved tools and knowledge-bases. Here we present a new genome annotation pipeline, strengthened with various tools and knowledge-bases that are capable of producing better quality annotations from the consensus of the predictions from different tools. This resource also perform various additional annotations, apart from the usual gene predictions and functional annotations, which involve SSRs, novel repeats, paralogs, proteins with transmembrane helices, signal peptides etc. This new annotation resource is trained to evaluate and integrate all the predictions together to resolve the overlaps and ambiguities of the boundaries. One of the important highlights of this resource is the capability of predicting the phylogenetic relations of the repeats using the evolutionary trace analysis and orthologous gene clusters. We also present a case study, of the pipeline, in which we upgrade the genome annotation of Nelumbo nucifera (sacred lotus. It is demonstrated that this resource is capable of producing an improved annotation for a better understanding of the biology of various organisms.

Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries

Science.gov (United States)

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 such as SSRs, SNPs and InDels in several model and non-model plant species. Yam (Dioscorea spp.) i...

The Need for Cooperation in Cereal Research

NARCIS (Netherlands)

Kamp, J.W. van der

2004-01-01

The trends and needs in cereal research as discussed in 2003 AACC annual meeting are presented. The seminar identified the need of feeding a growing world population with less arable land and under more adverse agronomic conditions. An urgent need of eliminating mycotoxins and coeliac diseases to

Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

Science.gov (United States)

Smith, David Roy

2017-05-01

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.

Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

Science.gov (United States)

Tzika, Athanasia C; Ullate-Agote, Asier; Grbic, Djordje; Milinkovitch, Michel C

2015-07-01

Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The eastern oyster genome: A resource for comparative genomics in shellfish aquaculture species

Science.gov (United States)

Oyster aquaculture is an important sector of world food production. As such, it is imperative to develop a high quality reference genome for the eastern oyster, Crassostrea virginica, to assist in the elucidation of the genomic basis of commercially important traits. All genetic, gene expression and...

Preventive and therapeutic potential of peptides from cereals against cancer.

Science.gov (United States)

Ortiz-Martinez, Margarita; Winkler, Robert; García-Lara, Silverio

2014-12-05

Epidemiological studies have shown that regular consumption of food based on whole-grain cereals and their products is associated with reduced risks of various types of degenerative chronic diseases. Food proteins are considered an important source of nutraceutical peptides and amino acids that can exert biological functions to promote health and prevent disease, including cancer. There have been several reports on peptides with anti-tumour activity in recent years. Plant-derived peptides, such as rapeseed, amaranth and soybean lunasin have received main attention. In this review, we extend this vision to analyse the evidence of current advances in peptides in cereals such as wheat, maize, rice, barley, rye and pseudocereals compared with soybean. We also show evidence of several mechanisms through which bioactive peptide exerts anti-tumour activity. Finally, we report the current status of major strategies for the fractionation, isolation and characterisation of bioactive peptides in cereals. In recent reports, it has been shown that peptides are an interesting alternative in the search for new treatments for cancer. One of the most studied sources of these peptides is food proteins; however, a review that includes more recent findings for cereals as a potential source of bioactive peptides in the treatment of cancer, the techniques for their isolation and characterisation and the assays used to prove their bioactivity is not available. This review can be used as a tool in the search for new sources of anti-cancer peptides. The authors have no conflicts of interest, financial or otherwise. Copyright © 2014 Elsevier B.V. All rights reserved.

Optimization of the composition of the powdered cereal sprouts mixtures

Directory of Open Access Journals (Sweden)

Tumbas-Šaponjac Vesna T.

2016-01-01

Full Text Available Sprouts of cereals have received significant attention as functional food due to their nutritional and functional value. Consumption of sprouts has become increasingly popular among people interested in improving and maintaining their health status by changing dietary habits. Cereal grains contain several classes of phytochemicals, i.e. phenolics, chlorophylls, and carotenoids. However, their nutritional and chemical profile is altered and improved during germination. The purpose of this study was to find the best ratio of the powdered wheat (WS, oat (OS and barley (BS sprouts for designing the cereal sprout mixture (CSM with the highest total phenolic content (TPh and antioxidant capacity (AC, using Simplex-Centroid experimental design and response surface methodology (RSM. Single- and multi-response optimizations showed that OS did not contribute to TPh or AC values of CSM and, therefore, was not included in any of the compositions of the optimized CSM. Single-response optimizations showed that the highest TPh was found for CSM containing 82% BS and 18% WS, while the best AC was found for pure BS. The predicted ratio of cereal sprout powders in CSM obtained by multi-response optimization was: 96% BS and 4% WS. This mixture possessed the highest predicted TPh and AC (372.32 mg GAE/100 g, 549.99 μmol TE/100 g, respectively, which was confirmed to be in accordance with the experimental values. Based on the results obtained in this study, a designed CSM is proposed as a convenient ingredient of functional food products, dietary supplements and nutraceuticals.

Probiotic potential of spontaneously fermented cereal based foods ...

African Journals Online (AJOL)

Probiotic potential of spontaneously fermented cereal based foods – A review. ... The realization that food has a role beyond provision of energy and body forming ... with growing interest in the research and development of functional foods.

Reference-quality genome sequence of Aegilops tauschii, the source of wheat D genome, shows that recombination shapes genome structure and evolution

Science.gov (United States)

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat and an important genetic resource for wheat. A reference-quality sequence for the Ae. tauschii genome was produced with a combination of ordered-clone sequencing, whole-genome shotgun sequencing, and BioNano optical geno...

Non-Alcoholic Beverages from Fermented Cereals with Increased Oligosaccharide Content

Directory of Open Access Journals (Sweden)

Grazina Juodeikiene

2016-01-01

Full Text Available The aim of this study is to develop a new technology for making traditional Lithuanian non-alcoholic beverage kvass from fermented cereals by extending the spectrum of raw materials (extruded rye and applying new biotechnological resources (xylanolytic enzymes and lactic acid bacteria (LAB to improve its functional properties. Arabinoxylans in extruded rye were very efficiently hydrolysed into oligosaccharides by xylanolytic complex Ceremix Plus MG. Using Ceremix Plus MG and LAB fermentation, the yield of arabinoxylooligosaccharides and xylooligosaccharides in beverage was increased to 300 and 1100 mg/L, respectively. Beverages fermented by LAB had lower pH values and ethanol volume fraction compared to the yeast-fermented beverage. The acceptability of the beverage fermented by Lactobacillus sakei was higher than of Pediococcus pentosaceus- or yeast-fermented beverages and similar to the acceptability of commercial kvass made from malt extract. The results showed that extruded rye, xylanolytic enzymes and LAB can be used for production of novel and safe high-value non-alcoholic beverages.

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/.

A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

Science.gov (United States)

2012-01-01

Background The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia

Arthropod genomic resources for the 21st century

Science.gov (United States)

Genome references are foundational for high quality entomological research today. Species, sub populations and taxonomy are defined by gene flow and genome sequences. Gene content in arthropods is often directly reflective of life history, for example, diet and symbiont related gene loss is observed...

IMPACTS OF SOCIODEMOGRAPHIC VARIABLES ON THE IMPLICIT VALUES OF BREAKFAST CEREAL CHARACTERISTICS

OpenAIRE

Shi, Hongqi; Price, David W.

1998-01-01

The implicit values of nutrient and nonnutrient characteristics of breakfast cereal were estimated using the 1987-88 household portion of the USDAÂ’'s Nationwide Food Consumption Survey data. The effects of sociodemographic variables on cereal characteristic values were also estimated. The conceptual framework of the hedonic price model, used for food products, has traditionally focused on the nutritional characteristics of these products. This framework was extended to incorporate nonnutriti...

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

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.

The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

Science.gov (United States)

Harb, Omar S; Roos, David S

2015-01-01

Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.

Development and Life History of Sitophilus zeamais (Coleoptera: Curculionidae on Cereal Crops

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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.

Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

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Wang Jintu

2011-04-01

Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

Science.gov (United States)

2011-01-01

Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of

Online detection and quatification of ergot bodies in cereals using near infrared hyperspectral imaging

NARCIS (Netherlands)

Vermeulen, Ph.; Fernandez - Pierna, J.A.; Egmond, van H.P.; Dardenne, P.; Baeten, V.

2012-01-01

The occurrence of ergot bodies (sclerotia of Claviceps purpurea) in cereals presents a high toxicity risk for animals and humans due to the alkaloid content. To reduce this risk, the European Commission fixed an ergot concentration limit of 0.1% in all feedstuffs containing unground cereals, and a

Strategies of Transition to Sustainable Agriculture in Iran I- Improving Resources Use Efficiency

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Alireza Koocheki

2017-12-01

Full Text Available Introduction Fast switch to sustainable agriculture patterns is not impossible for many farmers. However to achieve perfect sustainable in agro-ecosystems which are friendly with environment, changing conventional to sustainable agriculture should be carried slowly. For this purpose, three effective steps were mentioned: first level is increasing of inputs efficiency such as fertilizer and chemical pesticides which used in conventional agriculture now. Second level is related to changing inputs by friendly environmental inputs as alternative inputs and the final level is redesigning of the agro-ecosystems that its function is based on series of ecological process. On the other hand, achieving sustainable agriculture requires higher efficiency of inputs and many process should be replaced by friendly environmental inputs with chemical inputs and new system is designed based on ecological principles. The objective of this study was to offer approaches for improving inputs use efficiency as first step to transition from conventional to sustainable agriculture. Material and Methods In order to evaluate the transition status from conventional to sustainable agriculture in agro-ecosystems of Iran, scientific resource and researches that was performed about increasing of inputs efficiency as first step to transition from conventional to sustainable agriculture was studied. For this purpose, 177 studies that had been performed about using different inputs and its efficiency in various crops were assessed. Applied inputs included water, nitrogen and herbicides and studied plants included cereals (wheat, barley, rice, maize and sorghum, beans (bean, pea and lentil, oil crops (canola, sunflower, safflower and sesame, medicinal plants, potato, sugar beet and cotton. In this study, average and range of inputs use efficiency in different crops and also the relationship between increasing of inputs application with their use efficiency was assessed. In the

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

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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.

Marketing sugary cereals to children in the digital age: a content analysis of 17 child-targeted websites.

Science.gov (United States)

Cheyne, Andrew D; Dorfman, Lori; Bukofzer, Eliana; Harris, Jennifer L

2013-01-01

The Institute of Medicine has warned of the harm of food marketing to children from television to new media channels such as the Internet. The authors identified and analyzed the techniques used to engage children on websites from cereal companies--the third largest food marketer to children. The authors found that top breakfast cereal manufacturers maintain child-oriented websites, using strategies unique to the Internet to capture and maintain children's attention. These include branded engagement techniques such as advergames, videos, site registration, and viral marketing, including inviting friends to join the site. The authors found 3 progressive levels of telepresence on child-targeted cereal websites: sites with more than 1 engaging feature, multiple techniques present on individual pages, and the construction of a virtual world. Using Internet traffic data, the authors confirm that these techniques work: cereal marketers reach children online with lengthier and more sophisticated engagements than are possible with traditional, passive media such as television advertisements or product packaging. Despite the cereal manufacturer's self-regulatory pledge to improve their marketing to children, their marketing practices exploit children's susceptibility to advertising by almost exclusively promoting high-sugar cereals using deeply engaging techniques.

Detection of alien genetic introgressions in bread wheat using dot-blot genomic hybridisation.

Science.gov (United States)

Rey, María-Dolores; Prieto, Pilar

2017-01-01

Simple, reliable methods for the identification of alien genetic introgressions are required in plant breeding programmes. The use of genomic dot-blot hybridisation allows the detection of small Hordeum chilense genomic introgressions in the descendants of genetic crosses between wheat and H. chilense addition or substitution lines in wheat when molecular markers are difficult to use. Based on genomic in situ hybridisation, DNA samples from wheat lines carrying putatively H. chilense introgressions were immobilised on a membrane, blocked with wheat genomic DNA and hybridised with biotin-labelled H. chilense genomic DNA as a probe. This dot-blot screening reduced the number of plants necessary to be analysed by molecular markers or in situ hybridisation, saving time and money. The technique was sensitive enough to detect a minimum of 5 ng of total genomic DNA immobilised on the membrane or about 1/420 dilution of H. chilense genomic DNA in the wheat background. The robustness of the technique was verified by in situ hybridisation. In addition, the detection of other wheat relative species such as Hordeum vulgare , Secale cereale and Agropyron cristatum in the wheat background was also reported .

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

KAUST Repository

Bracken-Grissom, Heather; Collins, Allen G.; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Monica; Messing, Charles; O'Brien, Stephen J.; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W.; Ryan, Joseph F.; Schulze, Anja; Worheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E.; Diaz, M. Christina; Evans, Nathaniel; Flot, Jean-Francois; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y.; Laberge, Tammy; Lavrov, Dennis; Michonneau, Francois; Moroz, Leonid L.; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A.; Rhodes, Adelaide; Rodriguez-Lanetty, Mauricio; Santos, Scott R.; Satoh, Nori; Thacker, Robert W.; Van de Peer, Yves; Voolstra, Christian R.; Welch, David Mark; Winston, Judith; Zhou, Xin

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

CyanoClust: comparative genome resources of cyanobacteria and plastids

OpenAIRE

Sasaki, Naobumi V.; Sato, Naoki

2010-01-01

Cyanobacteria, which perform oxygen-evolving photosynthesis as do chloroplasts of plants and algae, are one of the best-studied prokaryotic phyla and one from which many representative genomes have been sequenced. Lack of a suitable comparative genomic database has been a problem in cyanobacterial genomics because many proteins involved in physiological functions such as photosynthesis and nitrogen fixation are not catalogued in commonly used databases, such as Clusters of Orthologous Protein...

Weed infestation of crops in different soils in the protective zone of Roztocze National Park. Part I. Winter and spring cereals

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Marta Ziemińska-Smyk

2013-12-01

Full Text Available The study on weed infestation of crops in different soils in the protective zone of RPN was conducted in the years 1991-1995. The characterization of weed infestation of winter and spring cereals was based on 306 phytosociological records. made with the use of Braun-Blanquet method. The degree of weed infestation in the fields in the protective zone of RPN depended on environment conditions. Both winter and spring cereals in majority of soils were most infested by: Cenaturea cyanus, Apera spica-venti and Vicia hirsta. In the lightest podsolic soils, made of loose sand and slightly loamy sand. winter and spring cereals were additionally infested by Equisetum arvense and two acidophylic species: Seleranthus annuus and Spergula arvensis. The crops in brown loess soil were infested by Matricaria maritima subsp. inodora. The most difficult weed species in brown soil formed from gaizes and limestone soil were: Convolvulus arvensis, Papaver rhoeas and Galium aparine. Moreover winter cercals in limestone soil showed high or medium infestation with Consolida regalis, Aethusa cynapium, Lathyrus tuberosus and low infestation with Apera spica-venti and Centaurea cyanus. Spring cereals were less infested than winter cereals. Apera spica-venti and Centaurea cyanus were less common with spring cereals than with winter cereals. Also, spring cereals showed high or medium infestation with Convolvulus arvensis. Spring cereals in some soil units were infested by Chenopodium album and Stellaria media. There was also higher infestation of spring cereals in limestone soils with Avena fatua, Veronica persica, Sinapis arvensis and Sonchus arvensis, compared to winter cereals in limestone soils.

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

DEFF Research Database (Denmark)

Olesen, Jørgen E; Børgesen, Christen Duus; Elsgaard, Lars

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...

Effects of Ready-to-Eat-Cereals on Key Nutritional and Health Outcomes : A Systematic Review

NARCIS (Netherlands)

Priebe, Marion G.; McMonagle, Jolene R.

2016-01-01

Background In many countries breakfast cereals are an important component of breakfast. This systematic review assesses the contribution of consumption of ready-to eat cereal (RTEC) to the recommended nutrient intake. Furthermore, the effects of RTEC consumption on key health parameters are

Long Term Evaluation of Yield Stability Trend for Cereal Crops in Iran

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mehdi nassiri mahalati

2016-05-01

Full Text Available During the last few decades cereals yield have increased drastically at the national level however, information about yield stability and its resistance to annual environmental variability are scare. In this study long term stability of grin yield of wheat, barley, rice, corn and overall cereals in Iran were evaluated during a 40-year period (1971-2011. Stability analysis was conducted using two different methods. In the first method the residuals of regression between crop yield and time (years were calculated as stability index. For this different segmented regression models including linear, bi-linear and tri-linear were fitted to yield trend data and the best model for each crop was selected based on statistical measures. Absolute residuals (the difference between actual and predicted yields for each year as well as relative residuals (absolute residuals as percent of predicted yield were estimated. In the second method yield stability was estimated from the slope of the regression line between average annual yield of all cereals (environmental index and the yield of each crop in the same year. Results indicted that in wheat and barley absolute and relative residuals were increased during the study period leading to reduction of stability despite considerable yield increment. However, for rice and corn residuals followed a decreasing trend and therefore yield stability of these crops was increased during the last 40 years. The same result was obtained with the environmental index but in this method reduction of yield stability in barley was lower than wheat. Based on the results, yield and yield stability of cereals crops in Iran increased during the last 40 years. However, the percentage increase in stability is lower than that of yield. Application of nitrogen fertilizers was led to reduction in stability. Yield stability of wheat, barley, rice, corn and overall cereals was improved with increasing their cultivated area.

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

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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.

Implications of publicly available genomic data resources in searching for therapeutic targets of obesity and type 2 diabetes.

Science.gov (United States)

Jung, Sungwon

2018-04-20

Obesity and type 2 diabetes (T2D) are two major conditions that are related to metabolic disorders and affect a large population. Although there have been significant efforts to identify their therapeutic targets, few benefits have come from comprehensive molecular profiling. This limited availability of comprehensive molecular profiling of obesity and T2D may be due to multiple challenges, as these conditions involve multiple organs and collecting tissue samples from subjects is more difficult in obesity and T2D than in other diseases, where surgical treatments are popular choices. While there is no repository of comprehensive molecular profiling data for obesity and T2D, multiple existing data resources can be utilized to cover various aspects of these conditions. This review presents studies with available genomic data resources for obesity and T2D and discusses genome-wide association studies (GWAS), a knockout (KO)-based phenotyping study, and gene expression profiles. These studies, based on their assessed coverage and characteristics, can provide insights into how such data can be utilized to identify therapeutic targets for obesity and T2D.

How Does Gender Affect Sustainable Intensification of Cereal Production in the West African Sahel? Evidence from Burkina Faso.

Science.gov (United States)

Theriault, Veronique; Smale, Melinda; Haider, Hamza

2017-04-01

Better understanding of gender differences in the adoption of agricultural intensification strategies is crucial for designing effective policies to close the gender gap while sustainably enhancing farm productivity. We examine gender differences in adoption rates, likelihood and determinants of adopting strategy sets that enhance yields, protect crops, and restore soils in the West African Sahel, based on analysis of cereal production in Burkina Faso. Applying a multivariate probit model to a nationally representative household panel, we exploit the individual plot as unit of analysis and control for plot manager characteristics along with other covariates. Reflecting the socio-cultural context of farming combined with the economic attributes of inputs, we find that female managers of individual cereal fields are less likely than their male counterparts to adopt yield-enhancing and soil-restoring strategies, although no differential is apparent for yield-protecting strategies. More broadly, gender-disaggregated regressions demonstrate that adoption determinants differ by gender. Plot manager characteristics, including age, marital status, and access to credit or extension services do influence adoption decisions. Furthermore, household resources influence the probability of adopting intensification strategy sets differently by gender of the plot manager. Variables expressing the availability of household labor strongly influence the adoption of soil-restoring strategies by female plot managers. By contrast, household resources such as extent of livestock owned, value of non-farm income, and area planted to cotton affect the adoption choices of male plot managers. Rectifying the male bias in extension services along with improving access to credit, income, and equipment to female plot managers could contribute to sustainable agricultural intensification.

Essential and toxic heavy metals in cereals and agricultural products marketed in Kermanshah, Iran, and human health risk assessment.

Science.gov (United States)

Pirsaheb, Meghdad; Fattahi, Nazir; Sharafi, Kiomars; Khamotian, Razieh; Atafar, Zahra

2016-01-01

Levels of some essential and toxic heavy metals such as lead, cadmium, chromium, nickel, zinc and copper in cereals and agricultural products obtained from the markets in Kermanshah city, west Iran, were determined by inductively coupled plasma-optical emission spectrometry (ICP-OES). The average concentrations for lead and cadmium in some cereals were higher than the maximum levels set by the Codex Alimentarius. A potential human health risk assessment was conducted by calculating estimated weekly intake (EWI) of the metals from eating cereals and comparison of these values with provisional tolerable weekly intake (PTWI) values. In combination with recent cereal consumption data, the EWIs of heavy metals were calculated for the Kermanshah population. EWI data for the studied metals through cereal consumption were lower than the PTWI values. Cr, Ni, Zn and Cu levels in all samples analysed were within the ranges reported for similar cereals from various parts of the world.

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...... 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...... 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....

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

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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. .

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...

EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes.

Science.gov (United States)

Clasen, Frederick Johannes; Pierneef, Rian Ewald; Slippers, Bernard; Reva, Oleg

2018-05-03

Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2.0 algorithm. Using SWGIS v2.0, GIs are then identified in 36 fungal, 22 protozoan and 8 invertebrate genomes. SWGIS v2.0 predicts GIs in large eukaryotic chromosomes based on the atypical nucleotide composition of these regions. Averages for predicting false negative and false positive GIs were 20.1% and 11.01% respectively. A total of 10,550 GIs were identified in 66 eukaryotic species with 5299 of these GIs coding for at least one functional protein. The EuGI web-resource, freely accessible at http://eugi.bi.up.ac.za , was developed that allows browsing the database created from identified GIs and genes within GIs through an interactive and visual interface. SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes.

Development of Genomic Resources in the Species of Trifolium L. and Its Application in Forage Legume Breeding

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Leif Skøt

2012-05-01

Full Text Available Clovers (genus Trifolium are a large and widespread genus of legumes. A number of clovers are of agricultural importance as forage crops in grassland agriculture, particularly temperate areas. White clover (Trifolium repens L. is used in grazed pasture and red clover (T. pratense L. is widely cut and conserved as a winter feed. For the diploid red clover, genetic and genomic tools and resources have developed rapidly over the last five years including genetic and physical maps, BAC (bacterial artificial chromosome end sequence and transcriptome sequence information. This has paved the way for the use of genome wide selection and high throughput phenotyping in germplasm development. For the allotetraploid white clover progress has been slower although marker assisted selection is in use and relatively robust genetic maps and QTL (quantitative trait locus information now exist. For both species the sequencing of the model legume Medicago truncatula gene space is an important development to aid genomic, biological and evolutionary studies. The first genetic maps of another species, subterranean clover (Trifolium subterraneum L. have also been published and its comparative genomics with red clover and M. truncatula conducted. Next generation sequencing brings the potential to revolutionize clover genomics, but international consortia and effective use of germplasm, novel population structures and phenomics will be required to carry out effective translation into breeding. Another avenue for clover genomic and genetic improvement is interspecific hybridization. This approach has considerable potential with regard to crop improvement but also opens windows of opportunity for studies of biological and evolutionary processes.

Probiotic potentials of cereal-based beverages.

Science.gov (United States)

Enujiugha, Victor N; Badejo, Adebanjo A

2017-03-04

Probiotics offer remarkable potential for the prevention and management of various infective and noninfective disorders. They are reported to play key roles in the suppression of gastrointestinal infections, antimicrobial activity, improvement in lactose metabolism, reduction in serum cholesterol, immune system stimulation, antimutagenic properties, anticarcinogenic properties, anti-diarrheal properties, and improvement in inflammatory bowel disease. Although probiotic foods are classically confined to beverages and cheese, containing live organisms of the lactic acid bacteria family, such health-promoting foods are traditionally dairy-based, comprising milk and its fermented products. However, recent research focuses on the probiotic potentials of fermented cereal-based beverages which are especially consumed in developing countries characterized by low nutritional security and high incidence of gut pathogen infections. Moreover, lactose intolerance and cholesterol content associated with dairy products, coupled with the vegetarian tendencies of diverse populations in the third world, tend to enforce the recent recourse to nondairy beverages. Probiotic microorganisms are mostly of human or animal origin; however, strains recognized as probiotics are also found in nondairy fermented substrates. This review examines the potentials of some traditional cereal-based beverages to serve as probiotic foods, their microbial and functional properties, as well as their process optimization and storage for enhanced utilization.

Genetics of cereal adaptation to the man-made habitat

International Nuclear Information System (INIS)

De Wet, J.M.J.

1989-01-01

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

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Energy Technology Data Exchange (ETDEWEB)

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

2013-01-24

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

Genome-Wide Association Mapping for Cell Wall Composition and Properties in Temperate Grasses

DEFF Research Database (Denmark)

Bellucci, Andrea

with a wide range of chemical bounds. At present the interest in plant cell wall is growing due to the possibility to convert ligno-cellulosic biomass (e.g. agricultural residues) into bioethanol but also for the benefits to human health of some cell wall constituents found in cereals, in particular beta......-glucans. Plant cell wall biosynthesis is regulated by a large number of genes and regulatory factors but very few of these are known and characterized. This PhD project aimed to the identification of putative candidate genes involved in plant cell wall composition and properties using a genome wide (GWAS......) approach. The species investigate were wheat, barley and B. distachyon, considered a model plant for temperate cereals. Agronomical traits as yield and plant height were also included in the analysis along with cell wall composition and saccharification properties. Several marker-trait associations were...

The complete chloroplast genome of an irreplaceable dietary and model crop, foxtail millet (Setaria italica).

Science.gov (United States)

Wang, Shuo; Gao, Li-Zhi

2016-11-01

The complete chloroplast genome sequence of foxtail millet (Setaria italica), an important food and fodder crop in the family Poaceae, is first reported in this study. The genome consists of 1 35 516 bp containing a pair of inverted repeats (IRs) of 21 804 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region of 79 896 bp and 12 012 bp, respectively. Coding sequences constitute 58.8% of the genome harboring 111 unique genes, 71 of which are protein-coding genes, 4 are rRNA genes, and 36 are tRNA genes. Phylogenetic analysis indicated foxtail millet clustered with Panicum virgatum and Echinochloa crus-galli belonging to the tribe Paniceae of the subfamily Panicoideae. This newly determined chloroplast genome will provide valuable information for the future breeding programs of valuable cereal crops in the family Poaceae.

Genome Variation Map: a data repository of genome variations in BIG Data Center

OpenAIRE

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2017-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

Effects of milling on the extraction efficiency of incurred pesticides in cereals

DEFF Research Database (Denmark)

Herrmann, Susan Strange; Hajeb, Parvaneh; Andersen, Gitte

2017-01-01

This study investigated the effects of particle size and milling temperature on the extraction efficiencies of pesticide residues from cereal flour. Samples of cereal grains (barley, oat, rye and wheat) were milled using a centrifugal mill with four different sieves (0.2, 1.0, 3.0 and 5.0 mm......) or a knife mill both at room temperature and after freezing of the grain at –80°C overnight. The incurred pesticides in the test materials were extracted by the QuEChERS method and analysed by LC-MS/MS and GC-MS/MS. The particle size distribution for the milled samples was determined using a vibratory sieve...... shaker. Based on the pesticide levels recovered from each of the different millings and the corresponding particle size distributions, it was confirmed that smaller average particle sizes increase the extraction efficiency up to 31%, with all other factors equal. The cereals milled at room temperature...

Aspects of the selection, design and use of high lysine cereals

International Nuclear Information System (INIS)

Munck, L.

1976-01-01

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)

The importance, biology and management of cereal cyst nematodes (Heterodera spp.

Directory of Open Access Journals (Sweden)

F. Mokrini

2018-01-01

Full Text Available Cereals are exposed to biotic and abiotic stresses. Among the biotic stresses, plant-parasitic nematodes play an important role in decreasing crop yield. Cereal cyst nematodes (CCNs are known to be a major constraint to wheat production in several parts of the world. Significant economic losses due to CCNs have been reported. Recognition and identification of CCNs are the first steps in nematode management. This paper reviews the current distribution of CCNs in different parts of the world and the recent advances in nematode identification. The different approaches for managing CCNs are also discussed.

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...

Genome-nutrition divergence: evolving understanding of the malnutrition spectrum.

Science.gov (United States)

Eaton, Jacob C; Iannotti, Lora L

2017-11-01

Humans adapted over a period of 2.3 million years to a diet high in quality and diversity. Genome-nutrition divergence describes the misalignment between modern global diets and the genome formed through evolution. A survey of hominin diets over time shows that humans have thrived on a broad range of foods. Earlier diets were highly diverse and nutrient dense, in contrast to modern food systems in which monotonous diets of staple cereals and ultraprocessed foods play a more prominent role. Applying the lens of genome-nutrition divergence to malnutrition reveals shared risk factors for undernutrition and overnutrition at nutrient, food, and environmental levels. Mechanisms for food system shifts, such as crop-neutral agricultural policy, agroecology, and social policy, are explored as a means to realign modern diets with the nutritional patterns to which humans may be better adapted to thrive. © The Author(s) 2017. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua

Directory of Open Access Journals (Sweden)

Lisa A. Beirn

2015-08-01

Full Text Available The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli, although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.

Effect of γ-irradiation on the occurrence of pathogenic microorganisms and nutritive value of four principal cereal grains

International Nuclear Information System (INIS)

Aziz, N.H.; Souzan, R.M.; Shahin Azza, A.

2006-01-01

The effects of 60 Co γ-photon-irradiation on the natural occurrence of pathogenic microorganisms in four principal cereal grains and on amino acids and vitamins in these cereals were investigated. The total numbers of aerobic bacteria were reduced by three logarithmic decades when grains were given a dose of 10 kGy. Coliforms and 'coagulase- positive' staphylococci were inhibited by a dose of 1 kGy, whereas fungi were inhibited by a dose of 5 kGy. The 15 kGy dose eliminated viable microorganisms in cereal grains, and about 10-30 colony-forming units of Clostridium sp. per gram of grain survived after this dose. The dose of 10 kGy did not cause any measurable destruction of total amino acids. Thiamin was reduced by 22-33% and riboflavin by 10-16% after a dose of 10 kGy. Irradiation did not increase the acid values significantly, but did increase the peroxide values, which was not accompanied by the off-odors of cereals. We conclude that the overall dose of 10 kGy is very effective for microbial decontamination of cereal grains, and does not adversely affect the nutritional quality of cereal grains

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

Science.gov (United States)

Lewis, Tony E; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L; Buchan, Daniel W A; Chothia, Cyrus; Cuff, Alison; Dana, Jose M; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T; Kelley, Lawrence A; Kleywegt, Gerard J; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G; Ochoa-Montaño, Bernardo; Rackham, Owen J L; Smith, James; Sternberg, Michael J E; Velankar, Sameer; Yeats, Corin; Orengo, Christine

2013-01-01

Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).

Assessing Impacts of National Scale Droughts on Cereal Production

Science.gov (United States)

Udmale, P. D.; Ichikawa, Y.

2017-12-01

Till date, several drought indices have been developed and used to monitor local to regional scale droughts on various temporal scales. However, there are no generalized criteria to define a threshold to declare a national level drought using drought indices. EM-DAT (a global database on natural and technological disasters) lists disasters (including drought) from 1900 until the present confirming one of the following criteria: 10 or more people dead; 100 or more people affected; the declaration of a state of emergency; or a call for international assistance. This data is gathered from various organizations like United Nations Institutes, Governments, etc. and do not cover all disasters or have political limitations that could affect the numbers. These criteria are neither objective nor quantitative, and accordingly may cause uncertainties when the data is used for further investigation on disaster impacts. Here we present a methodology to define drought at a national scale and its impacts on national level crop production (mainly cereals). We define drought based on the percentage of cropland area affected by drought in a country during its seasonal rainfall. For this purpose meteorological definition of drought in combination with country's cropland area is proposed to prepare a drought inventory for major cereal producing countries (1902-2012). This drought inventory together with FAO's Crop data is used to identify the impacts of drought on a national level cereal production (and yield) using Superposed Epoch Analysis for the period 1961-2012.

Research Ethics 2.0 : New Perspectives on Norms, Values, and Integrity in Genomic Research in Times of Even Scarcer Resources

NARCIS (Netherlands)

Brall, Caroline; Maeckelberghe, Els; Porz, Rouven; Makhoul, Jihad; Schröder-Bäck, Peter

Research ethics anew gained importance due to the changing scientific landscape and increasing demands and competition in the academic field. These changes are further exaggerated because of scarce(r) resources in some countries on the one hand and advances in genomics on the other. In this paper,

Antioxidant activity of commonly consumed cereals, millets, pulses and legumes in India.

Science.gov (United States)

Sreeramulu, D; Reddy, C Vijaya Kumar; Raghunath, M

2009-02-01

Plant foods are important due to their antioxidant activity (AOA) attributed to the phenolics which are known to protect organisms against harmful effects of oxygen radicals. However, information on antioxidant activity of Indian plant foods is scanty. Therefore, the present study evaluated the AOA of cereals, millets, pulses and legumes, commonly consumed in India and assessed the relationship with their total phenolic content (TPC). AOA was assessed by DPPH (2,2-Diphenyl-1-picryl hydrazyl) radical scavenging assay, ferric reducing antioxidant power (FRAP) assay and reducing power. DPPH scavenging activity ranged from 0.24 and 1.73 mg/g, whereas FRAP ranged from 16.21 to 471.71 micromoles/g. Finger millet (Eleusine cora cana) and Rajmah (Phaseolus vulgaris) had the highest FRAP 471.71, 372.76 and DPPH scavenging activity 1.73, 1.07. Similar trends were observed with reducing power. Among cereals and legumes, Finger millet (Ragi) and black gram dhal (Phaseolus mungo Roxb) had the highest TPC, the values being 373 and 418 mg/100 g respectively, while rice (Oryza sativa) and green gram dhal (Phaseolus aureus Roxb) showed the least (47.6 and 62.4 mg/100 g). In the present study, FRAP (r = 0.91) and reducing power (r = 0.90) showed significant correlation with TPC in cereals and millets, but not in pulses and legumes. The results suggest that TPC contributes significantly to the AOA of Indian cereals and millets.

Digesta characteristiscs and performance of African catfish (Clarias gariepinus) fed cereal grains that differ in viscosity

NARCIS (Netherlands)

Leenhouwers, J.I.; Veld, ter M.; Verreth, J.A.J.; Schrama, J.W.

2007-01-01

Inclusion of cereal grains in fish diets may induce changes in digesta characteristics with possible consequences for fish performance. Especially viscosity characteristics of the dietary ingredients may induce these changes. The aim of this study was to investigate effects of dietary cereal grains

Cereal bran fractionation: processing techniques for the recovery of functional components and their applications to the food industry.

Science.gov (United States)

Soukoulis, Christos; Aprea, Eugenio

2012-04-01

Bran is the outer part of cereal grains that is separated during the cereals de-hulling and milling processes. It was considered in the past a by-product of cereal industry employed mainly as animal feed. Cereal bran, being particularly rich in different functional biopolymers, bio-active compounds and essential fatty acids, attracted the interest of pharmaceutical and food industry. Furthermore, the peculiar techno-functional properties of brans together with their particular physiological and nutritional aspects have led to a great interest in their incorporation as main or secondary components in different groups of food products including bakery and confectionery products, breakfast cereals and extruded foodstuffs, emulsions and functional dairy products and pasta products. In the first part of the present work the main fractionation processes, bran fractions properties and their physicochemical and technological properties are briefly reviewed. In the second part, relevant applications, with emphasis on patents, in food industry are reviewed as well.

Regional diversity on the timing for the origins of cereal cultivation and domestication in southwest Asia

DEFF Research Database (Denmark)

Otaegui, Amaia Arranz; Colledge, Sue; Zapata, Lydia

2016-01-01

in regions such as the southern-central Levant and the Upper Euphrates area, but the plant-based subsistence in the eastern Fertile Crescent (southeast Turkey, Iran, and Iraq) focused on the exploitation of plants such as legumes, goatgrass, fruits, and nuts. Around 10.7–10.2 ka Cal BP (early Pre......-Pottery Neolithic B), the predominant exploitation of cereals continued in the southern-central Levant and is correlated with the appearance of significant proportions (∼30%) of domesticated-type cereal chaff in the archaeobotanical record. In the eastern Fertile Crescent exploitation of legumes, fruits, nuts......, and grasses continued, and in the Euphrates legumes predominated. In these two regions domesticated-type cereal chaff (>10%) is not identified until the middle and late Pre-Pottery Neolithic B (10.2–8.3 ka Cal BP). We propose that the cultivation of wild and domesticated cereals developed at different times...

Mineral Retention Values for Blends of Cereal Based ...

African Journals Online (AJOL)

Prof. Ogunji

household diets can be manipulated to enhance the micronutrients content or alter the levels of ... (2007) reported that fermentation for 72h increased most of the minerals in cereal based ... Production of Amylase Rich Flour (ARF): Amylase rich flour was produced by the method of Odumodu ..... Practical chemistry (3rd Ed).

Bioactive small molecules in commercially available cereal food

DEFF Research Database (Denmark)

Steffensen, Stine K.; Adhikari, Khem B.; Laursen, Bente B.

2017-01-01

processes. The concentrations of 11 BX compounds were determined by liquid chromatography–triple quadrupole mass spectrometry (LC–MS/MS) in 25 supermarket-available cereal food products. The total BX content varied from below the limit of detection to >500 μg/g dry matter (DM) with some degree of variation...

The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes.

Science.gov (United States)

Kapopoulou, Adamandia; Lew, Jocelyne M; Cole, Stewart T

2011-01-01

In this paper, we present the MycoBrowser portal (http://mycobrowser.epfl.ch/), a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. A central component of MycoBrowser is TubercuList (http://tuberculist.epfl.ch), which has recently benefited from a new data management system and web interface. These improvements were extended to all MycoBrowser databases. We provide an overview of the functionalities available and the different ways of interrogating the data then discuss how both the new information and the latest features are helping the mycobacterial research communities. Copyright © 2010 Elsevier Ltd. All rights reserved.

The Banana Genome Hub

Science.gov (United States)

Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

2013-01-01

Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

Influence of Higher Wheat Prices on Ready-to-Eat Cereal Companies in 2010

OpenAIRE

HERNANDEZ LOERA CHAVEZ, PABLO

2013-01-01

In 2010, sever droughts and fires destroyed 20 percent of Russia’s wheat crop. This incident increased dramatically the prices of wheat worldwide. This paper studies the financial consequences that these higher wheat prices brought to companies that use wheat to manufacture ready-to-eat cereal and wheat-related products. The international cereal companies selected for this study were Kellogg Company, Nestlé Group and Ralcorp Holdings, Inc., owner of Post Foods Company. Keywords: Wheat, ce...

Breakfast and Breakfast Cereal Choice and Its Impact on Nutrient and Sugar Intakes and Anthropometric Measures among a Nationally Representative Sample of Australian Children and Adolescents

Directory of Open Access Journals (Sweden)

Flavia Fayet-Moore

2017-09-01

Full Text Available There is limited evidence in Australia that compares the nutritional impact of a breakfast cereal breakfast to a non-cereal breakfast, and includes the type of cereal. This study investigated the impact of breakfast choice and the total sugar content of breakfast cereal on nutrient intakes and anthropometric measures among Australian children and adolescents. Data from 2 to 18-year-old in the 2011–2012 National Nutrition and Physical Activity Survey were used (n = 2821. Participants were classified as breakfast cereal consumers (minimally pre-sweetened (MPS or pre-sweetened (PS, non-cereal breakfast consumers, or breakfast skippers. Foods consumed for breakfast, foods added to the cereal bowl, and the impact of breakfast choice on daily nutrient intakes and anthropometric measures were determined. Although only 9% of children skipped breakfast, 61% of skippers were aged 14–18 years. Among breakfast consumers, 49% had breakfast cereal, and 62% of these exclusively consumed MPS cereal. Breakfast skippers had a higher saturated fat intake than breakfast cereal consumers, and lower intakes of dietary fibre and most micronutrients (p < 0.001. Compared with non-cereal breakfast consumers, breakfast cereal consumers had additional free sugars intake, lower sodium, and higher total sugars, carbohydrate, dietary fibre, and almost all other micronutrients (p < 0.001. The only difference in nutrient intakes between MPS and PS cereal consumers was higher folate among PS consumers. No associations between anthropometric measures and breakfast or breakfast cereal choice were found. The highest prevalence of breakfast skipping was among 14–18-year old. Breakfast cereal consumers had higher intakes of dietary fibre and most micronutrients compared with non-cereal breakfast consumers and skippers, and almost no differences were found between MPS and PS cereal consumers.

Barriers and incentives to the production of bioethanol from cereal straw: A farm business perspective

International Nuclear Information System (INIS)

Glithero, N.J.; Ramsden, S.J.; Wilson, P.

2013-01-01

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. - 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

National Human Genome Research Institute

Science.gov (United States)

... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing

Directory of Open Access Journals (Sweden)

Gang Nie

2017-01-01

Full Text Available Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57% unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis.

Seeds, hands and lands : maize genetic resources of highland Guatemala in space and time

NARCIS (Netherlands)

Etten, van J.

2006-01-01

Crop genetic resources are an important aspect of agricultural production. Agricultural innovation through plant breeding is generally seen as an efficient means to support food security and economic development in poor areas. Modern varieties of maize, a major cereal and the subject of this study,

Genome-wide identification, classification and expression profiling of nicotianamine synthase (NAS) gene family in maize

OpenAIRE

Zhou, Xiaojin; Li, Suzhen; Zhao, Qianqian; Liu, Xiaoqing; Zhang, Shaojun; Sun, Cheng; Fan, Yunliu; Zhang, Chunyi; Chen, Rumei

2013-01-01

Background Nicotianamine (NA), a ubiquitous molecule in plants, is an important metal ion chelator and the main precursor for phytosiderophores biosynthesis. Considerable progress has been achieved in cloning and characterizing the functions of nicotianamine synthase (NAS) in plants including barley, Arabidopsis and rice. Maize is not only an important cereal crop, but also a model plant for genetics and evolutionary study. The genome sequencing of maize was completed, and many gene families ...

Genome Variation Map: a data repository of genome variations in BIG Data Center.

Science.gov (United States)

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2018-01-04

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome Variation Map: a data repository of genome variations in BIG Data Center

Science.gov (United States)

Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

2018-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

The Sequenced Angiosperm Genomes and Genome Databases.

Science.gov (United States)

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

Development of cereals for animal feed technology

Directory of Open Access Journals (Sweden)

A. N. Ostrikov

2017-01-01

Full Text Available The technological process of cereals production used in the production of feed stuff, which includes the following basic steps: grain moistening; binning of moistened grain for redistribution of moisture in the bulk of kernel; steaming of moistened grain; rolling of steamed grain; drying and cooling of flakes – is developed. In the production of flakes from scoured barley and oat grain before feeding to the rolling line film removal from the grain of these crops and the separation of the husks is carried out by one the existing methods: the method of grinding, followed by sifting and eventilation of films from tail fractions or a method of peeling on special machines with a separation of films. Wet-heat treatment of grain, followed by rolling helps to improve taste and palatability of feed, improves the nutritional value of carbohydrate and protein complexes, reduces the exertion of the body to digest food nutrients, allows to inactivate antinutritional substances and free the grain from the pathogenic and other microorganisms. In the duration of rolling process splitting of complex carbohydrates occurs, starch loses its original structure and is easier exposed to enzymes. The dried and cooled flakes have satisfactory flowability, do not set up. Humidity of flakes is not more than 14%, the temperature is not more than 10 °C above the ambient temperature, bulk density is 350–400 kg/m3. Developed set of equipment allows producing cereal flakes, the use of which in feed stuff and rations of young cattle and pigs increases the productivity of animals by 15–20% while reducing feed costs by 12–15%. Cereal flakes are used in the manufacture of complete feed for piglets (pigs at the age of 10 to 60 days, feed concentrates for pigs under the age of 4 months, the calves under the age of 115 days, high-producing cows, sporting and trained horses and lactating mares.

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

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.

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.

Science.gov (United States)

Szczecińska, Monika; Sawicki, Jakub

2015-09-15

The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161-162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. The determination of complete

Sequence analysis of cereal sucrose synthase genes and isolation ...

African Journals Online (AJOL)

SERVER

2007-10-18

Oct 18, 2007 ... sequencing of sucrose synthase gene fragment from sor- ghum using primers designed at their conserved exons. MATERIALS AND METHODS. Multiple sequence alignment. Sucrose synthase gene sequences of various cereals like rice, maize, and barley were accessed from NCBI Genbank database.

From plant genomes to phenotypes

OpenAIRE

Bolger, Marie; Gundlach, Heidrun; Scholz, Uwe; Mayer, Klaus; Usadel, Björn; Schwacke, Rainer; Schmutzer, Thomas; Chen, Jinbo; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Fiorani, Fabio; Spannagl, Manuel

2017-01-01

Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.

Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies

Science.gov (United States)

Tian, Wenlan; Paudel, Dev

2017-01-01

Jatropha (Jatropha curcas L.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies. PMID:28154822

The impact of image-size manipulation and sugar content on children's cereal consumption.

Science.gov (United States)

Neyens, E; Aerts, G; Smits, T

2015-12-01

Previous studies have demonstrated that portion sizes and food energy-density influence children's eating behavior. However, the potential effects of front-of-pack image-sizes of serving suggestions and sugar content have not been tested. Using a mixed experimental design among young children, this study examines the effects of image-size manipulation and sugar content on cereal and milk consumption. Children poured and consumed significantly more cereal and drank significantly more milk when exposed to a larger sized image of serving suggestion as compared to a smaller image-size. Sugar content showed no main effects. Nevertheless, cereal consumption only differed significantly between small and large image-sizes when sugar content was low. An advantage of this study was the mundane setting in which the data were collected: a school's dining room instead of an artificial lab. Future studies should include a control condition, with children eating by themselves to reflect an even more natural context. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microdochium nivale and Microdochium majus in seed samples of Danish small grain cereals

DEFF Research Database (Denmark)

Nielsen, L. K.; Justesen, A. F.; Jensen, J. D.

2013-01-01

Microdochium nivale and Microdochium majus are two of fungal species found in the Fusarium Head Blight (FHB) complex infecting small grain cereals. Quantitative real-time PCR assays were designed to separate the two Microdochium species based on the translation elongation factor 1a gene (TEF-1a......) and used to analyse a total of 374 seed samples of wheat, barley, triticale, rye and oat sampled from farmers’ fields across Denmark from 2003 to 2007. Both fungal species were detected in the five cereal species but M. majus showed a higher prevalence compared to M. nivale in most years in all cereal...... species except rye, in which M. nivale represented a larger proportion of the biomass and was more prevalent than M. majus in some samples. Historical samples of wheat and barley from 1957 to 2000 similarly showed a strong prevalence of M. majus over M. nivale indicating that M. majus has been the main...

The genome of Chenopodium quinoa

KAUST Repository

Jarvis, David Erwin; Ho, Yung Shwen; Lightfoot, Damien; Schmö ckel, Sandra M.; Li, Bo; Borm, Theo J. A.; Ohyanagi, Hajime; Mineta, Katsuhiko; Michell, Craig; Saber, Noha; Kharbatia, Najeh M.; Rupper, Ryan R.; Sharp, Aaron R.; Dally, Nadine; Boughton, Berin A.; Woo, Yong; Gao, Ge; Schijlen, Elio G. W. M.; Guo, Xiujie; Momin, Afaque Ahmad Imtiyaz; Negrã o, Só nia; Al-Babili, Salim; Gehring, Christoph A; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T.; Gojobori, Takashi; Linden, C. Gerard van der; Loo, Eibertus N. van; Jellen, Eric N.; Maughan, Peter J.; Tester, Mark A.

2017-01-01

Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

The genome of Chenopodium quinoa

KAUST Repository

Jarvis, David Erwin

2017-02-08

Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

The genome of Chenopodium quinoa.

Science.gov (United States)

Jarvis, David E; Ho, Yung Shwen; Lightfoot, Damien J; Schmöckel, Sandra M; Li, Bo; Borm, Theo J A; Ohyanagi, Hajime; Mineta, Katsuhiko; Michell, Craig T; Saber, Noha; Kharbatia, Najeh M; Rupper, Ryan R; Sharp, Aaron R; Dally, Nadine; Boughton, Berin A; Woo, Yong H; Gao, Ge; Schijlen, Elio G W M; Guo, Xiujie; Momin, Afaque A; Negrão, Sónia; Al-Babili, Salim; Gehring, Christoph; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T; Gojobori, Takashi; Linden, C Gerard van der; van Loo, Eibertus N; Jellen, Eric N; Maughan, Peter J; Tester, Mark

2017-02-16

Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

Developing climate resilient rice through genomics assisted breeding

Directory of Open Access Journals (Sweden)

Valarmathi Muthu

2017-10-01

Full Text Available Rice is one of the major cereal food crops whose production has to be doubled to achieve the projected demand [1] and current yield trends are not sufficient to meet the projected growth in production. Increasing the rice production by 30% during 2030 needs overcoming challenges viz., yield plateau, declining land, water and labor resources and predicted effects of global climate change. Development of high performance rice genotypes with enhanced yield potential and resilience to climate change will help in sustained increase in rice production. Deployment of genomic technologies can accelerate development and delivery of improved germplasm with enhanced resilience and adaptability [2, 3]. In this context, the present study was undertaken with an aim of developing rice genotypes pyramided with QTLs/genes controlling tolerance against various biotic and abiotic stresses viz., bacterial leaf blight (xa13, Xa21, blast (Pi9, Gall midge (Gm4, drought (qDTY1.1 qDTY2.1, submergence (Sub1 and salinity (Saltol. CBMAS14065 an elite culture harboring QTLs controlling tolerance against drought, salinity and submergence was crossed with a donor harboring BLB, Blast and Gall midge resistant genes. True F1s were backcrossed with CBMAS14065 and BC1F1 progenies were subjected to foreground selection using markers linked to the target traits. Superior plants (18 of BC1F1 generation were subjected to background selection which revealed 71.42 - 86.90% recurrent parent (CBMAS14065 genome recovery. Selected BC1F1 plants were advanced to BC2F1 generation backcrossing with CBMAS14065. In BC2F1 generation, through foreground selection 6-8 QTL/gene positive plants have been selected and advanced for further evaluation. The superior lines with desired QTLs/genes will be subjected to rigorous phenotypic evaluation against target stresses and advanced further.

Finite element simulation of the compression behaviour of airy breakfast cereals

KAUST Repository

Mamlouk, Hedi

2013-07-01

In this paper we are concerned by the fragmentation study of five breakfast cereals from the market exhibiting differences in shape, formulation and texture. The experimental part of the study encompasses compression testing and fragment size evaluation using 2D image analysis. Structural information about the airy structure is then determined using X-ray tomography and related 3D image analysis. The numerical part has the ambition of assessing the fragmentation process using a damage-based mechanical model that simulates solid material rupture events as onset and growth of damage up to brittle failure. The model is based on a finite element scheme in which direct information of the 3D airy structure is encoded in the solid meshing. The force-displacement signature well shows competition between bending and compression driven failure depending on cereal shape. Our results show also large dispersion in the porous structure that affects significantly the result of the fragmentation. The numerical model is able to simulate the result of fragmentation at the cost of identifying two mechanical parameters, namely Young\\'s modulus and critical stress. These two quantities are proved to be product dependent and display a large range of variation. Industrial relevance The design of new food product becomes more and more based on functionality criteria. In a typical chewing process the need to understand the deformation mechanisms leading to fragmentation helps in understanding the role of the structure and, in turn, the processing conditions for building new transformed products. There is an increasing industrial demand in that sense especially knowing that some of the cereal products can be designed to meet these criteria for specific populations (old people with dental problems, infant feeding). Our work is, within this context, an attempt to set a numerical and experimental framework for studying the fragmentation of five selected breakfast cereals from the market. �

ArylexTM active – new herbicide active and base for new cereals herbicides: ZyparTM and Pixxaro™ EC to control wide range of broadleaf weeds in cereals in Europe

Directory of Open Access Journals (Sweden)

Dzikowski, Marcin

2016-02-01

Full Text Available Arylex™ active is a new auxinic herbicide for postemergence control of a range of important broadleaf weeds in cereals. It has been discovered and developed by Dow AgroSciences globally as a first member of the new ‘arylpicolinate‘ structural class. Arylex applied together with safener brings excellent crop safety and due to the rapid degradation in soil and plant tissue it does not limit the following crop choice. In Europe the first two herbicides containing this active are Zypar™ and Pixxaro™ EC. Zypar is a premix of Arylex and florasulam, delivering at the 1 L/ha maximum use rate 6 g ae/ha of Arylex and 5 g/ha of florasulam. It can be applied to all cereals, apart from oats, in autumn and spring. Spring application is allowed from BBCH 13 till BBCH 45, however the best performance is reached up to BBCH 32. Zypar’s spectrum of controlled weeds is very wide. Pixxaro EC is a combination of Arylex and fluroxypyr and at 0.5 l/ha dose rate delivers 6 g ae/ha of Arylex and 140 g ae/ha of fluroxypyr. It can be applied in all cereals, apart from oats, in spring from BBCH 13 till BBCH 45, while the best performance is observed between BBCH 30 and 45. Pixxaro EC shows excellent efficacy against key weeds, especially Galium aparine and at all growth stages. This herbicide brings a novel non-ALS solution and will be a key component of anti-resistance strategies for broadleaf weeds in cereals.

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.

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.

Inhibition of Orobanche crenata seed germination and radicle growth by allelochemicals identified in cereals.

Science.gov (United States)

Fernández-Aparicio, Mónica; Cimmino, Alessio; Evidente, Antonio; Rubiales, Diego

2013-10-16

Orobanche crenata is a parasitic weed that causes severe yield losses in important grain and forage legume crops. Cereals have been reported to inhibit O. crenata parasitism when grown intercropped with susceptible legumes, but the responsible metabolites have not been identified. A number of metabolites have been reported in cereals that have allelopathic properties against weeds, pests, and pathogens. We tested the effect of several allelochemicals identified in cereals on O. crenata seed germination and radicle development. We found that 2-benzoxazolinone, its derivative 6-chloroacetyl-2-benzoxazolinone, and scopoletin significantly inhibited O. crenata seed germination. Benzoxazolinones, l-tryptophan, and coumalic acid caused the stronger inhibition of radicle growth. Also, other metabolites reduced radicle length, this inhibition being dose-dependent. Only scopoletin caused cell necrotic-like darkening in the young radicles. Prospects for their application to parasitic weed management are discussed.

Rumen undegradable protein (RUP) and its intestinal digestibility after steam flaking of cereal grains

DEFF Research Database (Denmark)

Chrenková, M; Formelová, Z; Ceresnáková, Z

2018-01-01

While it is known that heat treatment of cereal grains generally improves the nutritional value for ruminants, simultaneous information on rumen degradability and intestinal digestibility of the rumen by-pass is scarce, especially for non-starch constituents. The effect of steam flaking at 90°C...... flaking on chemical composition of cereal grains (crude protein, acid detergent fibre, neutral detergent fibre, and starch) were observed. The protein fractions that are relevant to rumen degradability were significantly influenced by the steam flaking: the non-protein nitrogen fraction (A) was reduced (P...... hand, steam flaking markedly increased buffer insoluble but neutral detergent soluble protein fraction (B2) by 15–25% for all three cereal grains, whereas effects on B3 fraction were not significant. Steam flaking was also associated with an increase of the rumen undegradable protein fraction (C...

CHOgenome.org 2.0: Genome resources and website updates.

Science.gov (United States)

Kremkow, Benjamin G; Baik, Jong Youn; MacDonald, Madolyn L; Lee, Kelvin H

2015-07-01

Chinese hamster ovary (CHO) cells are a major host cell line for the production of therapeutic proteins, and CHO cell and Chinese hamster (CH) genomes have recently been sequenced using next-generation sequencing methods. CHOgenome.org was launched in 2011 (version 1.0) to serve as a database repository and to provide bioinformatics tools for the CHO community. CHOgenome.org (version 1.0) maintained GenBank CHO-K1 genome data, identified CHO-omics literature, and provided a CHO-specific BLAST service. Recent major updates to CHOgenome.org (version 2.0) include new sequence and annotation databases for both CHO and CH genomes, a more user-friendly website, and new research tools, including a proteome browser and a genome viewer. CHO cell-line specific sequences and annotations facilitate cell line development opportunities, several of which are discussed. Moving forward, CHOgenome.org will host the increasing amount of CHO-omics data and continue to make useful bioinformatics tools available to the CHO community. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimization of cereal-legume blend ratio to enhance the nutritional ...

African Journals Online (AJOL)

Optimization of cereal-legume blend ratio to enhance the nutritional quality and functional property of complementary food. ... Ethiopian Journal of Science and Technology. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current ...

CyanoClust: comparative genome resources of cyanobacteria and plastids.

Science.gov (United States)

Sasaki, Naobumi V; Sato, Naoki

2010-01-01

Cyanobacteria, which perform oxygen-evolving photosynthesis as do chloroplasts of plants and algae, are one of the best-studied prokaryotic phyla and one from which many representative genomes have been sequenced. Lack of a suitable comparative genomic database has been a problem in cyanobacterial genomics because many proteins involved in physiological functions such as photosynthesis and nitrogen fixation are not catalogued in commonly used databases, such as Clusters of Orthologous Proteins (COG). CyanoClust is a database of homolog groups in cyanobacteria and plastids that are produced by the program Gclust. We have developed a web-server system for the protein homology database featuring cyanobacteria and plastids. Database URL: http://cyanoclust.c.u-tokyo.ac.jp/.

BEHAVIOR OF CEREAL'S VARIETIES IN THE PRESENCE OF ...

African Journals Online (AJOL)

F. Labdelli

1 sept. 2017 ... ... of this nematode. Key words: Nematode; Heterodera; cereals; varieties; behaviour. .... L'essai est mené à l'air libre en conditions extérieures à raison de 08 répétitions pour les témoins et 08 ..... cyst nematode populations from north Africa and Asia . Nematology ... Research 2008, 6 (Special issue), 81-87.

Genomic imprinting, growth control and the allocation of nutritional resources: consequences for postnatal life.

Science.gov (United States)

Charalambous, Marika; da Rocha, Simão Teixeira; Ferguson-Smith, Anne C

2007-02-01

Genes subject to genomic imprinting are predominantly expressed from one of the two parental chromosomes, are often clustered in the genome, and their activity and repression are epigenetically regulated. The role of imprinted genes in growth control has been apparent since the discovery of imprinting in the early 1980s. Drawing from studies in the mouse, we propose three distinct classes of imprinted genes - those expressed, imprinted and acting predominantly within the placenta, those with no associated foetal growth effects that act postnatally to regulate metabolic processes, and those expressed in the embryo and placenta that programme the development of organs participating in metabolic processes. Members of this latter class may interact in functional networks regulating the interaction between the mother and the foetus, affecting generalized foetal well-being, growth and organ development; they may also coordinately regulate the development of particular organ systems. The mono-allelic behaviour and sensitivity to changes in regional epigenetic states renders imprinted genes adaptable and vulnerable; in all cases, their perturbed dosage can compromise prenatal and/or postnatal control of nutritional resources. This finding has implications for understanding the relationships between prenatal events and diseases later in life.

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...

Invertebrate communities in spring wheat and the identification of cereal aphid predators through molecular gut content analysis

Science.gov (United States)

Cereal aphid complexes are responsible for reducing wheat production worldwide; however, management against these species is rare in North America. Generalist predators may contribute to reducing cereal aphid numbers and preventing significant damage to crops. A two-year survey identifying the arth...

Does Regular Breakfast Cereal Consumption Help Children and Adolescents Stay Slimmer? A Systematic Review and Meta-Analysis

Directory of Open Access Journals (Sweden)

Anne de la Hunty

2013-03-01

Full Text Available Objective: To review systematically the evidence on breakfast cereal consumption and obesity in children and adolescents and assess whether the regular consumption of breakfast cereals could help to prevent excessive weight gain. Methods: A systematic review and meta-analysis of studies relating breakfast cereal consumption to BMI, BMI z-scores and prevalence of obesity as the outcomes. Results: 14 papers met the inclusion criteria. The computed effect size for mean BMI between high consumers and low or non-consumers over all 25 study subgroups was -1.13 kg/m2 (95% CI -0.81, -1.46, p Conclusion: Overall, the evidence reviewed is suggestive that regular consumption of breakfast cereals results in a lower BMI and a reduced likelihood of being overweight in children and adolescents. However, more evidence from long-term trials and investigations into mechanisms is needed to eliminate possible confounding factors and determine causality.

Genomics With Cloud Computing

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Sukhamrit Kaur

2015-04-01

Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

Resilience of cereal crops to abiotic stress: A review

African Journals Online (AJOL)

SAM

2014-07-16

Jul 16, 2014 ... Key words: Cereal crops, abiotic stresses, food insecurity, molecular breeding, quantitative trait loci (QTLs), salinity, water stress. ... production of genetically modified (GM) crops, exo- genous use of osmo protectants etc. ... stressful environments is important to fulfill food demand of the ever-increasing world ...

Regulation of abscisic acid metabolism in relation to the dormancy and germination of cereal grains

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Justyna Fidler

2015-03-01

Full Text Available Seed dormancy is of particular importance in the cultivation of cereals, as it directly affects the quality of crop yield. If the dormancy period is too short, this may lead to pre-harvest sprouting, whereas a dormancy period that is too long may cause uneven germination; both of these scenarios are associated with economic losses. Most enzymes engaged in the metabolism of abscisic acid (ABA have been identified, and significant progress has been made in understanding the role of this phytohormone in the induction and maintenance of dormancy, mainly as a result of research conducted in Arabidopsis. Much less is known about the metabolism and function of ABA in cereal grains, especially in relation to dormancy and germination. This review focuses on the regulation of ABA metabolism in dormant and non-dormant cereal grains, in both the dry state and upon imbibition. Moreover, this review describes the influence of factors such as after-ripening, light, temperature, nitric oxide, and reactive oxygen species (ROS on the dormancy and germination of cereal grains. These factors, with the exception of ROS, appear to affect the level of dormancy and germination of grains through regulation of ABA metabolism.

Model training across multiple breeding cycles significantly improves genomic prediction accuracy in rye (Secale cereale L.).

Science.gov (United States)

Auinger, Hans-Jürgen; Schönleben, Manfred; Lehermeier, Christina; Schmidt, Malthe; Korzun, Viktor; Geiger, Hartwig H; Piepho, Hans-Peter; Gordillo, Andres; Wilde, Peer; Bauer, Eva; Schön, Chris-Carolin

2016-11-01

Genomic prediction accuracy can be significantly increased by model calibration across multiple breeding cycles as long as selection cycles are connected by common ancestors. In hybrid rye breeding, application of genome-based prediction is expected to increase selection gain because of long selection cycles in population improvement and development of hybrid components. Essentially two prediction scenarios arise: (1) prediction of the genetic value of lines from the same breeding cycle in which model training is performed and (2) prediction of lines from subsequent cycles. It is the latter from which a reduction in cycle length and consequently the strongest impact on selection gain is expected. We empirically investigated genome-based prediction of grain yield, plant height and thousand kernel weight within and across four selection cycles of a hybrid rye breeding program. Prediction performance was assessed using genomic and pedigree-based best linear unbiased prediction (GBLUP and PBLUP). A total of 1040 S 2 lines were genotyped with 16 k SNPs and each year testcrosses of 260 S 2 lines were phenotyped in seven or eight locations. The performance gap between GBLUP and PBLUP increased significantly for all traits when model calibration was performed on aggregated data from several cycles. Prediction accuracies obtained from cross-validation were in the order of 0.70 for all traits when data from all cycles (N CS  = 832) were used for model training and exceeded within-cycle accuracies in all cases. As long as selection cycles are connected by a sufficient number of common ancestors and prediction accuracy has not reached a plateau when increasing sample size, aggregating data from several preceding cycles is recommended for predicting genetic values in subsequent cycles despite decreasing relatedness over time.

Dietary fibers and associated phytochemicals in cereals.

Science.gov (United States)

Bach Knudsen, Knud Erik; Nørskov, Natalja P; Bolvig, Anne Katrine; Hedemann, Mette Skou; Laerke, Helle Nygaard

2017-07-01

Epidemiological studies have linked whole-grain (WG) cereal consumption to a reduced risk of developing several chronic diseases-coronary heart disease, arteriosclerosis, type-2 diabetes, and some form of cancers. The underlying physiological mechanisms behind the protective effects of WG are unclear, but can most likely be assigned to a concerted action of dietary fiber (DF) and a wide variety of phytochemicals. Physiologically, it is important that soluble nonstarch polysaccharides contribute to higher viscosity in the small intestine as this may influence rate and extent of digestion and absorption. Associated with the DF matrix of cereals is an array of nonnutritive constituents predominantly concentrated in the bran fraction. Among them, the phenolic phytochemicals, benzoic acid and cinnamic derivatives and lignans, are of importance in a nutritional-health perspective. Only a small fraction of the phenolics is absorbed in the small intestine, but the availability can be increased by bioprocessing. The major part, however, is passed to the large intestine where the microbiota, which degrade and metabolize DF to SCFAs and gases, also convert the phenolic compounds into a range of other metabolites that are absorbed into the body and with the capability of influencing the metabolism at the cellular level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of the ``a'' Genome of Finger Millet Using Chloroplast DNA

Science.gov (United States)

Hilu, K. W.

1988-01-01

Finger millet (Eleusine corocana subsp. coracana), an important cereal in East Africa and India, is a tetraploid species with unknown genomic components. A recent cytogenetic study confirmed the direct origin of this millet from the tetraploid E. coracana subsp. africana but questioned Eleusine indica as a genomic donor. Chloroplast (ct) DNA sequence analysis using restriction fragment pattern was used to examine the phylogenetic relationships between E. coracana subsp. coracana (domesticated finger millet), E. coracana subspecies africana (wild finger millet), and E. indica. Eleusine tristachya was included since it is the only other annual diploid species in the genus with a basic chromosome number of x = 9 like finger millet. Eight of the ten restriction endonucleases used had 16 to over 30 restriction sites per genome and were informative. E. coracana subsp. coracana and subsp. africana and E. indica were identical in all the restriction sites surveyed, while the ct genome of E. tristachya differed consistently by at least one mutational event for each restriction enzyme surveyed. This random survey of the ct genomes of these species points out E. indica as one of the genome donors (maternal genome donor) of domesticated finger millet contrary to a previous cytogenetic study. The data also substantiate E. coracana subsp. africana as the progenitor of domesticated finger millet. The disparity between the cytogenetic and the molecular approaches is discussed in light of the problems associated with chromosome pairing and polyploidy. PMID:8608927

Identification of the "A" genome of finger millet using chloroplast DNA.

Science.gov (United States)

Hilu, K W

1988-01-01

Finger millet (Eleusine corocana subsp. coracana), an important cereal in East Africa and India, is a tetraploid species with unknown genomic components. A recent cytogenetic study confirmed the direct origin of this millet from the tetraploid E. coracana subsp. africana but questioned Eleusine indica as a genomic donor. Chloroplast (ct) DNA sequence analysis using restriction fragment pattern was used to examine the phylogenetic relationships between E. coracana subsp. coracana (domesticated finger millet), E. coracana subspecies africana (wild finger millet), and E. indica. Eleusine tristachya was included since it is the only other annual diploid species in the genus with a basic chromosome number of x = 9 like finger millet. Eight of the ten restriction endonucleases used had 16 to over 30 restriction sites per genome and were informative. E. coracana subsp. coracana and subsp. africana and E. indica were identical in all the restriction sites surveyed, while the ct genome of E, tristachya differed consistently by at least one mutational event for each restriction enzyme surveyed. This random survey of the ct genomes of these species points out E. indica as one of the genome donors (maternal genome donor) of domesticated finger millet contrary to a previous cytogenetic study. The data also substantiate E. coracana subsp. africana as the progenitor of domesticated finger millet. The disparity between the cytogenetic and the molecular approaches is discussed in light of the problems associated with chromosome pairing and polyploidy.

Prediction of cereal feed value by near infrared spectroscopy

DEFF Research Database (Denmark)

Jørgensen, Johannes Ravn

. NIRS is therefore appropriate as a quick method for the determination of FEsv and FEso, since it is rapid (approximately 1 minute per measurement of a ground test) and cheap. The aim is to develop a rapid method to analyse grain feed value. This will contribute to highlight the opportunities...... 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 bank of 1213 grain samples of wheat, triticale, barley and rye, and related chemical reference analyses to describe the feed value have been established...... with the error in the chemical analysis. Prediction error by NIRS prediction of feed value has been shown to be above the error of the chemical measurement. The conclusion is that it has proved possible to predict the feed value in cereals with NIRS quickly and cheaply, but prediction error with this method...

Optimization of cereal-legume blend ratio to enhance the nutritional ...

African Journals Online (AJOL)

Optimization of cereal-legume blend ratio to enhance the nutritional quality and functional ... The collected data were subjected to analysis of variance using SPSS ... Mean separation result showed that protein, fat, energy, crude fibre and ash ...

Simultaneous Determination of Multi-Mycotoxins in Cereal Grains Collected from South Korea by LC/MS/MS

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Dong-Ho Kim

2017-03-01

Full Text Available An improved analytical method compared with conventional ones was developed for simultaneous determination of 13 mycotoxins (deoxynivalenol, nivalenol, 3-acetylnivalenol, aflatoxin B1, aflatoxin B2, aflatoxin G1, aflatoxin G2, fumonisin B1, fumonisin B2, T-2, HT-2, zearalenone, and ochratoxin A in cereal grains by liquid chromatography-tandem mass spectrometry (LC/MS/MS after a single immunoaffinity column clean-up. The method showed a good linearity, sensitivity, specificity, and accuracy in mycotoxin determination by LC/MS/MS. The levels of 13 mycotoxins in 5 types of commercial grains (brown rice, maize, millet, sorghum, and mixed cereal from South Korea were determined in a total of 507 cereal grains. Mycotoxins produced from Fusarium sp. (fumonisins, deoxynivalenol, nivalenol, and zearalenone were more frequently (more than 5% and concurrently detected in all cereal grains along with higher mean levels (4.3–161.0 ng/g in positive samples than other toxins such as aflatoxins and ochratoxin A (less than 9% and below 5.2 ng/g in positive samples from other fungal species.

Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua)

Science.gov (United States)

The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread highly destructive, with infections by C. cereale resulting in extensive turfgrass loss. Comprehensive research aimed at controlling turfgrass a...

Cultivation with deliberation: cereals and their growing conditions in prehistory

Czech Academy of Sciences Publication Activity Database

Dreslerová, Dagmar; Kočár, Petr; Chuman, T.; Pokorná, Adéla

2017-01-01

Roč. 26, č. 5 (2017), s. 513-526 ISSN 0939-6314 Institutional support: RVO:67985912 Keywords : prehistory * arable farming * soils * archaeobotany * cereals Subject RIV: AC - Archeology, Anthropology, Ethnology OBOR OECD: Archaeology Impact factor: 1.908, year: 2016

Nitrate Leaching from Winter Cereal Cover Crops Using Undisturbed Soil-Column Lysimeters.

Science.gov (United States)

Meisinger, John J; Ricigliano, Kristin A

2017-05-01

Cover crops are important management practices for reducing nitrogen (N) leaching, especially in the Chesapeake Bay watershed, which is under total maximum daily load (TMDL) restraints. Winter cereals are common cool-season crops in the Bay watershed, but studies have not directly compared nitrate-N (NO-N) leaching losses from these species. A 3-yr cover crop lysimeter study was conducted in Beltsville, MD, to directly compare NO-N leaching from a commonly grown cultivar of barley ( L.), rye ( L.), and wheat ( L.), along with a no-cover control, using eight tension-drained undisturbed soil column lysimeters in a completely randomized design with two replicates. The lysimeters were configured to exclude runoff and to estimate NO-N leaching and flow-weighted NO-N concentration (FWNC). The temporal pattern of NO-N leaching showed a consistent highly significant ( leaching with cover crops compared with no cover but showed only small and periodically significant ( leaching was more affected by the quantity of establishment-season (mid-October to mid-December) precipitation than by cover crop species. For example, compared with no cover, winter cereal covers reduced NO-N leaching 95% in a dry year and 50% in wet years, with corresponding reductions in FWNC of 92 and 43%, respectively. These results are important for scientists, nutrient managers, and policymakers because they directly compare NO-N leaching from winter cereal covers and expand knowledge for developing management practices for winter cereals that can improve water quality and increase N efficiency in cropping systems. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Statistical Methods in Integrative Genomics

Science.gov (United States)

Richardson, Sylvia; Tseng, George C.; Sun, Wei

2016-01-01

Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531

Determinants of rural household marketed surplus for cereal crops ...

African Journals Online (AJOL)

... and supply of cereal crops to the market (market surplus). The study utilized cross sectional data obtained through multistage random sampling method. Ordinary least square method was used for the analysis. Finding revealed that the quantity of food crops reserved for home consumption by households increased their ...

[Soluble and insoluble dietary fiber in cereals and legumes cultivated in Chile].

Science.gov (United States)

Pak, N; Ayala, C; Vera, G; Pennacchiotti, I; Araya, H

1990-03-01

Insoluble, soluble and total dietary fiber (DF) were determined in 35 varieties of certified whole seeds (without processing) of cereals (rice, oat, rye, and wheat) and legumes (pea, cowpea, beans, chikpea, lentil and lupine). The enzymatic method of Asp, Johansson and Siljestrom was used, with modifications in relation to time of incubation with alpha amylase, filtration system and volumes of the filtrates. Results were expressed as g/100 g dry weight. Total DF for cereals showed a range from 10.1 (wheat var. Chasqui) to 22.2 (rice var Quella). Rye, var. Tetra Baer and oats var. Pony Baer presented the highest soluble fiber content (3.3 and 3.9, respectively). In legumes, total DF fluctuated between 12.7 (pea, var. yellow) and 36.6 (lupine, var. Multolupa). Bean, var. Pinto INIA and lupine var. Multolupa presented the highest soluble fiber values (5.8 for both). Based on the results of this research work, it might be concluded that great variation exists in regard to the amount of total soluble and insoluble DF in cereals and legumes, a fact which impedes generalization as to its content in each food item.

Fermented cereal beverages: from probiotic, prebiotic and synbiotic towards Nanoscience designed healthy drinks.

Science.gov (United States)

Salmerón, I

2017-08-01

The consumption of fermented foods by human kind goes a long way back in history and there are as many types of fermented food as civilizations. Food Science and Technology has progressed from designing nutritional foods towards food with health improvement characteristics such as functional foods. In this sense, the area of food with properties to improve gastrointestinal health such as probiotics, prebiotics and synbiotics has been the most important segment within functional foods. Most of these products are dairy-based so the development of nondairy gut improvement products has been of great interest for the food industry, resulting in the rise of cereal-based probiotic and synbiotic products. Finally, through Nanoscience and the application of Nanotechnology techniques in the food sector, it has been possible to design fermented beverages with synbiotic properties, and the incorporation of nanoparticles with unique and specific bioactivity, which has opened a new horizon in this segment of food created to improve human health and well-being. There is currently a great interest in producing healthy food in particular that which has an impact in improving the gastrointestinal health such as probiotics, prebiotics and synbiotics. Most of these functional foods are dairy based and have been greatly accepted worldwide. Nevertheless, there has been a need for the development of nondairy probiotic, prebiotic and synbiotic products. This has encouraged food scientists to study the feasibility of applying other fermenting substrates such as cereals for the development of innovative nondairy fermented functional foods. Therefore, in this review we have addressed the significance of applying cereals and their fractions for the development of probiotic, prebiotic and synbiotic beverages. Furthermore, we have presented the importance of including nanoscience and nanotechnology techniques for the creation of fermented cereal beverages that contain specific bioactive

Worldwide Occurrence of Mycotoxins in Cereals and Cereal-Derived Food Products: Public Health Perspectives of Their Co-occurrence.

Science.gov (United States)

Lee, Hyun Jung; Ryu, Dojin

2017-08-23

Cereal grains and their processed food products are frequently contaminated with mycotoxins. Among many, five major mycotoxins of aflatoxins, ochratoxins, fumonisins, deoxynivalenol, and zearalenone are of significant public health concern as they can cause adverse effects in humans. Being airborne or soilborne, the cosmopolitan nature of mycotoxigenic fungi contribute to the worldwide occurrence of mycotoxins. On the basis of the global occurrence data reported during the past 10 years, the incidences and maximum levels in raw cereal grains were 55% and 1642 μg/kg for aflatoxins, 29% and 1164 μg/kg for ochratoxin A, 61% and 71,121 μg/kg for fumonisins, 58% and 41,157 μg/kg, for deoxynivalenol, and 46% and 3049 μg/kg for zearalenone. The concentrations of mycotoxins tend to be lower in processed food products; the incidences varied depending on the individual mycotoxins, possibly due to the varying stability during processing and distribution of mycotoxins. It should be noted that more than one mycotoxin, produced by a single or several fungal species, may occur in various combinations in a given sample or food. Most studies reported additive or synergistic effects, suggesting that these mixtures may pose a significant threat to public health, particularly to infants and young children. Therefore, information on the co-occurrence of mycotoxins and their interactive toxicity is summarized in this paper.

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop.

Science.gov (United States)

Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; Sivarajan, Sajeevan Radha; Patrignani, Andrea; Grüter, Simon; Poveda, Lucy; Shimizu-Inatsugi, Rie; Baeten, John; Francoijs, Kees-Jan; Nataraja, Karaba N; Reddy, Yellodu A Nanja; Phadnis, Shamprasad; Ravikumar, Ramapura L; Schlapbach, Ralph; Sreeman, Sheshshayee M; Shimizu, Kentaro K

2017-09-05

Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

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Monika Szczecińska

2015-09-01

Full Text Available Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2 enabled the molecular delimitation of closely-related Pulsatilla

The genome of Eucalyptus grandis

Energy Technology Data Exchange (ETDEWEB)

Myburg, Alexander A.; Grattapaglia, Dario; Tuskan, Gerald A.; Hellsten, Uffe; Hayes, Richard D.; Grimwood, Jane; Jenkins, Jerry; Lindquist, Erika; Tice, Hope; Bauer, Diane; Goodstein, David M.; Dubchak, Inna; Poliakov, Alexandre; Mizrachi, Eshchar; Kullan, Anand R. K.; Hussey, Steven G.; Pinard, Desre; van der Merwe, Karen; Singh, Pooja; van Jaarsveld, Ida; Silva-Junior, Orzenil B.; Togawa, Roberto C.; Pappas, Marilia R.; Faria, Danielle A.; Sansaloni, Carolina P.; Petroli, Cesar D.; Yang, Xiaohan; Ranjan, Priya; Tschaplinski, Timothy J.; Ye, Chu-Yu; Li, Ting; Sterck, Lieven; Vanneste, Kevin; Murat, Florent; Soler, Marçal; Clemente, Hélène San; Saidi, Naijib; Cassan-Wang, Hua; Dunand, Christophe; Hefer, Charles A.; Bornberg-Bauer, Erich; Kersting, Anna R.; Vining, Kelly; Amarasinghe, Vindhya; Ranik, Martin; Naithani, Sushma; Elser, Justin; Boyd, Alexander E.; Liston, Aaron; Spatafora, Joseph W.; Dharmwardhana, Palitha; Raja, Rajani; Sullivan, Christopher; Romanel, Elisson; Alves-Ferreira, Marcio; Külheim, Carsten; Foley, William; Carocha, Victor; Paiva, Jorge; Kudrna, David; Brommonschenkel, Sergio H.; Pasquali, Giancarlo; Byrne, Margaret; Rigault, Philippe; Tibbits, Josquin; Spokevicius, Antanas; Jones, Rebecca C.; Steane, Dorothy A.; Vaillancourt, René E.; Potts, Brad M.; Joubert, Fourie; Barry, Kerrie; Pappas, Georgios J.; Strauss, Steven H.; Jaiswal, Pankaj; Grima-Pettenati, Jacqueline; Salse, Jérôme; Van de Peer, Yves; Rokhsar, Daniel S.; Schmutz, Jeremy

2014-06-11

Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

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.

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.

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

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

Science.gov (United States)

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

2012-01-01

The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: the 'DDBJ Omics Archive' (DOR; http://trace.ddbj.nig.ac.jp/dor) and BioProject (http://trace.ddbj.nig.ac.jp/bioproject). DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. In this article, we describe major changes and improvements introduced to the DDBJ services, and the launch of two new resources: DOR and BioProject.

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...

Evaluation of nutrient composition of some cereals and legumes ...

African Journals Online (AJOL)

The use of compost for horticultural crops production in Nigeria is beginning to gain some attention, since it has been reported to improve plant growth and yield. Some cereals and legumes crops residues with potentials of being used as compost materials such as Sorghum Stovers, Rice Straws, Maize Stovers, Millet ...

Seed protein improvement in cereals and grain legumes

International Nuclear Information System (INIS)

1979-01-01

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

Sensitization to cereals and peanut evidenced by skin prick test and specific IgE in food-tolerant, grass pollen allergic patients

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Martens Maria

2011-12-01

Full Text Available Abstract Background 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 history of, and clinically reactions to foods botanically related to grass. Methods 70 subjects (41 females; mean age 32 years and 20 healthy controls (13 females; mean age 24 years were tested by open food challenge (OFC with cereals and peanut. SPT and sIgE both with Immulite® (Siemens and ImmunoCAP® (Phadia to grass and birch pollen, cereals, peanut and bromelain were performed. Results Of the 65 OFC-negative subjects 29-46% (SPT, depending on cut-off, 20% (Immulite and 38% (ImmunoCAP had positive results to one or more of the foods tested. Controls were negative in all tests. Cross-reactive carbohydrate determinants (CCD as evidenced by reaction to bromelain could explain only a minority of the measured IgE-sensitizations. Conclusion Grass pollen allergic patients with documented food tolerance to cereals and peanut may express significant sensitization. False-positive cereal or peanut allergy diagnoses may be a quantitatively important problem both in routine clinical work and epidemiological studies.

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....

[Storage of cereal bars with mesquite cotyledon (Prosopis chilensis (Mol) Stuntz)].

Science.gov (United States)

Escobar, B; Estévez, A M; Guiñez, M A

2000-06-01

The use of walnut or peanut in the elaboration of cereal bars represents a possible risk of undesirable changes during their storage due to their high content of unsaturated fatty acids in the oil; oxidizing of the fatty acids is one of the main causes of deterioration. Development of new snack products implies the use of packages that should protect the food against the damage caused by light and reduce the oxygen concentration of in their interior. The objective of this investigation was to evaluate the physical, chemical and sensory changes in the storage of cereal bars with peanut or walnut and mezquite cotyledon subjected to two thermal treatments, packed in cellophane or milky polypropilene. Four types of bars were elaborated with 6% of mezquite cotyledon, treated by microwaves or toasted, and with 18% of peanut or walnut. The bars were stored for 90 days at room temperature; and each 30 days it was measured moisture content, peroxides index, water activity, sensory quality and acceptability. The peroxides values (4.9-13.8 meq/kg of oil) indicates that the shelf life of the bars in all the studied treatments was 90 days. The packaging materials used allows to maintain in good conditions, for 3 months, the cereals bars of moisture (7.4-11.2%), water activity (0.50-0.65) and sensory acceptability.

Challenges to develop nitrogen-fixing cereals by direct nif-gene transfer.

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Curatti, Leonardo; Rubio, Luis M

2014-08-01

Some regions of the developing world suffer low cereal production yields due to low fertilizer inputs, among other factors. Biological N2 fixation, catalyzed by the prokaryotic enzyme nitrogenase, is an alternative to the use of synthetic N fertilizers. The molybdenum nitrogenase is an O2-labile metalloenzyme composed of the NifDK and NifH proteins, which biosyntheses require a number of nif gene products. A challenging strategy to increase cereal crop productivity in a scenario of low N fertilization is the direct transfer of nif genes into cereals. The sensitivity of nitrogenase to O2 and the apparent complexity of nitrogenase biosynthesis are the main barriers identified so far. Expression of active NifH requires the products of nifM, nifH, and possibly nifU and nifS, whereas active NifDK requires the products of nifH, nifD, nifK, nifB, nifE, nifN, and possibly nifU, nifS, nifQ, nifV, nafY, nifW and nifZ. Plastids and mitochondria are potential subcellular locations for nitrogenase. Both could provide the ATP and electrons required for nitrogenase to function but they differ in their internal O2 levels and their ability to incorporate ammonium into amino acids. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Narrowing the harvest: Increasing sickle investment and the rise of domesticated cereal agriculture in the Fertile Crescent

Science.gov (United States)

Maeda, Osamu; Lucas, Leilani; Silva, Fabio; Tanno, Ken-Ichi; Fuller, Dorian Q.

2016-08-01

For the first time we integrate quantitative data on lithic sickles and archaeobotanical evidence for domestication and the evolution of plant economies from sites dated to the terminal Pleistocene and Early Holocene (ca. 12000-5000 cal. BCE) from throughout the Fertile Crescent region of Southwest Asia. We find a strong correlation in some regions, throughout the Levant, for increasing investment in sickles that tracks the evidence for increasing reliance on cereal crops, while evidence for morphological domestication in wheats (Triticum monococcum and Triticum dicoccum) and barley (Hordeum vulgare) was delayed in comparison to sickle use. These data indicate that while the co-increase of sickle blades and cereal crops support the protracted development of agricultural practice, sickles did not drive the initial stages of the domestication process but rather were a cultural adaptation to increasing reliance on cereals that were still undergoing selection for morphological change. For other regions, such as the Eastern Fertile Crescent and Cyprus such correlations are weaker or non-existent suggesting diverse cultural trajectories to cereal domestication. We conclude that sickles were an exaptation transferred to cereal harvesting and important in signalling a new cultural identity of "farmers". Furthermore, the protracted process of technological and agricultural evolution calls into question hypotheses that the transition to agriculture was caused by any particular climatic event.

Effect of temperature and precipitation on nitrate leaching from organic cereal cropping systems in Denmark

DEFF Research Database (Denmark)

Jabloun, Mohamed; Schelde, Kirsten; Tao, F

2015-01-01

The effect of variation in seasonal temperature and precipitation on soil water nitrate (NO3single bondN) concentration and leaching from winter and spring cereals cropping systems was investigated over three consecutive four-year crop rotation cycles from 1997 to 2008 in an organic farming crop...... rotation experiment in Denmark. Three experimental sites, varying in climate and soil type from coarse sand to sandy loam, were investigated. The experiment included experimental treatments with different rotations, manure rate and cover crop, and soil nitrate concentrations was monitored using suction......N concentration for winter and spring cereals, respectively, and 68% and 77% of the variation in the square root transform of annual NO3single bondN leaching for winter and spring cereals, respectively. Nitrate concentration and leaching were shown to be site specific and driven by climatic factors and crop...

Nutritional evaluation of cereal mutants

International Nuclear Information System (INIS)

1977-01-01

An advisory group of experts, comprising nutritionists, analysts and plant breeders, discussed the desirability of nutritional goals for plant breeding and attempted to specify the deficiencies of various cereal crops in essential nutrients. It considered the plant factors influencing the value for human and animal nutrition and the feasibility of improving these by genetic and plant breeding methods. Methods of assaying nutritional quality were discussed, particularly in relation to the need for rapid, inexpensive methods capable of being used as screening procedures in plant breeding programmes. The proceedings contain 9 scientific papers and a conclusion and recommendations, including a review of the chemical cuzymatic, microbiological and animal assay techniques that are available

Musa sebagai Model Genom

Directory of Open Access Journals (Sweden)

RITA MEGIA

2005-12-01

Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

Simultaneous determination of nitrogen and phosphorus in cereals using 14 MeV Neutron Activation Analysis

International Nuclear Information System (INIS)

Bejarano, R.

1992-01-01

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

Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement.

Science.gov (United States)

Gupta, Sonal; Nawaz, Kashif; Parween, Sabiha; Roy, Riti; Sahu, Kamlesh; Kumar Pole, Anil; Khandal, Hitaishi; Srivastava, Rishi; Kumar Parida, Swarup; Chattopadhyay, Debasis

2017-02-01

Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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)

Co-60 uptake in some young cereal plants

International Nuclear Information System (INIS)

Dumitru, R.O.

1998-01-01

The measure of Co-60 uptake by young cereal plants is dependent on the type of soil, plant and growth conditions. Depending on the size of the uptake, a plant can be used for industrial purposes, fodder, foodstuff or for possible decontamination of the soil. Although the requirement for cobalt in higher plants is little, their contamination with Co-60 can be of interest because this radionuclide belongs to the class of the radionuclides with a great radiotoxicity. The soil-to-plant transfer factor (TF) is a measure of the radionuclide uptake in the plant. In this paper the soil-to-plant TFs for Co-60 were determined for the whole aerial part of some young plants in the cereal class that, in this stage of the development, may be used as fodder. To determine soil-to-plant TFs, plants cultivated in pots in laboratory conditions were used. The method used is similar with the plantlet method of Neubauer and Schneider. We have determined some physical, chemical and mineralogical properties of the studied soil, a brown-reddish forest type soil. The soil-to-plant TFs were calculated on the basis of the Co-60 activities determined in plant and soil dried samples. For the vegetal samples the whole aerial part of the plants was measured in millet, wheat, barley and triticale. At harvest, only a few millet plants where flowered. The results of the measurements of soil-to-plant TFs of Co-60 are the following: 0.0315±0.0017 for millet, 0.0260±0.0014 for barley, 0.0140±0.0008 for wheat and 0.0491±0.0022 for triticale. These TFs were corrected for standard conditions and were compared with data from literature. The soil-to-plant TFs for Co-60 found in the aerial part of young cereals are close to those recommended for the fodder. The obtained values prove the strong dependence of the soil-to-plant TFs for Co-60 on the type of soil and plant. (author)

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.

Science.gov (United States)

Argout, X; Martin, G; Droc, G; Fouet, O; Labadie, K; Rivals, E; Aury, J M; Lanaud, C

2017-09-15

Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes. The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).

Validation and transferability study of a method based on near-infrared hyperspectral imaging for the detection and quantification of ergot bodies in cereals

NARCIS (Netherlands)

Vermeulen, Ph.; Fernández - Pierna, J.A.; Egmond, van H.P.; Zegers, J.; Dardenne, P.; Baeten, V.

2013-01-01

In recent years, near-infrared (NIR) hyperspectral imaging has proved its suitability for quality and safety control in the cereal sector by allowing spectroscopic images to be collected at single-kernel level, which is of great interest to cereal control laboratories. Contaminants in cereals

Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns

Directory of Open Access Journals (Sweden)

Hayashizaki Yoshihide

2009-06-01

Full Text Available Abstract Background Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs for wheat is becoming particularly important for functional genomics and molecular breeding. We prepared a comprehensive collection of ESTs from the various tissues that develop during the wheat life cycle and from tissues subjected to stress. We also examined their expression profiles in silico. As full-length cDNAs are indispensable to certify the collected ESTs and annotate the genes in the wheat genome, we performed a systematic survey and sequencing of the full-length cDNA clones. This sequence information is a valuable genetic resource for functional genomics and will enable carrying out comparative genomics in cereals. Results As part of the functional genomics and development of genomic wheat resources, we have generated a collection of full-length cDNAs from common wheat. By grouping the ESTs of recombinant clones randomly selected from the full-length cDNA library, we were able to sequence 6,162 independent clones with high accuracy. About 10% of the clones were wheat-unique genes, without any counterparts within the DNA database. Wheat clones that showed high homology to those of rice were selected in order to investigate their expression patterns in various tissues throughout the wheat life cycle and in response to abiotic-stress treatments. To assess the variability of genes that have evolved differently in wheat and rice, we calculated the substitution rate (Ka/Ks of the counterparts in wheat and rice. Genes that were preferentially expressed in certain tissues or treatments had higher Ka/Ks values than those in other tissues and treatments, which suggests that the genes with the higher variability expressed in these tissues is under adaptive selection. Conclusion We have generated a high-quality full-length cDNA resource for common wheat, which is essential for continuation of the

Synthetic biology approaches to engineering the nitrogen symbiosis in cereals.